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Sample records for dos modelos voxels

  1. En la búsqueda de características en eyecciones coronales de masa que discriminen entre dos paradigmas físicos en modelos de ECMs

    NASA Astrophysics Data System (ADS)

    Paissan, G.; Stenborg, G.; Rovira, M.

    Se conocen tres diferentes fenómenos de gran escala que ocurren en la atmósfera solar, denominados eyecciones coronales de masa (ECMs), protuberancias eruptivas y grandes fulguraciones de dos bandas. Estos fenómenos están estrechamente relacionados y podrían ser distintas manifestaciones de un único proceso físico. Las ECMs son definidas como eyecciones de gran escala de masa y flujo magnético desde la baja corona al espacio interplanetario. Desde su descubrimiento en los '70, muchos modelos han sido propuestos para explicar su origen y evolución. La explicación física de las ECMs es un tema de debate intenso. No obstante, los modelos pueden sintetizarse en dos grandes grupos: 1) los modelos de inyección de flujo y 2) los modelos de almacenamiento y liberación. En este trabajo, se presentan los estudios realizados con una serie de eventos observados con el coronógrafo MICA (Mirror Coronograph for Argentina), el telescopio en H-alfa HASTA (H-alpha Solar Telescope for Argentina) y los coronógrafos C2 y C3 de la sonda SOHO (Solar and Heliospheric Observatory). Los eventos que pudieron ser identificados como ECMs son contrastados dentro del esquema de los dos paradigmas teóricos propuestos.

  2. DOS.

    ERIC Educational Resources Information Center

    Traven, Bill

    1988-01-01

    Discusses using the DOS PATH command (for MS-DOS) to enable the microcomputer user to move from directory to directory on a hard drive. Lists the commands to be programed, gives examples, and explains the use of each. (MVL)

  3. Análise da aplicação e dos resultados do modelo OPM3® para a área da saúde

    PubMed Central

    Augusto dos Santos, Luis; de Fátima Marin, Heimar

    2015-01-01

    Esta pesquisa procurou analisar se um modelo de questionário criado por uma comunidade internacional de gerenciamento de projetos e se é aplicavél a organizações voltadas a área de saúde. O modelo OPM3® (Organizational Project Management Maturity Model) foi criado para que organizações de qualquer área ou porte pudessem identificar a presença, ou ausência, de boas práticas de gerenciamento. O objetivo da aplicação desse modelo é avaliar sempre a organização e não o entrevistado. No presente artigo, são apresentados os resultados da aplicação desse modelo em uma organização que possuía produtos e serviços de tecnologia da informação aplicados à área de saúde. Este estudo verificou que o modelo é aplicável de forma rápida e que a organização analisada possuía um número expressivo de boas práticas. PMID:26924862

  4. Intra voxel analysis in MRI

    NASA Astrophysics Data System (ADS)

    Ambrosanio, Michele; Baselice, Fabio; Ferraioli, Giampaolo; Pascazio, Vito

    2014-03-01

    A new application of Compressive Sensing (CS) in Magnetic Resonance Imaging (MRI) field is presented. In particular, first results of the Intra Voxel Analysis (IVA) technique are reported. The idea is to exploit CS peculiarities in order to distinguish different contributions inside the same resolution cell, instead of reconstructing images from not fully sampled k-space acquisition. Applied to MRI field, this means the possibility of estimating the presence of different tissues inside the same voxel, i.e. in one pixel of the obtained image. In other words, the method is the first attempt, as far as we know, of achieving Spectroscopy-like results starting from each pixel of MR images. In particular, tissues are distinguished each others by evaluating their spin-spin relaxation times. Within this manuscript, first results on clinical dataset, in particular a phantom made by aqueous solution and oil and an occipital brain lesion corresponding to a metastatic breast cancer nodule, are reported. Considering the phantom dataset, in particular focusing on the slice where the separation between water and oil occurs, the methodology is able to distinguish the two components with different spin-spin relaxation times. With respect to clinical dataset,focusing on a voxel of the lesion area, the approach is able to detect the presence of two tissues, namely the healthy and the cancer related ones, while in other location outside the lesion only the healthy tissue is detected. Of course, these are the first results of the proposed methodology, further studies on different types of clinical datasets are required in order to widely validate the approach. Although few datasets have been considered, results seem both interesting and promising.

  5. VoxelStats: A MATLAB Package for Multi-Modal Voxel-Wise Brain Image Analysis.

    PubMed

    Mathotaarachchi, Sulantha; Wang, Seqian; Shin, Monica; Pascoal, Tharick A; Benedet, Andrea L; Kang, Min Su; Beaudry, Thomas; Fonov, Vladimir S; Gauthier, Serge; Labbe, Aurélie; Rosa-Neto, Pedro

    2016-01-01

    In healthy individuals, behavioral outcomes are highly associated with the variability on brain regional structure or neurochemical phenotypes. Similarly, in the context of neurodegenerative conditions, neuroimaging reveals that cognitive decline is linked to the magnitude of atrophy, neurochemical declines, or concentrations of abnormal protein aggregates across brain regions. However, modeling the effects of multiple regional abnormalities as determinants of cognitive decline at the voxel level remains largely unexplored by multimodal imaging research, given the high computational cost of estimating regression models for every single voxel from various imaging modalities. VoxelStats is a voxel-wise computational framework to overcome these computational limitations and to perform statistical operations on multiple scalar variables and imaging modalities at the voxel level. VoxelStats package has been developed in Matlab(®) and supports imaging formats such as Nifti-1, ANALYZE, and MINC v2. Prebuilt functions in VoxelStats enable the user to perform voxel-wise general and generalized linear models and mixed effect models with multiple volumetric covariates. Importantly, VoxelStats can recognize scalar values or image volumes as response variables and can accommodate volumetric statistical covariates as well as their interaction effects with other variables. Furthermore, this package includes built-in functionality to perform voxel-wise receiver operating characteristic analysis and paired and unpaired group contrast analysis. Validation of VoxelStats was conducted by comparing the linear regression functionality with existing toolboxes such as glim_image and RMINC. The validation results were identical to existing methods and the additional functionality was demonstrated by generating feature case assessments (t-statistics, odds ratio, and true positive rate maps). In summary, VoxelStats expands the current methods for multimodal imaging analysis by allowing the

  6. VoxelStats: A MATLAB Package for Multi-Modal Voxel-Wise Brain Image Analysis

    PubMed Central

    Mathotaarachchi, Sulantha; Wang, Seqian; Shin, Monica; Pascoal, Tharick A.; Benedet, Andrea L.; Kang, Min Su; Beaudry, Thomas; Fonov, Vladimir S.; Gauthier, Serge; Labbe, Aurélie; Rosa-Neto, Pedro

    2016-01-01

    In healthy individuals, behavioral outcomes are highly associated with the variability on brain regional structure or neurochemical phenotypes. Similarly, in the context of neurodegenerative conditions, neuroimaging reveals that cognitive decline is linked to the magnitude of atrophy, neurochemical declines, or concentrations of abnormal protein aggregates across brain regions. However, modeling the effects of multiple regional abnormalities as determinants of cognitive decline at the voxel level remains largely unexplored by multimodal imaging research, given the high computational cost of estimating regression models for every single voxel from various imaging modalities. VoxelStats is a voxel-wise computational framework to overcome these computational limitations and to perform statistical operations on multiple scalar variables and imaging modalities at the voxel level. VoxelStats package has been developed in Matlab® and supports imaging formats such as Nifti-1, ANALYZE, and MINC v2. Prebuilt functions in VoxelStats enable the user to perform voxel-wise general and generalized linear models and mixed effect models with multiple volumetric covariates. Importantly, VoxelStats can recognize scalar values or image volumes as response variables and can accommodate volumetric statistical covariates as well as their interaction effects with other variables. Furthermore, this package includes built-in functionality to perform voxel-wise receiver operating characteristic analysis and paired and unpaired group contrast analysis. Validation of VoxelStats was conducted by comparing the linear regression functionality with existing toolboxes such as glim_image and RMINC. The validation results were identical to existing methods and the additional functionality was demonstrated by generating feature case assessments (t-statistics, odds ratio, and true positive rate maps). In summary, VoxelStats expands the current methods for multimodal imaging analysis by allowing the

  7. VoxelStats: A MATLAB Package for Multi-Modal Voxel-Wise Brain Image Analysis.

    PubMed

    Mathotaarachchi, Sulantha; Wang, Seqian; Shin, Monica; Pascoal, Tharick A; Benedet, Andrea L; Kang, Min Su; Beaudry, Thomas; Fonov, Vladimir S; Gauthier, Serge; Labbe, Aurélie; Rosa-Neto, Pedro

    2016-01-01

    In healthy individuals, behavioral outcomes are highly associated with the variability on brain regional structure or neurochemical phenotypes. Similarly, in the context of neurodegenerative conditions, neuroimaging reveals that cognitive decline is linked to the magnitude of atrophy, neurochemical declines, or concentrations of abnormal protein aggregates across brain regions. However, modeling the effects of multiple regional abnormalities as determinants of cognitive decline at the voxel level remains largely unexplored by multimodal imaging research, given the high computational cost of estimating regression models for every single voxel from various imaging modalities. VoxelStats is a voxel-wise computational framework to overcome these computational limitations and to perform statistical operations on multiple scalar variables and imaging modalities at the voxel level. VoxelStats package has been developed in Matlab(®) and supports imaging formats such as Nifti-1, ANALYZE, and MINC v2. Prebuilt functions in VoxelStats enable the user to perform voxel-wise general and generalized linear models and mixed effect models with multiple volumetric covariates. Importantly, VoxelStats can recognize scalar values or image volumes as response variables and can accommodate volumetric statistical covariates as well as their interaction effects with other variables. Furthermore, this package includes built-in functionality to perform voxel-wise receiver operating characteristic analysis and paired and unpaired group contrast analysis. Validation of VoxelStats was conducted by comparing the linear regression functionality with existing toolboxes such as glim_image and RMINC. The validation results were identical to existing methods and the additional functionality was demonstrated by generating feature case assessments (t-statistics, odds ratio, and true positive rate maps). In summary, VoxelStats expands the current methods for multimodal imaging analysis by allowing the

  8. Voxel-Based LIDAR Analysis and Applications

    NASA Astrophysics Data System (ADS)

    Hagstrom, Shea T.

    One of the greatest recent changes in the field of remote sensing is the addition of high-quality Light Detection and Ranging (LIDAR) instruments. In particular, the past few decades have been greatly beneficial to these systems because of increases in data collection speed and accuracy, as well as a reduction in the costs of components. These improvements allow modern airborne instruments to resolve sub-meter details, making them ideal for a wide variety of applications. Because LIDAR uses active illumination to capture 3D information, its output is fundamentally different from other modalities. Despite this difference, LIDAR datasets are often processed using methods appropriate for 2D images and that do not take advantage of its primary virtue of 3-dimensional data. It is this problem we explore by using volumetric voxel modeling. Voxel-based analysis has been used in many applications, especially medical imaging, but rarely in traditional remote sensing. In part this is because the memory requirements are substantial when handling large areas, but with modern computing and storage this is no longer a significant impediment. Our reason for using voxels to model scenes from LIDAR data is that there are several advantages over standard triangle-based models, including better handling of overlapping surfaces and complex shapes. We show how incorporating system position information from early in the LIDAR point cloud generation process allows radiometrically-correct transmission and other novel voxel properties to be recovered. This voxelization technique is validated on simulated data using the Digital Imaging and Remote Sensing Image Generation (DIRSIG) software, a first-principles based ray-tracer developed at the Rochester Institute of Technology. Voxel-based modeling of LIDAR can be useful on its own, but we believe its primary advantage is when applied to problems where simpler surface-based 3D models conflict with the requirement of realistic geometry. To

  9. Voxel2MCNP: software for handling voxel models for Monte Carlo radiation transport calculations.

    PubMed

    Hegenbart, Lars; Pölz, Stefan; Benzler, Andreas; Urban, Manfred

    2012-02-01

    Voxel2MCNP is a program that sets up radiation protection scenarios with voxel models and generates corresponding input files for the Monte Carlo code MCNPX. Its technology is based on object-oriented programming, and the development is platform-independent. It has a user-friendly graphical interface including a two- and three-dimensional viewer. A row of equipment models is implemented in the program. Various voxel model file formats are supported. Applications include calculation of counting efficiency of in vivo measurement scenarios and calculation of dose coefficients for internal and external radiation scenarios. Moreover, anthropometric parameters of voxel models, for instance chest wall thickness, can be determined. Voxel2MCNP offers several methods for voxel model manipulations including image registration techniques. The authors demonstrate the validity of the program results and provide references for previous successful implementations. The authors illustrate the reliability of calculated dose conversion factors and specific absorbed fractions. Voxel2MCNP is used on a regular basis to generate virtual radiation protection scenarios at Karlsruhe Institute of Technology while further improvements and developments are ongoing. PMID:22217596

  10. Voxel classification based airway tree segmentation

    NASA Astrophysics Data System (ADS)

    Lo, Pechin; de Bruijne, Marleen

    2008-03-01

    This paper presents a voxel classification based method for segmenting the human airway tree in volumetric computed tomography (CT) images. In contrast to standard methods that use only voxel intensities, our method uses a more complex appearance model based on a set of local image appearance features and Kth nearest neighbor (KNN) classification. The optimal set of features for classification is selected automatically from a large set of features describing the local image structure at several scales. The use of multiple features enables the appearance model to differentiate between airway tree voxels and other voxels of similar intensities in the lung, thus making the segmentation robust to pathologies such as emphysema. The classifier is trained on imperfect segmentations that can easily be obtained using region growing with a manual threshold selection. Experiments show that the proposed method results in a more robust segmentation that can grow into the smaller airway branches without leaking into emphysematous areas, and is able to segment many branches that are not present in the training set.

  11. Uncertainty driven probabilistic voxel selection for image registration.

    PubMed

    Oreshkin, Boris N; Arbel, Tal

    2013-10-01

    This paper presents a novel probabilistic voxel selection strategy for medical image registration in time-sensitive contexts, where the goal is aggressive voxel sampling (e.g., using less than 1% of the total number) while maintaining registration accuracy and low failure rate. We develop a Bayesian framework whereby, first, a voxel sampling probability field (VSPF) is built based on the uncertainty on the transformation parameters. We then describe a practical, multi-scale registration algorithm, where, at each optimization iteration, different voxel subsets are sampled based on the VSPF. The approach maximizes accuracy without committing to a particular fixed subset of voxels. The probabilistic sampling scheme developed is shown to manage the tradeoff between the robustness of traditional random voxel selection (by permitting more exploration) and the accuracy of fixed voxel selection (by permitting a greater proportion of informative voxels).

  12. DOS basics

    SciTech Connect

    O`Connor, P.

    1994-09-01

    DOS is an acronym for Disk Operating System. It is actually a set of programs that allows you to control your personal computer. DOS offers the capabilities to create and manage files; organize and maintain information placed on disks; use application programs such as WordPerfect, Lotus 123, Excel, Windows, etc. In addition, DOS provides the basic utilities needed to copy files from one area to another, delete files and list files. The latest version of DOS also offers more advanced features that include hard disk compression and memory management. Basic DOS commands are discussed.

  13. Schizophrenia Patients Demonstrate Both Inter-Voxel Level and Intra-Voxel Level White Matter Alterations.

    PubMed

    Zhuo, Chuanjun; Ma, Xiaolei; Qu, Hongru; Wang, Lina; Jia, Feng; Wang, Chunli

    2016-01-01

    Fractional anisotropy (FA) and mean diffusivity (MD) are the most frequently used metrics to investigate white matter impairments in mental disorders. However, these two metrics are derived from intra-voxel analyses and only reflect the diffusion properties solely within the voxel unit. Local diffusion homogeneity (LDH) is a newly developed inter-voxel metric which quantifies the local coherence of water molecule diffusion in a model-free manner. In this study, 94 schizophrenia patients and 91 sex- and age-matched healthy controls underwent diffusion tensor imaging (DTI) examinations. White matter integrity was assessed by FA, MD and LDH. Group differences in these metrics were compared using tract-based spatial statistics (TBSS). Compared with healthy controls, schizophrenia patients exhibited reduced FA and increased MD in the corpus callosum, cingulum, internal capsule, fornix and widespread superficial white matter in the frontal, parietal, occipital and temporal lobes. We also found decreased LDH in the corpus callosum, cingulum, internal capsule and fornix in schizophrenia. Our findings suggest that both intra-voxel and inter-voxel diffusion metrics are able to detect impairments in the anisotropic white matter regions, and intra-voxel diffusion metrics could detect additional impairments in the widespread isotropic white matter regions in schizophrenia. PMID:27618693

  14. Schizophrenia Patients Demonstrate Both Inter-Voxel Level and Intra-Voxel Level White Matter Alterations.

    PubMed

    Zhuo, Chuanjun; Ma, Xiaolei; Qu, Hongru; Wang, Lina; Jia, Feng; Wang, Chunli

    2016-01-01

    Fractional anisotropy (FA) and mean diffusivity (MD) are the most frequently used metrics to investigate white matter impairments in mental disorders. However, these two metrics are derived from intra-voxel analyses and only reflect the diffusion properties solely within the voxel unit. Local diffusion homogeneity (LDH) is a newly developed inter-voxel metric which quantifies the local coherence of water molecule diffusion in a model-free manner. In this study, 94 schizophrenia patients and 91 sex- and age-matched healthy controls underwent diffusion tensor imaging (DTI) examinations. White matter integrity was assessed by FA, MD and LDH. Group differences in these metrics were compared using tract-based spatial statistics (TBSS). Compared with healthy controls, schizophrenia patients exhibited reduced FA and increased MD in the corpus callosum, cingulum, internal capsule, fornix and widespread superficial white matter in the frontal, parietal, occipital and temporal lobes. We also found decreased LDH in the corpus callosum, cingulum, internal capsule and fornix in schizophrenia. Our findings suggest that both intra-voxel and inter-voxel diffusion metrics are able to detect impairments in the anisotropic white matter regions, and intra-voxel diffusion metrics could detect additional impairments in the widespread isotropic white matter regions in schizophrenia.

  15. Schizophrenia Patients Demonstrate Both Inter-Voxel Level and Intra-Voxel Level White Matter Alterations

    PubMed Central

    Wang, Lina; Jia, Feng; Wang, Chunli

    2016-01-01

    Fractional anisotropy (FA) and mean diffusivity (MD) are the most frequently used metrics to investigate white matter impairments in mental disorders. However, these two metrics are derived from intra-voxel analyses and only reflect the diffusion properties solely within the voxel unit. Local diffusion homogeneity (LDH) is a newly developed inter-voxel metric which quantifies the local coherence of water molecule diffusion in a model-free manner. In this study, 94 schizophrenia patients and 91 sex- and age-matched healthy controls underwent diffusion tensor imaging (DTI) examinations. White matter integrity was assessed by FA, MD and LDH. Group differences in these metrics were compared using tract-based spatial statistics (TBSS). Compared with healthy controls, schizophrenia patients exhibited reduced FA and increased MD in the corpus callosum, cingulum, internal capsule, fornix and widespread superficial white matter in the frontal, parietal, occipital and temporal lobes. We also found decreased LDH in the corpus callosum, cingulum, internal capsule and fornix in schizophrenia. Our findings suggest that both intra-voxel and inter-voxel diffusion metrics are able to detect impairments in the anisotropic white matter regions, and intra-voxel diffusion metrics could detect additional impairments in the widespread isotropic white matter regions in schizophrenia. PMID:27618693

  16. Modeling and analysis of caves using voxelization

    NASA Astrophysics Data System (ADS)

    Szeifert, Gábor; Szabó, Tivadar; Székely, Balázs

    2014-05-01

    Although there are many ways to create three dimensional representations of caves using modern information technology methods, modeling of caves has been challenging for researchers for a long time. One of these promising new alternative modeling methods is using voxels. We are using geodetic measurements as an input for our voxelization project. These geodetic underground surveys recorded the azimuth, altitude and distance of corner points of cave systems relative to each other. The diameter of each cave section is estimated from separate databases originating from different surveys. We have developed a simple but efficient method (it covers more than 99.9 % of the volume of the input model on the average) to convert these vector-type datasets to voxels. We have also developed software components to make visualization of the voxel and vector models easier. Since each cornerpoint position is measured relative to another cornerpoints positions, propagation of uncertainties is an important issue in case of long caves with many separate sections. We are using Monte Carlo simulations to analyze the effect of the error of each geodetic instrument possibly involved in a survey. Cross-sections of the simulated three dimensional distributions show, that even tiny uncertainties of individual measurements can result in high variation of positions that could be reduced by distributing the closing errors if such data are available. Using the results of our simulations, we can estimate cave volume and the error of the calculated cave volume depending on the complexity of the cave. Acknowledgements: the authors are grateful to Ariadne Karst and Cave Exploring Association and State Department of Environmental and Nature Protection of the Hungarian Ministry of Rural Development, Department of National Parks and Landscape Protection, Section Landscape and Cave Protection and Ecotourism for providing the cave measurement data. BS contributed as an Alexander von Humboldt Research

  17. Computer simulations for internal dosimetry using voxel models.

    PubMed

    Kinase, Sakae; Mohammadi, Akram; Takahashi, Masa; Saito, Kimiaki; Zankl, Maria; Kramer, Richard

    2011-07-01

    In the Japan Atomic Energy Agency, several studies have been conducted on the use of voxel models for internal dosimetry. Absorbed fractions (AFs) and S values have been evaluated for preclinical assessments of radiopharmaceuticals using human voxel models and a mouse voxel model. Computational calibration of in vivo measurement system has been also made using Japanese and Caucasian voxel models. In addition, for radiation protection of the environment, AFs have been evaluated using a frog voxel model. Each study was performed by using Monte Carlo simulations. Consequently, it was concluded that these data of Monte Carlo simulations and voxel models could adequately reproduce measurement results. Voxel models were found to be a significant tool for internal dosimetry since the models are anatomically realistic. This fact indicates that several studies on correction of the in vivo measurement efficiency for the variability of human subjects and interspecies scaling of organ doses will succeed.

  18. Fine-Resolution Voxel S Values for Constructing Absorbed Dose Distributions at Variable Voxel Size

    PubMed Central

    Dieudonné, Arnaud; Hobbs, Robert F.; Bolch, Wesley E.; Sgouros, George; Gardin, Isabelle

    2010-01-01

    This article presents a revised voxel S values (VSVs) approach for dosimetry in targeted radiotherapy, allowing dose calculation for any voxel size and shape of a given SPECT or PET dataset. This approach represents an update to the methodology presented in MIRD pamphlet no. 17. Methods VSVs were generated in soft tissue with a fine spatial sampling using the Monte Carlo (MC) code MCNPX for particle emissions of 9 radionuclides: 18F, 90Y, 99mTc, 111In, 123I, 131I, 177Lu, 186Re, and 201Tl. A specific resampling algorithm was developed to compute VSVs for desired voxel dimensions. The dose calculation was performed by convolution via a fast Hartley transform. The fine VSVs were calculated for cubic voxels of 0.5 mm for electrons and 1.0 mm for photons. Validation studies were done for 90Y and 131I VSV sets by comparing the revised VSV approach to direct MC simulations. The first comparison included 20 spheres with different voxel sizes (3.8–7.7 mm) and radii (4–64 voxels) and the second comparison a hepatic tumor with cubic voxels of 3.8 mm. MC simulations were done with MCNPX for both. The third comparison was performed on 2 clinical patients with the 3D-RD (3-Dimensional Radiobiologic Dosimetry) software using the EGSnrc (Electron Gamma Shower National Research Council Canada)-based MC implementation, assuming a homogeneous tissue-density distribution. Results For the sphere model study, the mean relative difference in the average absorbed dose was 0.20% ± 0.41% for 90Y and −0.36% ± 0.51% for 131I (n = 20). For the hepatic tumor, the difference in the average absorbed dose to tumor was 0.33% for 90Y and −0.61% for 131I and the difference in average absorbed dose to the liver was 0.25% for 90Y and −1.35% for 131I. The comparison with the 3D-RD software showed an average voxel-to-voxel dose ratio between 0.991 and 0.996. The calculation time was below 10 s with the VSV approach and 50 and 15 h with 3D-RD for the 2 clinical patients. Conclusion This new

  19. Computerized MRS voxel registration and partial volume effects in single voxel 1H-MRS.

    PubMed

    Lee, Hedok; Caparelli, Elisabeth; Li, Haifang; Mandal, Amit; Smith, S David; Zhang, Shaonan; Bilfinger, Thomas V; Benveniste, Helene

    2013-09-01

    Partial volume effects in proton magnetic resonance spectroscopy in the brain have been studied previously in terms of proper water concentration calculations, but there is a lack of disclosure in terms of voxel placement techniques that would affect the calculations. The purpose of this study is to facilitate a fully automated MRS voxel registration method which is time efficient, accurate, and can be extended to all imaging modalities. A total of thirteen healthy adults underwent single voxel 1H-MRS scans in 3.0T MRI scanners. Transposition of a MRS voxel onto an anatomical scan is derived along with a full calculation of water concentration with a correction term to account for the partial volume effects. Five metabolites (tNAA, Glx, tCr, mI, and tCho) known to yield high reliability are studied. Pearson's correlation analyses between tissue volume fractions and metabolite concentrations were statistically significant in parietal (tCr, Glx, and tNAA) lobe and occipital lobe (tNAA). MRS voxel overlaps quantified by dice metric over repeated visits yielded 60%~70% and coefficients of variance in metabolites concentration were 4%~10%. These findings reiterate an importance of considering the partial volume effects when tissue water is used as an internal concentration reference so as to avoid misinterpreting a morphometric difference as a metabolic difference.

  20. Influence of voxel size on specific absorbed fractions and S-values in a mouse voxel phantom.

    PubMed

    Mohammadi, A; Kinase, S

    2011-02-01

    Photon and electron specific absorbed fractions (SAFs) and S-values have been evaluated using mouse voxel phantoms. In voxel phantoms, it is important to choose the voxel size carefully since it affects the accuracy of results. In this study, two mouse voxel phantoms were constructed, with cubic voxels, one with 0.1-mm sides and the other with 0.4-mm sides. The sources were considered to be distributed uniformly in the main organs and the radiation transport was simulated using the Monte Carlo code EGS4. It was found that the effect of voxel size on SAFs for self-irradiation was not high (<10 %) for electrons and photons. However, it was appreciable for cross-irradiation especially for electrons. The effect of voxel size was investigated on S-values for some beta emitters such as (131)I, (153)Sm, (188)Re and (90)Y.

  1. Investigation of Nonuniform Dose Voxel Geometry in Monte Carlo Calculations.

    PubMed

    Yuan, Jiankui; Chen, Quan; Brindle, James; Zheng, Yiran; Lo, Simon; Sohn, Jason; Wessels, Barry

    2015-08-01

    The purpose of this work is to investigate the efficacy of using multi-resolution nonuniform dose voxel geometry in Monte Carlo (MC) simulations. An in-house MC code based on the dose planning method MC code was developed in C++ to accommodate the nonuniform dose voxel geometry package since general purpose MC codes use their own coupled geometry packages. We devised the package in a manner that the entire calculation volume was first divided into a coarse mesh and then the coarse mesh was subdivided into nonuniform voxels with variable voxel sizes based on density difference. We name this approach as multi-resolution subdivision (MRS). It generates larger voxels in small density gradient regions and smaller voxels in large density gradient regions. To take into account the large dose gradients due to the beam penumbra, the nonuniform voxels can be further split using ray tracing starting from the beam edges. The accuracy of the implementation of the algorithm was verified by comparing with the data published by Rogers and Mohan. The discrepancy was found to be 1% to 2%, with a maximum of 3% at the interfaces. Two clinical cases were used to investigate the efficacy of nonuniform voxel geometry in the MC code. Applying our MRS approach, we started with the initial voxel size of 5 × 5 × 3 mm(3), which was further divided into smaller voxels. The smallest voxel size was 1.25 × 1.25 × 3 mm(3). We found that the simulation time per history for the nonuniform voxels is about 30% to 40% faster than the uniform fine voxels (1.25 × 1.25 × 3 mm(3)) while maintaining similar accuracy.

  2. Multistep Lattice-Voxel method utilizing lattice function for Monte-Carlo treatment planning with pixel based voxel model.

    PubMed

    Kumada, H; Saito, K; Nakamura, T; Sakae, T; Sakurai, H; Matsumura, A; Ono, K

    2011-12-01

    Treatment planning for boron neutron capture therapy generally utilizes Monte-Carlo methods for calculation of the dose distribution. The new treatment planning system JCDS-FX employs the multi-purpose Monte-Carlo code PHITS to calculate the dose distribution. JCDS-FX allows to build a precise voxel model consisting of pixel based voxel cells in the scale of 0.4×0.4×2.0 mm(3) voxel in order to perform high-accuracy dose estimation, e.g. for the purpose of calculating the dose distribution in a human body. However, the miniaturization of the voxel size increases calculation time considerably. The aim of this study is to investigate sophisticated modeling methods which can perform Monte-Carlo calculations for human geometry efficiently. Thus, we devised a new voxel modeling method "Multistep Lattice-Voxel method," which can configure a voxel model that combines different voxel sizes by utilizing the lattice function over and over. To verify the performance of the calculation with the modeling method, several calculations for human geometry were carried out. The results demonstrated that the Multistep Lattice-Voxel method enabled the precise voxel model to reduce calculation time substantially while keeping the high-accuracy of dose estimation.

  3. The reference phantoms: voxel vs polygon.

    PubMed

    Kim, C H; Yeom, Y S; Nguyen, T T; Wang, Z J; Kim, H S; Han, M C; Lee, J K; Zankl, M; Petoussi-Henss, N; Bolch, W E; Lee, C; Chung, B S

    2016-06-01

    The International Commission on Radiological Protection (ICRP) reference male and female adult phantoms, described in Publication 110, are voxel phantoms based on whole-body computed tomography scans of a male and a female patient, respectively. The voxel in-plane resolution and the slice thickness, of the order of a few millimetres, are insufficient for proper segmentation of smaller tissues such as the lens of the eye, the skin, and the walls of some organs. The calculated doses for these tissues therefore present some limitations, particularly for weakly penetrating radiation. Similarly, the Publication 110 phantoms cannot represent 8-40-µm-thick target regions in respiratory or alimentary tract organs. Separate stylised models have been used to represent these tissues for calculation of the ICRP reference dose coefficients (DCs). ICRP Committee 2 recently initiated a research project, the ultimate goal of which is to convert the Publication 110 phantoms to a high-quality polygon-mesh (PM) format, including all source and target regions, even those of the 8-40-µm-thick alimentary and respiratory tract organs. It is expected that the converted phantoms would lead to the same or very similar DCs as the Publication 110 reference phantoms for penetrating radiation and, at the same time, provide more accurate DCs for weakly penetrating radiation and small tissues. Additionally, the reference phantoms in the PM format would be easily deformable and, as such, could serve as a starting point to create phantoms of various postures for use, for example, in accidental dose calculations. This paper will discuss the current progress of the phantom conversion project and its significance for ICRP DC calculations.

  4. Effects of voxelization on dose volume histogram accuracy

    NASA Astrophysics Data System (ADS)

    Sunderland, Kyle; Pinter, Csaba; Lasso, Andras; Fichtinger, Gabor

    2016-03-01

    PURPOSE: In radiotherapy treatment planning systems, structures of interest such as targets and organs at risk are stored as 2D contours on evenly spaced planes. In order to be used in various algorithms, contours must be converted into binary labelmap volumes using voxelization. The voxelization process results in lost information, which has little effect on the volume of large structures, but has significant impact on small structures, which contain few voxels. Volume differences for segmented structures affects metrics such as dose volume histograms (DVH), which are used for treatment planning. Our goal is to evaluate the impact of voxelization on segmented structures, as well as how factors like voxel size affects metrics, such as DVH. METHODS: We create a series of implicit functions, which represent simulated structures. These structures are sampled at varying resolutions, and compared to labelmaps with high sub-millimeter resolutions. We generate DVH and evaluate voxelization error for the same structures at different resolutions by calculating the agreement acceptance percentage between the DVH. RESULTS: We implemented tools for analysis as modules in the SlicerRT toolkit based on the 3D Slicer platform. We found that there were large DVH variation from the baseline for small structures or for structures located in regions with a high dose gradient, potentially leading to the creation of suboptimal treatment plans. CONCLUSION: This work demonstrates that labelmap and dose volume voxel size is an important factor in DVH accuracy, which must be accounted for in order to ensure the development of accurate treatment plans.

  5. Finding significantly connected voxels based on histograms of connection strengths

    NASA Astrophysics Data System (ADS)

    Kasenburg, Niklas; Pedersen, Morten Vester; Darkner, Sune

    2016-03-01

    We explore a new approach for structural connectivity based segmentations of subcortical brain regions. Connectivity based segmentations are usually based on fibre connections from a seed region to predefined target regions. We present a method for finding significantly connected voxels based on the distribution of connection strengths. Paths from seed voxels to all voxels in a target region are obtained from a shortest-path tractography. For each seed voxel we approximate the distribution with a histogram of path scores. We hypothesise that the majority of estimated connections are false-positives and that their connection strength is distributed differently from true-positive connections. Therefore, an empirical null-distribution is defined for each target region as the average normalized histogram over all voxels in the seed region. Single histograms are then tested against the corresponding null-distribution and significance is determined using the false discovery rate (FDR). Segmentations are based on significantly connected voxels and their FDR. In this work we focus on the thalamus and the target regions were chosen by dividing the cortex into a prefrontal/temporal zone, motor zone, somatosensory zone and a parieto-occipital zone. The obtained segmentations consistently show a sparse number of significantly connected voxels that are located near the surface of the anterior thalamus over a population of 38 subjects.

  6. ODVBA: optimally-discriminative voxel-based analysis.

    PubMed

    Zhang, Tianhao; Davatzikos, Christos

    2011-08-01

    Gaussian smoothing of images prior to applying voxel-based statistics is an important step in voxel-based analysis and statistical parametric mapping (VBA-SPM) and is used to account for registration errors, to Gaussianize the data and to integrate imaging signals from a region around each voxel. However, it has also become a limitation of VBA-SPM based methods, since it is often chosen empirically and lacks spatial adaptivity to the shape and spatial extent of the region of interest, such as a region of atrophy or functional activity. In this paper, we propose a new framework, named optimally-discriminative voxel-based analysis (ODVBA), for determining the optimal spatially adaptive smoothing of images, followed by applying voxel-based group analysis. In ODVBA, nonnegative discriminative projection is applied regionally to get the direction that best discriminates between two groups, e.g., patients and controls; this direction is equivalent to local filtering by an optimal kernel whose coefficients define the optimally discriminative direction. By considering all the neighborhoods that contain a given voxel, we then compose this information to produce the statistic for each voxel. Finally, permutation tests are used to obtain a statistical parametric map of group differences. ODVBA has been evaluated using simulated data in which the ground truth is known and with data from an Alzheimer's disease (AD) study. The experimental results have shown that the proposed ODVBA can precisely describe the shape and location of structural abnormality.

  7. Voxel-by-voxel analysis of brain SPECT perfusion in Fibromyalgia

    NASA Astrophysics Data System (ADS)

    Guedj, Eric; Taïeb, David; Cammilleri, Serge; Lussato, David; de Laforte, Catherine; Niboyet, Jean; Mundler, Olivier

    2007-02-01

    We evaluated brain perfusion SPECT at rest, without noxious stiumuli, in a homogeneous group of hyperalgesic FM patients. We performed a voxel-based analysis in comparison to a control group, matched for age and gender. Under such conditions, we made the assumption that significant cerebral perfusion abnormalities could be demonstrated, evidencing altered cerebral processing associated with spontaneous pain in FM patients. The secondary objective was to study the reversibility and the prognostic value of such possible perfusion abnormalities under specific treatment. Eighteen hyperalgesic FM women (mean age 48 yr; range 25-63 yr; ACR criteria) and 10 healthy women matched for age were enrolled in the study. A voxel-by-voxel group analysis was performed using SPM2 ( p<0.05, corrected for multiple comparisons). All brain SPECT were performed before any change was made in therapy in the pain care unit. A second SPECT was performed a month later after specific treatment by Ketamine. Compared to control subjects, we observed individual brain SPECT abnormalities in FM patients, confirmed by SPM2 analysis with hyperperfusion of the somatosensory cortex and hypoperfusion of the frontal, cingulate, medial temporal and cerebellar cortices. We also found that a medial frontal and anterior cingulate hypoperfusions were highly predictive (PPV=83%; NPV=91%) of non-response on Ketamine, and that only responders showed significant modification of brain perfusion, after treatment. In the present study performed without noxious stimuli in hyperalgesic FM patients, we found significant hyperperfusion in regions of the brain known to be involved in sensory dimension of pain processing and significant hypoperfusion in areas assumed to be associated with the affective dimension. As current pharmacological and non-pharmacological therapies act differently on both components of pain, we hypothesize that SPECT could be a valuable and readily available tool to guide individual therapeutic

  8. Rasterization and Voxelization of - and Three-Dimensional Space Partitionings

    NASA Astrophysics Data System (ADS)

    Gorte, Ben; Zlatanov, Sisi

    2016-06-01

    The paper presents a very straightforward and effective algorithm to convert a space partitioning, made up of polyhedral objects, into a 3D block of voxels, which is fully occupied, i.e. in which every voxel has a value. In addition to walls, floors, etc. there are 'air' voxels, which in turn may be distinguished as indoor and outdoor air. The method is a 3D extension of a 2D polygon-to-raster conversion algorithm. The input of the algorithm is a set of non-overlapping, closed polyhedra, which can be nested or touching. The air volume is not necessarily represented explicitly as a polyhedron (it can be treated as 'background', leading to the 'default' voxel value). The approach consists of two stages, the first being object (boundary) based, the second scan-line based. In addition to planar faces, other primitives, such as ellipsoids, can be accommodated in the first stage without affecting the second.

  9. A comparison between voxel-based cortical thickness and voxel-based morphometry in normal aging.

    PubMed

    Hutton, Chloe; Draganski, Bogdan; Ashburner, John; Weiskopf, Nikolaus

    2009-11-01

    The morphology of cortical grey matter is commonly assessed using T1-weighted MRI together with automated computerised methods such as voxel-based morphometry (VBM) and cortical thickness measures. In the presented study we investigate how grey matter changes identified using voxel-based cortical thickness (VBCT) measures compare with local grey matter volume changes identified using VBM. We use data from a healthy aging population to perform the comparison, focusing on brain regions where age-related changes have been observed in previous studies. Our results show that overall, in healthy aging, VBCT and VBM yield very consistent results but VBCT provides a more sensitive measure of age-associated decline in grey matter compared with VBM. Our findings suggest that while VBCT selectively investigates cortical thickness, VBM provides a mixed measure of grey matter including cortical surface area or cortical folding, as well as cortical thickness. We therefore propose that used together, these techniques can separate the underlying grey matter changes, highlighting the utility of combining these complementary methods. PMID:19559801

  10. Digital breast tomosynthesis reconstruction with an adaptive voxel grid

    NASA Astrophysics Data System (ADS)

    Claus, Bernhard; Chan, Heang-Ping

    2014-03-01

    In digital breast tomosynthesis (DBT) volume datasets are typically reconstructed with an anisotropic voxel size, where the in-plane voxel size usually reflects the detector pixel size (e.g., 0.1 mm), and the slice separation is generally between 0.5-1.0 mm. Increasing the tomographic angle is expected to give better 3D image quality; however, the slice spacing in the reconstruction should be reduced, otherwise one may risk losing fine-scale image detail (e.g., small microcalcifications). An alternative strategy consists of reconstructing on an adaptive voxel grid, where the voxel height at each location is adapted based on the backprojected data at this location, with the goal to improve image quality for microcalcifications. In this paper we present an approach for generating such an adaptive voxel grid. This approach is based on an initial reconstruction step that is performed at a finer slice-spacing combined with a selection of an "optimal" height for each voxel. This initial step is followed by a (potentially iterative) reconstruction acting now on the adaptive grid only.

  11. Voxel-based texture analysis of the brain.

    PubMed

    Maani, Rouzbeh; Yang, Yee Hong; Kalra, Sanjay

    2015-01-01

    This paper presents a novel voxel-based method for texture analysis of brain images. Texture analysis is a powerful quantitative approach for analyzing voxel intensities and their interrelationships, but has been thus far limited to analyzing regions of interest. The proposed method provides a 3D statistical map comparing texture features on a voxel-by-voxel basis. The validity of the method was examined on artificially generated effects as well as on real MRI data in Alzheimer's Disease (AD). The artificially generated effects included hyperintense and hypointense signals added to T1-weighted brain MRIs from 30 healthy subjects. The AD dataset included 30 patients with AD and 30 age/sex matched healthy control subjects. The proposed method detected artificial effects with high accuracy and revealed statistically significant differences between the AD and control groups. This paper extends the usage of texture analysis beyond the current region of interest analysis to voxel-by-voxel 3D statistical mapping and provides a hypothesis-free analysis tool to study cerebral pathology in neurological diseases.

  12. Voxel-Based Texture Analysis of the Brain

    PubMed Central

    Maani, Rouzbeh; Yang, Yee Hong; Kalra, Sanjay

    2015-01-01

    This paper presents a novel voxel-based method for texture analysis of brain images. Texture analysis is a powerful quantitative approach for analyzing voxel intensities and their interrelationships, but has been thus far limited to analyzing regions of interest. The proposed method provides a 3D statistical map comparing texture features on a voxel-by-voxel basis. The validity of the method was examined on artificially generated effects as well as on real MRI data in Alzheimer's Disease (AD). The artificially generated effects included hyperintense and hypointense signals added to T1-weighted brain MRIs from 30 healthy subjects. The AD dataset included 30 patients with AD and 30 age/sex matched healthy control subjects. The proposed method detected artificial effects with high accuracy and revealed statistically significant differences between the AD and control groups. This paper extends the usage of texture analysis beyond the current region of interest analysis to voxel-by-voxel 3D statistical mapping and provides a hypothesis-free analysis tool to study cerebral pathology in neurological diseases. PMID:25756621

  13. Coarse Point Cloud Registration by Egi Matching of Voxel Clusters

    NASA Astrophysics Data System (ADS)

    Wang, Jinhu; Lindenbergh, Roderik; Shen, Yueqian; Menenti, Massimo

    2016-06-01

    Laser scanning samples the surface geometry of objects efficiently and records versatile information as point clouds. However, often more scans are required to fully cover a scene. Therefore, a registration step is required that transforms the different scans into a common coordinate system. The registration of point clouds is usually conducted in two steps, i.e. coarse registration followed by fine registration. In this study an automatic marker-free coarse registration method for pair-wise scans is presented. First the two input point clouds are re-sampled as voxels and dimensionality features of the voxels are determined by principal component analysis (PCA). Then voxel cells with the same dimensionality are clustered. Next, the Extended Gaussian Image (EGI) descriptor of those voxel clusters are constructed using significant eigenvectors of each voxel in the cluster. Correspondences between clusters in source and target data are obtained according to the similarity between their EGI descriptors. The random sampling consensus (RANSAC) algorithm is employed to remove outlying correspondences until a coarse alignment is obtained. If necessary, a fine registration is performed in a final step. This new method is illustrated on scan data sampling two indoor scenarios. The results of the tests are evaluated by computing the point to point distance between the two input point clouds. The presented two tests resulted in mean distances of 7.6 mm and 9.5 mm respectively, which are adequate for fine registration.

  14. Laser-induced forward transfer (LIFT) of congruent voxels

    NASA Astrophysics Data System (ADS)

    Piqué, Alberto; Kim, Heungsoo; Auyeung, Raymond C. Y.; Beniam, Iyoel; Breckenfeld, Eric

    2016-06-01

    Laser-induced forward transfer (LIFT) of functional materials offers unique advantages and capabilities for the rapid prototyping of electronic, optical and sensor elements. The use of LIFT for printing high viscosity metallic nano-inks and nano-pastes can be optimized for the transfer of voxels congruent with the shape of the laser pulse, forming thin film-like structures non-lithographically. These processes are capable of printing patterns with excellent lateral resolution and thickness uniformity typically found in 3-dimensional stacked assemblies, MEMS-like structures and free-standing interconnects. However, in order to achieve congruent voxel transfer with LIFT, the particle size and viscosity of the ink or paste suspensions must be adjusted to minimize variations due to wetting and drying effects. When LIFT is carried out with high-viscosity nano-suspensions, the printed voxel size and shape become controllable parameters, allowing the printing of thin-film like structures whose shape is determined by the spatial distribution of the laser pulse. The result is a new level of parallelization beyond current serial direct-write processes whereby the geometry of each printed voxel can be optimized according to the pattern design. This work shows how LIFT of congruent voxels can be applied to the fabrication of 2D and 3D microstructures by adjusting the viscosity of the nano-suspension and laser transfer parameters.

  15. Modelo de galaxia disco

    NASA Astrophysics Data System (ADS)

    Ledesma, M.; Mosconi, M.

    El objetivo de este trabajo es estudiar la formación de galaxias anillo, a través de simulaciones numéricas. En el estudio numérico es necesario construir el modelo de una galaxia disco normal, en condición de equilibrio estable, que se ajuste a los parámetros observacionales disponibles de estos objetos. En dicho modelo se considera la galaxia constituída por un halo de materia oscura, un bulge y el disco propiamente dicho. A partir de perfiles de densidad obtenidos de las observaciones, se lleva a cabo la distribución espacial de las partículas, a través del ``Método del rechazo". La asignación de velocidades se realiza considerando que las partículas del disco están aproximadamente en equilibrio rotacional, y se agregan dispersiones de velocidad de acuerdo con el parámetro de Toomre Q=1.5.

  16. Compact encoding of 3-D voxel surfaces based on pattern code representation.

    PubMed

    Kim, Chang-Su; Lee, Sang-Uk

    2002-01-01

    In this paper, we propose a lossless compression algorithm for three-dimensional (3-D) binary voxel surfaces, based on the pattern code representation (PCR). In PCR, a voxel surface is represented by a series of pattern codes. The pattern of a voxel v is defined as the 3 x 3 x 3 array of voxels, centered on v. Therefore, the pattern code for informs of the local shape of the voxel surface around . The proposed algorithm can achieve the coding gain, since the patterns of adjacent voxels are highly correlated to each other. The performance of the proposed algorithm is evaluated using various voxel surfaces, which are scan-converted from triangular mesh models. It is shown that the proposed algorithm requires only 0.5 approximately 1 bits per black voxel (bpbv) to store or transmit the voxel surfaces.

  17. Selection of voxel size and photon number in voxel-based Monte Carlo method: criteria and applications

    NASA Astrophysics Data System (ADS)

    Li, Dong; Chen, Bin; Ran, Wei Yu; Wang, Guo Xiang; Wu, Wen Juan

    2015-09-01

    The voxel-based Monte Carlo method (VMC) is now a gold standard in the simulation of light propagation in turbid media. For complex tissue structures, however, the computational cost will be higher when small voxels are used to improve smoothness of tissue interface and a large number of photons are used to obtain accurate results. To reduce computational cost, criteria were proposed to determine the voxel size and photon number in 3-dimensional VMC simulations with acceptable accuracy and computation time. The selection of the voxel size can be expressed as a function of tissue geometry and optical properties. The photon number should be at least 5 times the total voxel number. These criteria are further applied in developing a photon ray splitting scheme of local grid refinement technique to reduce computational cost of a nonuniform tissue structure with significantly varying optical properties. In the proposed technique, a nonuniform refined grid system is used, where fine grids are used for the tissue with high absorption and complex geometry, and coarse grids are used for the other part. In this technique, the total photon number is selected based on the voxel size of the coarse grid. Furthermore, the photon-splitting scheme is developed to satisfy the statistical accuracy requirement for the dense grid area. Result shows that local grid refinement technique photon ray splitting scheme can accelerate the computation by 7.6 times (reduce time consumption from 17.5 to 2.3 h) in the simulation of laser light energy deposition in skin tissue that contains port wine stain lesions.

  18. Selection of voxel size and photon number in voxel-based Monte Carlo method: criteria and applications.

    PubMed

    Li, Dong; Chen, Bin; Ran, Wei Yu; Wang, Guo Xiang; Wu, Wen Juan

    2015-01-01

    The voxel-based Monte Carlo method (VMC) is now a gold standard in the simulation of light propagation in turbid media. For complex tissue structures, however, the computational cost will be higher when small voxels are used to improve smoothness of tissue interface and a large number of photons are used to obtain accurate results. To reduce computational cost, criteria were proposed to determine the voxel size and photon number in 3-dimensional VMC simulations with acceptable accuracy and computation time. The selection of the voxel size can be expressed as a function of tissue geometry and optical properties. The photon number should be at least 5 times the total voxel number. These criteria are further applied in developing a photon ray splitting scheme of local grid refinement technique to reduce computational cost of a nonuniform tissue structure with significantly varying optical properties. In the proposed technique, a nonuniform refined grid system is used, where fine grids are used for the tissue with high absorption and complex geometry, and coarse grids are used for the other part. In this technique, the total photon number is selected based on the voxel size of the coarse grid. Furthermore, the photon-splitting scheme is developed to satisfy the statistical accuracy requirement for the dense grid area. Result shows that local grid refinement technique photon ray splitting scheme can accelerate the computation by 7.6 times (reduce time consumption from 17.5 to 2.3 h) in the simulation of laser light energy deposition in skin tissue that contains port wine stain lesions. PMID:26417866

  19. Selection of voxel size and photon number in voxel-based Monte Carlo method: criteria and applications.

    PubMed

    Li, Dong; Chen, Bin; Ran, Wei Yu; Wang, Guo Xiang; Wu, Wen Juan

    2015-01-01

    The voxel-based Monte Carlo method (VMC) is now a gold standard in the simulation of light propagation in turbid media. For complex tissue structures, however, the computational cost will be higher when small voxels are used to improve smoothness of tissue interface and a large number of photons are used to obtain accurate results. To reduce computational cost, criteria were proposed to determine the voxel size and photon number in 3-dimensional VMC simulations with acceptable accuracy and computation time. The selection of the voxel size can be expressed as a function of tissue geometry and optical properties. The photon number should be at least 5 times the total voxel number. These criteria are further applied in developing a photon ray splitting scheme of local grid refinement technique to reduce computational cost of a nonuniform tissue structure with significantly varying optical properties. In the proposed technique, a nonuniform refined grid system is used, where fine grids are used for the tissue with high absorption and complex geometry, and coarse grids are used for the other part. In this technique, the total photon number is selected based on the voxel size of the coarse grid. Furthermore, the photon-splitting scheme is developed to satisfy the statistical accuracy requirement for the dense grid area. Result shows that local grid refinement technique photon ray splitting scheme can accelerate the computation by 7.6 times (reduce time consumption from 17.5 to 2.3 h) in the simulation of laser light energy deposition in skin tissue that contains port wine stain lesions.

  20. The influence of voxel size on atom probe tomography data.

    PubMed

    Torres, K L; Daniil, M; Willard, M A; Thompson, G B

    2011-05-01

    A methodology for determining the optimal voxel size for phase thresholding in nanostructured materials was developed using an atom simulator and a model system of a fixed two-phase composition and volume fraction. The voxel size range was banded by the atom count within each voxel. Some voxel edge lengths were found to be too large, resulting in an averaging of compositional fluctuations; others were too small with concomitant decreases in the signal-to-noise ratio for phase identification. The simulated methodology was then applied to the more complex experimentally determined data set collected from a (Co(0.95)Fe(0.05))(88)Zr(6)Hf(1)B(4)Cu(1) two-phase nanocomposite alloy to validate the approach. In this alloy, Zr and Hf segregated to an intergranular amorphous phase while Fe preferentially segregated to a crystalline phase during the isothermal annealing step that promoted primary crystallization. The atom probe data analysis of the volume fraction was compared to transmission electron microscopy (TEM) dark-field imaging analysis and a lever rule analysis of the volume fraction within the amorphous and crystalline phases of the ribbon.

  1. Geodesic Binding for Degenerate Character Geometry Using Sparse Voxelization.

    PubMed

    Dionne, Olivier; de Lasa, Martin

    2014-10-01

    We propose a fully automatic method for specifying influence weights for closed-form skinning methods, such as linear blend or dual quaternion skinning. Our method is designed to work with production meshes that may contain non-manifold geometry, be non-watertight, have intersecting triangles, or be comprised of multiple connected components. Starting from a character rest pose mesh and skeleton hierarchy, we first voxelize the input geometry. The resulting sparse voxelization is then used to calculate binding weights, based on the geodesic distance between each voxel lying on a skeleton "bone" and all non-exterior voxels. This yields smooth weights at interactive rates, without time-constants, iteration parameters, or costly optimization at bind or pose time. By decoupling weight assignment from distance computation we make it possible to modify weights interactively, at pose time, without additional pre-processing or computation. This allows artists to assess impact of weight selection in the context in which they are used. PMID:26357384

  2. Brain tissue segmentation in 4D CT using voxel classification

    NASA Astrophysics Data System (ADS)

    van den Boom, R.; Oei, M. T. H.; Lafebre, S.; Oostveen, L. J.; Meijer, F. J. A.; Steens, S. C. A.; Prokop, M.; van Ginneken, B.; Manniesing, R.

    2012-02-01

    A method is proposed to segment anatomical regions of the brain from 4D computer tomography (CT) patient data. The method consists of a three step voxel classification scheme, each step focusing on structures that are increasingly difficult to segment. The first step classifies air and bone, the second step classifies vessels and the third step classifies white matter, gray matter and cerebrospinal fluid. As features the time averaged intensity value and the temporal intensity change value were used. In each step, a k-Nearest-Neighbor classifier was used to classify the voxels. Training data was obtained by placing regions of interest in reconstructed 3D image data. The method has been applied to ten 4D CT cerebral patient data. A leave-one-out experiment showed consistent and accurate segmentation results.

  3. Real-time 3D human pose recognition from reconstructed volume via voxel classifiers

    NASA Astrophysics Data System (ADS)

    Yoo, ByungIn; Choi, Changkyu; Han, Jae-Joon; Lee, Changkyo; Kim, Wonjun; Suh, Sungjoo; Park, Dusik; Kim, Junmo

    2014-03-01

    This paper presents a human pose recognition method which simultaneously reconstructs a human volume based on ensemble of voxel classifiers from a single depth image in real-time. The human pose recognition is a difficult task since a single depth camera can capture only visible surfaces of a human body. In order to recognize invisible (self-occluded) surfaces of a human body, the proposed algorithm employs voxel classifiers trained with multi-layered synthetic voxels. Specifically, ray-casting onto a volumetric human model generates a synthetic voxel, where voxel consists of a 3D position and ID corresponding to the body part. The synthesized volumetric data which contain both visible and invisible body voxels are utilized to train the voxel classifiers. As a result, the voxel classifiers not only identify the visible voxels but also reconstruct the 3D positions and the IDs of the invisible voxels. The experimental results show improved performance on estimating the human poses due to the capability of inferring the invisible human body voxels. It is expected that the proposed algorithm can be applied to many fields such as telepresence, gaming, virtual fitting, wellness business, and real 3D contents control on real 3D displays.

  4. Monte Carlo study of voxel S factor dependence on tissue density and atomic composition

    NASA Astrophysics Data System (ADS)

    Amato, Ernesto; Italiano, Antonio; Baldari, Sergio

    2013-11-01

    Voxel dosimetry is a common approach to the internal dosimetry of non-uniform activity distributions in nuclear medicine therapies with radiopharmaceuticals and in the estimation of the radiation hazard due to internal contamination of radionuclides. Aim of the present work is to extend our analytical approach for the calculation of voxel S factors to materials different from the soft tissue. We used a Monte Carlo simulation in GEANT4 of a voxelized region of each material in which the source of monoenergetic electrons or photons was uniformly distributed within the central voxel, and the energy deposition was scored over the surrounding 11×11×11 voxels. Voxel S factors were obtained for the following standard ICRP materials: Adipose tissue, Bone cortical, Brain, Lung, Muscle skeletal and Tissue soft with 1 g cm-3 density. Moreover, we considered the standard ICRU materials: Bone compact and Muscle striated. Voxel S factors were represented as a function of the “normalized radius”, defined as the ratio between the source-target voxel distance and the voxel side. We found that voxel S factors and related analytical fit functions are mainly affected by the tissue density, while the material composition gives only a slight contribution to the difference between data series, which is negligible for practical purposes. Our results can help in broadening the dosimetric three-dimensional approach based on voxel S factors to other tissues where diagnostic and therapeutic radionuclides can be taken up and radiation can propagate.

  5. Fast construction of voxel-level functional connectivity graphs

    PubMed Central

    2014-01-01

    Background Graph-based analysis of fMRI data has recently emerged as a promising approach to study brain networks. Based on the assessment of synchronous fMRI activity at separate brain sites, functional connectivity graphs are constructed and analyzed using graph-theoretical concepts. Most previous studies investigated region-level graphs, which are computationally inexpensive, but bring along the problem of choosing sensible regions and involve blurring of more detailed information. In contrast, voxel-level graphs provide the finest granularity attainable from the data, enabling analyses at superior spatial resolution. They are, however, associated with considerable computational demands, which can render high-resolution analyses infeasible. In response, many existing studies investigating functional connectivity at the voxel-level reduced the computational burden by sacrificing spatial resolution. Methods Here, a novel, time-efficient method for graph construction is presented that retains the original spatial resolution. Performance gains are instead achieved through data reduction in the temporal domain based on dichotomization of voxel time series combined with tetrachoric correlation estimation and efficient implementation. Results By comparison with graph construction based on Pearson’s r, the technique used by the majority of previous studies, we find that the novel approach produces highly similar results an order of magnitude faster. Conclusions Its demonstrated performance makes the proposed approach a sensible and efficient alternative to customary practice. An open source software package containing the created programs is freely available for download. PMID:24947161

  6. A voxel visualization and analysis system based on AutoCAD

    NASA Astrophysics Data System (ADS)

    Marschallinger, Robert

    1996-05-01

    A collection of AutoLISP programs is presented which enable the visualization and analysis of voxel models by AutoCAD rel. 12/rel. 13. The programs serve as an interactive, graphical front end for manipulating the results of three-dimensional modeling software producing block estimation data. ASCII data files describing geometry and attributes per estimation block are imported and stored as a voxel array. Each voxel may contain multiple attributes, therefore different parameters may be incorporated in one voxel array. Voxel classification is implemented on a layer basis providing flexible treatment of voxel classes such as recoloring, peeling, or volumetry. A versatile clipping tool enables slicing voxel arrays according to combinations of three perpendicular clipping planes. The programs feature an up-to-date, graphical user interface for user-friendly operation by non AutoCAD specialists.

  7. Voxel-by-voxel correlations of perfusion, substrate, and metabolite signals in dynamic hyperpolarized (13) C imaging.

    PubMed

    Lau, Justin Y C; Chen, Albert P; Gu, Yi-Ping; Cunningham, Charles H

    2016-08-01

    In this study, a mixture of pyruvic acid and the perfusion agent HP001 was co-polarized for simultaneous assessment of perfusion and metabolism in vivo. The pre-polarized mixture was administered to rats with subcutaneous MDA-MB-231 breast cancer xenografts and imaged using an interleaved sequence with designed spectral-spatial pulses and flyback echo-planar readouts. Voxel-by-voxel signal correlations from 10 animals (15 data sets) were analyzed for tumour, kidney, and muscle regions of interest. The relationship between perfusion and hyperpolarized signal was explored on a voxel-by-voxel basis in various metabolically active tissues, including tumour, healthy kidneys, and skeletal muscle. Positive pairwise correlations between lactate, pyruvate, and HP001 observed in all 10 tumours suggested that substrate delivery was the dominant factor limiting the conversion of pyruvate to lactate in the tumour model used in this study. On the other hand, in cases where conversion is the limiting factor, such as in healthy kidneys, both pyruvate and lactate can act as excellent perfusion markers. In intermediate cases between the two limits, such as in skeletal muscle, some perfusion information may be inferred from the (pyruvate + lactate) signal distribution. Co-administration of pyruvate with a dynamic nuclear polarization (DNP) perfusion agent is an effective approach for distinguishing between slow metabolism and poor perfusion and a practical strategy for lactate signal normalization to account for substrate delivery, especially in cases of rapid pyruvate-to-lactate conversion and in poorly perfused regions with inadequate pyruvate signal-to-noise ratio for reliable determination of the lactate-to-pyruvate ratio. Copyright © 2016 John Wiley & Sons, Ltd.

  8. Comparing voxel-based iterative sensitivity and voxel-based morphometry to detect abnormalities in T2-weighted MRI.

    PubMed

    Diaz-de-Grenu, Lara Z; Acosta-Cabronero, Julio; Williams, Guy B; Nestor, Peter J

    2014-10-15

    This study aimed to test the superiority proposed by Abbott et al. (2011) of their Voxel based iterative sensitivity (VBIS) method over Voxel Based Morphometry using T2-weighted images (T2-VBM), in detecting intensity changes in Alzheimer's disease (AD). A comparison was made first in simulated intensity lesions and then in AD patients. Intensity changes were evaluated in the whole-brain with VBIS and with a simple intensity-based approach and in specific tissue classes with the conventional VBM method of using tissue probability segments. Results showed that VBIS performed well in the simulated environment though it showed no superiority in detecting the lesion compared to the much simpler VBM approach. The VBIS method, however, failed to detect any meaningful signal intensity reduction in AD patient data. Moreover, its whole brain approach was contaminated by the excess cerebrospinal fluid signal (very bright on T2-weighted scans) in areas of maximal measurable atrophy (mesial temporal lobes); this gave rise to spurious signal intensity increases in these regions in AD. The same artefact was observed for both intensity-based methods but not with the conventional VBM approach of performing statistics on grey matter segments. In conclusion, no evidence was found to indicate that VBIS offers benefits over T2-VBM in AD, nor in simulation intensity lesions. The study highlights the necessity of empirically testing voxel-based analysis techniques rather than merely claiming superiority of one method over another on theoretical grounds.

  9. Fast voxel and polygon ray-tracing algorithms in intensity modulated radiation therapy treatment planning

    SciTech Connect

    Fox, Christopher; Romeijn, H. Edwin; Dempsey, James F.

    2006-05-15

    We present work on combining three algorithms to improve ray-tracing efficiency in radiation therapy dose computation. The three algorithms include: An improved point-in-polygon algorithm, incremental voxel ray tracing algorithm, and stereographic projection of beamlets for voxel truncation. The point-in-polygon and incremental voxel ray-tracing algorithms have been used in computer graphics and nuclear medicine applications while the stereographic projection algorithm was developed by our group. These algorithms demonstrate significant improvements over the current standard algorithms in peer reviewed literature, i.e., the polygon and voxel ray-tracing algorithms of Siddon for voxel classification (point-in-polygon testing) and dose computation, respectively, and radius testing for voxel truncation. The presented polygon ray-tracing technique was tested on 10 intensity modulated radiation therapy (IMRT) treatment planning cases that required the classification of between 0.58 and 2.0 million voxels on a 2.5 mm isotropic dose grid into 1-4 targets and 5-14 structures represented as extruded polygons (a.k.a. Siddon prisms). Incremental voxel ray tracing and voxel truncation employing virtual stereographic projection was tested on the same IMRT treatment planning cases where voxel dose was required for 230-2400 beamlets using a finite-size pencil-beam algorithm. Between a 100 and 360 fold cpu time improvement over Siddon's method was observed for the polygon ray-tracing algorithm to perform classification of voxels for target and structure membership. Between a 2.6 and 3.1 fold reduction in cpu time over current algorithms was found for the implementation of incremental ray tracing. Additionally, voxel truncation via stereographic projection was observed to be 11-25 times faster than the radial-testing beamlet extent approach and was further improved 1.7-2.0 fold through point-classification using the method of translation over the cross product technique.

  10. Voxelization algorithms for geospatial applications: Computational methods for voxelating spatial datasets of 3D city models containing 3D surface, curve and point data models.

    PubMed

    Nourian, Pirouz; Gonçalves, Romulo; Zlatanova, Sisi; Ohori, Ken Arroyo; Vu Vo, Anh

    2016-01-01

    Voxel representations have been used for years in scientific computation and medical imaging. The main focus of our research is to provide easy access to methods for making large-scale voxel models of built environment for environmental modelling studies while ensuring they are spatially correct, meaning they correctly represent topological and semantic relations among objects. In this article, we present algorithms that generate voxels (volumetric pixels) out of point cloud, curve, or surface objects. The algorithms for voxelization of surfaces and curves are a customization of the topological voxelization approach [1]; we additionally provide an extension of this method for voxelization of point clouds. The developed software has the following advantages:•It provides easy management of connectivity levels in the resulting voxels.•It is not dependant on any external library except for primitive types and constructs; therefore, it is easy to integrate them in any application.•One of the algorithms is implemented in C++ and C for platform independence and efficiency.

  11. Voxelization algorithms for geospatial applications: Computational methods for voxelating spatial datasets of 3D city models containing 3D surface, curve and point data models.

    PubMed

    Nourian, Pirouz; Gonçalves, Romulo; Zlatanova, Sisi; Ohori, Ken Arroyo; Vu Vo, Anh

    2016-01-01

    Voxel representations have been used for years in scientific computation and medical imaging. The main focus of our research is to provide easy access to methods for making large-scale voxel models of built environment for environmental modelling studies while ensuring they are spatially correct, meaning they correctly represent topological and semantic relations among objects. In this article, we present algorithms that generate voxels (volumetric pixels) out of point cloud, curve, or surface objects. The algorithms for voxelization of surfaces and curves are a customization of the topological voxelization approach [1]; we additionally provide an extension of this method for voxelization of point clouds. The developed software has the following advantages:•It provides easy management of connectivity levels in the resulting voxels.•It is not dependant on any external library except for primitive types and constructs; therefore, it is easy to integrate them in any application.•One of the algorithms is implemented in C++ and C for platform independence and efficiency. PMID:27408832

  12. Mapping protein abundance patterns in the brain using voxelation combined with liquid chromatography and mass spectrometry

    SciTech Connect

    Petyuk, Vladislav A.; Qian, Weijun; Smith, Richard D.; Smith, Desmond J.

    2010-02-01

    Voxelation creates expression atlases by high-throughput analysis of spatially registered cubes or voxels harvested from the brain. The modality independence of voxelation allows a variety of bioanalytical techniques to be used to map abundance. Protein expression patterns in the brain can be obtained using liquid chromatography (LC) combined with mass spectrometry (MS). Here we describe the methodology of voxelation as it pertains particularly to LC-MS proteomic analysis: sample preparation, instrumental set up and analysis, peptide identification and protein relative abundance quantitation. We also briefly describe some of the advantages, limitations and insights into the brain that can be obtained using combined proteomic and transcriptomic maps

  13. WE-D-BRE-06: Quantification of Dose-Response for High Grade Esophagtis Patients Using a Novel Voxel-To-Voxel Method

    SciTech Connect

    Niedzielski, J; Martel, M; Tucker, S; Gomez, D; Court, L; Yang, J; Briere, T

    2014-06-15

    Purpose: Radiation induces an inflammatory response in the esophagus, discernible on CT studies. This work objectively quantifies the voxel esophageal radiation-response for patients with acute esophagitis. This knowledge is an important first-step towards predicting the effect of complex dose distributions on patient esophagitis symptoms. Methods: A previously validated voxel-based methodology of quantifying radiation esophagitis severity was used to identify the voxel dose-response for 18 NSCLC patients with severe esophagitis (CTCAE grading criteria, grade2 or higher). The response is quantified as percent voxel volume change for a given dose. During treatment (6–8 weeks), patients had weekly 4DCT studies and esophagitis scoring. Planning CT esophageal contours were deformed to each weekly CT using a demons DIR algorithm. An algorithm using the Jacobian Map from the DIR of the planning CT to all weekly CTs was used to quantify voxel-volume change, along with corresponding delivered voxel dose, to the planning voxel. Dose for each voxel for each time-point was calculated on each previous weekly CT image, and accumulated using DIR. Thus, for each voxel, the volume-change and delivered dose was calculated for each time-point. The data was binned according to when the volume-change first increased by a threshold volume (10%–100%, in 10% increments), and the average delivered dose calculated for each bin. Results: The average dose resulting in a voxel volume increase of 10–100% was 21.6 to 45.9Gy, respectively. The mean population dose to give a 50% volume increase was 36.3±4.4Gy, (range:29.8 to 43.5Gy). The average week of 50% response was 4.1 (range:4.9 to 2.8 weeks). All 18 patients showed similar dose to first response curves, showing a common trend in the initial inflammatoryresponse. Conclusion: We extracted the dose-response curve of the esophagus on a voxel-to-voxel level. This may be useful for estimating the esophagus response (and patient symptoms

  14. Single Voxel Proton Spectroscopy for Neurofeedback at 7 Tesla.

    PubMed

    Koush, Yury; Elliott, Mark A; Mathiak, Klaus

    2011-09-01

    Echo-planar imaging (EPI) in fMRI is regularly used to reveal BOLD activation in presubscribed regions of interest (ROI). The response is mediated by relative changes in T2* which appear as changes in the image pixel intensities. We have proposed an application of functional single-voxel proton spectroscopy (fSVPS) for real-time studies at ultra-high MR field which can be comparable to the EPI BOLD fMRI technique. A spin-echo SVPS protocol without water suppression was acquired with 310 repetitions on a 7T Siemens MR scanner (TE/TR = 20/1000 ms, flip angle α = 90°, voxel size 10 × 10 × 10 mm(3)). Transmitter reference voltage was optimized for the voxel location. Spectral processing of the water signal free induction decay (FID) using log-linear regression was used to estimate the T2* change between rest and activation of a functional task. The FID spectrum was filtered with a Gaussian window around the water peak, and log-linear regression was optimized for the particular ROI by adoption of the linearization length. The spectroscopic voxel was positioned on an ROI defined from a real-time fMRI EPI BOLD localizer. Additional online signal processing algorithms performed signal drift removal (exponential moving average), despiking and low-pass filtering (modified Kalman filter) and, finally, the dynamic feedback signal normalization. Two functional tasks were used to estimate the sensitivity of the SVPS method compared to BOLD signal changes, namely the primary motor cortex (PMC, left hand finger tapping) and visual cortex (VC, blinking checkerboard). Four healthy volunteers performed these tasks and an additional session using real-time signal feedback modulating their activation level of the PMC. Results show that single voxel spectroscopy is able to provide a good and reliable estimation of the BOLD signal changes. Small data size and FID signal processing instead of processing entire brain volumes as well as more information revealed from the acquired total

  15. Voxel Based Representation of Full-Waveform Airborne Laser Scanner Data for Forestry Applications

    NASA Astrophysics Data System (ADS)

    Stelling, N.; Richter, K.

    2016-06-01

    The advantages of using airborne full-waveform laser scanner data in forest applications, e.g. for the description of the vertical vegetation structure or accurate biomass estimation, have been emphasized in many publications. To exploit the full potential offered by airborne full-waveform laser scanning data, the development of voxel based methods for data analysis is essential. In contrast to existing approaches based on the extraction of discrete 3D points by a Gaussian decomposition, it is very promising to derive the voxel attributes from the digitised waveform directly. For this purpose, the waveform data have to be transferred into a 3D voxel representation. This requires a series of radiometric and geometric transformations of the raw full-waveform laser scanner data. Thus, the paper deals with the geometric aspects and describes a processing chain from the raw waveform data to an attenuationcorrected volumetric forest stand reconstruction. The integration of attenuation-corrected waveform data into the voxel space is realised with an efficient parametric voxel traversal method operating on an octree data structure. The voxel attributes are derived from the amplitudes of the attenuation-corrected waveforms. Additionally, a new 3D filtering approach is presented to eliminate non-object voxel. Applying these methods to real full-waveform laser scanning data, a voxel based representation of a spruce was generated combining three flight strips from different viewing directions.

  16. Probing the mysterious underpinnings of multi-voxel fMRI analyses.

    PubMed

    Op de Beeck, Hans P

    2010-04-01

    Various arguments have been proposed for or against sub-voxel sensitivity or hyperacuity in functional magnetic resonance imaging (fMRI) at standard resolution. Sub-voxel sensitivity might exist, but nevertheless the performance of multi-voxel fMRI analyses is very likely to be dominated by a larger-scale organization, even if this organization is very weak. Up to now, most arguments are indirect in nature: they do not in themselves proof or contradict sub-voxel sensitivity, but they are suggestive, seem consistent or not with sub-voxel sensitivity, or show that the principle might or might not work. Here the previously proposed smoothing argument against hyperacuity is extended with simulations that include more realistic signal, noise, and analysis properties than any of the simulations presented before. These simulations confirm the relevance of the smoothing approach to find out the scale of the functional maps that underlie the outcome of multi-voxel analyses, at least in relative terms (differences in the scale of different maps). However, image smoothing, like most other arguments in the literature, is an indirect argument, and at the end of the day such arguments are not sufficient to decide the issue on whether and how much sub-voxel maps contribute. A few suggestions are made about the type of evidence that is needed to help us understand the as yet mysterious underpinnings of multi-voxel fMRI analyses.

  17. 3D change detection in staggered voxels model for robotic sensing and navigation

    NASA Astrophysics Data System (ADS)

    Liu, Ruixu; Hampshire, Brandon; Asari, Vijayan K.

    2016-05-01

    3D scene change detection is a challenging problem in robotic sensing and navigation. There are several unpredictable aspects in performing scene change detection. A change detection method which can support various applications in varying environmental conditions is proposed. Point cloud models are acquired from a RGB-D sensor, which provides the required color and depth information. Change detection is performed on robot view point cloud model. A bilateral filter smooths the surface and fills the holes as well as keeps the edge details on depth image. Registration of the point cloud model is implemented by using Random Sample Consensus (RANSAC) algorithm. It uses surface normal as the previous stage for the ground and wall estimate. After preprocessing the data, we create a point voxel model which defines voxel as surface or free space. Then we create a color model which defines each voxel that has a color by the mean of all points' color value in this voxel. The preliminary change detection is detected by XOR subtract on the point voxel model. Next, the eight neighbors for this center voxel are defined. If they are neither all `changed' voxels nor all `no changed' voxels, a histogram of location and hue channel color is estimated. The experimental evaluations performed to evaluate the capability of our algorithm show promising results for novel change detection that indicate all the changing objects with very limited false alarm rate.

  18. Rapid three-dimensional quantification of voxel-wise collagen fiber orientation.

    PubMed

    Liu, Zhiyi; Quinn, Kyle P; Speroni, Lucia; Arendt, Lisa; Kuperwasser, Charlotte; Sonnenschein, Carlos; Soto, Ana M; Georgakoudi, Irene

    2015-07-01

    Defining fiber orientation at each voxel within a 3D biomedical image stack is potentially useful for a variety of applications, including cancer, wound healing and tissue regeneration. Current methods are typically computationally intensive or inaccurate. Herein, we present a 3D weighted orientation vector summation algorithm, which is a generalization of a previously reported 2D vector summation technique aimed at quantifying collagen fiber orientations simultaneously at each voxel of an image stack. As a result, voxel-wise fiber orientation information with 4° to 5° accuracy can be determined, and the computational time required to analyze a typical stack with the size of 512x512x100 voxels is less than 5 min. Thus, this technique enables the practical extraction of voxel-specific orientation data for characterizing structural anisotropy in 3D specimens. As examples, we use this approach to characterize the fiber organization in an excised mouse mammary gland and a 3D breast tissue model.

  19. Monte Carlo-based diffusion tensor tractography with a geometrically corrected voxel-centre connecting method

    NASA Astrophysics Data System (ADS)

    Bodammer, N. C.; Kaufmann, J.; Kanowski, M.; Tempelmann, C.

    2009-02-01

    Diffusion tensor tractography (DTT) allows one to explore axonal connectivity patterns in neuronal tissue by linking local predominant diffusion directions determined by diffusion tensor imaging (DTI). The majority of existing tractography approaches use continuous coordinates for calculating single trajectories through the diffusion tensor field. The tractography algorithm we propose is characterized by (1) a trajectory propagation rule that uses voxel centres as vertices and (2) orientation probabilities for the calculated steps in a trajectory that are obtained from the diffusion tensors of either two or three voxels. These voxels include the last voxel of each previous step and one or two candidate successor voxels. The precision and the accuracy of the suggested method are explored with synthetic data. Results clearly favour probabilities based on two consecutive successor voxels. Evidence is also provided that in any voxel-centre-based tractography approach, there is a need for a probability correction that takes into account the geometry of the acquisition grid. Finally, we provide examples in which the proposed fibre-tracking method is applied to the human optical radiation, the cortico-spinal tracts and to connections between Broca's and Wernicke's area to demonstrate the performance of the proposed method on measured data.

  20. Multi-voxel algorithm for quantitative bi-exponential MRI T1 estimation

    NASA Astrophysics Data System (ADS)

    Bladt, P.; Van Steenkiste, G.; Ramos-Llordén, G.; den Dekker, A. J.; Sijbers, J.

    2016-03-01

    Quantification of the spin-lattice relaxation time, T1, of tissues is important for characterization of tissues in clinical magnetic resonance imaging (MRI). In T1 mapping, T1 values are estimated from a set of T1-weighted MRI images. Due to the limited spatial resolution of the T1-weighted images, one voxel might consist of two tissues, causing partial volume effects (PVE). In conventional mono-exponential T1 estimation, these PVE result in systematic errors in the T1 map. To account for PVE, single-voxel bi-exponential estimators have been suggested. Unfortunately, in general, they suffer from low accuracy and precision. In this work, we propose a joint multi-voxel bi-exponential T1 estimator (JMBE) and compare its performance to a single-voxel bi-exponential T1 estimator (SBE). Results show that, in contrast to the SBE, and for clinically achievable single-voxel SNRs, the JMBE is accurate and efficient if four or more neighboring voxels are used in the joint estimation framework. This illustrates that, for clinically realistic SNRs, accurate results for quantitative biexponential T1 estimation are only achievable if information of neighboring voxels is incorporated.

  1. Influence of exposure factors on the variability of CBCT voxel values: a phantom study

    PubMed Central

    Freitas, D Q; Ambrosano, G M B; Haiter-Neto, F

    2014-01-01

    Objectives: To assess the influence of milliamperage and kilovolt peak (kVp) on the variability of cone beam CT (CBCT) voxel values. Methods: CBCT scans were obtained from radiographic phantoms in varying concentrations of dipotassium hydrogen phosphate solutions (200–1200 mg ml−1) under different protocols of milliamperage and kVp. In addition, scans were performed with and without a dental implant and exo-mass. The variability of CBCT voxel values was measured on each scan, and factorial analysis of variance and the post hoc Tukey test were performed (α = 0.05). Linear regression was performed to assess the relationship between voxel value variability and dipotassium hydrogen phosphate concentration. Results: milliamperage and the presence of a dental implant did not produce significant interference (p = 0.28 and 0.87, respectively) in voxel value variability. Scans at the highest kVp value presented a significant reduction (p ≤ 0.0001) in voxel value variability when only exo-mass was not present. Voxel value variability was not influenced by exo-mass in scans at the highest levels of milliamperage and kVp. The presence of exo-mass produced a significant reduction (p ≤ 0.0001) in voxel value variability in most of the scans. Higher concentrations yielded greater variations in voxel values in all scans, except for those operating at the highest levels of mAs and kVp. Conclusions: mAs did not influence the variability of CBCT voxel values; higher kVp reduced such variability when only the object was smaller than the field of view. PMID:24869906

  2. A voxel-based technique to estimate the volume of trees from terrestrial laser scanner data

    NASA Astrophysics Data System (ADS)

    Bienert, A.; Hess, C.; Maas, H.-G.; von Oheimb, G.

    2014-06-01

    The precise determination of the volume of standing trees is very important for ecological and economical considerations in forestry. If terrestrial laser scanner data are available, a simple approach for volume determination is given by allocating points into a voxel structure and subsequently counting the filled voxels. Generally, this method will overestimate the volume. The paper presents an improved algorithm to estimate the wood volume of trees using a voxel-based method which will correct for the overestimation. After voxel space transformation, each voxel which contains points is reduced to the volume of its surrounding bounding box. In a next step, occluded (inner stem) voxels are identified by a neighbourhood analysis sweeping in the X and Y direction of each filled voxel. Finally, the wood volume of the tree is composed by the sum of the bounding box volumes of the outer voxels and the volume of all occluded inner voxels. Scan data sets from several young Norway maple trees (Acer platanoides) were used to analyse the algorithm. Therefore, the scanned trees as well as their representing point clouds were separated in different components (stem, branches) to make a meaningful comparison. Two reference measurements were performed for validation: A direct wood volume measurement by placing the tree components into a water tank, and a frustum calculation of small trunk segments by measuring the radii along the trunk. Overall, the results show slightly underestimated volumes (-0.3% for a probe of 13 trees) with a RMSE of 11.6% for the individual tree volume calculated with the new approach.

  3. A free database of radionuclide voxel S values for the dosimetry of nonuniform activity distributions.

    PubMed

    Lanconelli, N; Pacilio, M; Lo Meo, S; Botta, F; Di Dia, A; Aroche, A Torres; Pérez, M A Coca; Cremonesi, M

    2012-01-21

    The increasing availability of SPECT/CT devices with advanced technology offers the opportunity for the accurate assessment of the radiation dose to the biological target volume during radionuclide therapy. Voxel dosimetry can be performed employing direct Monte Carlo radiation transport simulations, based on both morphological and functional images of the patient. On the other hand, for voxel dosimetry calculations the voxel S value method can be considered an easier approach than patient-specific Monte Carlo simulations, ensuring a good dosimetric accuracy at least for anatomic regions which are characterized by uniform density tissue. However, this approach has been limited because of the lack of tabulated S values for different voxel dimensions and radionuclides. The aim of this work is to provide a free dataset of values which can be used for voxel dosimetry in targeted radionuclide studies. Seven different radionuclides (89Sr, 90Y, 131I, 153Sm, 177Lu, 186Re, 188Re), and 13 different voxel sizes (2.21, 2.33, 2.4, 3, 3.59, 3.9, 4, 4.42, 4.8, 5, 6, 6.8 and 9.28 mm) are considered. Voxel S values are calculated performing simulations of monochromatic photon and electron sources in two different homogeneous tissues (soft tissue and bone) with DOSXYZnrc code, and weighting the contributions on the basis of the radionuclide emission spectra. The outcomes are validated by comparison with Monte Carlo simulations obtained with other codes (PENELOPE and MCNP4c) performing direct simulation of the radionuclide emission spectra. The differences among the different Monte Carlo codes are of the order of a few per cent when considering the source voxel and the bremsstrahlung tail, whereas the highest differences are observed at a distance close to the maximum continuous slowing down approximation range of electrons. These discrepancies would negligibly affect dosimetric assessments. The dataset of voxel S values can be freely downloaded from the website www.medphys.it.

  4. A free database of radionuclide voxel S values for the dosimetry of nonuniform activity distributions

    NASA Astrophysics Data System (ADS)

    Lanconelli, N.; Pacilio, M.; Lo Meo, S.; Botta, F.; Di Dia, A.; Torres Aroche, L. A.; Coca Pérez, M. A.; Cremonesi, M.

    2012-01-01

    The increasing availability of SPECT/CT devices with advanced technology offers the opportunity for the accurate assessment of the radiation dose to the biological target volume during radionuclide therapy. Voxel dosimetry can be performed employing direct Monte Carlo radiation transport simulations, based on both morphological and functional images of the patient. On the other hand, for voxel dosimetry calculations the voxel S value method can be considered an easier approach than patient-specific Monte Carlo simulations, ensuring a good dosimetric accuracy at least for anatomic regions which are characterized by uniform density tissue. However, this approach has been limited because of the lack of tabulated S values for different voxel dimensions and radionuclides. The aim of this work is to provide a free dataset of values which can be used for voxel dosimetry in targeted radionuclide studies. Seven different radionuclides (89Sr, 90Y, 131I, 153Sm, 177Lu, 186Re, 188Re), and 13 different voxel sizes (2.21, 2.33, 2.4, 3, 3.59, 3.9, 4, 4.42, 4.8, 5, 6, 6.8 and 9.28 mm) are considered. Voxel S values are calculated performing simulations of monochromatic photon and electron sources in two different homogeneous tissues (soft tissue and bone) with DOSXYZnrc code, and weighting the contributions on the basis of the radionuclide emission spectra. The outcomes are validated by comparison with Monte Carlo simulations obtained with other codes (PENELOPE and MCNP4c) performing direct simulation of the radionuclide emission spectra. The differences among the different Monte Carlo codes are of the order of a few per cent when considering the source voxel and the bremsstrahlung tail, whereas the highest differences are observed at a distance close to the maximum continuous slowing down approximation range of electrons. These discrepancies would negligibly affect dosimetric assessments. The dataset of voxel S values can be freely downloaded from the website www.medphys.it.

  5. What do differences between multi-voxel and univariate analysis mean? How subject-, voxel-, and trial-level variance impact fMRI analysis.

    PubMed

    Davis, Tyler; LaRocque, Karen F; Mumford, Jeanette A; Norman, Kenneth A; Wagner, Anthony D; Poldrack, Russell A

    2014-08-15

    Multi-voxel pattern analysis (MVPA) has led to major changes in how fMRI data are analyzed and interpreted. Many studies now report both MVPA results and results from standard univariate voxel-wise analysis, often with the goal of drawing different conclusions from each. Because MVPA results can be sensitive to latent multidimensional representations and processes whereas univariate voxel-wise analysis cannot, one conclusion that is often drawn when MVPA and univariate results differ is that the activation patterns underlying MVPA results contain a multidimensional code. In the current study, we conducted simulations to formally test this assumption. Our findings reveal that MVPA tests are sensitive to the magnitude of voxel-level variability in the effect of a condition within subjects, even when the same linear relationship is coded in all voxels. We also find that MVPA is insensitive to subject-level variability in mean activation across an ROI, which is the primary variance component of interest in many standard univariate tests. Together, these results illustrate that differences between MVPA and univariate tests do not afford conclusions about the nature or dimensionality of the neural code. Instead, targeted tests of the informational content and/or dimensionality of activation patterns are critical for drawing strong conclusions about the representational codes that are indicated by significant MVPA results. PMID:24768930

  6. What do differences between multi-voxel and univariate analysis mean? How subject-, voxel-, and trial-level variance impact fMRI analysis.

    PubMed

    Davis, Tyler; LaRocque, Karen F; Mumford, Jeanette A; Norman, Kenneth A; Wagner, Anthony D; Poldrack, Russell A

    2014-08-15

    Multi-voxel pattern analysis (MVPA) has led to major changes in how fMRI data are analyzed and interpreted. Many studies now report both MVPA results and results from standard univariate voxel-wise analysis, often with the goal of drawing different conclusions from each. Because MVPA results can be sensitive to latent multidimensional representations and processes whereas univariate voxel-wise analysis cannot, one conclusion that is often drawn when MVPA and univariate results differ is that the activation patterns underlying MVPA results contain a multidimensional code. In the current study, we conducted simulations to formally test this assumption. Our findings reveal that MVPA tests are sensitive to the magnitude of voxel-level variability in the effect of a condition within subjects, even when the same linear relationship is coded in all voxels. We also find that MVPA is insensitive to subject-level variability in mean activation across an ROI, which is the primary variance component of interest in many standard univariate tests. Together, these results illustrate that differences between MVPA and univariate tests do not afford conclusions about the nature or dimensionality of the neural code. Instead, targeted tests of the informational content and/or dimensionality of activation patterns are critical for drawing strong conclusions about the representational codes that are indicated by significant MVPA results.

  7. Calculation of Dose Deposition in 3D Voxels by Heavy Ions

    NASA Technical Reports Server (NTRS)

    Plante, Ianik; Cucinotta, Francis A.

    2010-01-01

    The biological response to high-LET radiation is very different from low-LET radiation, and can be partly attributed to the energy deposition by the radiation. Several experiments, notably detection of gamma-H2AX foci by immunofluorescence, has revealed important differences in the nature and in the spatial distribution of double-strand breaks (DSB) induced by low- and high-LET radiations. Many calculations, most of which are based on amorphous track models with radial dose, have been combined with chromosome models to calculate the number and distribution of DSB within nuclei and chromosome aberrations. In this work, the Monte-Carlo track structure simulation code RITRACKS have been used to calculate directly the energy deposition in voxels (3D pixels). A cubic volume of 5 micrometers of side was irradiated by 1) 450 (1)H+ ions of 300 MeV (LET is approximately 0.3 keV/micrometer) and 2) by 1 (56)Fe26+ ion of 1 GeV/amu (LET is approximately 150 keV/micrometer). In both cases, the dose deposited in the volume is approximately 1 Gy. All energy deposition events are recorded and dose is calculated in voxels of 20 micrometers of side. The voxels are then visualized in 3D by using a color scale to represent the intensity of the dose in a voxel. This simple approach has revealed several important points which may help understand experimental observations. In both simulations, voxels which receive low dose are the most numerous, and those corresponding to electron track ends received a dose which is in the higher range. The dose voxels are distributed randomly and scattered uniformly within the volume irradiated by low-LET radiation. The distribution of the voxels shows major differences for the (56)Fe26+ ion. The track structure can still be seen, and voxels with much higher dose are found in the region corresponding to the track "core". These high-dose voxels are not found in the low-LET irradiation simulation and may be responsible for DSB that are more difficult to

  8. Validation of voxel-based morphometry (VBM) based on MRI

    NASA Astrophysics Data System (ADS)

    Yang, Xueyu; Chen, Kewei; Guo, Xiaojuan; Yao, Li

    2007-03-01

    Voxel-based morphometry (VBM) is an automated and objective image analysis technique for detecting differences in regional concentration or volume of brain tissue composition based on structural magnetic resonance (MR) images. VBM has been used widely to evaluate brain morphometric differences between different populations, but there isn't an evaluation system for its validation until now. In this study, a quantitative and objective evaluation system was established in order to assess VBM performance. We recruited twenty normal volunteers (10 males and 10 females, age range 20-26 years, mean age 22.6 years). Firstly, several focal lesions (hippocampus, frontal lobe, anterior cingulate, back of hippocampus, back of anterior cingulate) were simulated in selected brain regions using real MRI data. Secondly, optimized VBM was performed to detect structural differences between groups. Thirdly, one-way ANOVA and post-hoc test were used to assess the accuracy and sensitivity of VBM analysis. The results revealed that VBM was a good detective tool in majority of brain regions, even in controversial brain region such as hippocampus in VBM study. Generally speaking, much more severity of focal lesion was, better VBM performance was. However size of focal lesion had little effects on VBM analysis.

  9. Investigation of mindfulness meditation practitioners with voxel-based morphometry.

    PubMed

    Hölzel, Britta K; Ott, Ulrich; Gard, Tim; Hempel, Hannes; Weygandt, Martin; Morgen, Katrin; Vaitl, Dieter

    2008-03-01

    Mindfulness meditators practice the non-judgmental observation of the ongoing stream of internal experiences as they arise. Using voxel-based morphometry, this study investigated MRI brain images of 20 mindfulness (Vipassana) meditators (mean practice 8.6 years; 2 h daily) and compared the regional gray matter concentration to that of non-meditators matched for sex, age, education and handedness. Meditators were predicted to show greater gray matter concentration in regions that are typically activated during meditation. Results confirmed greater gray matter concentration for meditators in the right anterior insula, which is involved in interoceptive awareness. This group difference presumably reflects the training of bodily awareness during mindfulness meditation. Furthermore, meditators had greater gray matter concentration in the left inferior temporal gyrus and right hippocampus. Both regions have previously been found to be involved in meditation. The mean value of gray matter concentration in the left inferior temporal gyrus was predictable by the amount of meditation training, corroborating the assumption of a causal impact of meditation training on gray matter concentration in this region. Results suggest that meditation practice is associated with structural differences in regions that are typically activated during meditation and in regions that are relevant for the task of meditation.

  10. Neuroanatomical voxel-based profile of schizophrenia and bipolar disorder.

    PubMed

    Maggioni, E; Bellani, M; Altamura, A C; Brambilla, P

    2016-08-01

    Although schizophrenia (SCZ) and bipolar disorder (BD) share elements of pathology (Ellison-Wright and Bullmore, 2009), the neural mechanisms underlying these disorders are still under investigation. Up until now, many neuroimaging studies investigated the brain structural differences of SCZ and BD compared with healthy controls (HC), trying to identify the possible neuroanatomical markers for the two disorders. However, just a few studies focused on the brain structural changes between the two diagnoses. The present review summarises the findings of the voxel-based grey matter (GM) comparisons between SCZ and BD, with the objective to highlight the possible consistent anatomical differences between the two disorders. While the comparisons between patients and HC highlighted overlapping areas of GM reduction in insula and anterior cingulate cortex, the SCZ-BD comparisons suggest the presence of more generalised GM deficits in SCZ compared with BD. Indeed, in a number of studies, SCZ patients showed lower GM volumes than BD patients in fronto-temporal cortex, thalamus, hippocampus and amygdala. Conversely, only a couple of studies reported GM deficits in BD compared with SCZ, both at the level of cerebellum. In summary, the two disorders exhibit both common and specific neuroanatomical characteristics, whose knowledge is mandatory to develop innovative diagnostic and treatment strategies. PMID:27095442

  11. Transformation Invariant Control of Voxel-Wise False Discovery Rate

    PubMed Central

    Li, Junning; Shi, Yonggang; Toga, Arthur W.

    2016-01-01

    Multiple testing for statistical maps remains a critical and challenging problem in brain mapping. Since the false discovery rate (FDR) criterion was introduced to the neuroimaging community a decade ago, many variations have been proposed, mainly to enhance detection power. However, a fundamental geometrical property known as transformation invariance has not been adequately addressed, especially for the voxel-wise FDR. Correction of multiple testing applied after spatial transformation is not necessarily equivalent to transformation applied after correction in the original space. Without the invariance property, assigning different testing spaces will yield different results. We find that normalized residuals of linear models with Gaussian noises are uniformly distributed on a unit high-dimensional sphere, independent of t-statistics and F-statistics. By defining volumetric measure in the hyper-spherical space mapped by normalized residuals, instead of the image’s Euclidean space, we can achieve invariant control of the FDR under diffeomorphic transformation. This hyper-spherical measure also reflects intrinsic “volume of randomness” in signals. Experiments with synthetic, semi-synthetic and real images demonstrate that our method significantly reduces FDR inconsistency introduced by the choice of testing spaces. PMID:27101602

  12. Difusión de Arnold en un modelo simple

    NASA Astrophysics Data System (ADS)

    Cincotta, P. M.; Nuñez, J. A.; Miloni, O.

    Investigadores como Merritt, Valluri, Pfenniger o Contopoulos (por citar los más relevantes) consideran seriamente la hipótesis que la difusión de Arnold juega un rol importante en la evolución dinámica de los sistemas estelares y planetarios. Sin embargo no existe ninguna evidencia. El mayor problema para investigar fenómenos como éste es que uno debe estudiar numéricamente sistemas multidimensionales (más de dos grados de libertad) y visualizar de alguna manera el espacio de fases (más de cuatro dimensiones). Más complicado aún es el caso de difusión de Arnold, donde deben considerarse tiempos de movimiento extremadamente largos y tratar con parámetros exponencialmente pequeños. El propósito de este trabajo es estudiar, en un modelo simple 3D, la existencia o no de difusión de Arnold mediante experimentos numéricos y estimaciones analíticas. Siguiendo los trabajos de Cincotta (2000) y Cincotta, Nuñez y Simo (2000), aquí se pretende ``visualizar" la difusión y, a la vez, determinar la escala de tiempo en la que ésta se podría manifestar. Este trabajo es el escalón inicial para luego abordar este problema en modelos.

  13. Distinct Cortical Pathways for Music and Speech Revealed by Hypothesis-Free Voxel Decomposition.

    PubMed

    Norman-Haignere, Sam; Kanwisher, Nancy G; McDermott, Josh H

    2015-12-16

    The organization of human auditory cortex remains unresolved, due in part to the small stimulus sets common to fMRI studies and the overlap of neural populations within voxels. To address these challenges, we measured fMRI responses to 165 natural sounds and inferred canonical response profiles ("components") whose weighted combinations explained voxel responses throughout auditory cortex. This analysis revealed six components, each with interpretable response characteristics despite being unconstrained by prior functional hypotheses. Four components embodied selectivity for particular acoustic features (frequency, spectrotemporal modulation, pitch). Two others exhibited pronounced selectivity for music and speech, respectively, and were not explainable by standard acoustic features. Anatomically, music and speech selectivity concentrated in distinct regions of non-primary auditory cortex. However, music selectivity was weak in raw voxel responses, and its detection required a decomposition method. Voxel decomposition identifies primary dimensions of response variation across natural sounds, revealing distinct cortical pathways for music and speech. PMID:26687225

  14. A genome-scale map of expression for a mouse brain section obtained using voxelation

    SciTech Connect

    Chin, Mark H.; Geng, Alex B.; Khan, Arshad H.; Qian, Weijun; Petyuk, Vladislav A.; Boline, Jyl; Levy, Shawn; Toga, Arthur W.; Smith, Richard D.; Leahy, Richard M.; Smith, Desmond J.

    2007-08-20

    Gene expression signatures in the mammalian brain hold the key to understanding neural development and neurological diseases. We have reconstructed 2- dimensional images of gene expression for 20,000 genes in a coronal slice of the mouse brain at the level of the striatum by using microarrays in combination with voxelation at a resolution of 1 mm3. Good reliability of the microarray results were confirmed using multiple replicates, subsequent quantitative RT-PCR voxelation, mass spectrometry voxelation and publicly available in situ hybridization data. Known and novel genes were identified with expression patterns localized to defined substructures within the brain. In addition, genes with unexpected patterns were identified and cluster analysis identified a set of genes with a gradient of dorsal/ventral expression not restricted to known anatomical boundaries. The genome-scale maps of gene expression obtained using voxelation will be a valuable tool for the neuroscience community.

  15. Distinct Cortical Pathways for Music and Speech Revealed by Hypothesis-Free Voxel Decomposition.

    PubMed

    Norman-Haignere, Sam; Kanwisher, Nancy G; McDermott, Josh H

    2015-12-16

    The organization of human auditory cortex remains unresolved, due in part to the small stimulus sets common to fMRI studies and the overlap of neural populations within voxels. To address these challenges, we measured fMRI responses to 165 natural sounds and inferred canonical response profiles ("components") whose weighted combinations explained voxel responses throughout auditory cortex. This analysis revealed six components, each with interpretable response characteristics despite being unconstrained by prior functional hypotheses. Four components embodied selectivity for particular acoustic features (frequency, spectrotemporal modulation, pitch). Two others exhibited pronounced selectivity for music and speech, respectively, and were not explainable by standard acoustic features. Anatomically, music and speech selectivity concentrated in distinct regions of non-primary auditory cortex. However, music selectivity was weak in raw voxel responses, and its detection required a decomposition method. Voxel decomposition identifies primary dimensions of response variation across natural sounds, revealing distinct cortical pathways for music and speech.

  16. Neural traffic as voxel-based measure of cerebral functional connectivity in fMRI.

    PubMed

    Beu, M; Baudrexel, S; Hautzel, H; Antke, Chr; Mueller, H-W

    2009-01-30

    To access functional connectivity by in vivo brain imaging voxel-by-voxel, we developed a novel approach named neural traffic (NT). NT depicts the intensity of functional connectivity on a voxel-by-voxel basis in the whole brain. Functional magnetic resonance imaging (fMRI) experiments were carried out on eight individuals during either hearing or viewing words. The blood oxygen level dependant (BOLD) signal was taken as measure of neural activity. For each voxel, functional connectivity with all other brain voxels was determined by calculating Pearson correlation coefficients at two connectivity thresholds (r=0.35 and 0.65). Then, NT images were derived by counting the number of suprathreshold connections for each individual voxel. Calculations based on random networks indicate that statistically reliable NT images can be derived in individuals. With regard to group analysis, at r=0.35 NT images are similar though not identical with the first component of principal component analysis (PCA), displaying a widespread but not ubiquitous pattern of functionally connected cortical areas. At r=0.65, NT group images display functional connectivity confined to circumscribed cortical regions which reach beyond the corresponding primary sensory areas, their known associated areas and the default network. In conclusion, NT goes beyond the approach of correlating the BOLD signal with the external stimulus-presentation time course by computing linear functional connectivity between all brain voxels based on any BOLD time course. First results demonstrate that the NT approach is likely - on an individual base - to reveal novel cortical and subcortical connectivities involved in stimulus processing.

  17. A novel, optimized approach of voxel division for water vapor tomography

    NASA Astrophysics Data System (ADS)

    Yao, Yibin; Zhao, Qingzhi

    2016-03-01

    Water vapor information with highly spatial and temporal resolution can be acquired using Global Navigation Satellite System (GNSS) water vapor tomography technique. Usually, the targeted tomographic area is discretized into a number of voxels and the water vapor distribution can be reconstructed using a large number of GNSS signals which penetrate the entire tomographic area. Due to the influence of geographic distribution of receivers and geometric location of satellite constellation, many voxels located at the bottom and the side of research area are not crossed by signals, which would undermine the quality of tomographic result. To alleviate this problem, a novel, optimized approach of voxel division is here proposed which increases the number of voxels crossed by signals. On the vertical axis, a 3D water vapor profile is utilized, which is derived from radiosonde data for many years, to identify the maximum height of tomography space. On the horizontal axis, the total number of voxel crossed by signal is enhanced, based on the concept of non-uniform symmetrical division of horizontal voxels. In this study, tomographic experiments are implemented using GPS data from Hong Kong Satellite Positioning Reference Station Network, and tomographic result is compared with water vapor derived from radiosonde and European Center for Medium-Range Weather Forecasting (ECMWF). The result shows that the Integrated Water Vapour (IWV), RMS, and error distribution of the proposed approach are better than that of traditional method.

  18. Effect of voxel size when calculating patient specific radionuclide dosimetry estimates using direct Monte Carlo simulation.

    PubMed

    Hickson, Kevin J; O'Keefe, Graeme J

    2014-09-01

    The scalable XCAT voxelised phantom was used with the GATE Monte Carlo toolkit to investigate the effect of voxel size on dosimetry estimates of internally distributed radionuclide calculated using direct Monte Carlo simulation. A uniformly distributed Fluorine-18 source was simulated in the Kidneys of the XCAT phantom with the organ self dose (kidney ← kidney) and organ cross dose (liver ← kidney) being calculated for a number of organ and voxel sizes. Patient specific dose factors (DF) from a clinically acquired FDG PET/CT study have also been calculated for kidney self dose and liver ← kidney cross dose. Using the XCAT phantom it was found that significantly small voxel sizes are required to achieve accurate calculation of organ self dose. It has also been used to show that a voxel size of 2 mm or less is suitable for accurate calculations of organ cross dose. To compensate for insufficient voxel sampling a correction factor is proposed. This correction factor is applied to the patient specific dose factors calculated with the native voxel size of the PET/CT study.

  19. Informational connectivity: identifying synchronized discriminability of multi-voxel patterns across the brain.

    PubMed

    Coutanche, Marc N; Thompson-Schill, Sharon L

    2013-01-01

    The fluctuations in a brain region's activation levels over a functional magnetic resonance imaging (fMRI) time-course are used in functional connectivity (FC) to identify networks with synchronous responses. It is increasingly recognized that multi-voxel activity patterns contain information that cannot be extracted from univariate activation levels. Here we present a novel analysis method that quantifies regions' synchrony in multi-voxel activity pattern discriminability, rather than univariate activation, across a timeseries. We introduce a measure of multi-voxel pattern discriminability at each time-point, which is then used to identify regions that share synchronous time-courses of condition-specific multi-voxel information. This method has the sensitivity and access to distributed information that multi-voxel pattern analysis enjoys, allowing it to be applied to data from conditions not separable by univariate responses. We demonstrate this by analyzing data collected while people viewed four different types of man-made objects (typically not separable by univariate analyses) using both FC and informational connectivity (IC) methods. IC reveals networks of object-processing regions that are not detectable using FC. The IC results support prior findings and hypotheses about object processing. This new method allows investigators to ask questions that are not addressable through typical FC, just as multi-voxel pattern analysis (MVPA) has added new research avenues to those addressable with the general linear model (GLM).

  20. Variation in voxel value distribution and effect of time between exposures in six CBCT units.

    PubMed

    Spin-Neto, R; Gotfredsen, E; Wenzel, A

    2014-01-01

    The aim of this study is to assess the variation in voxel value distribution in volumetric data sets obtained by six cone beam CT (CBCT) units, and the effect of time between exposures. Six CBCT units [Cranex(®) 3D (CRAN; Soredex Oy, Tuusula, Finland), Scanora(®) 3D (SCAN; Soredex Oy), NewTom™ 5G (NEWT; QR Srl, Verona, Italy), Promax(®) Dimax 3 (Planmeca Oy, Helsinki, Finland), i-CAT (Imaging Sciences International, Hatfield, PA) and 3D Accuitomo FPD80 (Morita, Kyoto, Japan)] were tested. Two volumetric data sets of a dry human skull embedded in acrylic were acquired by each CBCT unit in two sessions on separate days. Each session consisted of 20 exposures: 10 acquired with 30 min between exposures and 10 acquired immediately one after the other. CBCT data were exported as digital imaging and communications in medicine (DICOM) files and converted to text files. The text files were re-organized to contain x-, y- and z-position and grey shade for each voxel. The files were merged to contain 1 record per voxel position, including the voxel values from the 20 exposures in a session. For each voxel, subtractions were performed between Data Set 1 and the remaining 19 data sets (1 - 2, 1 - 3, etc) in a session. Means, medians, ranges and standard deviations for grey shade variation in the subtraction data sets were calculated for each unit and session. For all CBCT units, variation in voxel values was observed throughout the 20 exposures. A "fingerprint" for the grey shade variation was observed for CRAN, SCAN and NEWT. For the other units, the variation was (apparently) randomly distributed. Large discrepancies in voxel value distribution are seen in CBCT images. This variation should be considered in studies that assess minute changes in CBCT images. PMID:24678846

  1. Variation in voxel value distribution and effect of time between exposures in six CBCT units

    PubMed Central

    Gotfredsen, E; Wenzel, A

    2014-01-01

    The aim of this study is to assess the variation in voxel value distribution in volumetric data sets obtained by six cone beam CT (CBCT) units, and the effect of time between exposures. Six CBCT units [Cranex® 3D (CRAN; Soredex Oy, Tuusula, Finland), Scanora® 3D (SCAN; Soredex Oy), NewTom™ 5G (NEWT; QR Srl, Verona, Italy), Promax® Dimax 3 (Planmeca Oy, Helsinki, Finland), i-CAT (Imaging Sciences International, Hatfield, PA) and 3D Accuitomo FPD80 (Morita, Kyoto, Japan)] were tested. Two volumetric data sets of a dry human skull embedded in acrylic were acquired by each CBCT unit in two sessions on separate days. Each session consisted of 20 exposures: 10 acquired with 30 min between exposures and 10 acquired immediately one after the other. CBCT data were exported as digital imaging and communications in medicine (DICOM) files and converted to text files. The text files were re-organized to contain x-, y- and z-position and grey shade for each voxel. The files were merged to contain 1 record per voxel position, including the voxel values from the 20 exposures in a session. For each voxel, subtractions were performed between Data Set 1 and the remaining 19 data sets (1 − 2, 1 − 3, etc) in a session. Means, medians, ranges and standard deviations for grey shade variation in the subtraction data sets were calculated for each unit and session. For all CBCT units, variation in voxel values was observed throughout the 20 exposures. A “fingerprint” for the grey shade variation was observed for CRAN, SCAN and NEWT. For the other units, the variation was (apparently) randomly distributed. Large discrepancies in voxel value distribution are seen in CBCT images. This variation should be considered in studies that assess minute changes in CBCT images. PMID:24678846

  2. Variation in voxel value distribution and effect of time between exposures in six CBCT units.

    PubMed

    Spin-Neto, R; Gotfredsen, E; Wenzel, A

    2014-01-01

    The aim of this study is to assess the variation in voxel value distribution in volumetric data sets obtained by six cone beam CT (CBCT) units, and the effect of time between exposures. Six CBCT units [Cranex(®) 3D (CRAN; Soredex Oy, Tuusula, Finland), Scanora(®) 3D (SCAN; Soredex Oy), NewTom™ 5G (NEWT; QR Srl, Verona, Italy), Promax(®) Dimax 3 (Planmeca Oy, Helsinki, Finland), i-CAT (Imaging Sciences International, Hatfield, PA) and 3D Accuitomo FPD80 (Morita, Kyoto, Japan)] were tested. Two volumetric data sets of a dry human skull embedded in acrylic were acquired by each CBCT unit in two sessions on separate days. Each session consisted of 20 exposures: 10 acquired with 30 min between exposures and 10 acquired immediately one after the other. CBCT data were exported as digital imaging and communications in medicine (DICOM) files and converted to text files. The text files were re-organized to contain x-, y- and z-position and grey shade for each voxel. The files were merged to contain 1 record per voxel position, including the voxel values from the 20 exposures in a session. For each voxel, subtractions were performed between Data Set 1 and the remaining 19 data sets (1 - 2, 1 - 3, etc) in a session. Means, medians, ranges and standard deviations for grey shade variation in the subtraction data sets were calculated for each unit and session. For all CBCT units, variation in voxel values was observed throughout the 20 exposures. A "fingerprint" for the grey shade variation was observed for CRAN, SCAN and NEWT. For the other units, the variation was (apparently) randomly distributed. Large discrepancies in voxel value distribution are seen in CBCT images. This variation should be considered in studies that assess minute changes in CBCT images.

  3. Octree indexing of DICOM images for voxel number reduction and improvement of Monte Carlo simulation computing efficiency

    SciTech Connect

    Hubert-Tremblay, Vincent; Archambault, Louis; Tubic, Dragan; Roy, Rene; Beaulieu, Luc

    2006-08-15

    The purpose of the present study is to introduce a compression algorithm for the CT (computed tomography) data used in Monte Carlo simulations. Performing simulations on the CT data implies large computational costs as well as large memory requirements since the number of voxels in such data reaches typically into hundreds of millions voxels. CT data, however, contain homogeneous regions which could be regrouped to form larger voxels without affecting the simulation's accuracy. Based on this property we propose a compression algorithm based on octrees: in homogeneous regions the algorithm replaces groups of voxels with a smaller number of larger voxels. This reduces the number of voxels while keeping the critical high-density gradient area. Results obtained using the present algorithm on both phantom and clinical data show that compression rates up to 75% are possible without losing the dosimetric accuracy of the simulation.

  4. Voxel-Based Approach for Estimating Urban Tree Volume from Terrestrial Laser Scanning Data

    NASA Astrophysics Data System (ADS)

    Vonderach, C.; Voegtle, T.; Adler, P.

    2012-07-01

    The importance of single trees and the determination of related parameters has been recognized in recent years, e.g. for forest inventories or management. For urban areas an increasing interest in the data acquisition of trees can be observed concerning aspects like urban climate, CO2 balance, and environmental protection. Urban trees differ significantly from natural systems with regard to the site conditions (e.g. technogenic soils, contaminants, lower groundwater level, regular disturbance), climate (increased temperature, reduced humidity) and species composition and arrangement (habitus and health status) and therefore allometric relations cannot be transferred from natural sites to urban areas. To overcome this problem an extended approach was developed for a fast and non-destructive extraction of branch volume, DBH (diameter at breast height) and height of single trees from point clouds of terrestrial laser scanning (TLS). For data acquisition, the trees were scanned with highest scan resolution from several (up to five) positions located around the tree. The resulting point clouds (20 to 60 million points) are analysed with an algorithm based on voxel (volume elements) structure, leading to an appropriate data reduction. In a first step, two kinds of noise reduction are carried out: the elimination of isolated voxels as well as voxels with marginal point density. To obtain correct volume estimates, the voxels inside the stem and branches (interior voxels) where voxels contain no laser points must be regarded. For this filling process, an easy and robust approach was developed based on a layer-wise (horizontal layers of the voxel structure) intersection of four orthogonal viewing directions. However, this procedure also generates several erroneous "phantom" voxels, which have to be eliminated. For this purpose the previous approach was extended by a special region growing algorithm. In a final step the volume is determined layer-wise based on the extracted

  5. Modelos Teoricos de Linhas de Recombinacao EM Radio Frequencias Para Regioes H II

    NASA Astrophysics Data System (ADS)

    Abraham, Z.; Cancoro, A. C. O.

    1987-05-01

    Foram feitos modelos de linhas de recombinção provenientes de regiões HII nas frequências de rádio para distintos números quãnticos. Estes modelos consideram regrões H II esfericamente simétricas com variações radiais na densidade e temperatura eletrônica, efeitos de colisoes inelásticas dos eletrons (alargarnento por pressão), e afastarnento do equiliíbrio termodinâmico local. 0 bojetivo é construir o perfil da linha para cada ponto da nuvern e obter o valor médio resultante da sua convoluçã com o feixe da antena de tarnanho comparável corn o tarnanho angular da nuvern para posterIor cornpara o corn

  6. A multicriteria framework with voxel-dependent parameters for radiotherapy treatment plan optimization

    SciTech Connect

    Zarepisheh, Masoud; Uribe-Sanchez, Andres F.; Li, Nan; Jia, Xun; Jiang, Steve B.

    2014-04-15

    Purpose: To establish a new mathematical framework for radiotherapy treatment optimization with voxel-dependent optimization parameters. Methods: In the treatment plan optimization problem for radiotherapy, a clinically acceptable plan is usually generated by an optimization process with weighting factors or reference doses adjusted for a set of the objective functions associated to the organs. Recent discoveries indicate that adjusting parameters associated with each voxel may lead to better plan quality. However, it is still unclear regarding the mathematical reasons behind it. Furthermore, questions about the objective function selection and parameter adjustment to assure Pareto optimality as well as the relationship between the optimal solutions obtained from the organ-based and voxel-based models remain unanswered. To answer these questions, the authors establish in this work a new mathematical framework equipped with two theorems. Results: The new framework clarifies the different consequences of adjusting organ-dependent and voxel-dependent parameters for the treatment plan optimization of radiation therapy, as well as the impact of using different objective functions on plan qualities and Pareto surfaces. The main discoveries are threefold: (1) While in the organ-based model the selection of the objective function has an impact on the quality of the optimized plans, this is no longer an issue for the voxel-based model since the Pareto surface is independent of the objective function selection and the entire Pareto surface could be generated as long as the objective function satisfies certain mathematical conditions; (2) All Pareto solutions generated by the organ-based model with different objective functions are parts of a unique Pareto surface generated by the voxel-based model with any appropriate objective function; (3) A much larger Pareto surface is explored by adjusting voxel-dependent parameters than by adjusting organ-dependent parameters, possibly

  7. Rapid three-dimensional quantification of voxel-wise collagen fiber orientation

    PubMed Central

    Liu, Zhiyi; Quinn, Kyle P.; Speroni, Lucia; Arendt, Lisa; Kuperwasser, Charlotte; Sonnenschein, Carlos; Soto, Ana M.; Georgakoudi, Irene

    2015-01-01

    Defining fiber orientation at each voxel within a 3D biomedical image stack is potentially useful for a variety of applications, including cancer, wound healing and tissue regeneration. Current methods are typically computationally intensive or inaccurate. Herein, we present a 3D weighted orientation vector summation algorithm, which is a generalization of a previously reported 2D vector summation technique aimed at quantifying collagen fiber orientations simultaneously at each voxel of an image stack. As a result, voxel-wise fiber orientation information with 4° to 5° accuracy can be determined, and the computational time required to analyze a typical stack with the size of 512x512x100 voxels is less than 5 min. Thus, this technique enables the practical extraction of voxel-specific orientation data for characterizing structural anisotropy in 3D specimens. As examples, we use this approach to characterize the fiber organization in an excised mouse mammary gland and a 3D breast tissue model. PMID:26203362

  8. Mapping the Voxel-Wise Effective Connectome in Resting State fMRI

    PubMed Central

    Wu, Guo-Rong; Stramaglia, Sebastiano; Chen, Huafu; Liao, Wei; Marinazzo, Daniele

    2013-01-01

    A network approach to brain and dynamics opens new perspectives towards understanding of its function. The functional connectivity from functional MRI recordings in humans is widely explored at large scale, and recently also at the voxel level. The networks of dynamical directed connections are far less investigated, in particular at the voxel level. To reconstruct full brain effective connectivity network and study its topological organization, we present a novel approach to multivariate Granger causality which integrates information theory and the architecture of the dynamical network to efficiently select a limited number of variables. The proposed method aggregates conditional information sets according to community organization, allowing to perform Granger causality analysis avoiding redundancy and overfitting even for high-dimensional and short datasets, such as time series from individual voxels in fMRI. We for the first time depicted the voxel-wise hubs of incoming and outgoing information, called Granger causality density (GCD), as a complement to previous repertoire of functional and anatomical connectomes. Analogies with these networks have been presented in most part of default mode network; while differences suggested differences in the specific measure of centrality. Our findings could open the way to a new description of global organization and information influence of brain function. With this approach is thus feasible to study the architecture of directed networks at the voxel level and individuating hubs by investigation of degree, betweenness and clustering coefficient. PMID:24069220

  9. A visual LISP program for voxelizing AutoCAD solid models

    NASA Astrophysics Data System (ADS)

    Marschallinger, Robert; Jandrisevits, Carmen; Zobl, Fritz

    2015-01-01

    AutoCAD solid models are increasingly recognized in geological and geotechnical 3D modeling. In order to bridge the currently existing gap between AutoCAD solid models and the grid modeling realm, a Visual LISP program is presented that converts AutoCAD solid models into voxel arrays. Acad2Vox voxelizer works on a 3D-model that is made up of arbitrary non-overlapping 3D-solids. After definition of the target voxel array geometry, 3D-solids are scanned at grid positions and properties are streamed to an ASCII output file. Acad2Vox has a novel voxelization strategy that combines a hierarchical reduction of sampling dimensionality with an innovative use of AutoCAD-specific methods for a fast and memory-saving operation. Acad2Vox provides georeferenced, voxelized analogs of 3D design data that can act as regions-of-interest in later geostatistical modeling and simulation. The Supplement includes sample geological solid models with instructions for practical work with Acad2Vox.

  10. Influence of voxel size settings in X-Ray CT Imagery of soil in scaling properties

    NASA Astrophysics Data System (ADS)

    Heck, R.; Scaiff, N. T.; Andina, D.; Tarquis, A. M.

    2012-04-01

    Fundamental to the interpretation and comparison of X-ray CT imagery of soil is recognition of the objectivity and consistency of procedures used to generate the 3D models. Notably, there has been a lack of consistency in the size of voxels used for diverse interpretations of soils features and processes; in part, this is due to the ongoing evolution of instrumentation and computerized image processing capacity. Moreover, there is still need for discussion on whether standard voxels sizes should be recommended, and what those would be. Regardless of any eventual adoption of such standards, there is a need to also consider the manner in which voxel size is set in the 3D imagery. In the typical approaches to X-ray CT imaging, voxel size may be set at three stages: image acquisition (involving the position of the sample relative to the tube and detector), image reconstruction (where binning of pixels in the acquired images may occur), as well as post-reconstruction re-sampling (which may involve algorithms such as tri-cubic convolution). This research evaluates and compares the spatial distribution of intra-aggregate voids in 3D imagery as well as their scaling properties, of equivalent voxel size, generated using various combinations of the afore-mentioned approaches. Funding provided by Spanish Ministerio de Ciencia e Innovación (MICINN) through project no. AGL2010-21501/AGR is greatly appreciated.

  11. Voxel Based Morphometry Alterations in Mal de Debarquement Syndrome

    PubMed Central

    Cha, Yoon-Hee; Chakrapani, Shruthi

    2015-01-01

    Background Mal de debarquement syndrome (MdDS) is a disorder of chronic self-motion perception that occurs though entrainment to rhythmic background motion, such as from sea voyage, and involves the perception of low-frequency rocking that can last for months or years. The neural basis of this persistent sensory perception abnormality is not well understood. Methods We investigated grey matter volume differences underlying persistent MdDS by performing voxel-based morphometry on whole brain and pre-specified ROIs in 28 individuals with MdDS and comparing them to 18 age, sex, and handedness matched controls. Results MdDS participants exhibited greater grey matter volume in the left inferior parietal lobule, right inferior occipital gyrus (area V3v), right temporal pole, bilateral cerebellar hemispheric lobules VIII/IX and left lobule VIIa/VIIb. Grey matter volumes were lower in bilateral inferior frontal, orbitofrontal, pregenual anterior cingulate cortex (pgACC) and left superior medial gyri (t = 3.0, p<0.005uncorr). In ROI analyses, there were no volume differences in the middle occipital gyrus (region of V5/MT) or parietal operculum 2 (region of the parietoinsular vestibular cortex). Illness duration was positively related to grey matter volume in bilateral inferior frontal gyrus/anterior insula (IFG/AI), right posterior insula, superior parietal lobule, left middle occipital gyrus (V5/MT), bilateral postcentral gyrus, anterior cerebellum, and left cerebellar hemisphere and vermian lobule IX. In contrast, illness duration was negatively related to volume in pgACC, posterior middle cingulate gyrus (MCC), left middle frontal gyrus (dorsolateral prefrontal cortex-DLPFC), and right cerebellar hemispheric lobule VIIIb (t = 3.0, p<0.005uncorr). The most significant differences were decreased volume in the pgACC and increased volume in the left IFG/AI with longer illness duration (qFDRcorr <0.05). Concurrent medication use did not correlate with these findings or have a

  12. Two-Voxel Localization Sequence for in Vivo Two-Dimensional Homonuclear Correlation Spectroscopy

    NASA Astrophysics Data System (ADS)

    Delmas, Florence; Beloeil, Jean-Claude; van der Sanden, Boudewijn P. J.; Nicolay, Klaas; Gillet, Brigitte

    2001-03-01

    The combination of localized 2D 1H MR correlation spectroscopy and Hadamard encoding allows the simultaneous acquisition of multiple volumes of interest without an increase in the experimental duration, compared to single-voxel acquisition. In the present study, 2D correlation spectra were acquired simultaneously within 20 to 40 min in two voxels located in each hemisphere of the rat brain. An intervoxel distance of 20% of the voxel size was sufficient to limit spatial contamination. The following cerebral metabolites gave detectable crosspeaks: N-acetylaspartate, the glutamate/glutamine pool, aspartate, phosphoethanolamine, glucose, glutathione, taurine, myo-inositols, lactate, threonine, γ-aminobutyric acid, and alanine. Most of the metabolites were measured without contamination of other resonances.

  13. New hybrid voxelized/analytical primitive in Monte Carlo simulations for medical applications

    NASA Astrophysics Data System (ADS)

    Bert, Julien; Lemaréchal, Yannick; Visvikis, Dimitris

    2016-05-01

    Monte Carlo simulations (MCS) applied in particle physics play a key role in medical imaging and particle therapy. In such simulations, particles are transported through voxelized phantoms derived from predominantly patient CT images. However, such voxelized object representation limits the incorporation of fine elements, such as artificial implants from CAD modeling or anatomical and functional details extracted from other imaging modalities. In this work we propose a new hYbrid Voxelized/ANalytical primitive (YVAN) that combines both voxelized and analytical object descriptions within the same MCS, without the need to simultaneously run two parallel simulations, which is the current gold standard methodology. Given that YVAN is simply a new primitive object, it does not require any modifications on the underlying MC navigation code. The new proposed primitive was assessed through a first simple MCS. Results from the YVAN primitive were compared against an MCS using a pure analytical geometry and the layer mass geometry concept. A perfect agreement was found between these simulations, leading to the conclusion that the new hybrid primitive is able to accurately and efficiently handle phantoms defined by a mixture of voxelized and analytical objects. In addition, two application-based evaluation studies in coronary angiography and intra-operative radiotherapy showed that the use of YVAN was 6.5% and 12.2% faster than the layered mass geometry method, respectively, without any associated loss of accuracy. However, the simplification advantages and differences in computational time improvements obtained with YVAN depend on the relative proportion of the analytical and voxelized structures used in the simulation as well as the size and number of triangles used in the description of the analytical object meshes.

  14. Voxel size dependency, reproducibility and sensitivity of an in vivo bone loading estimation algorithm.

    PubMed

    Christen, Patrik; Schulte, Friederike A; Zwahlen, Alexander; van Rietbergen, Bert; Boutroy, Stephanie; Melton, L Joseph; Amin, Shreyasee; Khosla, Sundeep; Goldhahn, Jörg; Müller, Ralph

    2016-01-01

    A bone loading estimation algorithm was previously developed that provides in vivo loading conditions required for in vivo bone remodelling simulations. The algorithm derives a bone's loading history from its microstructure as assessed by high-resolution (HR) computed tomography (CT). This reverse engineering approach showed accurate and realistic results based on micro-CT and HR-peripheral quantitative CT images. However, its voxel size dependency, reproducibility and sensitivity still need to be investigated, which is the purpose of this study. Voxel size dependency was tested on cadaveric distal radii with micro-CT images scanned at 25 µm and downscaled to 50, 61, 75, 82, 100, 125 and 150 µm. Reproducibility was calculated with repeated in vitro as well as in vivo HR-pQCT measurements at 82 µm. Sensitivity was defined using HR-pQCT images from women with fracture versus non-fracture, and low versus high bone volume fraction, expecting similar and different loading histories, respectively. Our results indicate that the algorithm is voxel size independent within an average (maximum) error of 8.2% (32.9%) at 61 µm, but that the dependency increases considerably at voxel sizes bigger than 82 µm. In vitro and in vivo reproducibility are up to 4.5% and 10.2%, respectively, which is comparable to other in vitro studies and slightly higher than in other in vivo studies. Subjects with different bone volume fraction were clearly distinguished but not subjects with and without fracture. This is in agreement with bone adapting to customary loading but not to fall loads. We conclude that the in vivo bone loading estimation algorithm provides reproducible, sensitive and fairly voxel size independent results at up to 82 µm, but that smaller voxel sizes would be advantageous.

  15. New hybrid voxelized/analytical primitive in Monte Carlo simulations for medical applications.

    PubMed

    Bert, Julien; Lemaréchal, Yannick; Visvikis, Dimitris

    2016-05-01

    Monte Carlo simulations (MCS) applied in particle physics play a key role in medical imaging and particle therapy. In such simulations, particles are transported through voxelized phantoms derived from predominantly patient CT images. However, such voxelized object representation limits the incorporation of fine elements, such as artificial implants from CAD modeling or anatomical and functional details extracted from other imaging modalities. In this work we propose a new hYbrid Voxelized/ANalytical primitive (YVAN) that combines both voxelized and analytical object descriptions within the same MCS, without the need to simultaneously run two parallel simulations, which is the current gold standard methodology. Given that YVAN is simply a new primitive object, it does not require any modifications on the underlying MC navigation code. The new proposed primitive was assessed through a first simple MCS. Results from the YVAN primitive were compared against an MCS using a pure analytical geometry and the layer mass geometry concept. A perfect agreement was found between these simulations, leading to the conclusion that the new hybrid primitive is able to accurately and efficiently handle phantoms defined by a mixture of voxelized and analytical objects. In addition, two application-based evaluation studies in coronary angiography and intra-operative radiotherapy showed that the use of YVAN was 6.5% and 12.2% faster than the layered mass geometry method, respectively, without any associated loss of accuracy. However, the simplification advantages and differences in computational time improvements obtained with YVAN depend on the relative proportion of the analytical and voxelized structures used in the simulation as well as the size and number of triangles used in the description of the analytical object meshes. PMID:27032813

  16. New hybrid voxelized/analytical primitive in Monte Carlo simulations for medical applications.

    PubMed

    Bert, Julien; Lemaréchal, Yannick; Visvikis, Dimitris

    2016-05-01

    Monte Carlo simulations (MCS) applied in particle physics play a key role in medical imaging and particle therapy. In such simulations, particles are transported through voxelized phantoms derived from predominantly patient CT images. However, such voxelized object representation limits the incorporation of fine elements, such as artificial implants from CAD modeling or anatomical and functional details extracted from other imaging modalities. In this work we propose a new hYbrid Voxelized/ANalytical primitive (YVAN) that combines both voxelized and analytical object descriptions within the same MCS, without the need to simultaneously run two parallel simulations, which is the current gold standard methodology. Given that YVAN is simply a new primitive object, it does not require any modifications on the underlying MC navigation code. The new proposed primitive was assessed through a first simple MCS. Results from the YVAN primitive were compared against an MCS using a pure analytical geometry and the layer mass geometry concept. A perfect agreement was found between these simulations, leading to the conclusion that the new hybrid primitive is able to accurately and efficiently handle phantoms defined by a mixture of voxelized and analytical objects. In addition, two application-based evaluation studies in coronary angiography and intra-operative radiotherapy showed that the use of YVAN was 6.5% and 12.2% faster than the layered mass geometry method, respectively, without any associated loss of accuracy. However, the simplification advantages and differences in computational time improvements obtained with YVAN depend on the relative proportion of the analytical and voxelized structures used in the simulation as well as the size and number of triangles used in the description of the analytical object meshes.

  17. Automated voxelization of 3D atom probe data through kernel density estimation.

    PubMed

    Srinivasan, Srikant; Kaluskar, Kaustubh; Dumpala, Santoshrupa; Broderick, Scott; Rajan, Krishna

    2015-12-01

    Identifying nanoscale chemical features from atom probe tomography (APT) data routinely involves adjustment of voxel size as an input parameter, through visual supervision, making the final outcome user dependent, reliant on heuristic knowledge and potentially prone to error. This work utilizes Kernel density estimators to select an optimal voxel size in an unsupervised manner to perform feature selection, in particular targeting resolution of interfacial features and chemistries. The capability of this approach is demonstrated through analysis of the γ / γ' interface in a Ni-Al-Cr superalloy. PMID:25825028

  18. An automated voxelized dosimetry tool for radionuclide therapy based on serial quantitative SPECT/CT imaging

    SciTech Connect

    Jackson, Price A.; Kron, Tomas; Beauregard, Jean-Mathieu; Hofman, Michael S.; Hogg, Annette; Hicks, Rodney J.

    2013-11-15

    Purpose: To create an accurate map of the distribution of radiation dose deposition in healthy and target tissues during radionuclide therapy.Methods: Serial quantitative SPECT/CT images were acquired at 4, 24, and 72 h for 28 {sup 177}Lu-octreotate peptide receptor radionuclide therapy (PRRT) administrations in 17 patients with advanced neuroendocrine tumors. Deformable image registration was combined with an in-house programming algorithm to interpolate pharmacokinetic uptake and clearance at a voxel level. The resultant cumulated activity image series are comprised of values representing the total number of decays within each voxel's volume. For PRRT, cumulated activity was translated to absorbed dose based on Monte Carlo-determined voxel S-values at a combination of long and short ranges. These dosimetric image sets were compared for mean radiation absorbed dose to at-risk organs using a conventional MIRD protocol (OLINDA 1.1).Results: Absorbed dose values to solid organs (liver, kidneys, and spleen) were within 10% using both techniques. Dose estimates to marrow were greater using the voxelized protocol, attributed to the software incorporating crossfire effect from nearby tumor volumes.Conclusions: The technique presented offers an efficient, automated tool for PRRT dosimetry based on serial post-therapy imaging. Following retrospective analysis, this method of high-resolution dosimetry may allow physicians to prescribe activity based on required dose to tumor volume or radiation limits to healthy tissue in individual patients.

  19. The Attentional Field Revealed by Single-Voxel Modeling of fMRI Time Courses

    PubMed Central

    DeYoe, Edgar A.

    2015-01-01

    The spatial topography of visual attention is a distinguishing and critical feature of many theoretical models of visuospatial attention. Previous fMRI-based measurements of the topography of attention have typically been too crude to adequately test the predictions of different competing models. This study demonstrates a new technique to make detailed measurements of the topography of visuospatial attention from single-voxel, fMRI time courses. Briefly, this technique involves first estimating a voxel's population receptive field (pRF) and then “drifting” attention through the pRF such that the modulation of the voxel's fMRI time course reflects the spatial topography of attention. The topography of the attentional field (AF) is then estimated using a time-course modeling procedure. Notably, we are able to make these measurements in many visual areas including smaller, higher order areas, thus enabling a more comprehensive comparison of attentional mechanisms throughout the full hierarchy of human visual cortex. Using this technique, we show that the AF scales with eccentricity and varies across visual areas. We also show that voxels in multiple visual areas exhibit suppressive attentional effects that are well modeled by an AF having an enhancing Gaussian center with a suppressive surround. These findings provide extensive, quantitative neurophysiological data for use in modeling the psychological effects of visuospatial attention. PMID:25810532

  20. List-mode image reconstruction for positron emission tomography using tetrahedral voxels

    NASA Astrophysics Data System (ADS)

    Gillam, John E.; Angelis, Georgios I.; Meikle, Steven R.

    2016-09-01

    Image space decomposition based on tetrahedral voxels are interesting candidates for use in emission tomography. Tetrahedral voxels provide many of the advantages of point clouds with irregular spacing, such as being intrinsically multi-resolution, yet they also serve as a volumetric partition of the image space and so are comparable to more standard cubic voxels. Additionally, non-rigid displacement fields can be applied to the tetrahedral mesh in a straight-forward manner. So far studies incorporating tetrahedral decomposition of the image space have concentrated on pre-calculated, node-based, system matrix elements which reduces the flexibility of the tetrahedral approach and the capacity to accurately define regions of interest. Here, a list-mode on-the-fly calculation of the system matrix elements is described using a tetrahedral decomposition of the image space and volumetric elements—voxels. The algorithm is demonstrated in the context of awake animal PET which may require both rigid and non-rigid motion compensation, as well as quantification within small regions of the brain. This approach allows accurate, event based, motion compensation including non-rigid deformations.

  1. Towards a voxel-based geographic automata for the simulation of geospatial processes

    NASA Astrophysics Data System (ADS)

    Jjumba, Anthony; Dragićević, Suzana

    2016-07-01

    Many geographic processes evolve in a three dimensional space and time continuum. However, when they are represented with the aid of geographic information systems (GIS) or geosimulation models they are modelled in a framework of two-dimensional space with an added temporal component. The objective of this study is to propose the design and implementation of voxel-based automata as a methodological approach for representing spatial processes evolving in the four-dimensional (4D) space-time domain. Similar to geographic automata models which are developed to capture and forecast geospatial processes that change in a two-dimensional spatial framework using cells (raster geospatial data), voxel automata rely on the automata theory and use three-dimensional volumetric units (voxels). Transition rules have been developed to represent various spatial processes which range from the movement of an object in 3D to the diffusion of airborne particles and landslide simulation. In addition, the proposed 4D models demonstrate that complex processes can be readily reproduced from simple transition functions without complex methodological approaches. The voxel-based automata approach provides a unique basis to model geospatial processes in 4D for the purpose of improving representation, analysis and understanding their spatiotemporal dynamics. This study contributes to the advancement of the concepts and framework of 4D GIS.

  2. Select and Cluster: A Method for Finding Functional Networks of Clustered Voxels in fMRI

    PubMed Central

    DonGiovanni, Danilo

    2016-01-01

    Extracting functional connectivity patterns among cortical regions in fMRI datasets is a challenge stimulating the development of effective data-driven or model based techniques. Here, we present a novel data-driven method for the extraction of significantly connected functional ROIs directly from the preprocessed fMRI data without relying on a priori knowledge of the expected activations. This method finds spatially compact groups of voxels which show a homogeneous pattern of significant connectivity with other regions in the brain. The method, called Select and Cluster (S&C), consists of two steps: first, a dimensionality reduction step based on a blind multiresolution pairwise correlation by which the subset of all cortical voxels with significant mutual correlation is selected and the second step in which the selected voxels are grouped into spatially compact and functionally homogeneous ROIs by means of a Support Vector Clustering (SVC) algorithm. The S&C method is described in detail. Its performance assessed on simulated and experimental fMRI data is compared to other methods commonly used in functional connectivity analyses, such as Independent Component Analysis (ICA) or clustering. S&C method simplifies the extraction of functional networks in fMRI by identifying automatically spatially compact groups of voxels (ROIs) involved in whole brain scale activation networks.

  3. Voxel Advanced Digital-Manufacturing for Earth and Regolith in Space Project

    NASA Technical Reports Server (NTRS)

    Zeitlin, Nancy; Mueller, Robert P.

    2015-01-01

    A voxel is a discrete three-dimensional (3D) element of material that is used to construct a larger 3D object. It is the 3D equivalent of a pixel. This project will conceptualize and study various approaches in order to develop a proof of concept 3D printing device that utilizes regolith as the material of the voxels. The goal is to develop a digital printer head capable of placing discrete self-aligning voxels in additive layers in order to fabricate small parts that can be given structural integrity through a post-printing sintering or other binding process. The quicker speeds possible with the voxel 3D printing approach along with the utilization of regolith material as the substrate will advance the use of this technology to applications for In-Situ Resource Utilization (ISRU), which is key to reducing logistics from Earth to Space, thus making long-duration human exploration missions to other celestial bodies more possible.

  4. Voxel-wise quantification of myocardial perfusion by cardiac magnetic resonance. Feasibility and methods comparison.

    PubMed

    Zarinabad, Niloufar; Chiribiri, Amedeo; Hautvast, Gilion L T F; Ishida, Masaki; Schuster, Andreas; Cvetkovic, Zoran; Batchelor, Philip G; Nagel, Eike

    2012-12-01

    The purpose of this study is to enable high spatial resolution voxel-wise quantitative analysis of myocardial perfusion in dynamic contrast-enhanced cardiovascular MR, in particular by finding the most favorable quantification algorithm in this context. Four deconvolution algorithms--Fermi function modeling, deconvolution using B-spline basis, deconvolution using exponential basis, and autoregressive moving average modeling--were tested to calculate voxel-wise perfusion estimates. The algorithms were developed on synthetic data and validated against a true gold-standard using a hardware perfusion phantom. The accuracy of each method was assessed for different levels of spatial averaging and perfusion rate. Finally, voxel-wise analysis was used to generate high resolution perfusion maps on real data acquired from five patients with suspected coronary artery disease and two healthy volunteers. On both synthetic and perfusion phantom data, the B-spline method had the highest error in estimation of myocardial blood flow. The autoregressive moving average modeling and exponential methods gave accurate estimates of myocardial blood flow. The Fermi model was the most robust method to noise. Both simulations and maps in the patients and hardware phantom showed that voxel-wise quantification of myocardium perfusion is feasible and can be used to detect abnormal regions.

  5. Lattice Boltzmann modeling of permeability in porous materials with partially percolating voxels.

    PubMed

    Li, Ruru; Yang, Y Sam; Pan, Jinxiao; Pereira, Gerald G; Taylor, John A; Clennell, Ben; Zou, Caineng

    2014-09-01

    A partial-bounce-back lattice Boltzmann model has been used to simulate flow on a lattice consisting of cubic voxels with a locally varying effective percolating fraction. The effective percolating fraction of a voxel is the total response to the partial-bounce-back techniques for porous media flow due to subvoxel fine structures. The model has been verified against known analytic solutions on two- and three-dimensional regular geometries, and has been applied to simulate flow and permeabilities of two real-world rock samples. This enables quantitative determination of permeability for problems where voxels cannot be adequately segmented as discrete compositions. The voxel compositions are represented as volume fractions of various material phases and void. The numerical results have shown that, for the tight-sandstone sample, the bulk permeability is sensitive to the effective percolating fraction of calcite. That is, the subvoxel flow paths in the calcite phase are important for bulk permeability. On the other hand, flow in the calcite phase in the sandstone sample makes an insignificant contribution to the bulk permeability. The calculated permeability value for the sandstone sample is up to two orders of magnitude greater than the tight sandstone. This model is generic and could be applied to other oil and gas reservoir media or to material samples.

  6. Sparse and Adaptive Diffusion Dictionary (SADD) for recovering intra-voxel white matter structure.

    PubMed

    Aranda, Ramon; Ramirez-Manzanares, Alonso; Rivera, Mariano

    2015-12-01

    On the analysis of the Diffusion-Weighted Magnetic Resonance Images, multi-compartment models overcome the limitations of the well-known Diffusion Tensor model for fitting in vivo brain axonal orientations at voxels with fiber crossings, branching, kissing or bifurcations. Some successful multi-compartment methods are based on diffusion dictionaries. The diffusion dictionary-based methods assume that the observed Magnetic Resonance signal at each voxel is a linear combination of the fixed dictionary elements (dictionary atoms). The atoms are fixed along different orientations and diffusivity profiles. In this work, we present a sparse and adaptive diffusion dictionary method based on the Diffusion Basis Functions Model to estimate in vivo brain axonal fiber populations. Our proposal overcomes the following limitations of the diffusion dictionary-based methods: the limited angular resolution and the fixed shapes for the atom set. We propose to iteratively re-estimate the orientations and the diffusivity profile of the atoms independently at each voxel by using a simplified and easier-to-solve mathematical approach. As a result, we improve the fitting of the Diffusion-Weighted Magnetic Resonance signal. The advantages with respect to the former Diffusion Basis Functions method are demonstrated on the synthetic data-set used on the 2012 HARDI Reconstruction Challenge and in vivo human data. We demonstrate that improvements obtained in the intra-voxel fiber structure estimations benefit brain research allowing to obtain better tractography estimations. Hence, these improvements result in an accurate computation of the brain connectivity patterns.

  7. Neural Correlates of Communication Skill and Symptom Severity in Autism: A Voxel-Based Morphometry Study

    ERIC Educational Resources Information Center

    Parks, Lauren K.; Hill, Dina E.; Thoma, Robert J.; Euler, Matthew J.; Lewine, Jeffrey D.; Yeo, Ronald A.

    2009-01-01

    Although many studies have compared the brains of normal controls and individuals with autism, especially older, higher-functioning individuals with autism, little is known of the neural correlates of the vast clinical heterogeneity characteristic of the disorder. In this study, we used voxel-based morphometry (VBM) to examine gray matter…

  8. Physically constrained voxel-based penalty adaptation for ultra-fast IMRT planning.

    PubMed

    Wahl, Niklas; Bangert, Mark; Kamerling, Cornelis P; Ziegenhein, Peter; Bol, Gijsbert H; Raaymakers, Bas W; Oelfke, Uwe

    2016-07-08

    Conventional treatment planning in intensity-modulated radiation therapy (IMRT) is a trial-and-error process that usually involves tedious tweaking of optimization parameters. Here, we present an algorithm that automates part of this process, in particular the adaptation of voxel-based penalties within normal tissue. Thereby, the proposed algorithm explicitly considers a priori known physical limitations of photon irradiation. The efficacy of the developed algorithm is assessed during treatment planning studies comprising 16 prostate and 5 head and neck cases. We study the eradication of hot spots in the normal tissue, effects on target coverage and target conformity, as well as selected dose volume points for organs at risk. The potential of the proposed method to generate class solutions for the two indications is investigated. Run-times of the algorithms are reported. Physically constrained voxel-based penalty adaptation is an adequate means to automatically detect and eradicate hot-spots during IMRT planning while maintaining target coverage and conformity. Negative effects on organs at risk are comparably small and restricted to lower doses. Using physically constrained voxel-based penalty adaptation, it was possible to improve the generation of class solutions for both indications. Considering the reported run-times of less than 20 s, physically constrained voxel-based penalty adaptation has the potential to reduce the clinical workload during planning and automated treatment plan generation in the long run, facilitating adaptive radiation treatments.

  9. Select and Cluster: A Method for Finding Functional Networks of Clustered Voxels in fMRI

    PubMed Central

    DonGiovanni, Danilo

    2016-01-01

    Extracting functional connectivity patterns among cortical regions in fMRI datasets is a challenge stimulating the development of effective data-driven or model based techniques. Here, we present a novel data-driven method for the extraction of significantly connected functional ROIs directly from the preprocessed fMRI data without relying on a priori knowledge of the expected activations. This method finds spatially compact groups of voxels which show a homogeneous pattern of significant connectivity with other regions in the brain. The method, called Select and Cluster (S&C), consists of two steps: first, a dimensionality reduction step based on a blind multiresolution pairwise correlation by which the subset of all cortical voxels with significant mutual correlation is selected and the second step in which the selected voxels are grouped into spatially compact and functionally homogeneous ROIs by means of a Support Vector Clustering (SVC) algorithm. The S&C method is described in detail. Its performance assessed on simulated and experimental fMRI data is compared to other methods commonly used in functional connectivity analyses, such as Independent Component Analysis (ICA) or clustering. S&C method simplifies the extraction of functional networks in fMRI by identifying automatically spatially compact groups of voxels (ROIs) involved in whole brain scale activation networks. PMID:27656202

  10. Estudio de distintos modelos de protuberancias solares

    NASA Astrophysics Data System (ADS)

    Cirigliano, D.; Rovira, M.; Mauas, P.

    En este trabajo presentamos perfiles de líneas del CaII, MgII y HeI calculados para distintos modelos de protuberancias, y los comparamos con observaciones obtenidas por los satélites OSO 8 y SOHO. Para obtener las poblaciones de los distintos niveles de los átomos, utilizamos un código numérico que combina las ecuaciones de transporte de radiación y equilibrio estadístico en un único sistema de ecuaciones no lineal. Los modelos básicos que consideramos para las protuberancias consisten en placas homogéneas y unidimensionales apoyadas sobre la superficie del Sol. Dichas placas se hallan estratificadas en hebras y los modelos difieren entre sí en la temperatura y ancho de la placa, en la presión a la cual se halla el plasma y en el número de hebras. A partir de estos modelos se investiga cada uno de estos parámetros libres y como influyen en la atmósfera de las protuberancias solares y en el perfil de línea de cada especie estudiada, con el objetivo de determinar las condiciones en las que se halla el material atmosférico de estas protuberancias.

  11. A Voxel-Based Approach for Imaging Voids in Three-Dimensional Point Clouds

    NASA Astrophysics Data System (ADS)

    Salvaggio, Katie N.

    Geographically accurate scene models have enormous potential beyond that of just simple visualizations in regard to automated scene generation. In recent years, thanks to ever increasing computational efficiencies, there has been significant growth in both the computer vision and photogrammetry communities pertaining to automatic scene reconstruction from multiple-view imagery. The result of these algorithms is a three-dimensional (3D) point cloud which can be used to derive a final model using surface reconstruction techniques. However, the fidelity of these point clouds has not been well studied, and voids often exist within the point cloud. Voids exist in texturally difficult areas, as well as areas where multiple views were not obtained during collection, constant occlusion existed due to collection angles or overlapping scene geometry, or in regions that failed to triangulate accurately. It may be possible to fill in small voids in the scene using surface reconstruction or hole-filling techniques, but this is not the case with larger more complex voids, and attempting to reconstruct them using only the knowledge of the incomplete point cloud is neither accurate nor aesthetically pleasing. A method is presented for identifying voids in point clouds by using a voxel-based approach to partition the 3D space. By using collection geometry and information derived from the point cloud, it is possible to detect unsampled voxels such that voids can be identified. This analysis takes into account the location of the camera and the 3D points themselves to capitalize on the idea of free space, such that voxels that lie on the ray between the camera and point are devoid of obstruction, as a clear line of sight is a necessary requirement for reconstruction. Using this approach, voxels are classified into three categories: occupied (contains points from the point cloud), free (rays from the camera to the point passed through the voxel), and unsampled (does not contain points

  12. A novel neutron computed tomography partial volume voxel water quantification technique

    NASA Astrophysics Data System (ADS)

    Heller, Arthur Kevin

    Since neutrons are attenuated by small amounts of water, but readily penetrate most metals, neutron imaging is ideal for the observation and quantification of water mass in operating hydrogen-powered polymer electrolyte fuel cells (PEFCs). PEFC's have a special need for non-destructive analysis techniques for the imaging of liquid water because the liquid water stored in the porous media can be a source of reduced performance, degradation and cause more lethargic start-up from freezing conditions. Traditional two-dimensional (2D) neutron radioscopy has been successfully applied to the quantification of liquid water in PEFC's, but it suffers from the drawback of making it difficult to determine the exact "depth" within a PEFC the liquid water mass exists. Neutron computed tomography (NCT) produces a three-dimensional (3D) volumetric reconstruction that offers the ability to determine the exact spatial location of a liquid water mass within a PEFC. This makes possible the isolation of liquid water slugs that can block the channels of either the anode or cathode reactant flow fields. Water mass quantification of these slugs would provide insight into improving PEFC design. Thus, a method was developed for the precise quantification of water mass in neutron computed tomography (NCT) reconstructions. A three-dimensional (3D) volumetric reconstruction is comprised of individual volume elements, or voxels. The gray level value of a voxel represents the total macroscopic cross section, Sigmat, of the material present at the voxel's spatial location. For voxels along interfaces, the gray level represents a combination of Sigmats for the various materials present. The fractional amount of water, also known as a partial volume, represented by such a voxel must be quantified for an accurate result. This calculation requires removing or compensating for the influence of other materials on the voxel's gray level. This is accomplished by background normalizing the raw data used

  13. Voxel-Based Dose Reconstruction for Total Body Irradiation With Helical TomoTherapy

    SciTech Connect

    Chao Ming; Penagaricano, Jose; Yan Yulong; Moros, Eduardo G.; Corry, Peter; Ratanatharathorn, Vaneerat

    2012-04-01

    Purpose: We have developed a megavoltage CT (MVCT)-based dose reconstruction strategy for total body irradiation (TBI) with helical TomoTherapy (HT) using a deformable registration model to account for the patient's interfraction changes. The proposed technique serves as an efficient tool for delivered dose verification and, potentially, plan adaptation. Methods and Materials: Four patients with acute myelogenous leukemia treated with TBI using HT were selected for this study. The prescription was 12 Gy, 2 Gy/fraction, twice per day, given at least 6 h apart. The original plan achieved coverage of 80% of the clinical target volume (CTV) by the 12 Gy isodose surface. MVCTs were acquired prior to each treatment. Regions of interest were contoured on each MVCT. The dose for each fraction was calculated based on the MVCT using the HT planned adaptive station. B-spline deformable registration was conducted to establish voxel-to-voxel correspondence between the MVCT and the planning CT. The resultant deformation vector was employed to map the reconstructed dose from each fraction to the same point as the plan dose, and a voxel-to-voxel summed dose from all six fractions was obtained. The reconstructed dose distribution and its dosimetric parameters were compared with those of the original treatment plan. Results: While changes in CTV contours occurred in all patients, the reconstructed dose distribution showed that the dose-volume histogram for CTV coverage was close (<1.5%) to that of the original plan. For sensitive structures, the differences between the reconstructed and the planned doses were less than 3.0%. Conclusion: Voxel-based dose reconstruction strategy that takes into account interfraction anatomical changes using MVCTs is a powerful tool for treatment verification of the delivered doses. This proposed technique can also be applied to adaptive TBI therapy using HT.

  14. Quantitative myocardial perfusion PET parametric imaging at the voxel-level

    NASA Astrophysics Data System (ADS)

    Mohy-ud-Din, Hassan; Lodge, Martin A.; Rahmim, Arman

    2015-08-01

    Quantitative myocardial perfusion (MP) PET has the potential to enhance detection of early stages of atherosclerosis or microvascular dysfunction, characterization of flow-limiting effects of coronary artery disease (CAD), and identification of balanced reduction of flow due to multivessel stenosis. We aim to enable quantitative MP-PET at the individual voxel level, which has the potential to allow enhanced visualization and quantification of myocardial blood flow (MBF) and flow reserve (MFR) as computed from uptake parametric images. This framework is especially challenging for the 82Rb radiotracer. The short half-life enables fast serial imaging and high patient throughput; yet, the acquired dynamic PET images suffer from high noise-levels introducing large variability in uptake parametric images and, therefore, in the estimates of MBF and MFR. Robust estimation requires substantial post-smoothing of noisy data, degrading valuable functional information of physiological and pathological importance. We present a feasible and robust approach to generate parametric images at the voxel-level that substantially reduces noise without significant loss of spatial resolution. The proposed methodology, denoted physiological clustering, makes use of the functional similarity of voxels to penalize deviation of voxel kinetics from physiological partners. The results were validated using extensive simulations (with transmural and non-transmural perfusion defects) and clinical studies. Compared to post-smoothing, physiological clustering depicted enhanced quantitative noise versus bias performance as well as superior recovery of perfusion defects (as quantified by CNR) with minimal increase in bias. Overall, parametric images obtained from the proposed methodology were robust in the presence of high-noise levels as manifested in the voxel time-activity-curves.

  15. Quantitative myocardial perfusion PET parametric imaging at the voxel-level.

    PubMed

    Mohy-Ud-Din, Hassan; Lodge, Martin A; Rahmim, Arman

    2015-08-01

    Quantitative myocardial perfusion (MP) PET has the potential to enhance detection of early stages of atherosclerosis or microvascular dysfunction, characterization of flow-limiting effects of coronary artery disease (CAD), and identification of balanced reduction of flow due to multivessel stenosis. We aim to enable quantitative MP-PET at the individual voxel level, which has the potential to allow enhanced visualization and quantification of myocardial blood flow (MBF) and flow reserve (MFR) as computed from uptake parametric images. This framework is especially challenging for the (82)Rb radiotracer. The short half-life enables fast serial imaging and high patient throughput; yet, the acquired dynamic PET images suffer from high noise-levels introducing large variability in uptake parametric images and, therefore, in the estimates of MBF and MFR. Robust estimation requires substantial post-smoothing of noisy data, degrading valuable functional information of physiological and pathological importance. We present a feasible and robust approach to generate parametric images at the voxel-level that substantially reduces noise without significant loss of spatial resolution. The proposed methodology, denoted physiological clustering, makes use of the functional similarity of voxels to penalize deviation of voxel kinetics from physiological partners. The results were validated using extensive simulations (with transmural and non-transmural perfusion defects) and clinical studies. Compared to post-smoothing, physiological clustering depicted enhanced quantitative noise versus bias performance as well as superior recovery of perfusion defects (as quantified by CNR) with minimal increase in bias. Overall, parametric images obtained from the proposed methodology were robust in the presence of high-noise levels as manifested in the voxel time-activity-curves.

  16. 3D sensitive voxel detector of ionizing radiation based on Timepix device

    NASA Astrophysics Data System (ADS)

    Soukup, P.; Jakubek, J.; Vykydal, Z.

    2011-01-01

    Position sensitive detectors are evolving towards higher segmentation geometries from 0D (single pad) over 1D (strip) to 2D (pixel) detectors. Each step has brought up substantial expansion in the field of applications. The next logical step in this evolution is to design a 3D, i.e. voxel detector. The voxel detector can be constructed from 2D volume element detectors arranged in layers forming a 3D matrix of sensitive elements — voxels. Such detectors can effectively record tracks of energetic particles. By proper analysis of these tracks it is possible to determine the type, direction and energy of the primary particle. One of the prominent applications of such device is in the localization and identification of gamma and neutron sources in the environment. It can be also used for emission and transmission radiography in many fields where standard imagers are currently utilized. The qualitative properties of current imagers such as: spatial resolution, efficiency, directional sensitivity, energy sensitivity and selectivity (background suppression) can be improved. The first prototype of a voxel detector was built using a number of Timepix devices. Timepix is hybrid semiconductor detector consisting of a segmented semiconductor sensor bump-bonded to a readout chip. Each sensor contains 256x256 square pixels of 55 μm size. The voxel detector prototype was successfully tested to prove the concept functionality. The detector has a modular architecture with a daisy chain connection of the individual detector layers. This permits easy rearrangement due to its modularity, while keeping a single readout system for a variable number of detector layers. A limitation of this approach is the relatively large inter-layer distance (4 mm) compared to the pixel thickness (0.3 mm). Therefore the next step in the design is to decrease the space between the 2D detectors.

  17. Efficient voxel navigation for proton therapy dose calculation in TOPAS and Geant4

    PubMed Central

    Schümann, J.; Paganetti, H.; Shin, J.; Faddegon, B.; Perl, J.

    2012-01-01

    A key task within all Monte Carlo particle transport codes is Navigation, the calculation to determine at each particle step what volume the particle may be leaving and what volume the particle may be entering. Navigation should be optimized to the specific geometry at hand. For patient dose calculation, this geometry generally involves voxelized computed tomography (CT) data. We investigated the effciency of navigation algorithms on currently available voxel geometry parameterizations in the Monte Carlo simulation package Geant4: G4VPVParameterisation, G4VNestedParameterisation and G4PhantomParameterisation, the latter with and without boundary skipping, a method where neighboring voxels with the same Hounsfield Unit are combined into one larger voxel. A fourth parameterization approach (MGHParameterization), developed in-house before the latter two parameterizations became available in Geant4, was also included in this study. All simulations were performed using TOPAS, a TOol for PArticle Simulations layered on top of Geant4. Runtime comparisons were performed on three distinct patient CT data sets: A head and neck, a liver, and a prostate patient. We included an additional version of these three patients where all voxels, including the air voxels outside of the patient, were uniformly set to water in the runtime study. The G4VPVParameterisation offers two optimization options. One option has a 60-150 times slower simulation speed. The other is compatible in speed but requires 15-19 times more memory compared to the other parameterizations. We found the average CPU time used for the simulation relative to G4VNestedParameterisation to be 1.014 for G4PhantomParameterisation without boundary skipping and 1.015 for MGHParameterization. The average run time ratio for G4PhantomParamererisation with and without boundary skipping for our heterogeneous data was = 0:97 : 1. The calculated dose distributions agreed with the reference distribution for all but the G4Phantom

  18. Prediction of fMRI time series of a single voxel using radial basis function neural network

    NASA Astrophysics Data System (ADS)

    Song, Sutao; Zhang, Jiacai; Yao, Li

    2011-03-01

    A great deal of current literature regarding functional neuroimaging has elucidated the relationships of neurons distributed all over the brain. Modern neuroimaging techniques, such as the functional MRI (fMRI), provide a convenient tool for people to study the correlation among different voxels as well as the spatio-temporal patterns of brain activity. In this study, we present a computational model using radial basis function neural network (RBF-NN) to predict the fMRI voxel activation with the activation of other voxels acquired at the same time. The fMRI data from a visual images stimuli presentation experiment was separated into two sets; one was used to train the model, and the other to validate the accuracy or generalizability of the model. In the visual stimuli presentation experiment, the subject did simple one-back-repetition tasks when four categories of stimuli (houses, faces, cars, and cats) were presented. Voxel sets A and B were selected from fMRI data by two different voxel selection criterion: (1) Voxel set A are those activated for any kind of object stronger than the other three objects in regions of interest (ROIs) without correction (P=0.001); (2) Voxel set B are those activated for at least one of the categories of stimuli within the ROIs (FWE correction, P=0.05). RBF-NN regression models construct the nonlinear relationship between the activation of voxels in A and B. Our test results showed that RBF-NN can capture the nonlinear relationship existing in neurons and reveal the relationship between voxel's activation from different brain regions.

  19. Linguistic Summarization of Video for Fall Detection Using Voxel Person and Fuzzy Logic.

    PubMed

    Anderson, Derek; Luke, Robert H; Keller, James M; Skubic, Marjorie; Rantz, Marilyn; Aud, Myra

    2009-01-01

    In this paper, we present a method for recognizing human activity from linguistic summarizations of temporal fuzzy inference curves representing the states of a three-dimensional object called voxel person. A hierarchy of fuzzy logic is used, where the output from each level is summarized and fed into the next level. We present a two level model for fall detection. The first level infers the states of the person at each image. The second level operates on linguistic summarizations of voxel person's states and inference regarding activity is performed. The rules used for fall detection were designed under the supervision of nurses to ensure that they reflect the manner in which elders perform these activities. The proposed framework is extremely flexible. Rules can be modified, added, or removed, allowing for per-resident customization based on knowledge about their cognitive and physical ability.

  20. Denoising Intra-voxel Axon Fiber Orientations by Means of ECQMMF Method

    NASA Astrophysics Data System (ADS)

    Ramirez-Manzanares, Alonso; Rivera, Mariano; Gee, James C.

    Diffusion weighted magnetic resonance imaging is widely used in the study of the structure of the fiber pathways in brain white matter. In this work we present a new method for denoising intra-voxel axon fiber tracks. In order to improve local (voxelwise) estimations, we use the general-purpose segmentation method called Entropy-Controlled Quadratic Markov Measure Field Models. Our proposal is capable of spatially-regularize multiple axon fiber orientations (intra-voxel orientations). In order to provide the best as possible local axon orientations to our spatial regularization procedure, we evaluate two optimization methods for fitting a Diffusion Basis Function model. We present qualitative results on real human Diffusion Weighted MRI data where the ground-truth is not available, and we quantitatively validate our results by synthetic experiments.

  1. Linguistic Summarization of Video for Fall Detection Using Voxel Person and Fuzzy Logic

    PubMed Central

    Anderson, Derek; Luke, Robert H.; Keller, James M.; Skubic, Marjorie; Rantz, Marilyn; Aud, Myra

    2009-01-01

    In this paper, we present a method for recognizing human activity from linguistic summarizations of temporal fuzzy inference curves representing the states of a three-dimensional object called voxel person. A hierarchy of fuzzy logic is used, where the output from each level is summarized and fed into the next level. We present a two level model for fall detection. The first level infers the states of the person at each image. The second level operates on linguistic summarizations of voxel person’s states and inference regarding activity is performed. The rules used for fall detection were designed under the supervision of nurses to ensure that they reflect the manner in which elders perform these activities. The proposed framework is extremely flexible. Rules can be modified, added, or removed, allowing for per-resident customization based on knowledge about their cognitive and physical ability. PMID:20046216

  2. Modelo analítico del efecto de PRS sobre satélites GPS

    NASA Astrophysics Data System (ADS)

    Meza, A.; Brunini, C.; Usandivaras, J. C.

    El sistema GPS (Global Position System) es, hoy en día, la herramienta de navegación y posicionamiento más potente y lo será sin duda en la próxima década. Gran parte de su valiosa utilidad se debe a la alta precisión que permite lograr y ésta, a su vez, depende, entre otras causas, de la precisión con que se conocen las órbitas de los satélites. La presión de radiación solar (PRS) fija el límite de la precisión con que pueden calcularse en la actualidad las efemérides satelitarias. El objetivo de este trabajo es proponer una mejor resolución de este fenómeno. El modelo analítico aquí presentado, se basa en el análisis del comportamiento de los residuos de un ajuste por mínimos cuadrados en el que se utiliza el modelo de PRS propuesto por Beutler. El mismo consiste en un modelo determinista del fenómeno con dos parámetros libres. Los resultados obtenidos ponen de manifiesto que, aún después de aplicar dichos parámetros, prevalecen en los residuos efectos semidiurnos en las componentes radial,tangencial y normal. Estos resultados obtenidos se comparan con los de un trabajo desarrollado por el Instituto de Berne (Beutler et al., 1994), en el que se utilizaron como pseudo-observaciones las órbitas precisas del IGS (CODE). El intervalo de integración escogido por este centro fueron las semanas 680 y 681. En resumen se tienen arcos de 14 días para todos los satélites, donde las efemérides precisas de los mismos para los 14 días fueron utilizados como pseudo-observaciones. El modelo de fuerza que empleó dicho centro fue básicamente el tradicional en lo que respecta al modelo de las fuerzas gravitacionales, y para la PRS utilizo el modelo standard de Beutler. Los parámetros de este modelo junto con las 6 condiciones iniciales (posición y velocidad) fueron ajustados por el método general de mínimos cuadrados. Los residuos en la componente radial, tangencial y normal, para los satélites con un buen comportamiento, presentan una

  3. Sweeping Raster Cross Sections Along Trajectories in Three-Dimensional Voxel Models

    NASA Astrophysics Data System (ADS)

    Gorte, B.; Zlatanova, S.; Leidner, A.

    2016-10-01

    The paper presents a new algorithm to reconstruct elongated objects defined by cross sections and trajectories in gridded threedimensional models represented as voxels. Examples of such objects are the elements of underground infrastructure in urban environments, such as pipes, conduits and tunnels. Starting from a basic methodology, which is based on distance transformations, the algorithm is extended in three ways on the basis of Voronoi datasets being produced alongside.

  4. A voxel-wise encoding model for early visual areas decodes mental images of remembered scenes.

    PubMed

    Naselaris, Thomas; Olman, Cheryl A; Stansbury, Dustin E; Ugurbil, Kamil; Gallant, Jack L

    2015-01-15

    Recent multi-voxel pattern classification (MVPC) studies have shown that in early visual cortex patterns of brain activity generated during mental imagery are similar to patterns of activity generated during perception. This finding implies that low-level visual features (e.g., space, spatial frequency, and orientation) are encoded during mental imagery. However, the specific hypothesis that low-level visual features are encoded during mental imagery is difficult to directly test using MVPC. The difficulty is especially acute when considering the representation of complex, multi-object scenes that can evoke multiple sources of variation that are distinct from low-level visual features. Therefore, we used a voxel-wise modeling and decoding approach to directly test the hypothesis that low-level visual features are encoded in activity generated during mental imagery of complex scenes. Using fMRI measurements of cortical activity evoked by viewing photographs, we constructed voxel-wise encoding models of tuning to low-level visual features. We also measured activity as subjects imagined previously memorized works of art. We then used the encoding models to determine if putative low-level visual features encoded in this activity could pick out the imagined artwork from among thousands of other randomly selected images. We show that mental images can be accurately identified in this way; moreover, mental image identification accuracy depends upon the degree of tuning to low-level visual features in the voxels selected for decoding. These results directly confirm the hypothesis that low-level visual features are encoded during mental imagery of complex scenes. Our work also points to novel forms of brain-machine interaction: we provide a proof-of-concept demonstration of an internet image search guided by mental imagery.

  5. Using Edge Voxel Information to Improve Motion Regression for rs-fMRI Connectivity Studies.

    PubMed

    Patriat, Rémi; Molloy, Erin K; Birn, Rasmus M

    2015-11-01

    Recent fMRI studies have outlined the critical impact of in-scanner head motion, particularly on estimates of functional connectivity. Common strategies to reduce the influence of motion include realignment as well as the inclusion of nuisance regressors, such as the 6 realignment parameters, their first derivatives, time-shifted versions of the realignment parameters, and the squared parameters. However, these regressors have limited success at noise reduction. We hypothesized that using nuisance regressors consisting of the principal components (PCs) of edge voxel time series would be better able to capture slice-specific and nonlinear signal changes, thus explaining more variance, improving data quality (i.e., lower DVARS and temporal SNR), and reducing the effect of motion on default-mode network connectivity. Functional MRI data from 22 healthy adult subjects were preprocessed using typical motion regression approaches as well as nuisance regression derived from edge voxel time courses. Results were evaluated in the presence and absence of both global signal regression and motion censoring. Nuisance regressors derived from signal intensity time courses at the edge of the brain significantly improved motion correction compared to using only the realignment parameters and their derivatives. Of the models tested, only the edge voxel regression models were able to eliminate significant differences in default-mode network connectivity between high- and low-motion subjects regardless of the use of global signal regression or censoring.

  6. An Eye Model for Computational Dosimetry Using A Multi-Scale Voxel Phantom

    NASA Astrophysics Data System (ADS)

    Caracappa, Peter F.; Rhodes, Ashley; Fiedler, Derek

    2014-06-01

    The lens of the eye is a radiosensitive tissue with cataract formation being the major concern. Recently reduced recommended dose limits to the lens of the eye have made understanding the dose to this tissue of increased importance. Due to memory limitations, the voxel resolution of computational phantoms used for radiation dose calculations is too large to accurately represent the dimensions of the eye. A revised eye model is constructed using physiological data for the dimensions of radiosensitive tissues, and is then transformed into a high-resolution voxel model. This eye model is combined with an existing set of whole body models to form a multi-scale voxel phantom, which is used with the MCNPX code to calculate radiation dose from various exposure types. This phantom provides an accurate representation of the radiation transport through the structures of the eye. Two alternate methods of including a high-resolution eye model within an existing whole body model are developed. The accuracy and performance of each method is compared against existing computational phantoms.

  7. Multi-resolution voxel phantom modeling: a high-resolution eye model for computational dosimetry

    NASA Astrophysics Data System (ADS)

    Caracappa, Peter F.; Rhodes, Ashley; Fiedler, Derek

    2014-09-01

    Voxel models of the human body are commonly used for simulating radiation dose with a Monte Carlo radiation transport code. Due to memory limitations, the voxel resolution of these computational phantoms is typically too large to accurately represent the dimensions of small features such as the eye. Recently reduced recommended dose limits to the lens of the eye, which is a radiosensitive tissue with a significant concern for cataract formation, has lent increased importance to understanding the dose to this tissue. A high-resolution eye model is constructed using physiological data for the dimensions of radiosensitive tissues, and combined with an existing set of whole-body models to form a multi-resolution voxel phantom, which is used with the MCNPX code to calculate radiation dose from various exposure types. This phantom provides an accurate representation of the radiation transport through the structures of the eye. Two alternate methods of including a high-resolution eye model within an existing whole-body model are developed. The accuracy and performance of each method is compared against existing computational phantoms.

  8. A reference workpiece for voxel size correction in x-ray computed tomography

    NASA Astrophysics Data System (ADS)

    Lifton, Joseph J.; Cross, Kevin J.; Malcolm, Andrew A.; McBride, John W.

    2013-06-01

    X-ray computed tomography (CT) is increasingly used for dimensional metrology, allowing the inspection of both interior and exterior features impossible to observe using traditional optical and tactile measurement techniques. X-ray CT offers many benefits over traditional instruments as a visual inspection tool, however, extracting dimensional information from the reconstructed data-sets must be approached with caution due to error sources that can propagate through the image reconstruction processes. One error source originates from values of the source-to-object and source-to-detector distances; these are critical inputs as they define the voxel size, a global scalar directly influencing all dimensions extracted from the data. To reduce voxel size errors a reference workpiece can be scanned using the same measurement settings as the actual workpiece. By reconstructing the reference workpiece a reference dimension can be evaluated and this then used to adjust the voxel size of the actual workpiece. This reference dimension must be threshold independent, namely it is determined without the influence of edge detection thresholds. This paper offers a reference workpiece designed for measurement in an X-ray CT system, a coordinate measuring machine (CMM), and an optical profiler. Repeated measurements are made of the reference workpiece using all three instruments and

  9. Dynamic Isosurface Extraction and Level-of-Detail in Voxel Space

    SciTech Connect

    Lamphere, P.B.; Linebarger, J.M.

    1999-03-01

    A new visualization representation is described, which dramatically improves interactivity for scientific visualizations of structured grid data sets by creating isosurfaces at interactive speeds and with dynamically changeable levels-of-detail (LOD). This representation enables greater interactivity by allowing an analyst to dynamically specify both the desired isosurface threshold and required level-of-detail to be used while rendering the image. A scientist can therefore view very large isosurfaces at interactive speeds (with a low level-of-detail), but has the full data set always available for analysis. The key idea is that various levels-of-detail are represented as differently sized hexahedral virtual voxels, which are stored in a three-dimensional binary tree, or kd-tree; thus the level-of-detail representation is done in voxel space instead of the traditional approach which relies on surface or geometry space decimations. Utilizing the voxel space is an essential step to moving from a post-processing visualization paradigm to a quantitative, real-time paradigm. This algorithm has been implemented as an integral component of the EIGEN/VR project at Sandia National Laboratories, which provides a rich environment for scientists to interactively explore and visualize the results of very large-scale simulations performed on massively parallel supercomputers.

  10. Dynamic isosurface extraction and level-of-detail in voxel space

    SciTech Connect

    Linebarger, J.M.; Lamphere, P.B.; Breckenridge, A.R.

    1998-06-01

    A new visualization technique is reported, which dramatically improves interactivity for scientific visualizations by working directly with voxel data and by employing efficient algorithms and data structures. This discussion covers the research software, the file structures, examples of data creation, data search, and triangle rendering codes that allow geometric surfaces to be extracted from volumetric data. Uniquely, these methods enable greater interactivity by allowing an analyst to dynamically specify both the desired isosurface threshold and required level-of-detail to be used while rendering the image. The key idea behind this visualization paradigm is that various levels-of-detail are represented as differently sized hexahedral virtual voxels, which are stored in a three-dimensional kd-tree; thus the level-of-detail representation is done in voxel space instead of the traditional approach which relies on surface or geometry space decimations. This algorithm has been implemented as an integral component in the EIGEN/VR project at Sandia National Laboratories, which provides a rich environment for scientists to interactively explore and visualize the results of very large-scale simulations performed on massively parallel supercomputers.

  11. VS: a surface-based system for topological analysis, quantization and visualization of voxel data.

    PubMed

    Cohen, Itay; Gordon, Dan

    2009-04-01

    VS is a simple system consisting of several techniques for various volumetric problems. Based on the marching cubes algorithm, it operates with one space sweep through the voxels and extracts all topological information: detection of all isosurfaces, partitioning the data into connected components on the basis of surface connectivity, and association of surfaces with any internal surfaces to arbitrary levels of nesting. VS extends Baker's "Weaving Wall" method by associating topological cavities with their outer surface, and by using efficient data structures for the voxel traversal and for the connected component detection. Its runtime, on average, is only about 2% more than the speeded-up marching cubes algorithm. VS operates on the original voxels without using the contour tree required by other approaches. Using linear-time preprocessing, VS constructs a data structure which can be utilized for any isovalue or interval of isovalues. An accurate estimate of each component's volume is based on the volume enclosed by the outer surface, minus the volume of any internal cavities. VS enables noise reduction by eliminating components (and cavities) with a small volume. Different components can be rendered with different visual attributes, and cutaway views by arbitrary cut-planes are displayed as if the objects were solid, without adding any new surface patches to match the intersection. PMID:19083261

  12. A Voxel-based Method for Forest Change Detection after Fire Using LiDAR Data

    NASA Astrophysics Data System (ADS)

    Xu, Z.

    2015-12-01

    A Voxel-based Method for Forest Change Detection after Fire Using LiDAR DataZewei Xu and Jonathan A. Greenberg Traditional methods of forest fire modeling focus on the patterns of burning in two-dimensions at relatively coarse resolutions. However, fires spread in complex, three-dimensional patterns related to the horizontal and vertical distributions of woody fuel as well as the prevailing climate conditions, and the micro-scale patterns of fuel distributions over scales of only meters can determine the path that fire can take through a complex landscape. One challenge in understanding the full three-dimensional (3D) path that a fire takes through a landscape is a lack of data at landscape scales of these burns. Remote sensing approaches, while operating at landscape scales, typically focus on two-dimensional analyses using standard image-based change detection techniques. In this research, we develop a 3D voxel-based change detection method applied to multitemporal LiDAR data collected before and after forest fires in California to quantify the full 3D pattern of vegetation loss. By changing the size of the voxel, forest loss at different spatial scales is revealed. The 3D tunnel of fuel loss created by the fire was used to examine ground-to-crown transitions, firebreaks, and other three-dimensional aspects of a forest fire.

  13. Effective dose evaluation for BNCT brain tumor treatment based on voxel phantoms.

    PubMed

    Wang, Jeng-Ning; Lee, Kuo-Wei; Jiang, Shiang-Huei

    2014-06-01

    For BNCT treatments, in addition to tumor target doses, non-negligible doses will result in all the remaining organs of the body. This work aims to evaluate the effective dose as well as the average absorbed doses of each of organs of patients with brain tumor treated in the BNCT epithermal neutron beam at THOR. The effective doses were evaluated according to the definitions of ICRP Publications 60 and 103 for the reference male and female computational phantoms developed in ICRP Publication 110 by using the MCNP5 Monte Carlo code with the THOR-Y09 beam source. The effective dose acquired in this work was compared with the results of our previous work calculated for an adult hermaphrodite mathematical phantom. It was found that the effective dose for the female voxel phantom is larger than that for the male voxel phantom by a factor of 1.2-1.5 and the effective dose for the voxel phantom is larger than that for the mathematical phantom by a factor of 1.3-1.6. For a typical brain tumor BNCT, the effective dose was calculated to be 1.51Sv and the average absorbed dose for eye lenses was 1.07Gy.

  14. Voxel-level reproducibility assessment of modality independent elastography in a pre-clinical murine model

    NASA Astrophysics Data System (ADS)

    Flint, Katelyn M.; Weis, Jared A.; Yankeelov, Thomas E.; Miga, Michael I.

    2015-03-01

    Changes in tissue mechanical properties, measured non-invasively by elastography methods, have been shown to be an important diagnostic tool, particularly for cancer. Tissue elasticity information, tracked over the course of therapy, may be an important prognostic indicator of tumor response to treatment. While many elastography techniques exist, this work reports on the use of a novel form of elastography that uses image texture to reconstruct elastic property distributions in tissue (i.e., a modality independent elastography (MIE) method) within the context of a pre-clinical breast cancer system.1,2 The elasticity results have previously shown good correlation with independent mechanical testing.1 Furthermore, MIE has been successfully utilized to localize and characterize lesions in both phantom experiments and simulation experiments with clinical data.2,3 However, the reproducibility of this method has not been characterized in previous work. The goal of this study is to evaluate voxel-level reproducibility of MIE in a pre-clinical model of breast cancer. Bland-Altman analysis of co-registered repeat MIE scans in this preliminary study showed a reproducibility index of 24.7% (scaled to a percent of maximum stiffness) at the voxel level. As opposed to many reports in the magnetic resonance elastography (MRE) literature that speak to reproducibility measures of the bulk organ, these results establish MIE reproducibility at the voxel level; i.e., the reproducibility of locally-defined mechanical property measurements throughout the tumor volume.

  15. VIDA: a voxel-based dosimetry method for targeted radionuclide therapy using Geant4.

    PubMed

    Kost, Susan D; Dewaraja, Yuni K; Abramson, Richard G; Stabin, Michael G

    2015-02-01

    We have developed the Voxel-Based Internal Dosimetry Application (VIDA) to provide patient-specific dosimetry in targeted radionuclide therapy performing Monte Carlo simulations of radiation transport with the Geant4 toolkit. The code generates voxel-level dose rate maps using anatomical and physiological data taken from individual patients. Voxel level dose rate curves are then fit and integrated to yield a spatial map of radiation absorbed dose. In this article, we present validation studies using established dosimetry results, including self-dose factors (DFs) from the OLINDA/EXM program for uniform activity in unit density spheres and organ self- and cross-organ DFs in the Radiation Dose Assessment Resource (RADAR) reference adult phantom. The comparison with reference data demonstrated agreement within 5% for self-DFs to spheres and reference phantom source organs for four common radionuclides used in targeted therapy ((131)I, (90)Y, (111)In, (177)Lu). Agreement within 9% was achieved for cross-organ DFs. We also present dose estimates to normal tissues and tumors from studies of two non-Hodgkin Lymphoma patients treated by (131)I radioimmunotherapy, with comparison to results generated independently with another dosimetry code. A relative difference of 12% or less was found between methods for mean absorbed tumor doses accounting for tumor regression.

  16. Preliminary studies on neutron conversion coefficients calculated with MCNPX in NORMAN voxel phantom.

    PubMed

    Gualdrini, G; Ferrari, P

    2007-01-01

    Effective dose is the main radiation protection quantity. Progresses in radiation studies brought ICRP to revise ICRP 60 recommendations. A new publication, already circulated in form of draft, is expected to change some aspects of effective dose evaluation method. The organ absorbed doses for neutrons at various energies and incidence angles, necessary to estimate the effective dose, have been published in ICRU 57 and ICRP 74 reports for ADAM and EVA analytical male and female phantoms and similar calculations were also performed, based on the MCNP code, for VIP-MAN voxel phantom. The NORMAN voxel phantom, developed on the basis of magnetic resonance data of an adult male at HPA (formerly NRPB), is an accurate model (with a voxel element of approximately 8 mm(3)), which well approximates the standard man and has been already employed for radiation protection studies with photons. In the present paper, a modified version, called NORMAN-05, including a new organ, the salivary glands (as suggested in the mentioned ICRP draft), and a more detailed skeletal description, especially devoted to red bone marrow dose evaluation, has been employed with the Monte Carlo code MCNPX to calculate neutron conversion coefficients from thermal energies to 20 MeV. Some preliminary results, for antero-posterior and postero-anterior irradiation conditions, are presented and compared with the available published data. PMID:17502319

  17. VIDA: A Voxel-Based Dosimetry Method for Targeted Radionuclide Therapy Using Geant4

    PubMed Central

    Dewaraja, Yuni K.; Abramson, Richard G.; Stabin, Michael G.

    2015-01-01

    Abstract We have developed the Voxel-Based Internal Dosimetry Application (VIDA) to provide patient-specific dosimetry in targeted radionuclide therapy performing Monte Carlo simulations of radiation transport with the Geant4 toolkit. The code generates voxel-level dose rate maps using anatomical and physiological data taken from individual patients. Voxel level dose rate curves are then fit and integrated to yield a spatial map of radiation absorbed dose. In this article, we present validation studies using established dosimetry results, including self-dose factors (DFs) from the OLINDA/EXM program for uniform activity in unit density spheres and organ self- and cross-organ DFs in the Radiation Dose Assessment Resource (RADAR) reference adult phantom. The comparison with reference data demonstrated agreement within 5% for self-DFs to spheres and reference phantom source organs for four common radionuclides used in targeted therapy (131I, 90Y, 111In, 177Lu). Agreement within 9% was achieved for cross-organ DFs. We also present dose estimates to normal tissues and tumors from studies of two non-Hodgkin Lymphoma patients treated by 131I radioimmunotherapy, with comparison to results generated independently with another dosimetry code. A relative difference of 12% or less was found between methods for mean absorbed tumor doses accounting for tumor regression. PMID:25594357

  18. Quantification of Vasa Vasorum Density in Multi-Slice Computed Tomographic Coronary Angiograms: Role of Computed Tomographic Image Voxel Size

    SciTech Connect

    Moritz, R.; Eaker, D; Langheinrich, A; Jorgensen, S; Bohle, R; Ritman, E

    2010-01-01

    This study is motivated by the possibility of using computed tomography (CT) to detect early coronary atherosclerosis by the increased CT values within the arterial wall resulting from vasa vasorum proliferation. Coronary arteries (n = 5) with early atherosclerotic changes were injected with Microfil and scanned (micro-CT). Noise was added to the CT projection data sets (to represent the radiation exposure of current clinical CT scanners) and then reconstructed to generate 3-dimensional images at different voxel sizes. Higher CT values were detected because of contrast agent in vasa vasorum if voxel size was less than (150 {micro}m){sup 3}. Contrast in the main lumen increased the CT values dramatically at voxels greater than (100 {micro}m){sup 3}, whereas CT values of the same specimen without contrast in the main lumen remained constant. Voxel sizes less than (200 {micro}m){sup 3} are needed to quantitate arterial wall opacification due to vasa vasorum proliferation.

  19. Chord-based versus voxel-based methods of electron transport in the skeletal tissues

    SciTech Connect

    Shah, Amish P.; Jokisch, Derek W.; Rajon, Didier A.; Watchman, Christopher J.; Patton, Phillip W.; Bolch, Wesley E.

    2005-10-15

    Anatomic models needed for internal dose assessment have traditionally been developed using mathematical surface equations to define organ boundaries, shapes, and their positions within the body. Many researchers, however, are now advocating the use of tomographic models created from segmented patient computed tomography (CT) or magnetic resonance (MR) scans. In the skeleton, however, the tissue structures of the bone trabeculae, marrow cavities, and endosteal layer are exceedingly small and of complex shape, and thus do not lend themselves easily to either stylistic representations or in-vivo CT imaging. Historically, the problem of modeling the skeletal tissues has been addressed through the development of chord-based methods of radiation particle transport, as given by studies at the University of Leeds (Leeds, UK) using a 44-year male subject. We have proposed an alternative approach to skeletal dosimetry in which excised sections of marrow-intact cadaver spongiosa are imaged directly via microCT scanning. The cadaver selected for initial investigation of this technique was a 66-year male subject of nominal body mass index (22.7 kg m{sup -2}). The objectives of the present study were to compare chord-based versus voxel-based methods of skeletal dosimetry using data from the UF 66-year male subject. Good agreement between chord-based and voxel-based transport was noted for marrow irradiation by either bone surface or bone volume sources up to 500-1000 keV (depending upon the skeletal site). In contrast, chord-based models of electron transport yielded consistently lower values of the self-absorbed fraction to marrow tissues than seen under voxel-based transport at energies above 100 keV, a feature directly attributed to the inability of chord-based models to account for nonlinear electron trajectories. Significant differences were also noted in the dosimetry of the endosteal layer (for all source tissues), with chord-based transport predicting a higher fraction

  20. In vitro comparison of cone beam computed tomography with different voxel sizes for detection of simulated external root resorption.

    PubMed

    Neves, Frederico S; de Freitas, Deborah Q; Campos, Paulo S F; de Almeida, Solange M; Haiter-Neto, Francisco

    2012-09-01

    The present study compared the efficacy of cone beam computed tomography using different voxel sizes in the diagnosis of simulated external root resorption. The presence or absence of simulated defects on buccal, mesial and distal root surfaces of 20 premolars was evaluated. The defects were small (0.26 mm in diameter and 0.08 mm deep), medium (0.62 mm in diameter and 0.19 mm deep) and large (1.05 mm in diameter and 0.24 mm deep), equally distributed on each root surface. Images were obtained using Classic i-CAT cone beam computed tomography with different voxel sizes: 0.12, 0.20, 0.25 and 0.30 mm. Five oral radiologists evaluated the images. Accuracy, sensitivity, specificity, positive and negative predictive values were determined. The sensitivity decreased and specificity increased as voxel size increased. Accuracy values were the highest for the smallest voxel size (0.12 mm). The results for voxel sizes 0.20 mm and 0.25 mm were similar. Positive and negative predictive values were similar in all protocols, except with 0.30 mm, in which they were the lowest. In conclusion, external root resorption was more easily diagnosed when a smaller voxel size was used.

  1. How does an fMRI voxel sample the neuronal activity pattern: compact-kernel or complex spatiotemporal filter?

    PubMed

    Kriegeskorte, Nikolaus; Cusack, Rhodri; Bandettini, Peter

    2010-02-01

    Recent studies suggested that fMRI voxel patterns can convey information represented in columnar-scale neuronal population codes, even when spatial resolution is insufficient to directly image the patterns of columnar selectivity (Kamitani and Tong, 2005; Haynes and Rees, 2005). Sensitivity to subvoxel-scale pattern information, or "fMRI hyperacuity," would greatly enhance the power of fMRI when combined with pattern information analysis techniques (Kriegeskorte and Bandettini, 2007). An individual voxel might weakly reflect columnar-level information if the columns within its boundaries constituted a slightly unbalanced sample of columnar selectivities (Kamitani and Tong, 2005), providing a possible mechanism for fMRI hyperacuity. However, Op de Beeck (2009) suggests that a coarse-scale neuronal organization rather than fMRI hyperacuity may explain the presence of the information in the fMRI patterns. Here we argue (a) that the present evidence does not rule out fMRI hyperacuity, (b) that the mechanism originally suggested for fMRI hyperacuity (biased sampling by averaging within each voxel's boundaries; Kamitani and Tong, 2005) will only produce very weak sensitivity to fine-grained pattern information, and (c) that an alternative mechanism (voxel as complex spatiotemporal filter) is physiologically more accurate and promises stronger sensitivity to fine-grained pattern information: We know that each voxel samples the neuronal activity pattern through a unique fine-grained structure of venous vessels that supply its blood oxygen level-dependent signal. At the simplest level, the drainage domain of a venous vessel may sample the neuronal pattern with a selectivity bias (Gardner, 2009; Shmuel et al., 2009). Beyond biased drainage domains, we illustrate with a simple simulation how temporal properties of the hemodynamics (e.g., the speed of the blood in the capillary bed) can shape spatial properties of a voxel's filter (e.g., how finely structured it is). This

  2. All about FAX: a Female Adult voXel phantom for Monte Carlo calculation in radiation protection dosimetry.

    PubMed

    Kramer, R; Khoury, H J; Vieira, J W; Loureiro, E C M; Lima, V J M; Lima, F R A; Hoff, G

    2004-12-01

    The International Commission on Radiological Protection (ICRP) has created a task group on dose calculations, which, among other objectives, should replace the currently used mathematical MIRD phantoms by voxel phantoms. Voxel phantoms are based on digital images recorded from scanning of real persons by computed tomography or magnetic resonance imaging (MRI). Compared to the mathematical MIRD phantoms, voxel phantoms are true to the natural representations of a human body. Connected to a radiation transport code, voxel phantoms serve as virtual humans for which equivalent dose to organs and tissues from exposure to ionizing radiation can be calculated. The principal database for the construction of the FAX (Female Adult voXel) phantom consisted of 151 CT images recorded from scanning of trunk and head of a female patient, whose body weight and height were close to the corresponding data recommended by the ICRP in Publication 89. All 22 organs and tissues at risk, except for the red bone marrow and the osteogenic cells on the endosteal surface of bone ('bone surface'), have been segmented manually with a technique recently developed at the Departamento de Energia Nuclear of the UFPE in Recife, Brazil. After segmentation the volumes of the organs and tissues have been adjusted to agree with the organ and tissue masses recommended by ICRP for the Reference Adult Female in Publication 89. Comparisons have been made with the organ and tissue masses of the mathematical EVA phantom, as well as with the corresponding data for other female voxel phantoms. The three-dimensional matrix of the segmented images has eventually been connected to the EGS4 Monte Carlo code. Effective dose conversion coefficients have been calculated for exposures to photons, and compared to data determined for the mathematical MIRD-type phantoms, as well as for other voxel phantoms.

  3. Identification of Voxels Confounded by Venous Signals Using Resting-State fMRI Functional Connectivity Graph Community Identification.

    PubMed

    Kalcher, Klaudius; Boubela, Roland N; Huf, Wolfgang; Našel, Christian; Moser, Ewald

    2015-01-01

    Identifying venous voxels in fMRI datasets is important to increase the specificity of fMRI analyses to microvasculature in the vicinity of the neural processes triggering the BOLD response. This is, however, difficult to achieve in particular in typical studies where magnitude images of BOLD EPI are the only data available. In this study, voxelwise functional connectivity graphs were computed on minimally preprocessed low TR (333 ms) multiband resting-state fMRI data, using both high positive and negative correlations to define edges between nodes (voxels). A high correlation threshold for binarization ensures that most edges in the resulting sparse graph reflect the high coherence of signals in medium to large veins. Graph clustering based on the optimization of modularity was then employed to identify clusters of coherent voxels in this graph, and all clusters of 50 or more voxels were then interpreted as corresponding to medium to large veins. Indeed, a comparison with SWI reveals that 75.6±5.9% of voxels within these large clusters overlap with veins visible in the SWI image or lie outside the brain parenchyma. Some of the remaining differences between the two modalities can be explained by imperfect alignment or geometric distortions between the two images. Overall, the graph clustering based method for identifying venous voxels has a high specificity as well as the additional advantages of being computed in the same voxel grid as the fMRI dataset itself and not needing any additional data beyond what is usually acquired (and exported) in standard fMRI experiments. PMID:26733787

  4. Identification of Voxels Confounded by Venous Signals Using Resting-State fMRI Functional Connectivity Graph Community Identification

    PubMed Central

    Kalcher, Klaudius; Boubela, Roland N.; Huf, Wolfgang; Našel, Christian; Moser, Ewald

    2015-01-01

    Identifying venous voxels in fMRI datasets is important to increase the specificity of fMRI analyses to microvasculature in the vicinity of the neural processes triggering the BOLD response. This is, however, difficult to achieve in particular in typical studies where magnitude images of BOLD EPI are the only data available. In this study, voxelwise functional connectivity graphs were computed on minimally preprocessed low TR (333 ms) multiband resting-state fMRI data, using both high positive and negative correlations to define edges between nodes (voxels). A high correlation threshold for binarization ensures that most edges in the resulting sparse graph reflect the high coherence of signals in medium to large veins. Graph clustering based on the optimization of modularity was then employed to identify clusters of coherent voxels in this graph, and all clusters of 50 or more voxels were then interpreted as corresponding to medium to large veins. Indeed, a comparison with SWI reveals that 75.6±5.9% of voxels within these large clusters overlap with veins visible in the SWI image or lie outside the brain parenchyma. Some of the remaining differences between the two modalities can be explained by imperfect alignment or geometric distortions between the two images. Overall, the graph clustering based method for identifying venous voxels has a high specificity as well as the additional advantages of being computed in the same voxel grid as the fMRI dataset itself and not needing any additional data beyond what is usually acquired (and exported) in standard fMRI experiments. PMID:26733787

  5. Object category classification of fMRI data using support vector machine combined with deactivation voxel selection

    NASA Astrophysics Data System (ADS)

    Yan, Caifeng; Song, Sutao; Li, Yao; Guo, Xiaojuan

    2012-03-01

    Support Vector Machine (SVM) is an accurate pattern recognition method which has been widely used in functional MRI (fMRI) data classification. Voxel selection is a very important part in classification. In general, voxel selection is based on brain regions associated with activation caused by different experiment conditions or stimulations. However, negative blood oxygenation level-dependent responses (deactivation) which have also been found in humans or animals contribute to the classification of different cognitive tasks. Different from traditional studies which focused merely on the activation voxel selection methods, our aim is to investigate the deactivation voxel selection methods in the classification of fMRI data using SVM. In this study, three different voxel selection methods (deactivation, activation, the combination of deactivation and activation) are applied to decide which voxel is included in SVM classifier with linear kernel in classifying 4-category objects on fMRI data. The average accuracies of deactivation classification were 73.36%(house vs. face), 60.34%(house vs. car), 60.94%(house vs. cat), 71.43%(face vs. car), 63.17%(face vs. cat) and 61.61%(car vs. cat). The classification results of deactivation were significantly above the chance level which implies the deactivation is informative. The accuracies of combination of activation and deactivation method were close to that of activation method, and it was even better for some representative subjects. These results suggest deactivation provides useful information in the object category classification on fMRI data and the method of voxel selection based on both activation and deactivation will be a significant method in classification in the future.

  6. Identification of Voxels Confounded by Venous Signals Using Resting-State fMRI Functional Connectivity Graph Community Identification.

    PubMed

    Kalcher, Klaudius; Boubela, Roland N; Huf, Wolfgang; Našel, Christian; Moser, Ewald

    2015-01-01

    Identifying venous voxels in fMRI datasets is important to increase the specificity of fMRI analyses to microvasculature in the vicinity of the neural processes triggering the BOLD response. This is, however, difficult to achieve in particular in typical studies where magnitude images of BOLD EPI are the only data available. In this study, voxelwise functional connectivity graphs were computed on minimally preprocessed low TR (333 ms) multiband resting-state fMRI data, using both high positive and negative correlations to define edges between nodes (voxels). A high correlation threshold for binarization ensures that most edges in the resulting sparse graph reflect the high coherence of signals in medium to large veins. Graph clustering based on the optimization of modularity was then employed to identify clusters of coherent voxels in this graph, and all clusters of 50 or more voxels were then interpreted as corresponding to medium to large veins. Indeed, a comparison with SWI reveals that 75.6±5.9% of voxels within these large clusters overlap with veins visible in the SWI image or lie outside the brain parenchyma. Some of the remaining differences between the two modalities can be explained by imperfect alignment or geometric distortions between the two images. Overall, the graph clustering based method for identifying venous voxels has a high specificity as well as the additional advantages of being computed in the same voxel grid as the fMRI dataset itself and not needing any additional data beyond what is usually acquired (and exported) in standard fMRI experiments.

  7. A study of bipolar disorder using magnetization transfer imaging and voxel-based morphometry.

    PubMed

    Bruno, S D; Barker, G J; Cercignani, M; Symms, M; Ron, M A

    2004-11-01

    Bipolar disorder (BP) traditionally has been considered as a recurrent illness with full recovery between episodes, and the absence of neuropathological abnormalities has usually been taken for granted. In recent times, the realization that, for many BP carries a poor prognosis, that cognitive deficits are often persistent and that structural brain abnormalities are detectable with modern imaging techniques has spurred the search for its neuropathological substrate. The shortcomings of post-mortem studies make the use of imaging techniques sensitive to neuropathological changes compelling. We report here the first study of BP patients using two such techniques in conjunction: magnetization transfer imaging (MTI) and voxel-based morphometry (VBM). Thirty-nine patients with BP (13 males and 26 females; 28 with BPI and 11 with BPII) and 35 healthy controls were investigated. Both high-resolution volumetric T1-weighted images and MT images were acquired from all subjects. Images were processed using a voxel-by-voxel analysis in statistical parametric mapping 2 (SPM2). The magnetization transfer ratio MTR, an index indicative of loss of macromolecular density, was reduced in the right subgenual anterior cingulate and adjacent white matter in bipolar patients compared with controls. VBM did not reveal significant volumetric differences between BP patients and controls in grey and white matter, but white matter density was significantly reduced bilaterally in prefrontal areas encompassing fronto-striatal connections. Our findings suggest that subtle abnormalities are present in the anterior cingulate and subgyral white matter in patients with BP in the absence of significant volumetric changes. These findings are in keeping with those of previously reported neuropathological studies and illustrate important similarities (involvement of the anterior cingulate) and differences (lack of widespread cortical abnormalities in BP) with our previous studies in schizophrenic

  8. MicroCT-Based Skeletal Models for Use in Tomographic Voxel Phantoms for Radiological Protection

    SciTech Connect

    Bolch, Wesley

    2010-03-30

    The University of Florida (UF) proposes to develop two high-resolution image-based skeletal dosimetry models for direct use by ICRP Committee 2’s Task Group on Dose Calculation in their forthcoming Reference Voxel Male (RVM) and Reference Voxel Female (RVF) whole-body dosimetry phantoms. These two phantoms are CT-based, and thus do not have the image resolution to delineate and perform radiation transport modeling of the individual marrow cavities and bone trabeculae throughout their skeletal structures. Furthermore, new and innovative 3D microimaging techniques will now be required for the skeletal tissues following Committee 2’s revision of the target tissues of relevance for radiogenic bone cancer induction. This target tissue had been defined in ICRP Publication 30 as a 10-μm cell layer on all bone surfaces of trabecular and cortical bone. The revised target tissue is now a 50-μm layer within the marrow cavities of trabecular bone only and is exclusive of the marrow adipocytes. Clearly, this new definition requires the use of 3D microimages of the trabecular architecture not available from past 2D optical studies of the adult skeleton. With our recent acquisition of two relatively young cadavers (males of age 18-years and 40-years), we will develop a series of reference skeletal models that can be directly applied to (1) the new ICRP reference voxel man and female phantoms developed for the ICRP, and (2) pediatric phantoms developed to target the ICRP reference children. Dosimetry data to be developed will include absorbed fractions for internal beta and alpha-particle sources, as well as photon and neutron fluence-to-dose response functions for direct use in external dosimetry studies of the ICRP reference workers and members of the general public

  9. Comparing the Effect of Different Voxel Resolutions for Assessment of Vertical Root Fracture of Permanent Teeth

    PubMed Central

    Uzun, Ismail; Gunduz, Kaan; Celenk, Peruze; Avsever, Hakan; Orhan, Kaan; Canitezer, Gozde; Ozmen, Bilal; Cicek, Ersan; Egrioglu, Erol

    2015-01-01

    Background: The teeth with undiagnosed vertical root fractures (VRFs) are likely to receive endodontic treatment or retreatment, leading to frustration and inappropriate endodontic therapies. Moreover, many cases of VRFs cannot be diagnosed definitively until the extraction of tooth. Objectives: This study aimed to assess the use of different voxel resolutions of two different cone beam computerized tomography (CBCT) units in the detection VRFs in vitro. Materials and Methods: The study material comprised 74 extracted human mandibular single rooted premolar teeth without root fractures that had not undergone any root-canal treatment. Images were obtained by two different CBCT units. Four image sets were obtained as follows: 1) 3D Accuitomo 170, 4 × 4 cm field of view (FOV) (0.080 mm3); 2) 3D Accuitomo 170. 6 × 6 cm FOV (0.125 mm3); 3) NewTom 3G, 6˝ (0.16 mm3) and 4) NewTom 3G, 9˝ FOV (0.25 mm3). Kappa coefficients were calculated to assess both intra- and inter-observer agreements for each image set. Results: No significant differences were found among observers or voxel sizes, with high average Z (Az) results being reported for all groups. Both intra- and inter-observer agreement values were relatively better for 3D Accuitomo 170 images than the images from NewTom 3G. The highest Az and kappa values were obtained with 3D Accuitomo 170, 4 × 4 cm FOV (0.080 mm3) images. Conclusion: No significant differences were found among observers or voxel sizes, with high Az results reported for all groups. PMID:26557279

  10. Micro-CT Pore Scale Study Of Flow In Porous Media: Effect Of Voxel Resolution

    NASA Astrophysics Data System (ADS)

    Shah, S.; Gray, F.; Crawshaw, J.; Boek, E.

    2014-12-01

    In the last few years, pore scale studies have become the key to understanding the complex fluid flow processes in the fields of groundwater remediation, hydrocarbon recovery and environmental issues related to carbon storage and capture. A pore scale study is often comprised of two key procedures: 3D pore scale imaging and numerical modelling techniques. The essence of a pore scale study is to test the physics implemented in a model of complicated fluid flow processes at one scale (microscopic) and then apply the model to solve the problems associated with water resources and oil recovery at other scales (macroscopic and field). However, the process of up-scaling from the pore scale to the macroscopic scale has encountered many challenges due to both pore scale imaging and modelling techniques. Due to the technical limitations in the imaging method, there is always a compromise between the spatial (voxel) resolution and the physical volume of the sample (field of view, FOV) to be scanned by the imaging methods, specifically X-ray micro-CT (XMT) in our case In this study, a careful analysis was done to understand the effect of voxel size, using XMT to image the 3D pore space of a variety of porous media from sandstones to carbonates scanned at different voxel resolution (4.5 μm, 6.2 μm, 8.3 μm and 10.2 μm) but keeping the scanned FOV constant for all the samples. We systematically segment the micro-CT images into three phases, the macro-pore phase, an intermediate phase (unresolved micro-pores + grains) and the grain phase and then study the effect of voxel size on the structure of the macro-pore and the intermediate phases and the fluid flow properties using lattice-Boltzmann (LB) and pore network (PN) modelling methods. We have also applied a numerical coarsening algorithm (up-scale method) to reduce the computational power and time required to accurately predict the flow properties using the LB and PN method.

  11. A voxel-based multiscale model to simulate the radiation response of hypoxic tumors

    SciTech Connect

    Espinoza, I.; Peschke, P.; Karger, C. P.

    2015-01-15

    Purpose: In radiotherapy, it is important to predict the response of tumors to irradiation prior to the treatment. This is especially important for hypoxic tumors, which are known to be highly radioresistant. Mathematical modeling based on the dose distribution, biological parameters, and medical images may help to improve this prediction and to optimize the treatment plan. Methods: A voxel-based multiscale tumor response model for simulating the radiation response of hypoxic tumors was developed. It considers viable and dead tumor cells, capillary and normal cells, as well as the most relevant biological processes such as (i) proliferation of tumor cells, (ii) hypoxia-induced angiogenesis, (iii) spatial exchange of cells leading to tumor growth, (iv) oxygen-dependent cell survival after irradiation, (v) resorption of dead cells, and (vi) spatial exchange of cells leading to tumor shrinkage. Oxygenation is described on a microscopic scale using a previously published tumor oxygenation model, which calculates the oxygen distribution for each voxel using the vascular fraction as the most important input parameter. To demonstrate the capabilities of the model, the dependence of the oxygen distribution on tumor growth and radiation-induced shrinkage is investigated. In addition, the impact of three different reoxygenation processes is compared and tumor control probability (TCP) curves for a squamous cells carcinoma of the head and neck (HNSSC) are simulated under normoxic and hypoxic conditions. Results: The model describes the spatiotemporal behavior of the tumor on three different scales: (i) on the macroscopic scale, it describes tumor growth and shrinkage during radiation treatment, (ii) on a mesoscopic scale, it provides the cell density and vascular fraction for each voxel, and (iii) on the microscopic scale, the oxygen distribution may be obtained in terms of oxygen histograms. With increasing tumor size, the simulated tumors develop a hypoxic core. Within the

  12. Fast Monte Carlo simulation on a voxelized human phantom deformed to a patient

    PubMed Central

    Bueno, G.; Déniz, O.; Carrascosa, C. B.; Delgado, J. M.; Brualla, L.

    2009-01-01

    Purpose: A method for performing fast simulations of absorbed dose using a patient’s computerized tomography (CT) scan without explicitly relying on a calibration curve is presented. Methods: The method is based on geometrical deformations performed on a standard voxelized human phantom. This involves spatially transforming the human phantom to align it with the patient CT image. Since the chemical composition and density of each voxel are given in the phantom data, a calibration curve is not used in the proposed method. For this study, the Monte Carlo (MC) code PENELOPE has been used as the simulation of reference. The results obtained with PENELOPE simulations are compared to those obtained with PENFAST and with the collapsed cone convolution algorithm implemented in a commercial treatment planning system. Results: The comparisons of the absorbed doses calculated with the different algorithms on two patient CTs and the corresponding deformed phantoms show a maximum distance to agreement of 2 mm, and in general, the obtained absorbed dose distributions are compatible within the reached statistical uncertainty. The validity of the deformation method for a broad range of patients is shown using MC simulations in random density phantoms. A PENFAST simulation of a 6 MV photon beam impinging on a patient CT reaches 2% statistical uncertainty in the absorbed dose, in a 0.1 cm3 voxel along the central axis, in 10 min running on a single core of a 2.8 GHz CPU. Conclusions: The proposed method of the absorbed dose calculation in a deformed voxelized phantom allows for dosimetric studies in the geometry of a patient CT scan. This is due to the fact that the chemical composition and material density of the phantom are known. Furthermore, simulation using the phantom geometry can provide dosimetric information for each organ. The method can be used for quality assurance procedures. In relation to PENFAST, it is shown that a purely condensed-history algorithm (class I) can

  13. Reference dosimetry calculations for neutron capture therapy with comparison of analytical and voxel models.

    PubMed

    Goorley, J T; Kiger, W S; Zamenhof, R G

    2002-02-01

    As clinical trials of Neutron Capture Therapy (NCT) are initiated in the U.S. and other countries, new treatment planning codes are being developed to calculate detailed dose distributions in patient-specific models. The thorough evaluation and comparison of treatment planning codes is a critical step toward the eventual standardization of dosimetry, which, in turn, is an essential element for the rational comparison of clinical results from different institutions. In this paper we report development of a reference suite of computational test problems for NCT dosimetry and discuss common issues encountered in these calculations to facilitate quantitative evaluations and comparisons of NCT treatment planning codes. Specifically, detailed depth-kerma rate curves were calculated using the Monte Carlo radiation transport code MCNP4B for four different representations of the modified Snyder head phantom, an analytic, multishell, ellipsoidal model, and voxel representations of this model with cubic voxel sizes of 16, 8, and 4 mm. Monoenergetic and monodirectional beams of 0.0253 eV, 1, 2, 10, 100, and 1000 keV neutrons, and 0.2, 0.5, 1, 2, 5, and 10 MeV photons were individually simulated to calculate kerma rates to a statistical uncertainty of <1% (1 std. dev.) in the center of the head model. In addition, a "generic" epithermal neutron beam with a broad neutron spectrum, similar to epithermal beams currently used or proposed for NCT clinical trials, was computed for all models. The thermal neutron, fast neutron, and photon kerma rates calculated with the 4 and 8 mm voxel models were within 2% and 4%, respectively, of those calculated for the analytical model. The 16 mm voxel model produced unacceptably large discrepancies for all dose components. The effects from different kerma data sets and tissue compositions were evaluated. Updating the kerma data from ICRU 46 to ICRU 63 data produced less than 2% difference in kerma rate profiles. The depth-dose profile data

  14. A fast algorithm for voxel-based deterministic simulation of X-ray imaging

    NASA Astrophysics Data System (ADS)

    Li, Ning; Zhao, Hua-Xia; Cho, Sang-Hyun; Choi, Jung-Gil; Kim, Myoung-Hee

    2008-04-01

    Deterministic method based on ray tracing technique is known as a powerful alternative to the Monte Carlo approach for virtual X-ray imaging. The algorithm speed is a critical issue in the perspective of simulating hundreds of images, notably to simulate tomographic acquisition or even more, to simulate X-ray radiographic video recordings. We present an algorithm for voxel-based deterministic simulation of X-ray imaging using voxel-driven forward and backward perspective projection operations and minimum bounding rectangles (MBRs). The algorithm is fast, easy to implement, and creates high-quality simulated radiographs. As a result, simulated radiographs can typically be obtained in split seconds with a simple personal computer. Program summaryProgram title: X-ray Catalogue identifier: AEAD_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEAD_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 416 257 No. of bytes in distributed program, including test data, etc.: 6 018 263 Distribution format: tar.gz Programming language: C (Visual C++) Computer: Any PC. Tested on DELL Precision 380 based on a Pentium D 3.20 GHz processor with 3.50 GB of RAM Operating system: Windows XP Classification: 14, 21.1 Nature of problem: Radiographic simulation of voxelized objects based on ray tracing technique. Solution method: The core of the simulation is a fast routine for the calculation of ray-box intersections and minimum bounding rectangles, together with voxel-driven forward and backward perspective projection operations. Restrictions: Memory constraints. There are three programs in all. A. Program for test 3.1(1): Object and detector have axis-aligned orientation; B. Program for test 3.1(2): Object in arbitrary orientation; C. Program for test 3.2: Simulation of X-ray video

  15. A DOS Primer for Librarians.

    ERIC Educational Resources Information Center

    Beecher, Henry

    1989-01-01

    Presents a basic orientation to the functions and capabilities of disk operating systems (DOS), aimed at the nontechnically oriented user of IBM personal computers and compatible microcomputers. Areas discussed include booting up, the use of floppy and hard disks, file storage and manipulation, and directories. Further readings are provided. (CLB)

  16. Comparison of internal dose estimates obtained using organ-level, voxel S value, and Monte Carlo techniques

    SciTech Connect

    Grimes, Joshua; Celler, Anna

    2014-09-15

    Purpose: The authors’ objective was to compare internal dose estimates obtained using the Organ Level Dose Assessment with Exponential Modeling (OLINDA/EXM) software, the voxel S value technique, and Monte Carlo simulation. Monte Carlo dose estimates were used as the reference standard to assess the impact of patient-specific anatomy on the final dose estimate. Methods: Six patients injected with{sup 99m}Tc-hydrazinonicotinamide-Tyr{sup 3}-octreotide were included in this study. A hybrid planar/SPECT imaging protocol was used to estimate {sup 99m}Tc time-integrated activity coefficients (TIACs) for kidneys, liver, spleen, and tumors. Additionally, TIACs were predicted for {sup 131}I, {sup 177}Lu, and {sup 90}Y assuming the same biological half-lives as the {sup 99m}Tc labeled tracer. The TIACs were used as input for OLINDA/EXM for organ-level dose calculation and voxel level dosimetry was performed using the voxel S value method and Monte Carlo simulation. Dose estimates for {sup 99m}Tc, {sup 131}I, {sup 177}Lu, and {sup 90}Y distributions were evaluated by comparing (i) organ-level S values corresponding to each method, (ii) total tumor and organ doses, (iii) differences in right and left kidney doses, and (iv) voxelized dose distributions calculated by Monte Carlo and the voxel S value technique. Results: The S values for all investigated radionuclides used by OLINDA/EXM and the corresponding patient-specific S values calculated by Monte Carlo agreed within 2.3% on average for self-irradiation, and differed by as much as 105% for cross-organ irradiation. Total organ doses calculated by OLINDA/EXM and the voxel S value technique agreed with Monte Carlo results within approximately ±7%. Differences between right and left kidney doses determined by Monte Carlo were as high as 73%. Comparison of the Monte Carlo and voxel S value dose distributions showed that each method produced similar dose volume histograms with a minimum dose covering 90% of the volume (D90

  17. A 12-step user guide for analyzing voxel-wise gray matter asymmetries in statistical parametric mapping (SPM).

    PubMed

    Kurth, Florian; Gaser, Christian; Luders, Eileen

    2015-02-01

    Voxel-based morphometry (VBM) has been proven capable of capturing cerebral gray matter asymmetries with a high (voxel-wise) regional specificity. However, a standardized reference on how to conduct voxel-wise asymmetry analyses is missing. This protocol provides the scientific community with a carefully developed guide describing, in 12 distinct steps, how to take structural images from data pre-processing, via statistical analysis, to the final interpretation of the significance maps. Key adaptations compared with the standard VBM workflow involve establishing a voxel-wise hemispheric correspondence, capturing the direction and degree of asymmetry and preventing a blurring of information across hemispheres. The workflow incorporates the most recent methodological developments, including high-dimensional spatial normalization and partial volume estimations. Although the protocol is primarily designed to enable relatively inexperienced users to conduct a voxel-based asymmetry analysis on their own, it may also be useful to experienced users who wish to efficiently adapt their existing scripts or pipelines.

  18. Multi-Voxel Pattern Analysis of Noun and Verb Differences in Ventral Temporal Cortex Marked Revision

    PubMed Central

    Boylan, Christine; Trueswell, John C.; Thompson-Schill, Sharon L.

    2014-01-01

    Recent evidence suggests a probabilistic relationship exists between the phonological/orthographic form of a word and its lexical-syntactic category (specifically nouns vs. verbs) such that syntactic prediction may elicit form-based estimates in sensory cortex. We tested this hypothesis by conducting multi-voxel pattern analysis (MVPA) of fMRI data from early visual cortex (EVC), left ventral temporal (VT) cortex, and a subregion of the latter - the left mid fusiform gyrus (mid FG), sometimes called the “visual word form area.” Crucially, we examined only those volumes sampled when subjects were predicting, but not viewing, nouns and verbs. This allowed us to investigate prediction effects in visual areas without any bottom-up orthographic input. We found that voxels in VT and mid FG, but not in EVC, were able to classify noun-predictive trials vs. verb-predictive trials in sentence contexts, suggesting that sentence-level predictions are sufficient to generate word form-based estimates in visual areas. PMID:25156159

  19. On the evolution of cured voxel in bulk photopolymerization upon focused Gaussian laser exposure

    NASA Astrophysics Data System (ADS)

    Bhole, Kiran; Gandhi, Prasanna; Kundu, T.

    2014-07-01

    Unconstrained depth photopolymerization is emerging as a promising technique for fabrication of several polymer microstructures such as self propagating waveguides, 3D freeform structures by bulk lithography, and polymer nanoparticles by flash exposure. Experimental observations reveal governing physics beyond Beer Lambert's law and scattering effects. This paper seeks to model unconstrained depth photopolymerization using classical nonlinear Schrödinger equation coupled with transient diffusion phenomenon. The beam propagation part of the proposed model considers scattering effects induced due to spatial variation of the refractive index as a function of the beam intensity. The critical curing energy model is used to further predict profile of polymerized voxel. Profiles of photopolymerized voxel simulated using proposed model are compared with the corresponding experimental results for several cases of exposure dose and duration. The comparison shows close match leading to conclusion that the experimentally observed deviation from Beer Lambert's law is indeed due to combined effect of diffusion of photoinitiator and scattering of light because of change in the refractive index.

  20. Regional gray matter abnormalities in patients with schizophrenia determined with optimized voxel-based morphometry

    NASA Astrophysics Data System (ADS)

    Guo, XiaoJuan; Yao, Li; Jin, Zhen; Chen, Kewei

    2006-03-01

    This study examined regional gray matter abnormalities across the whole brain in 19 patients with schizophrenia (12 males and 7 females), comparing with 11 normal volunteers (7 males and 4 females). The customized brain templates were created in order to improve spatial normalization and segmentation. Then automated preprocessing of magnetic resonance imaging (MRI) data was conducted using optimized voxel-based morphometry (VBM). The statistical voxel based analysis was implemented in terms of two-sample t-test model. Compared with normal controls, regional gray matter concentration in patients with schizophrenia was significantly reduced in the bilateral superior temporal gyrus, bilateral middle frontal and inferior frontal gyrus, right insula, precentral and parahippocampal areas, left thalamus and hypothalamus as well as, however, significant increases in gray matter concentration were not observed across the whole brain in the patients. This study confirms and extends some earlier findings on gray matter abnormalities in schizophrenic patients. Previous behavior and fMRI researches on schizophrenia have suggested that cognitive capacity decreased and self-conscious weakened in schizophrenic patients. These regional gray matter abnormalities determined through structural MRI with optimized VBM may be potential anatomic underpinnings of schizophrenia.

  1. Voxel-based analysis in neuroferritinopathy expands the phenotype and determines radiological correlates of disease severity.

    PubMed

    Keogh, M J; Aribisala, B S; He, J; Tulip, E; Butteriss, D; Morris, C; Gorman, G; Horvath, R; Chinnery, P F; Blamire, Andrew M

    2015-10-01

    Neuroferritinopathy is an autosomal dominant adult-onset movement disorder which occurs due to mutations in the ferritin light chain gene (FTL). Extensive iron deposition and cavitation are observed post-mortem in the basal ganglia, but whether more widespread pathological changes occur, and whether they correlate with disease severity is unknown. 3D-T1w and quantitative T2 whole brain MRI scans were performed in 10 clinically symptomatic patients with the 460InsA FTL mutation and 10 age-matched controls. Voxel-based morphometry (VBM) and voxel-based relaxometry (VBR) were subsequently performed. Clinical assessment using the Unified Dystonia Rating Scale (UDRS) and Unified Huntington's Disease Rating Scale (UHDRS) was undertaken in all patients. VBM detected significant tissue changes within the substantia nigra, midbrain and dentate together with significant cerebellar atrophy in patients (FWE, p < 0.05). Iron deposition in the caudate head and cavitation in the lateral globus pallidus correlated with UDRS score (p < 0.001). There were no differences between groups with VBR. Our data show that progressive iron accumulation in the caudate nucleus, and cavitation of the globus pallidus correlate with disease severity in neuroferritinopathy. We also confirm sub-clinical cerebellar atrophy as a feature of the disease. We suggest that VBM is an effective technique to detect regions of iron deposition and cavitation, with potential wider utility to determine radiological markers of disease severity for all NBIA disorders. PMID:26142024

  2. Spatial indices for measuring three-dimensional patterns in a voxel-based space

    NASA Astrophysics Data System (ADS)

    Jjumba, Anthony; Dragićević, Suzana

    2016-07-01

    Spatial indices are used to quantitatively describe the spatial arrangements of the features within a study region. However, most of the indices used are two-dimensional in their representation of the surface characteristics, and this is insufficient to quantify the three-dimensional properties of an area or geospatial features. With the increased availability of 3D data from laser scanning and other collection methods, a voxel-based representation of space is an important methodology that allows for an intuitive visualization of geospatial features and their analysis with 3D GIS techniques. The objective of this study is to conceptualize, develop, and implement indices that can characterize three-dimensional space and can be used to analyze the structure of spatial features in a landscape. The indices for three-dimensional space that are implemented are, namely, surface area volume, fractal dimension, lacunarity, and Moran's I which are all useful in the quantification of spatial organization found in ecological landscapes. In addition to providing the quantitative descriptors, the results indicate that a voxel-based representation provides a straightforward means of characterizing the form and composition of the spatial features using 3D indices.

  3. Multi-atlas registration and adaptive hexahedral voxel discretization for fast bioluminescence tomography.

    PubMed

    Ren, Shenghan; Hu, Haihong; Li, Gen; Cao, Xu; Zhu, Shouping; Chen, Xueli; Liang, Jimin

    2016-04-01

    Bioluminescence tomography (BLT) has been a valuable optical molecular imaging technique to non-invasively depict the cellular and molecular processes in living animals with high sensitivity and specificity. Due to the inherent ill-posedness of BLT, a priori information of anatomical structure is usually incorporated into the reconstruction. The structural information is usually provided by computed tomography (CT) or magnetic resonance imaging (MRI). In order to obtain better quantitative results, BLT reconstruction with heterogeneous tissues needs to segment the internal organs and discretize them into meshes with the finite element method (FEM). It is time-consuming and difficult to handle the segmentation and discretization problems. In this paper, we present a fast reconstruction method for BLT based on multi-atlas registration and adaptive voxel discretization to relieve the complicated data processing procedure involved in the hybrid BLT/CT system. A multi-atlas registration method is first adopted to estimate the internal organ distribution of the imaged animal. Then, the animal volume is adaptively discretized into hexahedral voxels, which are fed into FEM for the following BLT reconstruction. The proposed method is validated in both numerical simulation and an in vivo study. The results demonstrate that the proposed method can reconstruct the bioluminescence source efficiently with satisfactory accuracy. PMID:27446674

  4. On the evolution of cured voxel in bulk photopolymerization upon focused Gaussian laser exposure

    SciTech Connect

    Bhole, Kiran Gandhi, Prasanna; Kundu, T.

    2014-07-28

    Unconstrained depth photopolymerization is emerging as a promising technique for fabrication of several polymer microstructures such as self propagating waveguides, 3D freeform structures by bulk lithography, and polymer nanoparticles by flash exposure. Experimental observations reveal governing physics beyond Beer Lambert's law and scattering effects. This paper seeks to model unconstrained depth photopolymerization using classical nonlinear Schrödinger equation coupled with transient diffusion phenomenon. The beam propagation part of the proposed model considers scattering effects induced due to spatial variation of the refractive index as a function of the beam intensity. The critical curing energy model is used to further predict profile of polymerized voxel. Profiles of photopolymerized voxel simulated using proposed model are compared with the corresponding experimental results for several cases of exposure dose and duration. The comparison shows close match leading to conclusion that the experimentally observed deviation from Beer Lambert's law is indeed due to combined effect of diffusion of photoinitiator and scattering of light because of change in the refractive index.

  5. Surface mesh to voxel data registration for patient-specific anatomical modeling

    NASA Astrophysics Data System (ADS)

    de Oliveira, Júlia E. E.; Giessler, Paul; Keszei, András.; Herrler, Andreas; Deserno, Thomas M.

    2016-03-01

    Virtual Physiological Human (VPH) models are frequently used for training, planning, and performing medical procedures. The Regional Anaesthesia Simulator and Assistant (RASimAs) project has the goal of increasing the application and effectiveness of regional anesthesia (RA) by combining a simulator of ultrasound-guided and electrical nerve-stimulated RA procedures and a subject-specific assistance system through an integration of image processing, physiological models, subject-specific data, and virtual reality. Individualized models enrich the virtual training tools for learning and improving regional anaesthesia (RA) skills. Therefore, we suggest patient-specific VPH models that are composed by registering the general mesh-based models with patient voxel data-based recordings. Specifically, the pelvis region has been focused for the support of the femoral nerve block. The processing pipeline is composed of different freely available toolboxes such as MatLab, the open Simulation framework (SOFA), and MeshLab. The approach of Gilles is applied for mesh-to-voxel registration. Personalized VPH models include anatomical as well as mechanical properties of the tissues. Two commercial VPH models (Zygote and Anatomium) were used together with 34 MRI data sets. Results are presented for the skin surface and pelvic bones. Future work will extend the registration procedure to cope with all model tissue (i.e., skin, muscle, bone, vessel, nerve, fascia) in a one-step procedure and extrapolating the personalized models to body regions actually being out of the captured field of view.

  6. Rhesus Macaque Brain Morphometry: A Methodological Comparison of Voxel-Wise Approaches

    PubMed Central

    McLaren, Donald G.; Kosmatka, Kristopher J.; Kastman, Erik K.; Bendlin, Barbara B.; Johnson, Sterling C.

    2009-01-01

    Voxel-based morphometry studies have become increasingly common in human neuroimaging over the past several years; however, few studies have utilized this method to study morphometry changes in non-human primates. Here we describe the application of voxel-wise morphometry methods to the rhesus macaque (Macaca mulatta) using the 112RM-SL template and priors (McLaren et al. 2009) and as an illustrative example we describe age-associated changes in grey matter morphometry. Specifically, we evaluated the unified segmentation routine implemented using Statistical Parametric Mapping (SPM) software and the FMRIB’s Automated Segmentation Tool (FAST) in the FMRIB Software Library (FSL); the effect of varying the smoothing kernel; and the effect of the normalization routine. We found that when studying non-human primates, brain images need less smoothing than in human studies, 2–4mm FWHM. Using flow field deformations (DARTEL) improved inter-subject alignment leading to results that were more likely due to morphometry differences as opposed to registration differences. PMID:19883763

  7. Voxel-based morphometry reveals reduced grey matter volume in the temporal cortex of developmental prosopagnosics

    PubMed Central

    Furl, Nicholas; Draganski, Bogdan; Weiskopf, Nikolaus; Stevens, John; Tan, Geoffrey Chern-Yee; Driver, Jon; Dolan, Ray J.; Duchaine, Bradley

    2009-01-01

    Individuals with developmental prosopagnosia exhibit severe and lasting difficulties in recognizing faces despite the absence of apparent brain abnormalities. We used voxel-based morphometry to investigate whether developmental prosopagnosics show subtle neuroanatomical differences from controls. An analysis based on segmentation of T1-weighted images from 17 developmental prosopagnosics and 18 matched controls revealed that they had reduced grey matter volume in the right anterior inferior temporal lobe and in the superior temporal sulcus/middle temporal gyrus bilaterally. In addition, a voxel-based morphometry analysis based on the segmentation of magnetization transfer parameter maps showed that developmental prosopagnosics also had reduced grey matter volume in the right middle fusiform gyrus and the inferior temporal gyrus. Multiple regression analyses relating three distinct behavioural component scores, derived from a principal component analysis, to grey matter volume revealed an association between a component related to facial identity and grey matter volume in the left superior temporal sulcus/middle temporal gyrus plus the right middle fusiform gyrus/inferior temporal gyrus. Grey matter volume in the lateral occipital cortex was associated with component scores related to object recognition tasks. Our results demonstrate that developmental prosopagnosics have reduced grey matter volume in several regions known to respond selectively to faces and provide new evidence that integrity of these areas relates to face recognition ability. PMID:19887506

  8. Voxel-Based Morphometry ALE meta-analysis of Bipolar Disorder

    NASA Astrophysics Data System (ADS)

    Magana, Omar; Laird, Robert

    2012-03-01

    A meta-analysis was performed independently to view the changes in gray matter (GM) on patients with Bipolar disorder (BP). The meta-analysis was conducted on a Talairach Space using GingerALE to determine the voxels and their permutation. In order to achieve the data acquisition, published experiments and similar research studies were uploaded onto the online Voxel-Based Morphometry database (VBM). By doing so, coordinates of activation locations were extracted from Bipolar disorder related journals utilizing Sleuth. Once the coordinates of given experiments were selected and imported to GingerALE, a Gaussian was performed on all foci points to create the concentration points of GM on BP patients. The results included volume reductions and variations of GM between Normal Healthy controls and Patients with Bipolar disorder. A significant amount of GM clusters were obtained in Normal Healthy controls over BP patients on the right precentral gyrus, right anterior cingulate, and the left inferior frontal gyrus. In future research, more published journals could be uploaded onto the database and another VBM meta-analysis could be performed including more activation coordinates or a variation of age groups.

  9. Direct voxel-based comparisons between grey matter shrinkage and glucose hypometabolism in chronic alcoholism.

    PubMed

    Ritz, Ludivine; Segobin, Shailendra; Lannuzel, Coralie; Boudehent, Céline; Vabret, François; Eustache, Francis; Beaunieux, Hélène; Pitel, Anne L

    2016-09-01

    Alcoholism is associated with widespread brain structural abnormalities affecting mainly the frontocerebellar and the Papez's circuits. Brain glucose metabolism has received limited attention, and few studies used regions of interest approach and showed reduced global brain metabolism predominantly in the frontal and parietal lobes. Even though these studies have examined the relationship between grey matter shrinkage and hypometabolism, none has performed a direct voxel-by-voxel comparison between the degrees of structural and metabolic abnormalities. Seventeen alcoholic patients and 16 control subjects underwent both structural magnetic resonance imaging and (18)F-2-fluoro-deoxy-glucose-positron emission tomography examinations. Structural abnormalities and hypometabolism were examined in alcoholic patients compared with control subjects using two-sample t-tests. Then, these two patterns of brain damage were directly compared with a paired t-test. Compared to controls, alcoholic patients had grey matter shrinkage and hypometabolism in the fronto-cerebellar circuit and several nodes of Papez's circuit. The direct comparison revealed greater shrinkage than hypometabolism in the cerebellum, cingulate cortex, thalamus and hippocampus and parahippocampal gyrus. Conversely, hypometabolism was more severe than shrinkage in the dorsolateral, premotor and parietal cortices. The distinct profiles of abnormalities found within the Papez's circuit, the fronto-cerebellar circuit and the parietal gyrus in chronic alcoholism suggest the involvement of different pathological mechanisms. PMID:26661206

  10. Clinical Relevance of Single-Voxel 1H MRS Metabolites in Discriminating Suprasellar Tumors

    PubMed Central

    Virani, Rahul A

    2016-01-01

    Introdution Spatially resolved metabolic data obtained from Proton Magnetic Resonance Spectroscopy (1H MRS) provides information which increases the diagnostic accuracy of imaging sequences in predicting the histology of suprasellar tumors. Aim To evaluate the role of 1H MRS in the diagnosis of various suprasellar tumors. Materials and Methods Sixty cases of various suprasellar, hypothalamic and third ventricular neoplasms were investigated with long-echo single voxel 1H -MRS using 1.5 Tesla clinical imager. Single-voxel spectroscopic examinations were guided by T1-weighted or T2-weighted images. Statistical analysis was carried out using IBM SPSS software version 19. Results We observed that whenever brain tissue was damaged or replaced by any process, NAA was markedly reduced. Extra-axial lesions which do not infiltrate brain or contain neuroglial tissue, didn’t demonstrate any NAA resonances. Cr was used as an internal standard for semi-quantitative evaluation of metabolic changes of other brain metabolites. Increased Cho was seen in processes with elevated cell-membrane turnover. Conclusion Spectra obtained from different tumors exhibit reproducible differences while histologically similar tumors yield characteristic spectra with only minor differences. Pituitary tumors were typically characterized by significant reduction of NAA, Cr peak and moderate elevation of Cho peak. Gliomas were typically characterized by decrease of NAA and Cr peaks and increase of Cho peak. Craniopharyngiomas were typically characterized by significant decrease of all metabolites. PMID:27630921

  11. Automated Voxel Model from Point Clouds for Structural Analysis of Cultural Heritage

    NASA Astrophysics Data System (ADS)

    Bitelli, G.; Castellazzi, G.; D'Altri, A. M.; De Miranda, S.; Lambertini, A.; Selvaggi, I.

    2016-06-01

    In the context of cultural heritage, an accurate and comprehensive digital survey of a historical building is today essential in order to measure its geometry in detail for documentation or restoration purposes, for supporting special studies regarding materials and constructive characteristics, and finally for structural analysis. Some proven geomatic techniques, such as photogrammetry and terrestrial laser scanning, are increasingly used to survey buildings with different complexity and dimensions; one typical product is in form of point clouds. We developed a semi-automatic procedure to convert point clouds, acquired from laserscan or digital photogrammetry, to a filled volume model of the whole structure. The filled volume model, in a voxel format, can be useful for further analysis and also for the generation of a Finite Element Model (FEM) of the surveyed building. In this paper a new approach is presented with the aim to decrease operator intervention in the workflow and obtain a better description of the structure. In order to achieve this result a voxel model with variable resolution is produced. Different parameters are compared and different steps of the procedure are tested and validated in the case study of the North tower of the San Felice sul Panaro Fortress, a monumental historical building located in San Felice sul Panaro (Modena, Italy) that was hit by an earthquake in 2012.

  12. Multi-atlas registration and adaptive hexahedral voxel discretization for fast bioluminescence tomography

    PubMed Central

    Ren, Shenghan; Hu, Haihong; Li, Gen; Cao, Xu; Zhu, Shouping; Chen, Xueli; Liang, Jimin

    2016-01-01

    Bioluminescence tomography (BLT) has been a valuable optical molecular imaging technique to non-invasively depict the cellular and molecular processes in living animals with high sensitivity and specificity. Due to the inherent ill-posedness of BLT, a priori information of anatomical structure is usually incorporated into the reconstruction. The structural information is usually provided by computed tomography (CT) or magnetic resonance imaging (MRI). In order to obtain better quantitative results, BLT reconstruction with heterogeneous tissues needs to segment the internal organs and discretize them into meshes with the finite element method (FEM). It is time-consuming and difficult to handle the segmentation and discretization problems. In this paper, we present a fast reconstruction method for BLT based on multi-atlas registration and adaptive voxel discretization to relieve the complicated data processing procedure involved in the hybrid BLT/CT system. A multi-atlas registration method is first adopted to estimate the internal organ distribution of the imaged animal. Then, the animal volume is adaptively discretized into hexahedral voxels, which are fed into FEM for the following BLT reconstruction. The proposed method is validated in both numerical simulation and an in vivo study. The results demonstrate that the proposed method can reconstruct the bioluminescence source efficiently with satisfactory accuracy. PMID:27446674

  13. Sensitivity study of voxel-based PET image comparison to image registration algorithms

    SciTech Connect

    Yip, Stephen Chen, Aileen B.; Berbeco, Ross; Aerts, Hugo J. W. L.

    2014-11-01

    Purpose: Accurate deformable registration is essential for voxel-based comparison of sequential positron emission tomography (PET) images for proper adaptation of treatment plan and treatment response assessment. The comparison may be sensitive to the method of deformable registration as the optimal algorithm is unknown. This study investigated the impact of registration algorithm choice on therapy response evaluation. Methods: Sixteen patients with 20 lung tumors underwent a pre- and post-treatment computed tomography (CT) and 4D FDG-PET scans before and after chemoradiotherapy. All CT images were coregistered using a rigid and ten deformable registration algorithms. The resulting transformations were then applied to the respective PET images. Moreover, the tumor region defined by a physician on the registered PET images was classified into progressor, stable-disease, and responder subvolumes. Particularly, voxels with standardized uptake value (SUV) decreases >30% were classified as responder, while voxels with SUV increases >30% were progressor. All other voxels were considered stable-disease. The agreement of the subvolumes resulting from difference registration algorithms was assessed by Dice similarity index (DSI). Coefficient of variation (CV) was computed to assess variability of DSI between individual tumors. Root mean square difference (RMS{sub rigid}) of the rigidly registered CT images was used to measure the degree of tumor deformation. RMS{sub rigid} and DSI were correlated by Spearman correlation coefficient (R) to investigate the effect of tumor deformation on DSI. Results: Median DSI{sub rigid} was found to be 72%, 66%, and 80%, for progressor, stable-disease, and responder, respectively. Median DSI{sub deformable} was 63%–84%, 65%–81%, and 82%–89%. Variability of DSI was substantial and similar for both rigid and deformable algorithms with CV > 10% for all subvolumes. Tumor deformation had moderate to significant impact on DSI for progressor

  14. Permutation and parametric tests for effect sizes in voxel-based morphometry of gray matter volume in brain structural MRI.

    PubMed

    Dickie, David A; Mikhael, Shadia; Job, Dominic E; Wardlaw, Joanna M; Laidlaw, David H; Bastin, Mark E

    2015-12-01

    Permutation testing has been widely implemented in voxel-based morphometry (VBM) tools. However, this type of non-parametric inference has yet to be thoroughly compared with traditional parametric inference in VBM studies of brain structure. Here we compare both types of inference and investigate what influence the number of permutations in permutation testing has on results in an exemplar study of how gray matter proportion changes with age in a group of working age adults. High resolution T1-weighted volume scans were acquired from 80 healthy adults aged 25-64years. Using a validated VBM procedure and voxel-based permutation testing for Pearson product-moment coefficient, the effect sizes of changes in gray matter proportion with age were assessed using traditional parametric and permutation testing inference with 100, 500, 1000, 5000, 10000 and 20000 permutations. The statistical significance was set at P<0.05 and false discovery rate (FDR) was used to correct for multiple comparisons. Clusters of voxels with statistically significant (PFDR<0.05) declines in gray matter proportion with age identified with permutation testing inference (N≈6000) were approximately twice the size of those identified with parametric inference (N=3221voxels). Permutation testing with 10000 (N=6251voxels) and 20000 (N=6233voxels) permutations produced clusters that were generally consistent with each other. However, with 1000 permutations there were approximately 20% more statistically significant voxels (N=7117voxels) than with ≥10000 permutations. Permutation testing inference may provide a more sensitive method than traditional parametric inference for identifying age-related differences in gray matter proportion. Based on the results reported here, at least 10000 permutations should be used in future univariate VBM studies investigating age related changes in gray matter to avoid potential false findings. Additional studies using permutation testing in large imaging databanks

  15. Evaluation of a deterministic grid-based Boltzmann solver (GBBS) for voxel-level absorbed dose calculations in nuclear medicine

    NASA Astrophysics Data System (ADS)

    Mikell, Justin; Cheenu Kappadath, S.; Wareing, Todd; Erwin, William D.; Titt, Uwe; Mourtada, Firas

    2016-06-01

    To evaluate the 3D Grid-based Boltzmann Solver (GBBS) code ATTILA ® for coupled electron and photon transport in the nuclear medicine energy regime for electron (beta, Auger and internal conversion electrons) and photon (gamma, x-ray) sources. Codes rewritten based on ATTILA are used clinically for both high-energy photon teletherapy and 192Ir sealed source brachytherapy; little information exists for using the GBBS to calculate voxel-level absorbed doses in nuclear medicine. We compared DOSXYZnrc Monte Carlo (MC) with published voxel-S-values to establish MC as truth. GBBS was investigated for mono-energetic 1.0, 0.1, and 0.01 MeV electron and photon sources as well as 131I and 90Y radionuclides. We investigated convergence of GBBS by analyzing different meshes ({{M}0},{{M}1},{{M}2} ), energy group structures ({{E}0},{{E}1},{{E}2} ) for each radionuclide component, angular quadrature orders (≤ft. {{S}4},{{S}8},{{S}16}\\right) , and scattering order expansions ({{P}0} –{{P}6} ); higher indices imply finer discretization. We compared GBBS to MC in (1) voxel-S-value geometry for soft tissue, lung, and bone, and (2) a source at the interface between combinations of lung, soft tissue, and bone. Excluding Auger and conversion electrons, MC agreed within  ≈5% of published source voxel absorbed doses. For the finest discretization, most GBBS absorbed doses in the source voxel changed by less than 1% compared to the next finest discretization along each phase space variable indicating sufficient convergence. For the finest discretization, agreement with MC in the source voxel ranged from  ‑3% to  ‑20% with larger differences at lower energies (‑3% for 1 MeV electron in lung to  ‑20% for 0.01 MeV photon in bone); similar agreement was found for the interface geometries. Differences between GBBS and MC in the source voxel for 90Y and 131I were  ‑6%. The GBBS ATTILA was benchmarked against MC in the nuclear medicine regime. GBBS can be a

  16. Evaluation of a deterministic grid-based Boltzmann solver (GBBS) for voxel-level absorbed dose calculations in nuclear medicine

    NASA Astrophysics Data System (ADS)

    Mikell, Justin; Cheenu Kappadath, S.; Wareing, Todd; Erwin, William D.; Titt, Uwe; Mourtada, Firas

    2016-06-01

    To evaluate the 3D Grid-based Boltzmann Solver (GBBS) code ATTILA ® for coupled electron and photon transport in the nuclear medicine energy regime for electron (beta, Auger and internal conversion electrons) and photon (gamma, x-ray) sources. Codes rewritten based on ATTILA are used clinically for both high-energy photon teletherapy and 192Ir sealed source brachytherapy; little information exists for using the GBBS to calculate voxel-level absorbed doses in nuclear medicine. We compared DOSXYZnrc Monte Carlo (MC) with published voxel-S-values to establish MC as truth. GBBS was investigated for mono-energetic 1.0, 0.1, and 0.01 MeV electron and photon sources as well as 131I and 90Y radionuclides. We investigated convergence of GBBS by analyzing different meshes ({{M}0},{{M}1},{{M}2} ), energy group structures ({{E}0},{{E}1},{{E}2} ) for each radionuclide component, angular quadrature orders (≤ft. {{S}4},{{S}8},{{S}16}\\right) , and scattering order expansions ({{P}0} -{{P}6} ); higher indices imply finer discretization. We compared GBBS to MC in (1) voxel-S-value geometry for soft tissue, lung, and bone, and (2) a source at the interface between combinations of lung, soft tissue, and bone. Excluding Auger and conversion electrons, MC agreed within  ≈5% of published source voxel absorbed doses. For the finest discretization, most GBBS absorbed doses in the source voxel changed by less than 1% compared to the next finest discretization along each phase space variable indicating sufficient convergence. For the finest discretization, agreement with MC in the source voxel ranged from  -3% to  -20% with larger differences at lower energies (-3% for 1 MeV electron in lung to  -20% for 0.01 MeV photon in bone); similar agreement was found for the interface geometries. Differences between GBBS and MC in the source voxel for 90Y and 131I were  -6%. The GBBS ATTILA was benchmarked against MC in the nuclear medicine regime. GBBS can be a viable

  17. Evaluation of a deterministic grid-based Boltzmann solver (GBBS) for voxel-level absorbed dose calculations in nuclear medicine.

    PubMed

    Mikell, Justin; Cheenu Kappadath, S; Wareing, Todd; Erwin, William D; Titt, Uwe; Mourtada, Firas

    2016-06-21

    To evaluate the 3D Grid-based Boltzmann Solver (GBBS) code ATTILA (®) for coupled electron and photon transport in the nuclear medicine energy regime for electron (beta, Auger and internal conversion electrons) and photon (gamma, x-ray) sources. Codes rewritten based on ATTILA are used clinically for both high-energy photon teletherapy and (192)Ir sealed source brachytherapy; little information exists for using the GBBS to calculate voxel-level absorbed doses in nuclear medicine. We compared DOSXYZnrc Monte Carlo (MC) with published voxel-S-values to establish MC as truth. GBBS was investigated for mono-energetic 1.0, 0.1, and 0.01 MeV electron and photon sources as well as (131)I and (90)Y radionuclides. We investigated convergence of GBBS by analyzing different meshes ([Formula: see text]), energy group structures ([Formula: see text]) for each radionuclide component, angular quadrature orders ([Formula: see text], and scattering order expansions ([Formula: see text]-[Formula: see text]); higher indices imply finer discretization. We compared GBBS to MC in (1) voxel-S-value geometry for soft tissue, lung, and bone, and (2) a source at the interface between combinations of lung, soft tissue, and bone. Excluding Auger and conversion electrons, MC agreed within  ≈5% of published source voxel absorbed doses. For the finest discretization, most GBBS absorbed doses in the source voxel changed by less than 1% compared to the next finest discretization along each phase space variable indicating sufficient convergence. For the finest discretization, agreement with MC in the source voxel ranged from  -3% to  -20% with larger differences at lower energies (-3% for 1 MeV electron in lung to  -20% for 0.01 MeV photon in bone); similar agreement was found for the interface geometries. Differences between GBBS and MC in the source voxel for (90)Y and (131)I were  -6%. The GBBS ATTILA was benchmarked against MC in the nuclear medicine regime. GBBS can be a

  18. Evaluation of a deterministic grid-based Boltzmann solver (GBBS) for voxel-level absorbed dose calculations in nuclear medicine.

    PubMed

    Mikell, Justin; Cheenu Kappadath, S; Wareing, Todd; Erwin, William D; Titt, Uwe; Mourtada, Firas

    2016-06-21

    To evaluate the 3D Grid-based Boltzmann Solver (GBBS) code ATTILA (®) for coupled electron and photon transport in the nuclear medicine energy regime for electron (beta, Auger and internal conversion electrons) and photon (gamma, x-ray) sources. Codes rewritten based on ATTILA are used clinically for both high-energy photon teletherapy and (192)Ir sealed source brachytherapy; little information exists for using the GBBS to calculate voxel-level absorbed doses in nuclear medicine. We compared DOSXYZnrc Monte Carlo (MC) with published voxel-S-values to establish MC as truth. GBBS was investigated for mono-energetic 1.0, 0.1, and 0.01 MeV electron and photon sources as well as (131)I and (90)Y radionuclides. We investigated convergence of GBBS by analyzing different meshes ([Formula: see text]), energy group structures ([Formula: see text]) for each radionuclide component, angular quadrature orders ([Formula: see text], and scattering order expansions ([Formula: see text]-[Formula: see text]); higher indices imply finer discretization. We compared GBBS to MC in (1) voxel-S-value geometry for soft tissue, lung, and bone, and (2) a source at the interface between combinations of lung, soft tissue, and bone. Excluding Auger and conversion electrons, MC agreed within  ≈5% of published source voxel absorbed doses. For the finest discretization, most GBBS absorbed doses in the source voxel changed by less than 1% compared to the next finest discretization along each phase space variable indicating sufficient convergence. For the finest discretization, agreement with MC in the source voxel ranged from  -3% to  -20% with larger differences at lower energies (-3% for 1 MeV electron in lung to  -20% for 0.01 MeV photon in bone); similar agreement was found for the interface geometries. Differences between GBBS and MC in the source voxel for (90)Y and (131)I were  -6%. The GBBS ATTILA was benchmarked against MC in the nuclear medicine regime. GBBS can be a

  19. Hitchhiker’s Guide to Voxel Segmentation for Partial Volume Correction of In Vivo Magnetic Resonance Spectroscopy

    PubMed Central

    Quadrelli, Scott; Mountford, Carolyn; Ramadan, Saadallah

    2016-01-01

    Partial volume effects have the potential to cause inaccuracies when quantifying metabolites using proton magnetic resonance spectroscopy (MRS). In order to correct for cerebrospinal fluid content, a spectroscopic voxel needs to be segmented according to different tissue contents. This article aims to detail how automated partial volume segmentation can be undertaken and provides a software framework for researchers to develop their own tools. While many studies have detailed the impact of partial volume correction on proton magnetic resonance spectroscopy quantification, there is a paucity of literature explaining how voxel segmentation can be achieved using freely available neuroimaging packages. PMID:27147822

  20. Development of the voxel computational phantoms of pediatric patients and their application to organ dose assessment

    NASA Astrophysics Data System (ADS)

    Lee, Choonik

    A series of realistic voxel computational phantoms of pediatric patients were developed and then used for the radiation risk assessment for various exposure scenarios. The high-resolution computed tomographic images of live patients were utilized for the development of the five voxel phantoms of pediatric patients, 9-month male, 4-year female, 8-year female, 11-year male, and 14-year male. The phantoms were first developed as head and torso phantoms and then extended into whole body phantoms by utilizing computed tomographic images of a healthy adult volunteer. The whole body phantom series was modified to have the same anthropometrics with the most recent reference data reported by the international commission on radiological protection. The phantoms, named as the University of Florida series B, are the first complete set of the pediatric voxel phantoms having reference organ masses and total heights. As part of the dosimetry study, the investigation on skeletal tissue dosimetry methods was performed for better understanding of the radiation dose to the active bone marrow and bone endosteum. All of the currently available methodologies were inter-compared and benchmarked with the paired-image radiation transport model. The dosimetric characteristics of the phantoms were investigated by using Monte Carlo simulation of the broad parallel beams of external phantom in anterior-posterior, posterior-anterior, left lateral, right lateral, rotational, and isotropic angles. Organ dose conversion coefficients were calculated for extensive photon energies and compared with the conventional stylized pediatric phantoms of Oak Ridge National Laboratory. The multi-slice helical computed tomography exams were simulated using Monte Carlo simulation code for various exams protocols, head, chest, abdomen, pelvis, and chest-abdomen-pelvis studies. Results have found realistic estimates of the effective doses for frequently used protocols in pediatric radiology. The results were very

  1. A hybrid approach for rapid, accurate, and direct kilovoltage radiation dose calculations in CT voxel space

    SciTech Connect

    Kouznetsov, Alexei; Tambasco, Mauro

    2011-03-15

    Purpose: To develop and validate a fast and accurate method that uses computed tomography (CT) voxel data to estimate absorbed radiation dose at a point of interest (POI) or series of POIs from a kilovoltage (kV) imaging procedure. Methods: The authors developed an approach that computes absorbed radiation dose at a POI by numerically evaluating the linear Boltzmann transport equation (LBTE) using a combination of deterministic and Monte Carlo (MC) techniques. This hybrid approach accounts for material heterogeneity with a level of accuracy comparable to the general MC algorithms. Also, the dose at a POI is computed within seconds using the Intel Core i7 CPU 920 2.67 GHz quad core architecture, and the calculations are performed using CT voxel data, making it flexible and feasible for clinical applications. To validate the method, the authors constructed and acquired a CT scan of a heterogeneous block phantom consisting of a succession of slab densities: Tissue (1.29 cm), bone (2.42 cm), lung (4.84 cm), bone (1.37 cm), and tissue (4.84 cm). Using the hybrid transport method, the authors computed the absorbed doses at a set of points along the central axis and x direction of the phantom for an isotropic 125 kVp photon spectral point source located along the central axis 92.7 cm above the phantom surface. The accuracy of the results was compared to those computed with MCNP, which was cross-validated with EGSnrc, and served as the benchmark for validation. Results: The error in the depth dose ranged from -1.45% to +1.39% with a mean and standard deviation of -0.12% and 0.66%, respectively. The error in the x profile ranged from -1.3% to +0.9%, with standard deviations of -0.3% and 0.5%, respectively. The number of photons required to achieve these results was 1x10{sup 6}. Conclusions: The voxel-based hybrid method evaluates the LBTE rapidly and accurately to estimate the absorbed x-ray dose at any POI or series of POIs from a kV imaging procedure.

  2. A causa das estações do ano: modelos mentais

    NASA Astrophysics Data System (ADS)

    de Campos, J. A. S.; de Araujo, J. F. S.

    2003-08-01

    A década de 70 do século passado foi marcada pelo estudo das concepções alternativas que os alunos trazem para a sala de aula. A identificação destas concepções foi o ponto de partida para promover a mudança conceitual, onde as pré-concepções seriam trocadas pelas concepções científicas. Na década seguinte, surgiram muitas propostas de estratégias educacionais para facilitar esta troca, na sua maioria baseadas na idéia do conflito cognitivo, proposta por Piaget. Entretanto, os resultados pouco animadores conduziram à percepção de que a mudança conceitual é um processo mais complexo. Pelas idéias da Ciência Cognitiva, a mudança conceitual é uma mudança progressiva dos modelos mentais que o aluno tem sobre o mundo físico, através de enriquecimento e revisão. A causa das Estações do Ano é um tópico sobre o qual a maioria dos estudantes apresenta concepções alternativas. Os autores fizeram um levantamento sobre as pré-concepções encontradas em trabalhos sobre o tema (16 referências), procurando encontrar elementos comuns que indicassem a presença de modelos mentais específicos. As pré-concepções encontradas na literatura foram obtidas usando-se diversas metodologias (desde entrevistas clínicas até questionários de múltipla escolha) e envolvendo alunos e professores de diferentes regiões geográficas. A partir de uma análise aprofundada de cada trabalho, e utilizando-se a técnica das Redes Sistêmicas, chegou-se a conclusão que as diversas pré-concepções identificadas (em torno de 50), poderiam ser representadas por 6 modelos mentais, onde a explicação da causa das estações do ano tem um mecanismo causal responsável. Os mecanismos causais identificados foram: a dependência da distância, a dependência da orientação, a dependência conjunta da distância e orientação, a dependência da obstrução, a dependência da velocidade e a dependência da inclinação dos raios solares. Foram ainda identificadas

  3. A voxel-based finite element model for the prediction of bladder deformation

    SciTech Connect

    Chai Xiangfei; Herk, Marcel van; Hulshof, Maarten C. C. M.; Bel, Arjan

    2012-01-15

    Purpose: A finite element (FE) bladder model was previously developed to predict bladder deformation caused by bladder filling change. However, two factors prevent a wide application of FE models: (1) the labor required to construct a FE model with high quality mesh and (2) long computation time needed to construct the FE model and solve the FE equations. In this work, we address these issues by constructing a low-resolution voxel-based FE bladder model directly from the binary segmentation images and compare the accuracy and computational efficiency of the voxel-based model used to simulate bladder deformation with those of a classical FE model with a tetrahedral mesh. Methods: For ten healthy volunteers, a series of MRI scans of the pelvic region was recorded at regular intervals of 10 min over 1 h. For this series of scans, the bladder volume gradually increased while rectal volume remained constant. All pelvic structures were defined from a reference image for each volunteer, including bladder wall, small bowel, prostate (male), uterus (female), rectum, pelvic bone, spine, and the rest of the body. Four separate FE models were constructed from these structures: one with a tetrahedral mesh (used in previous study), one with a uniform hexahedral mesh, one with a nonuniform hexahedral mesh, and one with a low-resolution nonuniform hexahedral mesh. Appropriate material properties were assigned to all structures and uniform pressure was applied to the inner bladder wall to simulate bladder deformation from urine inflow. Performance of the hexahedral meshes was evaluated against the performance of the standard tetrahedral mesh by comparing the accuracy of bladder shape prediction and computational efficiency. Results: FE model with a hexahedral mesh can be quickly and automatically constructed. No substantial differences were observed between the simulation results of the tetrahedral mesh and hexahedral meshes (<1% difference in mean dice similarity coefficient to

  4. Voxel based morphometry in optical coherence tomography: validation and core findings

    NASA Astrophysics Data System (ADS)

    Antony, Bhavna J.; Chen, Min; Carass, Aaron; Jedynak, Bruno M.; Al-Louzi, Omar; Solomon, Sharon D.; Saidha, Shiv; Calabresi, Peter A.; Prince, Jerry L.

    2016-03-01

    Optical coherence tomography (OCT) of the human retina is now becoming established as an important modality for the detection and tracking of various ocular diseases. Voxel based morphometry (VBM) is a long standing neuroimaging analysis technique that allows for the exploration of the regional differences in the brain. There has been limited work done in developing registration based methods for OCT, which has hampered the advancement of VBM analyses in OCT based population studies. Following on from our recent development of an OCT registration method, we explore the potential benefits of VBM analysis in cohorts of healthy controls (HCs) and multiple sclerosis (MS) patients. Specifically, we validate the stability of VBM analysis in two pools of HCs showing no significant difference between the two populations. Additionally, we also present a retrospective study of age and sex matched HCs and relapsing remitting MS patients, demonstrating results consistent with the reported literature while providing insight into the retinal changes associated with this MS subtype.

  5. Gray matter correlates of dispositional optimism: a voxel-based morphometry study.

    PubMed

    Yang, Junyi; Wei, Dongtao; Wang, Kangcheng; Qiu, Jiang

    2013-10-11

    Dispositional optimism is an important product of human evolution. This individual difference variable plays a core role in human experience. Dispositional optimism is beneficial to physical and psychological wellbeing. Previous task-related neuroimaging studies on dispositional optimism were limited by small sample sizes, and did not examine individual differences in dispositional optimism related to brain structure. Thus, the current study used voxel-based morphometry and the revised Life Orientation Test to investigate individual dispositional optimism and its association with brain structure in 361 healthy participants. The results showed that individual dispositional optimism was associated with larger gray matter volume of a cluster of areas that included the left thalamus/left pulvinar that extended to the left parahippocampal gyrus. These findings suggest a biological basis for individual dispositional optimism, distributed across different gray matter regions of the brain.

  6. Feasibility of voxel-based statistical analysis method for myocardial PET

    NASA Astrophysics Data System (ADS)

    Ram Yu, A.; Kim, Jin Su; Paik, Chang H.; Kim, Kyeong Min; Moo Lim, Sang

    2014-09-01

    Although statistical parametric mapping (SPM) analysis is widely used in neuroimaging studies, to our best knowledge, there was no application to myocardial PET data analysis. In this study, we developed the voxel based statistical analysis method for myocardial PET which provides statistical comparison results between groups in image space. PET Emission data of normal and myocardial infarction rats were acquired For the SPM analysis, a rat heart template was created. In addition, individual PET data was spatially normalized and smoothed. Two sample t-tests were performed to identify the myocardial infarct region. This developed SPM method was compared with conventional ROI methods. Myocardial glucose metabolism was decreased in the lateral wall of the left ventricle. In the result of ROI analysis, the mean value of the lateral wall was 29% decreased. The newly developed SPM method for myocardial PET could provide quantitative information in myocardial PET study.

  7. Studying Sub-Dendrograms of Resting-State Functional Networks with Voxel-Wise Hierarchical Clustering

    PubMed Central

    Wang, Yanlu; Msghina, Mussie; Li, Tie-Qiang

    2016-01-01

    Hierarchical clustering is a useful data-driven approach to classify complex data and has been used to analyze resting-state functional magnetic resonance imaging (fMRI) data and derive functional networks of the human brain at very large scale, such as the entire visual or sensory-motor cortex. In this study, we developed a voxel-wise, whole-brain hierarchical clustering framework to perform multi-stage analysis of group-averaged resting-state fMRI data in different levels of detail. With the framework we analyzed particularly the somatosensory motor and visual systems in fine details and constructed the corresponding sub-dendrograms, which corroborate consistently with the known modular organizations from previous clinical and experimental studies. The framework provides a useful tool for data-driven analysis of resting-state fMRI data to gain insight into the hierarchical organization and degree of functional modulation among the sub-units. PMID:27014015

  8. Determining organ dose conversion coefficients for external neutron irradiation by using a voxel mouse model

    PubMed Central

    Zhang, Xiaomin; Xie, Xiangdong; Qu, Decheng; Ning, Jing; Zhou, Hongmei; Pan, Jie; Yang, Guoshan

    2016-01-01

    A set of fluence-to-dose conversion coefficients has been calculated for neutrons with energies <20 MeV using a developed voxel mouse model and Monte Carlo N-particle code (MCNP), for the purpose of neutron radiation effect evaluation. The calculation used 37 monodirectional monoenergetic neutron beams in the energy range 10−9 MeV to 20 MeV, under five different source irradiation configurations: left lateral, right lateral, dorsal–ventral, ventral–dorsal, and isotropic. Neutron fluence-to-dose conversion coefficients for selected organs of the body were presented in the paper, and the effect of irradiation geometry conditions, neutron energy and the organ location on the organ dose was discussed. The results indicated that neutron dose conversion coefficients clearly show sensitivity to irradiation geometry at neutron energy below 1 MeV. PMID:26661852

  9. Dose conversion coefficients for ICRP110 voxel phantom in the Geant4 Monte Carlo code

    NASA Astrophysics Data System (ADS)

    Martins, M. C.; Cordeiro, T. P. V.; Silva, A. X.; Souza-Santos, D.; Queiroz-Filho, P. P.; Hunt, J. G.

    2014-02-01

    The reference adult male voxel phantom recommended by International Commission on Radiological Protection no. 110 was implemented in the Geant4 Monte Carlo code. Geant4 was used to calculate Dose Conversion Coefficients (DCCs) expressed as dose deposited in organs per air kerma for photons, electrons and neutrons in the Annals of the ICRP. In this work the AP and PA irradiation geometries of the ICRP male phantom were simulated for the purpose of benchmarking the Geant4 code. Monoenergetic photons were simulated between 15 keV and 10 MeV and the results were compared with ICRP 110, the VMC Monte Carlo code and the literature data available, presenting a good agreement.

  10. Voxel-based morphometry predicts shifts in dendritic spine density and morphology with auditory fear conditioning.

    PubMed

    Keifer, O P; Hurt, R C; Gutman, D A; Keilholz, S D; Gourley, S L; Ressler, K J

    2015-07-07

    Neuroimaging has provided compelling data about the brain. Yet the underlying mechanisms of many neuroimaging techniques have not been elucidated. Here we report a voxel-based morphometry (VBM) study of Thy1-YFP mice following auditory fear conditioning complemented by confocal microscopy analysis of cortical thickness, neuronal morphometric features and nuclei size/density. Significant VBM results included the nuclei of the amygdala, the insula and the auditory cortex. There were no significant VBM changes in a control brain area. Focusing on the auditory cortex, confocal analysis showed that fear conditioning led to a significantly increased density of shorter and wider dendritic spines, while there were no spine differences in the control area. Of all the morphology metrics studied, the spine density was the only one to show significant correlation with the VBM signal. These data demonstrate that learning-induced structural changes detected by VBM may be partially explained by increases in dendritic spine density.

  11. Scattered radiation in flat-detector based cone-beam CT: analysis of voxelized patient simulations

    NASA Astrophysics Data System (ADS)

    Wiegert, Jens; Bertram, Matthias

    2006-03-01

    This paper presents a systematic assessment of scattered radiation in flat-detector based cone-beam CT. The analysis is based on simulated scatter projections of voxelized CT images of different body regions allowing to accurately quantify scattered radiation of realistic and clinically relevant patient geometries. Using analytically computed primary projection data of high spatial resolution in combination with Monte-Carlo simulated scattered radiation, practically noise-free reference data sets are computed with and without inclusion of scatter. The impact of scatter is studied both in the projection data and in the reconstructed volume for the head, thorax, and pelvis regions. Currently available anti-scatter grid geometries do not sufficiently compensate scatter induced cupping and streak artifacts, requiring additional software-based scatter correction. The required accuracy of scatter compensation approaches increases with increasing patient size.

  12. Voxel-based analysis of grey and white matter degeneration in cervical spondylotic myelopathy

    PubMed Central

    Grabher, Patrick; Mohammadi, Siawoosh; Trachsler, Aaron; Friedl, Susanne; David, Gergely; Sutter, Reto; Weiskopf, Nikolaus; Thompson, Alan J.; Curt, Armin; Freund, Patrick

    2016-01-01

    In this prospective study, we made an unbiased voxel-based analysis to investigate above-stenosis spinal degeneration and its relation to impairment in patients with cervical spondylotic myelopathy (CSM). Twenty patients and 18 controls were assessed with high-resolution MRI protocols above the level of stenosis. Cross-sectional areas of grey matter (GM), white matter (WM), and posterior columns (PC) were measured to determine atrophy. Diffusion indices assessed tract-specific integrity of PC and lateral corticospinal tracts (CST). Regression analysis was used to reveal relationships between MRI measures and clinical impairment. Patients showed mainly sensory impairment. Atrophy was prominent within the cervical WM (13.9%, p = 0.004), GM (7.2%, p = 0.043), and PC (16.1%, p = 0.005). Fractional anisotropy (FA) was reduced in the PC (−11.98%, p = 0.006) and lateral CST (−12.96%, p = 0.014). In addition, radial (+28.47%, p = 0.014), axial (+14.72%, p = 0.005), and mean (+16.50%, p = 0.001) diffusivities were increased in the PC. Light-touch score was associated with atrophy (R2 = 0.3559, p = 0.020) and FA (z score 3.74, p = 0.003) in the PC, as was functional independence and FA in the lateral CST (z score 3.68, p = 0.020). This study demonstrates voxel-based degeneration far above the stenosis at a level not directly affected by the compression and provides unbiased readouts of tract-specific changes that relate to impairment. PMID:27095134

  13. Voxel-based analysis of grey and white matter degeneration in cervical spondylotic myelopathy.

    PubMed

    Grabher, Patrick; Mohammadi, Siawoosh; Trachsler, Aaron; Friedl, Susanne; David, Gergely; Sutter, Reto; Weiskopf, Nikolaus; Thompson, Alan J; Curt, Armin; Freund, Patrick

    2016-04-20

    In this prospective study, we made an unbiased voxel-based analysis to investigate above-stenosis spinal degeneration and its relation to impairment in patients with cervical spondylotic myelopathy (CSM). Twenty patients and 18 controls were assessed with high-resolution MRI protocols above the level of stenosis. Cross-sectional areas of grey matter (GM), white matter (WM), and posterior columns (PC) were measured to determine atrophy. Diffusion indices assessed tract-specific integrity of PC and lateral corticospinal tracts (CST). Regression analysis was used to reveal relationships between MRI measures and clinical impairment. Patients showed mainly sensory impairment. Atrophy was prominent within the cervical WM (13.9%, p = 0.004), GM (7.2%, p = 0.043), and PC (16.1%, p = 0.005). Fractional anisotropy (FA) was reduced in the PC (-11.98%, p = 0.006) and lateral CST (-12.96%, p = 0.014). In addition, radial (+28.47%, p = 0.014), axial (+14.72%, p = 0.005), and mean (+16.50%, p = 0.001) diffusivities were increased in the PC. Light-touch score was associated with atrophy (R(2) = 0.3559, p = 0.020) and FA (z score 3.74, p = 0.003) in the PC, as was functional independence and FA in the lateral CST (z score 3.68, p = 0.020). This study demonstrates voxel-based degeneration far above the stenosis at a level not directly affected by the compression and provides unbiased readouts of tract-specific changes that relate to impairment.

  14. Wear Pattern Observations from TDR Retrievals Using Autoregistration of Voxel Data

    PubMed Central

    Shkolnikov, Yakov P.; Bowden, Anton; MacDonald, Daniel; Kurtz, Steve

    2010-01-01

    Due to their unique geometry, characterization of wear damage in total disc replacement (TDR) is difficult. In the paper, we developed and validated an automated damage calculation technique for explanted TDR components. Eight polyethylene cores implanted from 4.6 to 16.0 years were using cone-beam microCT imaging (SCANCO Medical, Switzerland). The nominal uniform voxel size for the implant under investigation was 18 microns, however with a smaller sample size increased resolutions (10 micron nominal voxel size) could be achieved using the same microCT imaging hardware. Nominal surface data for both sizes of TDR components we examined were obtained from manufacturer’s drawings (Link, Germany) and converted to highly discretized triangular meshes. The damage calculation technique utilized an initial alignment phase, followed by a pointwise calculation of the linear damage at each 3D surface point. During the alignment phase, a three-dimensional surface of the undamaged component was automatically aligned with volumetric image data from the damaged component. The alignment algorithm maximized the contact area between undamaged portions of the implant and its nominal surface using an iterative optimization technique. Linear damage at each triangle on the nominal surface was computed by moving along the local normal of the surface both inward and outward direction for a distance much less than the size of the implant. For the retrieved components, the maximum damage occurred away from the central axis of the dome close to the rim. Penetrations of up to 0.8 mm were observed in this region. Lower magnitude penetrations were observed near the pole of the dome. In conclusion, we have developed an analytical method to automatically align and measure three-dimensional surface damage with both high resolution and accuracy on implants with complicated, non-parametric, surface geometry and used this technique to analyze eight implants. PMID:20586080

  15. Voxel Based Analysis of Surgical Revascularization for Moyamoya Disease: Pre- and Postoperative SPECT Studies.

    PubMed

    Fushimi, Yasutaka; Okada, Tomohisa; Takagi, Yasushi; Funaki, Takeshi; Takahashi, Jun C; Miyamoto, Susumu; Togashi, Kaori

    2016-01-01

    Moyamoya disease (MMD) is a chronic, progressive, cerebrovascular occlusive disease that causes abnormal enlargement of collateral pathways (moyamoya vessels) in the region of the basal ganglia and thalamus. Cerebral revascularization procedures remain the preferred treatment for patients with MMD, improving the compromised cerebral blood flow (CBF). However, voxel based analysis (VBA) of revascularization surgery for MMD based on data from pre- and postoperative data has not been established. The latest algorithm called as Diffeomorphic Anatomical Registration Through Exponentiated Lie Algebra (DARTEL) has been introduced for VBA as the function of statistical parametric mapping (SPM8), and improved registration has been achieved by SPM8 with DARTEL. In this study, VBA was conducted to evaluate pre- and postoperative single photon emission computed tomography (SPECT) images for MMD by SPM8 with DARTEL algorithm, and the results were compared with those from SPM8 without DARTEL (a conventional method). Thirty-two patients with MMD who underwent superficial temporal artery-middle cerebral artery (STA-MCA) bypass surgery as the first surgery were included and all patients underwent pre- and postoperative 3D T1-weighted imaging and SPECT. Pre- and postoperative SPECT images were registered to 3D T1-weighted images, then VBA was conducted. Postoperative SPECT showed more statistically increased CBF areas in the bypassed side cerebral hemisphere by using SPM8 with DARTEL (58,989 voxels; P<0.001), and increased ratio of CBF after operation was less than 15%. Meanwhile, postoperative SPECT showed less CBF increased areas by SPM8 without DARTEL. In conclusion, VBA was conducted for patients with MMD, and SPM8 with DARTEL revealed that postoperative SPECT showed statistically significant CBF increases over a relatively large area and with at most 15% increase ratio. PMID:26867219

  16. Voxel-based population analysis for correlating local dose and rectal toxicity in prostate cancer radiotherapy

    NASA Astrophysics Data System (ADS)

    Acosta, Oscar; Drean, Gael; Ospina, Juan D.; Simon, Antoine; Haigron, Pascal; Lafond, Caroline; de Crevoisier, Renaud

    2013-04-01

    The majority of current models utilized for predicting toxicity in prostate cancer radiotherapy are based on dose-volume histograms. One of their main drawbacks is the lack of spatial accuracy, since they consider the organs as a whole volume and thus ignore the heterogeneous intra-organ radio-sensitivity. In this paper, we propose a dose-image-based framework to reveal the relationships between local dose and toxicity. In this approach, the three-dimensional (3D) planned dose distributions across a population are non-rigidly registered into a common coordinate system and compared at a voxel level, therefore enabling the identification of 3D anatomical patterns, which may be responsible for toxicity, at least to some extent. Additionally, different metrics were employed in order to assess the quality of the dose mapping. The value of this approach was demonstrated by prospectively analyzing rectal bleeding (⩾Grade 1 at 2 years) according to the CTCAE v3.0 classification in a series of 105 patients receiving 80 Gy to the prostate by intensity modulated radiation therapy (IMRT). Within the patients presenting bleeding, a significant dose excess (6 Gy on average, p < 0.01) was found in a region of the anterior rectal wall. This region, close to the prostate (1 cm), represented less than 10% of the rectum. This promising voxel-wise approach allowed subregions to be defined within the organ that may be involved in toxicity and, as such, must be considered during the inverse IMRT planning step.

  17. Voxel-based lesion-symptom mapping of stroke lesions underlying somatosensory deficits

    PubMed Central

    Meyer, Sarah; Kessner, Simon S.; Cheng, Bastian; Bönstrup, Marlene; Schulz, Robert; Hummel, Friedhelm C.; De Bruyn, Nele; Peeters, Andre; Van Pesch, Vincent; Duprez, Thierry; Sunaert, Stefan; Schrooten, Maarten; Feys, Hilde; Gerloff, Christian; Thomalla, Götz; Thijs, Vincent; Verheyden, Geert

    2015-01-01

    The aim of this study was to investigate the relationship between stroke lesion location and the resulting somatosensory deficit. We studied exteroceptive and proprioceptive somatosensory symptoms and stroke lesions in 38 patients with first-ever acute stroke. The Erasmus modified Nottingham Sensory Assessment was used to clinically evaluate somatosensory functioning in the arm and hand within the first week after stroke onset. Additionally, more objective measures such as the perceptual threshold of touch and somatosensory evoked potentials were recorded. Non-parametric voxel-based lesion-symptom mapping was performed to investigate lesion contribution to different somatosensory deficits in the upper limb. Additionally, structural connectivity of brain areas that demonstrated the strongest association with somatosensory symptoms was determined, using probabilistic fiber tracking based on diffusion tensor imaging data from a healthy age-matched sample. Voxels with a significant association to somatosensory deficits were clustered in two core brain regions: the central parietal white matter, also referred to as the sensory component of the superior thalamic radiation, and the parietal operculum close to the insular cortex, representing the secondary somatosensory cortex. Our objective recordings confirmed findings from clinical assessments. Probabilistic tracking connected the first region to thalamus, internal capsule, brain stem, postcentral gyrus, cerebellum, and frontal pathways, while the second region demonstrated structural connections to thalamus, insular and primary somatosensory cortex. This study reveals that stroke lesions in the sensory fibers of the superior thalamocortical radiation and the parietal operculum are significantly associated with multiple exteroceptive and proprioceptive deficits in the arm and hand. PMID:26900565

  18. The small-voxel tracking algorithm for simulating chemical reactions among diffusing molecules

    SciTech Connect

    Gillespie, Daniel T. Gillespie, Carol A.; Seitaridou, Effrosyni

    2014-12-21

    Simulating the evolution of a chemically reacting system using the bimolecular propensity function, as is done by the stochastic simulation algorithm and its reaction-diffusion extension, entails making statistically inspired guesses as to where the reactant molecules are at any given time. Those guesses will be physically justified if the system is dilute and well-mixed in the reactant molecules. Otherwise, an accurate simulation will require the extra effort and expense of keeping track of the positions of the reactant molecules as the system evolves. One molecule-tracking algorithm that pays careful attention to the physics of molecular diffusion is the enhanced Green's function reaction dynamics (eGFRD) of Takahashi, Tănase-Nicola, and ten Wolde [Proc. Natl. Acad. Sci. U.S.A. 107, 2473 (2010)]. We introduce here a molecule-tracking algorithm that has the same theoretical underpinnings and strategic aims as eGFRD, but a different implementation procedure. Called the small-voxel tracking algorithm (SVTA), it combines the well known voxel-hopping method for simulating molecular diffusion with a novel procedure for rectifying the unphysical predictions of the diffusion equation on the small spatiotemporal scale of molecular collisions. Indications are that the SVTA might be more computationally efficient than eGFRD for the problematic class of non-dilute systems. A widely applicable, user-friendly software implementation of the SVTA has yet to be developed, but we exhibit some simple examples which show that the algorithm is computationally feasible and gives plausible results.

  19. Organ doses from environmental exposures calculated using voxel phantoms of adults and children

    NASA Astrophysics Data System (ADS)

    Petoussi-Henss, Nina; Schlattl, H.; Zankl, M.; Endo, A.; Saito, K.

    2012-09-01

    This paper presents effective and organ dose conversion coefficients for members of the public due to environmental external exposures, calculated using the ICRP adult male and female reference computational phantoms as well as voxel phantoms of a baby, two children and four adult individual phantoms--one male and three female, one of them pregnant. Dose conversion coefficients are given for source geometries representing environmental radiation exposures, i.e. whole body irradiations from a volume source in air, representing a radioactive cloud, a plane source in the ground at a depth of 0.5 g cm-2, representing ground contamination by radioactive fall-out, and uniformly distributed natural sources in the ground. The organ dose conversion coefficients were calculated employing the Monte Carlo code EGSnrc simulating the photon transport in the voxel phantoms, and are given as effective and equivalent doses normalized to air kerma free-in-air at height 1 m above the ground in Sv Gy-1. The findings showed that, in general, the smaller the body mass of the phantom, the higher the dose. The difference in effective dose between an adult and an infant is 80-90% at 50 keV and less than 40% above 100 keV. Furthermore, dose equivalent rates for photon exposures of several radionuclides for the above environmental exposures were calculated with the most recent nuclear decay data. Data are shown for effective dose, thyroid, colon and red bone marrow. The results are expected to facilitate regulation of exposure to radiation, relating activities of radionuclides distributed in air and ground to dose of the public due to external radiation as well as the investigation of the radiological effects of major radiation accidents such as the recent one in Fukushima and the decision making of several committees.

  20. S values for 131I based on the ICRP adult voxel phantoms.

    PubMed

    Lamart, Stephanie; Simon, Steven L; Bouville, Andre; Moroz, Brian E; Lee, Choonsik

    2016-01-01

    To improve the estimates of organ doses from nuclear medicine procedures using (131)I, the authors calculated a comprehensive set of (131)I S values, defined as absorbed doses in target tissues per unit of nuclear transition in source regions, for different source and target combinations. The authors used the latest reference adult male and female voxel phantoms published by the International Commission on Radiological Protection (ICRP Publication 110) and the (131)I photon and electron spectra from the ICRP Publication 107 to perform Monte Carlo radiation transport calculations using MCNPX2.7 to compute the S values. For each phantom, the authors simulated 55 source regions with an assumed uniform distribution of (131)I. They computed the S values for 42 target tissues directly, without calculating specific absorbed fractions. From these calculations, the authors derived a comprehensive set of S values for (131)I for 55 source regions and 42 target tissues in the ICRP male and female voxel phantoms. Compared with the stylised phantoms from Oak Ridge National Laboratory (ORNL) that consist of 22 source regions and 24 target regions, the new data set includes 1662 additional S values corresponding to additional combinations of source-target tissues that are not available in the stylised phantoms. In a comparison of S values derived from the ICRP and ORNL phantoms, the authors found that the S values to the radiosensitive tissues in the ICRP phantoms were 1.1 (median, female) and 1.3 (median, male) times greater than the values based on the ORNL phantoms. However, for several source-target pairs, the difference was up to 10-fold. The new set of S values can be applied prospectively or retrospectively to the calculation of radiation doses in adults internally exposed to (131)I, including nuclear medicine patients treated for thyroid cancer or hyperthyroidism.

  1. Voxel Based Analysis of Surgical Revascularization for Moyamoya Disease: Pre- and Postoperative SPECT Studies

    PubMed Central

    Fushimi, Yasutaka; Okada, Tomohisa; Takagi, Yasushi; Funaki, Takeshi; Takahashi, Jun C.; Miyamoto, Susumu; Togashi, Kaori

    2016-01-01

    Moyamoya disease (MMD) is a chronic, progressive, cerebrovascular occlusive disease that causes abnormal enlargement of collateral pathways (moyamoya vessels) in the region of the basal ganglia and thalamus. Cerebral revascularization procedures remain the preferred treatment for patients with MMD, improving the compromised cerebral blood flow (CBF). However, voxel based analysis (VBA) of revascularization surgery for MMD based on data from pre- and postoperative data has not been established. The latest algorithm called as Diffeomorphic Anatomical Registration Through Exponentiated Lie Algebra (DARTEL) has been introduced for VBA as the function of statistical parametric mapping (SPM8), and improved registration has been achieved by SPM8 with DARTEL. In this study, VBA was conducted to evaluate pre- and postoperative single photon emission computed tomography (SPECT) images for MMD by SPM8 with DARTEL algorithm, and the results were compared with those from SPM8 without DARTEL (a conventional method). Thirty-two patients with MMD who underwent superficial temporal artery-middle cerebral artery (STA-MCA) bypass surgery as the first surgery were included and all patients underwent pre- and postoperative 3D T1-weighted imaging and SPECT. Pre- and postoperative SPECT images were registered to 3D T1-weighted images, then VBA was conducted. Postoperative SPECT showed more statistically increased CBF areas in the bypassed side cerebral hemisphere by using SPM8 with DARTEL (58,989 voxels; P<0.001), and increased ratio of CBF after operation was less than 15%. Meanwhile, postoperative SPECT showed less CBF increased areas by SPM8 without DARTEL. In conclusion, VBA was conducted for patients with MMD, and SPM8 with DARTEL revealed that postoperative SPECT showed statistically significant CBF increases over a relatively large area and with at most 15% increase ratio. PMID:26867219

  2. An information theoretic approach for non-rigid image registration using voxel class probabilities.

    PubMed

    D'Agostino, Emiliano; Maes, Frederik; Vandermeulen, Dirk; Suetens, Paul

    2006-06-01

    We propose two information theoretic similarity measures that allow to incorporate tissue class information in non-rigid image registration. The first measure assumes that tissue class probabilities have been assigned to each of the images to be registered by prior segmentation of both of them. One image is then non-rigidly deformed to match the other such that the fuzzy overlap of corresponding voxel object labels becomes similar to the ideal case whereby the tissue probability maps of both images are identical. Image similarity is assessed during registration by the divergence between the ideal and actual joint class probability distributions of both images. A second registration measure is proposed that applies in case a segmentation is available for only one of the images, for instance an atlas image that is to be matched to a study image to guide the segmentation thereof. Intensities in one image are matched to the fuzzy class labels in the other image by minimizing the conditional entropy of the intensities in the first image given the class labels in the second image. We derive analytic expressions for the gradient of each measure with respect to individual voxel displacements to derive a force field that drives the registration process, which is regularized by a viscous fluid model. The performance of the class-based measures is evaluated in the context of non-rigid inter-subject registration and atlas-based segmentation of MR brain images and compared with maximization of mutual information using only intensity information. Our results demonstrate that incorporation of class information in the registration measure significantly improves the overlap between corresponding tissue classes after non-rigid matching. The methods proposed here open new perspectives for integrating segmentation and registration in a single process, whereby the output of one is used to guide the other.

  3. Cortical abnormalities in bipolar disorder investigated with MRI and voxel-based morphometry.

    PubMed

    Nugent, Allison C; Milham, Michael P; Bain, Earle E; Mah, Linda; Cannon, Dara M; Marrett, Sean; Zarate, Carlos A; Pine, Daniel S; Price, Joseph L; Drevets, Wayne C

    2006-04-01

    Bipolar disorder (BD) has been associated with abnormalities of brain structure. Specifically, in vivo volumetric MRI and/or post mortem studies of BD have reported abnormalities of gray matter (GM) volume in the medial prefrontal cortex (PFC), amygdala, hippocampal subiculum and ventral striatum. These structures share anatomical connections with each other and form part of a "visceromotor" network modulating emotional behavior. Areas of the lateral orbital, superior temporal and posterior cingulate cortices project to this network, but morphometric abnormalities in these areas have not been established in BD. The current study assessed tissue volumes within these areas in BD using MRI and voxel-based morphometry (VBM). MRI images were obtained from 36 BD subjects and 65 healthy controls. To account for possible neurotrophic and neuroprotective effects of psychotropic medications, BD subjects were divided into medicated and unmedicated groups. Images were segmented into tissue compartments, which were examined on a voxel-wise basis to determine the location and extent of morphometric changes. The GM was reduced in the posterior cingulate/retrosplenial cortex and superior temporal gyrus of unmedicated BD subjects relative to medicated BD subjects and in the lateral orbital cortex of medicated BD subjects relative to controls. White matter (WM) was increased in the orbital and posterior cingulate cortices, which most likely reflected alterations in gyral morphology resulting from the reductions in the associated GM. The morphometric abnormalities in the posterior cingulate, superior temporal and lateral orbital cortices in BD support the hypothesis that the extended network of neuroanatomical structures subserving visceromotor regulation contains structural alterations in BD. Additionally, localization of morphometric abnormalities to areas known to exhibit increased metabolism in depression supports the hypothesis that repeated stress and elevated glucocorticoid

  4. The Neural Basis of Reversible Sentence Comprehension: Evidence from Voxel-Based Lesion Symptom Mapping in Aphasia

    ERIC Educational Resources Information Center

    Thothathiri, Malathi; Kimberg, Daniel Y.; Schwartz, Myrna F.

    2012-01-01

    We explored the neural basis of reversible sentence comprehension in a large group of aphasic patients (n = 79). Voxel-based lesion symptom mapping revealed a significant association between damage in temporo-parietal cortex and impaired sentence comprehension. This association remained after we controlled for phonological working memory. We…

  5. Voxel2MCNP: a framework for modeling, simulation and evaluation of radiation transport scenarios for Monte Carlo codes.

    PubMed

    Pölz, Stefan; Laubersheimer, Sven; Eberhardt, Jakob S; Harrendorf, Marco A; Keck, Thomas; Benzler, Andreas; Breustedt, Bastian

    2013-08-21

    The basic idea of Voxel2MCNP is to provide a framework supporting users in modeling radiation transport scenarios using voxel phantoms and other geometric models, generating corresponding input for the Monte Carlo code MCNPX, and evaluating simulation output. Applications at Karlsruhe Institute of Technology are primarily whole and partial body counter calibration and calculation of dose conversion coefficients. A new generic data model describing data related to radiation transport, including phantom and detector geometries and their properties, sources, tallies and materials, has been developed. It is modular and generally independent of the targeted Monte Carlo code. The data model has been implemented as an XML-based file format to facilitate data exchange, and integrated with Voxel2MCNP to provide a common interface for modeling, visualization, and evaluation of data. Also, extensions to allow compatibility with several file formats, such as ENSDF for nuclear structure properties and radioactive decay data, SimpleGeo for solid geometry modeling, ImageJ for voxel lattices, and MCNPX's MCTAL for simulation results have been added. The framework is presented and discussed in this paper and example workflows for body counter calibration and calculation of dose conversion coefficients is given to illustrate its application.

  6. Comparison of the influence of FOV sizes and different voxel resolutions for the assessment of periodontal defects

    PubMed Central

    Kolsuz, M E; Bagis, N; Avsever, H; Demiralp, K Ö

    2015-01-01

    Objectives: This study assessed the influence of different voxel resolutions of two different CBCT units on the in vitro detection of periodontal defects. Methods: The study used 12 dry skulls with a maxilla and a mandible. Artificial defects (dehiscence, tunnel, fenestration) were separately created on the anterior, premolar and molar teeth using burrs. A total of 14 dehiscences, 13 fenestrations, 8 tunnels and 16 non-defect controls were used in the study. Images were obtained from two different CBCT units in six voxel sizes (voxel size: 0.080, 0.100, 0.125, 0.150, 0.160 and 0.200 mm3). Kappa coefficients were calculated to assess both intra- and interobserver agreements for each image set. Results: Overall intraobserver kappa coefficients ranged between 0.978 and 0.973 for the 0.080-mm3 images and between 0.751 and 0.737 for the 0.160-mm3 images, suggesting notably high intraobserver agreement for detecting periodontal defects. CBCT performed significantly better at detecting fenestrations (p < 0.05) than tunnel and dehiscence defects. No statistically significant difference was found between the detection of dehiscence and tunnel defects (p > 0.05). Conclusions: A voxel size of 0.150 mm3 was identified as the cut-off point for overall detection of periodontal defects. CBCT should be considered the most reliable imaging modality for the diagnosis of periodontal defects. PMID:25900235

  7. Voxel-Wise Functional Connectomics Using Arterial Spin Labeling Functional Magnetic Resonance Imaging: The Role of Denoising.

    PubMed

    Liang, Xiaoyun; Connelly, Alan; Calamante, Fernando

    2015-11-01

    The objective of this study was to investigate voxel-wise functional connectomics using arterial spin labeling (ASL) functional magnetic resonance imaging (fMRI). Since ASL signal has an intrinsically low signal-to-noise ratio (SNR), the role of denoising is evaluated; in particular, a novel denoising method, dual-tree complex wavelet transform (DT-CWT) combined with the nonlocal means (NLM) algorithm is implemented and evaluated. Simulations were conducted to evaluate the performance of the proposed method in denoising images and in detecting functional networks from noisy data (including the accuracy and sensitivity of detection). In addition, denoising was applied to in vivo ASL datasets, followed by network analysis using graph theoretical approaches. Efficiencies cost was used to evaluate the performance of denoising in detecting functional networks from in vivo ASL fMRI data. Simulations showed that denoising is effective in detecting voxel-wise functional networks from low SNR data and/or from data with small total number of time points. The capability of denoised voxel-wise functional connectivity analysis was also demonstrated with in vivo data. We concluded that denoising is important for voxel-wise functional connectivity using ASL fMRI and that the proposed DT-CWT-NLM method should be a useful ASL preprocessing step.

  8. Abnormal Functional Specialization within Medial Prefrontal Cortex in High-Functioning Autism: A Multi-Voxel Similarity Analysis

    ERIC Educational Resources Information Center

    Gilbert, Sam J.; Meuwese, Julia D. I.; Towgood, Karren J.; Frith, Christopher D.; Burgess, Paul W.

    2009-01-01

    Multi-voxel pattern analyses have proved successful in "decoding" mental states from fMRI data, but have not been used to examine brain differences associated with atypical populations. We investigated a group of 16 (14 males) high-functioning participants with autism spectrum disorder (ASD) and 16 non-autistic control participants (12 males)…

  9. Diagnosis of a multifocal B cell lymphoma with preceding demyelinating central nervous system lesions by single voxel proton MR spectroscopy

    PubMed Central

    Kuhlmann, T; Schroter, A; Dechent, P; Weber, F; Rustenbeck, H; Fuzesi, L; Bruck, W; Ehrenreich, H; Frahm, J

    2001-01-01

    Single voxel proton magnetic resonance spectroscopy (MRS) provides a rapid non-invasive fingerprint of tissue chemistry. A case history is presented in which a B cell lymphoma with antecedent demyelinating lesions of the CNS was suspected by MRS and confirmed by neuropathological examination and immunoglobulin gene rearrangement.

 PMID:11160483

  10. Dyslexia and Voxel-Based Morphometry: Correlations between Five Behavioural Measures of Dyslexia and Gray and White Matter Volumes

    ERIC Educational Resources Information Center

    Tamboer, Peter; Scholte, H. Steven; Vorst, Harrie C. M.

    2015-01-01

    In voxel-based morphometry studies of dyslexia, the relation between causal theories of dyslexia and gray matter (GM) and white matter (WM) volume alterations is still under debate. Some alterations are consistently reported, but others failed to reach significance. We investigated GM alterations in a large sample of Dutch students (37 dyslexics…

  11. Calculation of Dose Deposition in 3D Voxels by Heavy Ions and Simulation of gamma-H2AX Experiments

    NASA Technical Reports Server (NTRS)

    Plante, I.; Ponomarev, A. L.; Wang, M.; Cucinotta, F. A.

    2011-01-01

    The biological response to high-LET radiation is different from low-LET radiation due to several factors, notably difference in energy deposition and formation of radiolytic species. Of particular importance in radiobiology is the formation of double-strand breaks (DSB), which can be detected by -H2AX foci experiments. These experiments has revealed important differences in the spatial distribution of DSB induced by low- and high-LET radiations [1,2]. To simulate -H2AX experiments, models based on amorphous track with radial dose are often combined with random walk chromosome models [3,4]. In this work, a new approach using the Monte-Carlo track structure code RITRACKS [5] and chromosome models have been used to simulate DSB formation. At first, RITRACKS have been used to simulate the irradiation of a cubic volume of 5 m by 1) 450 1H+ ions of 300 MeV (LET 0.3 keV/ m) and 2) by 1 56Fe26+ ion of 1 GeV/amu (LET 150 keV/ m). All energy deposition events are recorded to calculate dose in voxels of 20 m. The dose voxels are distributed randomly and scattered uniformly within the volume irradiated by low-LET radiation. Many differences are found in the spatial distribution of dose voxels for the 56Fe26+ ion. The track structure can be distinguished, and voxels with very high dose are found in the region corresponding to the track "core". These high-dose voxels are not found in the low-LET irradiation simulation and indicate clustered energy deposition, which may be responsible for complex DSB. In the second step, assuming that DSB will be found only in voxels where energy is deposited by the radiation, the intersection points between voxels with dose > 0 and simulated chromosomes were obtained. The spatial distribution of the intersection points is similar to -H2AX foci experiments. These preliminary results suggest that combining stochastic track structure and chromosome models could be a good approach to understand radiation-induced DSB and chromosome aberrations.

  12. A high-resolution voxel model for predicting local tissue temperatures in humans subjected to warm and hot environments.

    PubMed

    Nelson, D A; Charbonnel, S; Curran, A R; Marttila, E A; Fiala, D; Mason, P A; Ziriax, J M

    2009-04-01

    This work describes and presents results from a new three-dimensional whole-body model of human thermoregulation. The model has been implemented using a version of the "Brooks Man" anatomical data set, consisting of 1.3x10(8) cubic volume elements (voxels) measuring 0.2 cm/side. The model simulates thermoregulation through passive mechanisms (metabolism, blood flow, respiration, and transpiration) and active mechanisms (vasodilatation, vasoconstriction, sweating, and shivering). Compared with lumped or compartment models, a voxel model is capable of high spatial resolution and can capture a level of anatomical detail not achievable otherwise. A high spatial resolution model can predict detailed heating patterns from localized or nonuniform heating patterns, such as from some radio frequency sources. Exposures to warm and hot environments (ambient temperatures of 33-48 degrees C) were simulated with the current voxel model and with a recent compartment model. Results from the two models (core temperature, skin temperature, metabolic rate, and evaporative cooling rate) were compared with published experimental results obtained under similar conditions. Under the most severe environmental conditions considered (47.8 degrees C, 27% RH for 2 h), the voxel model predicted a rectal temperature increase of 0.56 degrees C, compared with a core temperature increase of 0.45 degrees C from the compartment model and an experimental mean rectal temperature increase of 0.6 degrees C. Similar, good agreement was noted for other thermal variables and under other environmental conditions. Results suggest that the voxel model is capable of predicting temperature response (core temperature and skin temperature) to certain warm or hot environments, with accuracy comparable to that of a compartment model. In addition, the voxel model is able to predict internal tissue temperatures and surface temperatures, over time, with a level of specificity and spatial resolution not achievable with

  13. Effect of micro-computed tomography voxel size and segmentation method on trabecular bone microstructure measures in mice.

    PubMed

    Christiansen, Blaine A

    2016-12-01

    Micro-computed tomography (μCT) is currently the gold standard for determining trabecular bone microstructure in small animal models. Numerous parameters associated with scanning and evaluation of μCT scans can strongly affect morphologic results obtained from bone samples. However, the effect of these parameters on specific trabecular bone outcomes is not well understood. This study investigated the effect of μCT scanning with nominal voxel sizes between 6-30 μm on trabecular bone outcomes quantified in mouse vertebral body trabecular bone. Additionally, two methods for determining a global segmentation threshold were compared: based on qualitative assessment of 2D images, or based on quantitative assessment of image histograms. It was found that nominal voxel size had a strong effect on several commonly reported trabecular bone parameters, in particular connectivity density, trabecular thickness, and bone tissue mineral density. Additionally, the two segmentation methods provided similar trabecular bone outcomes for scans with small nominal voxel sizes, but considerably different outcomes for scans with larger voxel sizes. The Qualitatively Selected segmentation method more consistently estimated trabecular bone volume fraction (BV/TV) and trabecular thickness across different voxel sizes, but the Histogram segmentation method more consistently estimated trabecular number, trabecular separation, and structure model index. Altogether, these results suggest that high-resolution scans be used whenever possible to provide the most accurate estimation of trabecular bone microstructure, and that the limitations of accurately determining trabecular bone outcomes should be considered when selecting scan parameters and making conclusions about inter-group variance or between-group differences in studies of trabecular bone microstructure in small animals. PMID:27430011

  14. Effect of micro-computed tomography voxel size and segmentation method on trabecular bone microstructure measures in mice.

    PubMed

    Christiansen, Blaine A

    2016-12-01

    Micro-computed tomography (μCT) is currently the gold standard for determining trabecular bone microstructure in small animal models. Numerous parameters associated with scanning and evaluation of μCT scans can strongly affect morphologic results obtained from bone samples. However, the effect of these parameters on specific trabecular bone outcomes is not well understood. This study investigated the effect of μCT scanning with nominal voxel sizes between 6-30 μm on trabecular bone outcomes quantified in mouse vertebral body trabecular bone. Additionally, two methods for determining a global segmentation threshold were compared: based on qualitative assessment of 2D images, or based on quantitative assessment of image histograms. It was found that nominal voxel size had a strong effect on several commonly reported trabecular bone parameters, in particular connectivity density, trabecular thickness, and bone tissue mineral density. Additionally, the two segmentation methods provided similar trabecular bone outcomes for scans with small nominal voxel sizes, but considerably different outcomes for scans with larger voxel sizes. The Qualitatively Selected segmentation method more consistently estimated trabecular bone volume fraction (BV/TV) and trabecular thickness across different voxel sizes, but the Histogram segmentation method more consistently estimated trabecular number, trabecular separation, and structure model index. Altogether, these results suggest that high-resolution scans be used whenever possible to provide the most accurate estimation of trabecular bone microstructure, and that the limitations of accurately determining trabecular bone outcomes should be considered when selecting scan parameters and making conclusions about inter-group variance or between-group differences in studies of trabecular bone microstructure in small animals.

  15. Skeletal dosimetry in a voxel-based rat phantom for internal exposures to photons and electrons

    SciTech Connect

    Xie Tianwu; Han Dao; Liu Yang; Sun Wenjuan; Liu Qian

    2010-05-15

    Purpose: The skeleton makes a significant contribution to the whole body absorbed dose evaluation of rats, since the bone marrow and bone surface in the skeleton express high radiosensitivity and are considered to be important dose-limiting tissues. The bone marrow can be categorized as red bone marrow (RBM) and yellow bone marrow (YBM). It is important to investigate the bone marrow in skeletal dosimetry. Methods: Cryosectional color images of the skeleton of a 156 g rat were segmented into mineral bone (including cortical bone and trabecular bone), RBM, and YBM. These three tissue types were identified at 40 different bone sites and integrated into a previously developed voxel-based rat computational phantom. Photon and electron skeletal absorbed fractions were then calculated using the MCNPX Monte Carlo code. Results: Absorbed fraction (AF) and specific absorbed fraction (SAF) for mineral bone, RBM, and YBM at the 40 different bone sites were established for monoenergetic photon and electron sources placed in 18 organs and seven bone sites. Discrete photon energy was varied from 0.01 to 5.0 MeV in 21 discrete steps, while 21 discrete electron energies were studied, from 0.1 to 10.0 MeV. The trends and values found were consistent with the results of other researchers [M. G. Stabin, T. E. Peterson, G. E. Holburn, and M. A. Emmons, ''Voxel-based mouse and rat models for internal dose calculations,'' J. Nucl. Med. 47, 655-659 (2006)]. S-factors for the radionuclides {sup 169}Er, {sup 143}Pr, {sup 89}Sr, {sup 32}P, and {sup 90}Y, located in 18 organs and seven bone sites for the skeleton, were calculated and are provided in detail. Conclusions: For internal dose calculations, the AF data reveal that the mineral bone in the rat skeletal system is responsible for significant attenuation of gamma rays, especially at low energies. The photon SAF curves of RBM show that, for photon energies greater than 0.6 MeV, there is an increase in secondary photons emitted from the

  16. An MR image-guided, voxel-based partial volume correction method for PET images

    PubMed Central

    Wang, Hesheng; Fei, Baowei

    2012-01-01

    Purpose: Partial volume effect in positron emission tomography (PET) can cause incorrect quantification of radiopharmaceutical uptake in functional imaging. A PET partial volume correction method is presented to attenuate partial volume blurring and to yield voxel-based corrected PET images. Methods: By modeling partial volume effect as a convolution of point spread function of the PET scanner, the reconstructed PET images are corrected by iterative deconvolution with an edge-preserving smoothness constraint. The constraint is constructed to restore discontinuities extracted from coregistered MR images but maintains the smoothness in radioactivity distribution. The correction is implemented in a Bayesian deconvolution framework and is solved by a conjugate gradient method. The performance of the method was compared with the geometric transfer matrix (GTM) method on a simulated dataset. The method was evaluated on synthesized brain FDG–PET data and phantom MRI–PET experiments. Results: The true PET activity of objects with a size of greater than the full-width at half maximum of the point spread function has been effectively restored in the simulated data. The partial volume correction method is quantitatively comparable to the GTM method. For synthesized FDG–PET with true activity 0 μci/cc for cerebrospinal fluid (CSF), 228 μci/cc for white matter (WM), and 621 μci/cc for gray matter (GM), the method has improved the radioactivity quantification from 186 ± 16 μci/cc to 30 ± 7 μci/cc in CSF, 317 ± 15 μci/cc to 236 ± 10 μci/cc for WM, 438 ± 4 μci/cc to 592 ± 5 μci/cc for GM. Both visual and quantitative assessments show improvement of partial volume correction in the synthesized and phantom experiments. Conclusions: The partial volume correction method improves the quantification of PET images. The method is comparable to the GTM method but does not need MR image segmentation or prior tracer distribution information. The

  17. SU-E-CAMPUS-I-02: Estimation of the Dosimetric Error Caused by the Voxelization of Hybrid Computational Phantoms Using Triangle Mesh-Based Monte Carlo Transport

    SciTech Connect

    Lee, C; Badal, A

    2014-06-15

    Purpose: Computational voxel phantom provides realistic anatomy but the voxel structure may result in dosimetric error compared to real anatomy composed of perfect surface. We analyzed the dosimetric error caused from the voxel structure in hybrid computational phantoms by comparing the voxel-based doses at different resolutions with triangle mesh-based doses. Methods: We incorporated the existing adult male UF/NCI hybrid phantom in mesh format into a Monte Carlo transport code, penMesh that supports triangle meshes. We calculated energy deposition to selected organs of interest for parallel photon beams with three mono energies (0.1, 1, and 10 MeV) in antero-posterior geometry. We also calculated organ energy deposition using three voxel phantoms with different voxel resolutions (1, 5, and 10 mm) using MCNPX2.7. Results: Comparison of organ energy deposition between the two methods showed that agreement overall improved for higher voxel resolution, but for many organs the differences were small. Difference in the energy deposition for 1 MeV, for example, decreased from 11.5% to 1.7% in muscle but only from 0.6% to 0.3% in liver as voxel resolution increased from 10 mm to 1 mm. The differences were smaller at higher energies. The number of photon histories processed per second in voxels were 6.4×10{sup 4}, 3.3×10{sup 4}, and 1.3×10{sup 4}, for 10, 5, and 1 mm resolutions at 10 MeV, respectively, while meshes ran at 4.0×10{sup 4} histories/sec. Conclusion: The combination of hybrid mesh phantom and penMesh was proved to be accurate and of similar speed compared to the voxel phantom and MCNPX. The lowest voxel resolution caused a maximum dosimetric error of 12.6% at 0.1 MeV and 6.8% at 10 MeV but the error was insignificant in some organs. We will apply the tool to calculate dose to very thin layer tissues (e.g., radiosensitive layer in gastro intestines) which cannot be modeled by voxel phantoms.

  18. Role of Disgust Proneness in Parkinson’s Disease: A Voxel-Based Morphometry Study

    PubMed Central

    Ille, Rottraut; Wabnegger, Albert; Schwingenschuh, Petra; Katschnig-Winter, Petra; Kögl-Wallner, Mariella; Wenzel, Karoline; Schienle, Anne

    2015-01-01

    The knowledge about personality traits in Parkinson’s disease (PD) is still limited. In particular, disgust proneness has not been investigated as well as its neuronal correlates. Although several morphometric studies demonstrated that PD is associated with gray matter volume (GMV) reduction in olfactory and gustatory regions involved in disgust processing, a possible correlation with disgust proneness has not been investigated. We conducted a voxel-based morphometry analysis to compare GMV between 16 cognitively normal male PD patients with mild to moderate symptoms and 24 matched control subjects. All participants had answered questionnaires for the assessment of disgust proneness, trait anger and trait anxiety. We correlated questionnaire scores with GMV in both groups. The clinical group reported selectively reduced disgust proneness toward olfactory stimuli associated with spoilage. Moreover, they showed GMV reduction in the central olfactory system [orbitofrontal cortex (OFC) and piriform cortex]. Disgust items referring to olfactory processing were positively correlated with OFC volume in PD patients. Our data suggest an association between PD-associated neurodegeneration and olfactory related facets of the personality trait disgust proneness. PMID:25908177

  19. MRI Correlates of Parkinson's Disease Progression: A Voxel Based Morphometry Study

    PubMed Central

    Fioravanti, Valentina; Benuzzi, Francesca; Codeluppi, Luca; Contardi, Sara; Cavallieri, Francesco; Nichelli, Paolo; Valzania, Franco

    2015-01-01

    We investigated structural brain differences between a group of early-mild PD patients at different phases of the disease and healthy subjects using voxel-based morphometry (VBM). 20 mild PD patients compared to 15 healthy at baseline and after 2 years of follow-up. VBM is a fully automated technique, which allows the identification of regional differences in the gray matter enabling an objective analysis of the whole brain between groups of subjects. With respect to controls, PD patients exhibited decreased GM volumes in right putamen and right parietal cortex. After 2 years of disease, the same patients confirmed GM loss in the putamen and parietal cortex; a significant difference was also observed in the area of pedunculopontine nucleus (PPN) and in the mesencephalic locomotor region (MLR). PD is associated with brain morphological changes in cortical and subcortical structures. The first regions to be affected in PD seem to be the parietal cortex and the putamen. A third structure that undergoes atrophy is the part of the inferior-posterior midbrain, attributable to the PPN and MLR. Our findings provide new insight into the brain involvement in PD and could contribute to a better understanding of the sequence of events occurring in these patients. PMID:25628916

  20. NOTE: SAR in a child voxel phantom from exposure to wireless computer networks (Wi-Fi)

    NASA Astrophysics Data System (ADS)

    Findlay, R. P.; Dimbylow, P. J.

    2010-08-01

    Specific energy absorption rate (SAR) values have been calculated in a 10 year old sitting voxel model from exposure to electromagnetic fields at 2.4 and 5 GHz, frequencies commonly used by Wi-Fi devices. Both plane-wave exposure of the model and irradiation from antennas in the near field were investigated for a variety of exposure conditions. In all situations studied, the SAR values calculated were considerably below basic restrictions. For a typical Wi-Fi exposure scenario using an inverted F antenna operating at 100 mW, a duty factor of 0.1 and an antenna-body separation of 34 cm, the maximum peak localized SAR was found to be 3.99 mW kg-1 in the torso region. At 2.4 GHz, using a power of 100 mW and a duty factor of 1, the highest localized SAR value in the head was calculated as 5.7 mW kg-1. This represents less than 1% of the SAR previously calculated in the head for a typical mobile phone exposure condition.

  1. Multi-voxel patterns of visual category representation during episodic encoding are predictive of subsequent memory

    PubMed Central

    Kuhl, Brice A.; Rissman, Jesse; Wagner, Anthony D.

    2012-01-01

    Successful encoding of episodic memories is thought to depend on contributions from prefrontal and temporal lobe structures. Neural processes that contribute to successful encoding have been extensively explored through univariate analyses of neuroimaging data that compare mean activity levels elicited during the encoding of events that are subsequently remembered vs. those subsequently forgotten. Here, we applied pattern classification to fMRI data to assess the degree to which distributed patterns of activity within prefrontal and temporal lobe structures elicited during the encoding of word-image pairs were diagnostic of the visual category (Face or Scene) of the encoded image. We then assessed whether representation of category information was predictive of subsequent memory. Classification analyses indicated that temporal lobe structures contained information robustly diagnostic of visual category. Information in prefrontal cortex was less diagnostic of visual category, but was nonetheless associated with highly reliable classifier-based evidence for category representation. Critically, trials associated with greater classifier-based estimates of category representation in temporal and prefrontal regions were associated with a higher probability of subsequent remembering. Finally, consideration of trial-by-trial variance in classifier-based measures of category representation revealed positive correlations between prefrontal and temporal lobe representations, with the strength of these correlations varying as a function of the category of image being encoded. Together, these results indicate that multi-voxel representations of encoded information can provide unique insights into how visual experiences are transformed into episodic memories. PMID:21925190

  2. Analytical calculation of proton linear energy transfer in voxelized geometries including secondary protons

    NASA Astrophysics Data System (ADS)

    Sanchez-Parcerisa, D.; Cortés-Giraldo, M. A.; Dolney, D.; Kondrla, M.; Fager, M.; Carabe, A.

    2016-02-01

    In order to integrate radiobiological modelling with clinical treatment planning for proton radiotherapy, we extended our in-house treatment planning system FoCa with a 3D analytical algorithm to calculate linear energy transfer (LET) in voxelized patient geometries. Both active scanning and passive scattering delivery modalities are supported. The analytical calculation is much faster than the Monte-Carlo (MC) method and it can be implemented in the inverse treatment planning optimization suite, allowing us to create LET-based objectives in inverse planning. The LET was calculated by combining a 1D analytical approach including a novel correction for secondary protons with pencil-beam type LET-kernels. Then, these LET kernels were inserted into the proton-convolution-superposition algorithm in FoCa. The analytical LET distributions were benchmarked against MC simulations carried out in Geant4. A cohort of simple phantom and patient plans representing a wide variety of sites (prostate, lung, brain, head and neck) was selected. The calculation algorithm was able to reproduce the MC LET to within 6% (1 standard deviation) for low-LET areas (under 1.7 keV μm-1) and within 22% for the high-LET areas above that threshold. The dose and LET distributions can be further extended, using radiobiological models, to include radiobiological effectiveness (RBE) calculations in the treatment planning system. This implementation also allows for radiobiological optimization of treatments by including RBE-weighted dose constraints in the inverse treatment planning process.

  3. Loss aversion is associated with bilateral insula volume. A voxel based morphometry study.

    PubMed

    Markett, S; Heeren, G; Montag, C; Weber, B; Reuter, M

    2016-04-21

    Loss aversion is a decision bias, reflecting a greater sensitivity to losses than to gains in a decision situation. Recent neuroscientific research has shown that mesocorticolimbic structures like ventromedial prefrontal cortex and the ventral striatum constitute a bidirectional neural system that processes gains and losses and exhibits a neural basis of loss aversion. On a functional and structural level, the amygdala and insula also seem to play an important role in the processing of loss averse behavior. By applying voxel-based morphometry to structural brain images in N=41 healthy participants, the current study provides further evidence for the relationship of brain structure and loss aversion. The results show a negative correlation of gray matter volume in bilateral posterior insula as well as left medial frontal gyrus with individual loss aversion. Hence, higher loss aversion is associated with lower gray matter volume in these brain areas. Both structures have been discussed to play important roles in the brain's salience network, where the posterior insula is involved in interoception and the detection of salience. The medial frontal gyrus might impact decision making through its dense connections with the anterior cingulate cortex. A possible explanation for the present finding is that structural differences in these regions alter the processing of losses and salience, possibly biasing decision making towards avoidance of negative outcomes. PMID:27012426

  4. Parahippocampal gray matter alterations in Spinocerebellar Ataxia Type 2 identified by voxel based morphometry.

    PubMed

    Mercadillo, Roberto E; Galvez, Víctor; Díaz, Rosalinda; Hernández-Castillo, Carlos Roberto; Campos-Romo, Aurelio; Boll, Marie-Catherine; Pasaye, Erick H; Fernandez-Ruiz, Juan

    2014-12-15

    Spinocerebellar Ataxia Type 2 (SCA2) is a genetic disorder causing cerebellar degeneration that result in motor and cognitive alterations. Voxel-based morphometry (VBM) analyses have found neurodegenerative patterns associated to SCA2, but they show some discrepancies. Moreover, behavioral deficits related to non-cerebellar functions are scarcely discussed in those reports. In this work we use behavioral and cognitive tests and VBM to identify and confirm cognitive and gray matter alterations in SCA2 patients compared with control subjects. Also, we discuss the cerebellar and non-cerebellar functions affected by this disease. Our results confirmed gray matter reduction in the cerebellar vermis, pons, and insular, frontal, parietal and temporal cortices. However, our analysis also found unreported loss of gray matter in the parahippocampal gyrus bilaterally. Motor performance test ratings correlated with total gray and white matter reductions, but executive performance and clinical features such as CAG repetitions and disease progression did not show any correlation. This pattern of cerebellar and non-cerebellar morphological alterations associated with SCA2 has to be considered to fully understand the motor and non-motor deficits that include language production and comprehension and some social skill changes that occur in these patients. PMID:25263602

  5. Regional gray matter density associated with emotional intelligence: evidence from voxel-based morphometry.

    PubMed

    Takeuchi, Hikaru; Taki, Yasuyuki; Sassa, Yuko; Hashizume, Hiroshi; Sekiguchi, Atsushi; Fukushima, Ai; Kawashima, Ryuta

    2011-09-01

    Emotional Intelligence (EI) is the ability to monitor one's own and others' emotions and the ability to use the gathered information to guide one's thinking and action. EI is thought to be important for social life making it a popular subject of research. However, despite the existence of previous functional imaging studies on EI, the relationship between regional gray matter morphology and EI has never been investigated. We used voxel-based morphometry (VBM) and a questionnaire (Emotional Intelligence Scale) to measure EI to identify the gray matter correlates of each factor of individual EI (Intrapersonal factor, Interpersonal factor, Situation Management factor). We found significant negative relationships between the Intrapersonal factor and regional gray matter density (rGMD) (1-a) in an anatomical cluster that included the right anterior insula, (1-b) in the right cerebellum, (1-c) in an anatomical cluster that extends from the cuneus to the precuneus, (1-d) and in an anatomical cluster that extends from the medial prefrontal cortex to the left lateral fronto-polar cortex. We also found significant positive correlations between the Interpersonal factor and rGMD in the right superior temporal sulcus, and significant negative correlations between the Situation Management factor and rGMD in the ventromedial prefrontal cortex. These findings suggest that each factor of EI in healthy young people is related to the specific brain regions known to be involved in the networks of social cognition and self-related recognition, and in the somatic marker circuitry.

  6. A combined voxel and surface based method for topology correction of brain surfaces

    NASA Astrophysics Data System (ADS)

    Gris, Florence; Favreau, Jean-Marie; Acosta, Oscar; Barra, Vincent; Salvado, Olivier

    2010-03-01

    Brain surfaces provide a reliable representation for cortical mapping. The construction of correct surfaces from magnetic resonance images (MRI) segmentation is a challenging task, especially when genus zero surfaces are required for further processing such as parameterization, partial inflation and registration. The generation of such surfaces has been approached either by correcting a binary image as part of the segmentation pipeline or by modifying the mesh representing the surface. During this task, the preservation of the structure may be compromised because of the convoluted nature of the brain and noisy/imperfect segmentations. In this paper, we propose a combined, voxel and surfacebased, topology correction method which preserves the structure of the brain while yielding genus zero surfaces. The topology of the binary segmentation is first corrected using a set of topology preserving operators applied sequentially. This results in a white matter/gray matter binary set with correct sulci delineation, homotopic to a filled sphere. Using the corrected segmentation, a marching cubes mesh is then generated and the tunnels and handles resulting from the meshing are finally removed with an algorithm based on the detection of nonseparating loops. The approach was validated using 20 young individuals MRI from the OASIS database, acquired at two different time-points. Reproducibility and robustness were evaluated using global and local criteria such as surface area, curvature and point to point distance. Results demonstrated the method capability to produce genus zero meshes while preserving geometry, two fundamental properties for reliable and accurate cortical mapping and further clinical studies.

  7. MATSIM -The Development and Validation of a Numerical Voxel Model based on the MATROSHKA Phantom

    NASA Astrophysics Data System (ADS)

    Beck, Peter; Rollet, Sofia; Berger, Thomas; Bergmann, Robert; Hajek, Michael; Latocha, Marcin; Vana, Norbert; Zechner, Andrea; Reitz, Guenther

    The AIT Austrian Institute of Technology coordinates the project MATSIM (MATROSHKA Simulation) in collaboration with the Vienna University of Technology and the German Aerospace Center. The aim of the project is to develop a voxel-based model of the MATROSHKA anthro-pomorphic torso used at the International Space Station (ISS) as foundation to perform Monte Carlo high-energy particle transport simulations for different irradiation conditions. Funded by the Austrian Space Applications Programme (ASAP), MATSIM is a co-investigation with the European Space Agency (ESA) ELIPS project MATROSHKA, an international collaboration of more than 18 research institutes and space agencies from all over the world, under the science and project lead of the German Aerospace Center. The MATROSHKA facility is designed to determine the radiation exposure of an astronaut onboard ISS and especially during an ex-travehicular activity. The numerical model developed in the frame of MATSIM is validated by reference measurements. In this report we give on overview of the model development and compare photon and neutron irradiations of the detector-equipped phantom torso with Monte Carlo simulations using FLUKA. Exposure to Co-60 photons was realized in the standard ir-radiation laboratory at Seibersdorf, while investigations with neutrons were performed at the thermal column of the Vienna TRIGA Mark-II reactor. The phantom was loaded with passive thermoluminescence dosimeters. In addition, first results of the calculated dose distribution within the torso are presented for a simulated exposure in low-Earth orbit.

  8. Regional gray matter density associated with emotional conflict resolution: evidence from voxel-based morphometry.

    PubMed

    Deng, Z; Wei, D; Xue, S; Du, X; Hitchman, G; Qiu, J

    2014-09-01

    Successful emotion regulation is a fundamental prerequisite for well-being and dysregulation may lead to psychopathology. The ability to inhibit spontaneous emotions while behaving in accordance with desired goals is an important dimension of emotion regulation and can be measured using emotional conflict resolution tasks. Few studies have investigated the gray matter correlates underlying successful emotional conflict resolution at the whole-brain level. We had 190 adults complete an emotional conflict resolution task (face-word task) and examined the brain regions significantly correlated with successful emotional conflict resolution using voxel-based morphometry. We found successful emotional conflict resolution was associated with increased regional gray matter density in widely distributed brain regions. These regions included the dorsal anterior cingulate/dorsal medial prefrontal cortex, ventral medial prefrontal cortex, supplementary motor area, amygdala, ventral striatum, precuneus, posterior cingulate cortex, inferior parietal lobule, superior temporal gyrus and fusiform face area. Together, our results indicate that individual differences in emotional conflict resolution ability may be attributed to regional structural differences across widely distributed brain regions.

  9. Neural correlates of post-conventional moral reasoning: a voxel-based morphometry study.

    PubMed

    Prehn, Kristin; Korczykowski, Marc; Rao, Hengyi; Fang, Zhuo; Detre, John A; Robertson, Diana C

    2015-01-01

    Going back to Kohlberg, moral development research affirms that people progress through different stages of moral reasoning as cognitive abilities mature. Individuals at a lower level of moral reasoning judge moral issues mainly based on self-interest (personal interests schema) or based on adherence to laws and rules (maintaining norms schema), whereas individuals at the post-conventional level judge moral issues based on deeper principles and shared ideals. However, the extent to which moral development is reflected in structural brain architecture remains unknown. To investigate this question, we used voxel-based morphometry and examined the brain structure in a sample of 67 Master of Business Administration (MBA) students. Subjects completed the Defining Issues Test (DIT-2) which measures moral development in terms of cognitive schema preference. Results demonstrate that subjects at the post-conventional level of moral reasoning were characterized by increased gray matter volume in the ventromedial prefrontal cortex and subgenual anterior cingulate cortex, compared with subjects at a lower level of moral reasoning. Our findings support an important role for both cognitive and emotional processes in moral reasoning and provide first evidence for individual differences in brain structure according to the stages of moral reasoning first proposed by Kohlberg decades ago. PMID:26039547

  10. Voxel-based Morphometry of Brain MRI in Normal Aging and Alzheimer's Disease.

    PubMed

    Matsuda, Hiroshi

    2013-02-01

    Voxel-based morphometry (VBM) using structural brain MRI has been widely used for assessment of normal aging and Alzheimer's disease (AD). VBM of MRI data comprises segmentation into gray matter, white matter, and cerebrospinal fluid partitions, anatomical standardization of all the images to the same stereotactic space using linear affine transformation and further non-linear warping, smoothing, and finally performing a statistical analysis. Two techniques for VBM are commonly used, optimized VBM using statistical parametric mapping (SPM) 2 or SPM5 with non-linear warping based on discrete cosine transforms and SPM8 plus non-linear warping based on diffeomorphic anatomical registration using exponentiated Lie algebra (DARTEL). In normal aging, most cortical regions prominently in frontal and insular areas have been reported to show age-related gray matter atrophy. In contrast, specific structures such as amygdala, hippocampus, and thalamus have been reported to be preserved in normal aging. On the other hand, VBM studies have demonstrated progression of atrophy mapping upstream to Braak's stages of neurofibrillary tangle deposition in AD. The earliest atrophy takes place in medial temporal structures. Stand-alone VBM software using SPM8 plus DARTEL running on Windows has been newly developed as an adjunct to the clinical assessment of AD. This software provides a Z-score map as a consequence of comparison of a patient's MRI with a normal database. PMID:23423504

  11. Role of disgust proneness in Parkinson's disease: a voxel-based morphometry study.

    PubMed

    Ille, Rottraut; Wabnegger, Albert; Schwingenschuh, Petra; Katschnig-Winter, Petra; Kögl-Wallner, Mariella; Wenzel, Karoline; Schienle, Anne

    2015-04-01

    The knowledge about personality traits in Parkinson's disease (PD) is still limited. In particular, disgust proneness has not been investigated as well as its neuronal correlates. Although several morphometric studies demonstrated that PD is associated with gray matter volume (GMV) reduction in olfactory and gustatory regions involved in disgust processing, a possible correlation with disgust proneness has not been investigated. We conducted a voxel-based morphometry analysis to compare GMV between 16 cognitively normal male PD patients with mild to moderate symptoms and 24 matched control subjects. All participants had answered questionnaires for the assessment of disgust proneness, trait anger and trait anxiety. We correlated questionnaire scores with GMV in both groups. The clinical group reported selectively reduced disgust proneness toward olfactory stimuli associated with spoilage. Moreover, they showed GMV reduction in the central olfactory system [orbitofrontal cortex (OFC) and piriform cortex]. Disgust items referring to olfactory processing were positively correlated with OFC volume in PD patients. Our data suggest an association between PD-associated neurodegeneration and olfactory related facets of the personality trait disgust proneness.

  12. Voxel-based Morphometry of Brain MRI in Normal Aging and Alzheimer's Disease.

    PubMed

    Matsuda, Hiroshi

    2013-02-01

    Voxel-based morphometry (VBM) using structural brain MRI has been widely used for assessment of normal aging and Alzheimer's disease (AD). VBM of MRI data comprises segmentation into gray matter, white matter, and cerebrospinal fluid partitions, anatomical standardization of all the images to the same stereotactic space using linear affine transformation and further non-linear warping, smoothing, and finally performing a statistical analysis. Two techniques for VBM are commonly used, optimized VBM using statistical parametric mapping (SPM) 2 or SPM5 with non-linear warping based on discrete cosine transforms and SPM8 plus non-linear warping based on diffeomorphic anatomical registration using exponentiated Lie algebra (DARTEL). In normal aging, most cortical regions prominently in frontal and insular areas have been reported to show age-related gray matter atrophy. In contrast, specific structures such as amygdala, hippocampus, and thalamus have been reported to be preserved in normal aging. On the other hand, VBM studies have demonstrated progression of atrophy mapping upstream to Braak's stages of neurofibrillary tangle deposition in AD. The earliest atrophy takes place in medial temporal structures. Stand-alone VBM software using SPM8 plus DARTEL running on Windows has been newly developed as an adjunct to the clinical assessment of AD. This software provides a Z-score map as a consequence of comparison of a patient's MRI with a normal database.

  13. Neurostructural correlates of two subtypes of specific phobia: a voxel-based morphometry study.

    PubMed

    Hilbert, Kevin; Evens, Ricarda; Maslowski, Nina Isabel; Wittchen, Hans-Ulrich; Lueken, Ulrike

    2015-02-28

    The animal and blood-injection-injury (BII) subtypes of specific phobia are both characterized by subjective fear but distinct autonomic reactions to threat. Previous functional neuroimaging studies have related these characteristic responses to shared and non-shared neural underpinnings. However, no comparative structural data are available. This study aims to fill this gap by comparing the two subtypes and also comparing them with a non-phobic control group. Gray and white matter data of 33 snake phobia subjects (SP), 26 dental phobia subjects (DP), and 37 healthy control (HC) subjects were analyzed with voxel-based morphometry. Especially DP differed from HC and SP by showing significantly increased grey matter volumes in widespread areas including the right subgenual anterior cingulate gyrus, left insula, left orbitofrontal and left prefrontal (PFC) cortices. In addition, white matter volume was significantly increased in the left PFC in DP compared with SP. These results are in line with functional changes observed in dental phobia and point toward those brain circuits associated with emotional processing and regulation. Future studies should aim to further delineate functional and structural connectivity alterations in specific phobia.

  14. The Neuroanatomical Basis of Panic Disorder and Social Phobia in Schizophrenia: A Voxel Based Morphometric Study

    PubMed Central

    Picado, Marisol; Carmona, Susanna; Hoekzema, Elseline; Pailhez, Guillem; Bergé, Daniel; Mané, Anna; Fauquet, Jordi; Hilferty, Joseph; Moreno, Ana; Cortizo, Romina; Vilarroya, Oscar; Bulbena, Antoni

    2015-01-01

    Objective It is known that there is a high prevalence of certain anxiety disorders among schizophrenic patients, especially panic disorder and social phobia. However, the neural underpinnings of the comorbidity of such anxiety disorders and schizophrenia remain unclear. Our study aims to determine the neuroanatomical basis of the co-occurrence of schizophrenia with panic disorder and social phobia. Methods Voxel-based morphometry was used in order to examine brain structure and to measure between-group differences, comparing magnetic resonance images of 20 anxious patients, 20 schizophrenic patients, 20 schizophrenic patients with comorbid anxiety, and 20 healthy control subjects. Results Compared to the schizophrenic patients, we observed smaller grey-matter volume (GMV) decreases in the dorsolateral prefrontal cortex and precentral gyrus in the schizophrenic-anxiety group. Additionally, the schizophrenic group showed significantly reduced GMV in the dorsolateral prefrontal cortex, precentral gyrus, orbitofrontal cortex, temporal gyrus and angular/inferior parietal gyrus when compared to the control group. Conclusions Our findings suggest that the comorbidity of schizophrenia with panic disorder and social phobia might be characterized by specific neuroanatomical and clinical alterations that may be related to maladaptive emotion regulation related to anxiety. Even thought our findings need to be replicated, our study suggests that the identification of neural abnormalities involved in anxiety, schizophrenia and schizophrenia-anxiety may lead to an improved diagnosis and management of these conditions. PMID:25774979

  15. Parallel Solutions for Voxel-Based Simulations of Reaction-Diffusion Systems

    PubMed Central

    D'Agostino, Daniele; Pasquale, Giulia; Clematis, Andrea; Maj, Carlo; Mosca, Ettore; Milanesi, Luciano; Merelli, Ivan

    2014-01-01

    There is an increasing awareness of the pivotal role of noise in biochemical processes and of the effect of molecular crowding on the dynamics of biochemical systems. This necessity has given rise to a strong need for suitable and sophisticated algorithms for the simulation of biological phenomena taking into account both spatial effects and noise. However, the high computational effort characterizing simulation approaches, coupled with the necessity to simulate the models several times to achieve statistically relevant information on the model behaviours, makes such kind of algorithms very time-consuming for studying real systems. So far, different parallelization approaches have been deployed to reduce the computational time required to simulate the temporal dynamics of biochemical systems using stochastic algorithms. In this work we discuss these aspects for the spatial TAU-leaping in crowded compartments (STAUCC) simulator, a voxel-based method for the stochastic simulation of reaction-diffusion processes which relies on the Sτ-DPP algorithm. In particular we present how the characteristics of the algorithm can be exploited for an effective parallelization on the present heterogeneous HPC architectures. PMID:25045716

  16. Gray matter correlates of creative potential: A latent variable voxel-based morphometry study

    PubMed Central

    Jauk, Emanuel; Neubauer, Aljoscha C.; Dunst, Beate; Fink, Andreas; Benedek, Mathias

    2015-01-01

    There is increasing research interest in the structural and functional brain correlates underlying creative potential. Recent investigations found that interindividual differences in creative potential relate to volumetric differences in brain regions belonging to the default mode network, such as the precuneus. Yet, the complex interplay between creative potential, intelligence, and personality traits and their respective neural bases is still under debate. We investigated regional gray matter volume (rGMV) differences that can be associated with creative potential in a heterogeneous sample of N = 135 individuals using voxel-based morphometry (VBM). By means of latent variable modeling and consideration of recent psychometric advancements in creativity research, we sought to disentangle the effects of ideational originality and fluency as two independent indicators of creative potential. Intelligence and openness to experience were considered as common covariates of creative potential. The results confirmed and extended previous research: rGMV in the precuneus was associated with ideational originality, but not with ideational fluency. In addition, we found ideational originality to be correlated with rGMV in the caudate nucleus. The results indicate that the ability to produce original ideas is tied to default-mode as well as dopaminergic structures. These structural brain correlates of ideational originality were apparent throughout the whole range of intellectual ability and thus not moderated by intelligence. In contrast, structural correlates of ideational fluency, a quantitative marker of creative potential, were observed only in lower intelligent individuals in the cuneus/lingual gyrus. PMID:25676914

  17. Analytical calculation of proton linear energy transfer in voxelized geometries including secondary protons.

    PubMed

    Sanchez-Parcerisa, D; Cortés-Giraldo, M A; Dolney, D; Kondrla, M; Fager, M; Carabe, A

    2016-02-21

    In order to integrate radiobiological modelling with clinical treatment planning for proton radiotherapy, we extended our in-house treatment planning system FoCa with a 3D analytical algorithm to calculate linear energy transfer (LET) in voxelized patient geometries. Both active scanning and passive scattering delivery modalities are supported. The analytical calculation is much faster than the Monte-Carlo (MC) method and it can be implemented in the inverse treatment planning optimization suite, allowing us to create LET-based objectives in inverse planning. The LET was calculated by combining a 1D analytical approach including a novel correction for secondary protons with pencil-beam type LET-kernels. Then, these LET kernels were inserted into the proton-convolution-superposition algorithm in FoCa. The analytical LET distributions were benchmarked against MC simulations carried out in Geant4. A cohort of simple phantom and patient plans representing a wide variety of sites (prostate, lung, brain, head and neck) was selected. The calculation algorithm was able to reproduce the MC LET to within 6% (1 standard deviation) for low-LET areas (under 1.7 keV μm(-1)) and within 22% for the high-LET areas above that threshold. The dose and LET distributions can be further extended, using radiobiological models, to include radiobiological effectiveness (RBE) calculations in the treatment planning system. This implementation also allows for radiobiological optimization of treatments by including RBE-weighted dose constraints in the inverse treatment planning process.

  18. Global and regional gray matter reductions in ADHD: a voxel-based morphometric study.

    PubMed

    Carmona, S; Vilarroya, O; Bielsa, A; Trèmols, V; Soliva, J C; Rovira, M; Tomàs, J; Raheb, C; Gispert, J D; Batlle, S; Bulbena, A

    2005-12-01

    Attention deficit hyperactivity disorder (ADHD) is a developmental disorder characterized by inattentiveness, motor hyperactivity and impulsivity. According to neuroimaging data, the neural substrate underlying ADHD seems to involve fronto-striatal circuits and the cerebellum. However, there are important discrepancies between various studies, probably due to the use of different techniques. The aim of this study is to examine cerebral gray (GM) and white (WM) matter abnormalities in a group of ADHD children using a voxel-based morphometry protocol. The sample consisted of 25 children/adolescents with DSM-IV TR diagnosis of ADHD (medicated, aged 6-16 years) who were compared with 25 healthy volunteer children/adolescents. ADHD brains on an average showed a global volume decrease of 5.4% as compared to controls. Additionally, there were regionally specific effects in the left fronto-parietal areas (left motor, premotor and somatosensory cortex), left cingulate cortex (anterior/middle/posterior cingulate), parietal lobe (precuneus bilaterally), temporal cortices (right middle temporal gyrus, left parahippocampal gyrus), and the cerebellum (bilateral posterior). There were no differences in WM volume between ADHD children and control subjects. The results are consistent with previous studies that used different techniques, and may represent a possible neural basis for some of the motor and attentional deficits commonly found in ADHD.

  19. Neural correlates of post-conventional moral reasoning: a voxel-based morphometry study.

    PubMed

    Prehn, Kristin; Korczykowski, Marc; Rao, Hengyi; Fang, Zhuo; Detre, John A; Robertson, Diana C

    2015-01-01

    Going back to Kohlberg, moral development research affirms that people progress through different stages of moral reasoning as cognitive abilities mature. Individuals at a lower level of moral reasoning judge moral issues mainly based on self-interest (personal interests schema) or based on adherence to laws and rules (maintaining norms schema), whereas individuals at the post-conventional level judge moral issues based on deeper principles and shared ideals. However, the extent to which moral development is reflected in structural brain architecture remains unknown. To investigate this question, we used voxel-based morphometry and examined the brain structure in a sample of 67 Master of Business Administration (MBA) students. Subjects completed the Defining Issues Test (DIT-2) which measures moral development in terms of cognitive schema preference. Results demonstrate that subjects at the post-conventional level of moral reasoning were characterized by increased gray matter volume in the ventromedial prefrontal cortex and subgenual anterior cingulate cortex, compared with subjects at a lower level of moral reasoning. Our findings support an important role for both cognitive and emotional processes in moral reasoning and provide first evidence for individual differences in brain structure according to the stages of moral reasoning first proposed by Kohlberg decades ago.

  20. Voxel-based morphometry to detect brain atrophy in progressive mild cognitive impairment.

    PubMed

    Hämäläinen, Anne; Tervo, Susanna; Grau-Olivares, Marta; Niskanen, Eini; Pennanen, Corina; Huuskonen, Jari; Kivipelto, Miia; Hänninen, Tuomo; Tapiola, Mia; Vanhanen, Matti; Hallikainen, Merja; Helkala, Eeva-Liisa; Nissinen, Aulikki; Vanninen, Ritva; Soininen, Hilkka

    2007-10-01

    Recent research has shown an increased rate of conversion to dementia in subjects with mild cognitive impairment (MCI) compared to controls. However, there are no specific methods to predict who will later develop dementia. In the present study, 22 controls and 56 MCI subjects were followed on average for 37 months (max. 60 months) and studied with magnetic resonance imaging (MRI) at baseline to assess changes in brain structure associated to later progression to dementia. Voxel-based morphometry (VBM) was used to investigate gray matter atrophy. During the follow-up, 13 subjects progressed to dementia. At baseline, no differences were detected in age or education between the control and MCI subjects, but they differed by several neuropsychological tests. The stable and progressive MCI subjects differed only by CDR sum of boxes scores and delayed verbal recall, which were also significant predictors of conversion to dementia. At the baseline imaging, the MCI subjects showed reduced gray matter density in medial temporal, temporoparietal as well as in frontal cortical areas compared to controls. Interestingly, the progressive MCI subjects showed atrophy in the left temporoparietal and posterior cingulate cortices and in the precuneus bilaterally, and a trend for hippocampal atrophy when compared to the stable MCI subjects. We conclude that widespread cortical atrophy is present already two and a half years before a clinical diagnosis of dementia can be set.

  1. Investigating the brain basis of facial expression perception using multi-voxel pattern analysis.

    PubMed

    Wegrzyn, Martin; Riehle, Marcel; Labudda, Kirsten; Woermann, Friedrich; Baumgartner, Florian; Pollmann, Stefan; Bien, Christian G; Kissler, Johanna

    2015-08-01

    Humans can readily decode emotion expressions from faces and perceive them in a categorical manner. The model by Haxby and colleagues proposes a number of different brain regions with each taking over specific roles in face processing. One key question is how these regions directly compare to one another in successfully discriminating between various emotional facial expressions. To address this issue, we compared the predictive accuracy of all key regions from the Haxby model using multi-voxel pattern analysis (MVPA) of functional magnetic resonance imaging (fMRI) data. Regions of interest were extracted using independent meta-analytical data. Participants viewed four classes of facial expressions (happy, angry, fearful and neutral) in an event-related fMRI design, while performing an orthogonal gender recognition task. Activity in all regions allowed for robust above-chance predictions. When directly comparing the regions to one another, fusiform gyrus and superior temporal sulcus (STS) showed highest accuracies. These results underscore the role of the fusiform gyrus as a key region in perception of facial expressions, alongside STS. The study suggests the need for further specification of the relative role of the various brain areas involved in the perception of facial expression. Face processing appears to rely on more interactive and functionally overlapping neural mechanisms than previously conceptualised. PMID:26046623

  2. Multi-Voxel Decoding and the Topography of Maintained Information During Visual Working Memory.

    PubMed

    Lee, Sue-Hyun; Baker, Chris I

    2016-01-01

    The ability to maintain representations in the absence of external sensory stimulation, such as in working memory, is critical for guiding human behavior. Human functional brain imaging studies suggest that visual working memory can recruit a network of brain regions from visual to parietal to prefrontal cortex. In this review, we focus on the maintenance of representations during visual working memory and discuss factors determining the topography of those representations. In particular, we review recent studies employing multi-voxel pattern analysis (MVPA) that demonstrate decoding of the maintained content in visual cortex, providing support for a "sensory recruitment" model of visual working memory. However, there is some evidence that maintained content can also be decoded in areas outside of visual cortex, including parietal and frontal cortex. We suggest that the ability to maintain representations during working memory is a general property of cortex, not restricted to specific areas, and argue that it is important to consider the nature of the information that must be maintained. Such information-content is critically determined by the task and the recruitment of specific regions during visual working memory will be both task- and stimulus-dependent. Thus, the common finding of maintained information in visual, but not parietal or prefrontal, cortex may be more of a reflection of the need to maintain specific types of visual information and not of a privileged role of visual cortex in maintenance.

  3. Parahippocampal gray matter alterations in Spinocerebellar Ataxia Type 2 identified by voxel based morphometry.

    PubMed

    Mercadillo, Roberto E; Galvez, Víctor; Díaz, Rosalinda; Hernández-Castillo, Carlos Roberto; Campos-Romo, Aurelio; Boll, Marie-Catherine; Pasaye, Erick H; Fernandez-Ruiz, Juan

    2014-12-15

    Spinocerebellar Ataxia Type 2 (SCA2) is a genetic disorder causing cerebellar degeneration that result in motor and cognitive alterations. Voxel-based morphometry (VBM) analyses have found neurodegenerative patterns associated to SCA2, but they show some discrepancies. Moreover, behavioral deficits related to non-cerebellar functions are scarcely discussed in those reports. In this work we use behavioral and cognitive tests and VBM to identify and confirm cognitive and gray matter alterations in SCA2 patients compared with control subjects. Also, we discuss the cerebellar and non-cerebellar functions affected by this disease. Our results confirmed gray matter reduction in the cerebellar vermis, pons, and insular, frontal, parietal and temporal cortices. However, our analysis also found unreported loss of gray matter in the parahippocampal gyrus bilaterally. Motor performance test ratings correlated with total gray and white matter reductions, but executive performance and clinical features such as CAG repetitions and disease progression did not show any correlation. This pattern of cerebellar and non-cerebellar morphological alterations associated with SCA2 has to be considered to fully understand the motor and non-motor deficits that include language production and comprehension and some social skill changes that occur in these patients.

  4. Multi-Voxel Decoding and the Topography of Maintained Information During Visual Working Memory

    PubMed Central

    Lee, Sue-Hyun; Baker, Chris I.

    2016-01-01

    The ability to maintain representations in the absence of external sensory stimulation, such as in working memory, is critical for guiding human behavior. Human functional brain imaging studies suggest that visual working memory can recruit a network of brain regions from visual to parietal to prefrontal cortex. In this review, we focus on the maintenance of representations during visual working memory and discuss factors determining the topography of those representations. In particular, we review recent studies employing multi-voxel pattern analysis (MVPA) that demonstrate decoding of the maintained content in visual cortex, providing support for a “sensory recruitment” model of visual working memory. However, there is some evidence that maintained content can also be decoded in areas outside of visual cortex, including parietal and frontal cortex. We suggest that the ability to maintain representations during working memory is a general property of cortex, not restricted to specific areas, and argue that it is important to consider the nature of the information that must be maintained. Such information-content is critically determined by the task and the recruitment of specific regions during visual working memory will be both task- and stimulus-dependent. Thus, the common finding of maintained information in visual, but not parietal or prefrontal, cortex may be more of a reflection of the need to maintain specific types of visual information and not of a privileged role of visual cortex in maintenance. PMID:26912997

  5. Effect of Experimental Thyrotoxicosis on Brain Gray Matter: A Voxel-Based Morphometry Study

    PubMed Central

    Göbel, Anna; Heldmann, Marcus; Göttlich, Martin; Dirk, Anna-Luise; Brabant, Georg; Münte, Thomas F.

    2015-01-01

    Background Hyper-as well hypothyroidism have an effect on behavior and brain function. Moreover, during development thyroid hormones influence brain structure. Objectives This study aimed to demonstrate an effect of experimentally induced hyperthyroidism on brain gray matter in healthy adult humans. Methods High-resolution 3D T1-weighted images were acquired in 29 healthy young subjects prior to as well as after receiving 250 µg of T4 per day for 8 weeks. Voxel-based morphometry analysis was performed using Statistical Parametric Mapping 8 (SPM8). Results Laboratory testing confirmed the induction of hyperthyroidism. In the hyperthyroid condition, gray matter volumes were increased in the right posterior cerebellum (lobule VI) and decreased in the bilateral visual cortex and anterior cerebellum (lobules I-IV) compared to the euthyroid condition. Conclusions Our study provides evidence that short periods of hyperthyroidism induce distinct alterations in brain structures of cerebellar regions that have been associated with sensorimotor functions as well as working memory in the literature. PMID:26601082

  6. Gray Matter Volume Decreases in Elderly Patients with Schizophrenia: A Voxel-based Morphometry Study

    PubMed Central

    Schuster, Caroline; Schuller, Anne Marie; Paulos, Carlos; Namer, Izzie; Pull, Charles; Danion, Jean Marie; Foucher, Jack René

    2012-01-01

    Background: Aged patients (>50 years old) with residual schizophrenic symptoms differ from young patients. They represent a subpopulation with a more unfavorable Kraepelinian course and have an increased risk (up to 30%) for dementia of unknown origin. However, our current understanding of age-related brain changes in schizophrenia is derived from studies that included less than 17% of patients who were older than 50 years of age. This study investigated the anatomical distribution of gray matter (GM) brain deficits in aged patients with ongoing schizophrenia. Methods: Voxel-based morphometry was applied to 3D-T1 magnetic resonance images obtained from 27 aged patients with schizophrenia (mean age of 60 years) and 40 age-matched normal controls. Results: Older patients with schizophrenia showed a bilateral reduction of GM volume in the thalamus, the prefrontal cortex, and in a large posterior region centered on the occipito-temporo-parietal junction. Only the latter region showed accelerated GM volume loss with increasing age. None of these results could be accounted for by institutionalization, antipsychotic medication, or cognitive scores. Conclusions: This study replicated most common findings in patients with schizophrenia with regard to thalamic and frontal GM deficits. However, it uncovered an unexpected large region of GM atrophy in the posterior tertiary cortices. The latter observation may be specific to this aged and chronically symptomatic subpopulation, as atrophy in this region is rarely reported in younger patients and is accelerated with age. PMID:21205677

  7. A voxel-based lesion study on facial emotion recognition after penetrating brain injury

    PubMed Central

    Dal Monte, Olga; Solomon, Jeffrey M.; Schintu, Selene; Knutson, Kristine M.; Strenziok, Maren; Pardini, Matteo; Leopold, Anne; Raymont, Vanessa; Grafman, Jordan

    2013-01-01

    The ability to read emotions in the face of another person is an important social skill that can be impaired in subjects with traumatic brain injury (TBI). To determine the brain regions that modulate facial emotion recognition, we conducted a whole-brain analysis using a well-validated facial emotion recognition task and voxel-based lesion symptom mapping (VLSM) in a large sample of patients with focal penetrating TBIs (pTBIs). Our results revealed that individuals with pTBI performed significantly worse than normal controls in recognizing unpleasant emotions. VLSM mapping results showed that impairment in facial emotion recognition was due to damage in a bilateral fronto-temporo-limbic network, including medial prefrontal cortex (PFC), anterior cingulate cortex, left insula and temporal areas. Beside those common areas, damage to the bilateral and anterior regions of PFC led to impairment in recognizing unpleasant emotions, whereas bilateral posterior PFC and left temporal areas led to impairment in recognizing pleasant emotions. Our findings add empirical evidence that the ability to read pleasant and unpleasant emotions in other people's faces is a complex process involving not only a common network that includes bilateral fronto-temporo-limbic lobes, but also other regions depending on emotional valence. PMID:22496440

  8. Cancer risk estimation in Digital Breast Tomosynthesis using GEANT4 Monte Carlo simulations and voxel phantoms.

    PubMed

    Ferreira, P; Baptista, M; Di Maria, S; Vaz, P

    2016-05-01

    The aim of this work was to estimate the risk of radiation induced cancer following the Portuguese breast screening recommendations for Digital Mammography (DM) when applied to Digital Breast Tomosynthesis (DBT) and to evaluate how the risk to induce cancer could influence the energy used in breast diagnostic exams. The organ doses were calculated by Monte Carlo simulations using a female voxel phantom and considering the acquisition of 25 projection images. Single organ cancer incidence risks were calculated in order to assess the total effective radiation induced cancer risk. The screening strategy techniques considered were: DBT in Cranio-Caudal (CC) view and two-view DM (CC and Mediolateral Oblique (MLO)). The risk of cancer incidence following the Portuguese screening guidelines (screening every two years in the age range of 50-80years) was calculated by assuming a single CC DBT acquisition view as standalone screening strategy and compared with two-view DM. The difference in the total effective risk between DBT and DM is quite low. Nevertheless in DBT an increase of risk for the lung is observed with respect to DM. The lung is also the organ that is mainly affected when non-optimal beam energy (in terms of image quality and absorbed dose) is used instead of an optimal one. The use of non-optimal energies could increase the risk of lung cancer incidence by a factor of about 2. PMID:27133140

  9. Regional gray matter density associated with emotional intelligence: evidence from voxel-based morphometry.

    PubMed

    Takeuchi, Hikaru; Taki, Yasuyuki; Sassa, Yuko; Hashizume, Hiroshi; Sekiguchi, Atsushi; Fukushima, Ai; Kawashima, Ryuta

    2011-09-01

    Emotional Intelligence (EI) is the ability to monitor one's own and others' emotions and the ability to use the gathered information to guide one's thinking and action. EI is thought to be important for social life making it a popular subject of research. However, despite the existence of previous functional imaging studies on EI, the relationship between regional gray matter morphology and EI has never been investigated. We used voxel-based morphometry (VBM) and a questionnaire (Emotional Intelligence Scale) to measure EI to identify the gray matter correlates of each factor of individual EI (Intrapersonal factor, Interpersonal factor, Situation Management factor). We found significant negative relationships between the Intrapersonal factor and regional gray matter density (rGMD) (1-a) in an anatomical cluster that included the right anterior insula, (1-b) in the right cerebellum, (1-c) in an anatomical cluster that extends from the cuneus to the precuneus, (1-d) and in an anatomical cluster that extends from the medial prefrontal cortex to the left lateral fronto-polar cortex. We also found significant positive correlations between the Interpersonal factor and rGMD in the right superior temporal sulcus, and significant negative correlations between the Situation Management factor and rGMD in the ventromedial prefrontal cortex. These findings suggest that each factor of EI in healthy young people is related to the specific brain regions known to be involved in the networks of social cognition and self-related recognition, and in the somatic marker circuitry. PMID:20740644

  10. Anatomical correlates of quality of life: evidence from voxel-based morphometry.

    PubMed

    Takeuchi, Hikaru; Taki, Yasuyuki; Nouchi, Rui; Hashizume, Hiroshi; Sassa, Yuko; Sekiguchi, Atsushi; Kotozaki, Yuka; Nakagawa, Seishu; Nagase, Tomomi; Miyauchi, Carlos Makoto; Kawashima, Ryuta

    2014-05-01

    Quality of life (QOL) has been defined in many ways, and these definitions usually emphasize happiness and satisfaction with life. Health-related problems are known to cause lower QOL. However, the neural mechanisms underlying individual differences in QOL measured by questionnaire (QOLMQ) in young healthy subjects are unknown. QOL is essential to our well-being, and investigation of the neural mechanisms underlying QOL in uncompromised subjects is obviously of great scientific and social interest. We used voxel-based morphometry to investigate the association between regional gray matter volume (rGMV) and QOLMQ across the brain in healthy young adults (age, 21.4 ± 1.8 years) men (n = 88) and women (n = 68) in humans. We found significant negative relationships between QOLMQ and rGMV in a region in the left rostrolateral prefrontal cortex and regions in the dorsal part of the anterior cingulate gyrus and contingent cingulate regions. These findings show that structural variations in regions associated with processing of negative emotions such as fear and anger as well as those associated with evaluation of internally generated information are associated with QOLMQ. These findings suggest that these processes might be related to QOLMQ in healthy young adults. PMID:23671021

  11. Differential effects of surface area, gyrification and cortical thickness on voxel based morphometric deficits in schizophrenia.

    PubMed

    Palaniyappan, Lena; Liddle, Peter F

    2012-03-01

    Voxel Based Morphometry (VBM) and Surface Based Morphometry (SBM) are the two most commonly used methods to study the structure of gray matter in various disease states such as schizophrenia. Though overlapping changes have been observed in same datasets using the two procedures, the proportional contribution of the anatomical properties of the cortical mantle such as thickness, surface area and gyrification to the group differences in gray matter volume (GMV) observed using VBM is unknown. In the present study, we investigate the relationship between the GMV and the anatomical properties of the cortical mantle in regions showing significant VBM changes in schizophrenia using a sample of 57 patients and 41 healthy controls. To this end, we obtained significant clusters showing VBM changes in schizophrenia and studied the contribution of the three anatomical properties derived from SBM to the observed group differences in the GMV using a multiple mediation analysis. Our results suggest that while SBM measures make distinct but regionally variable contribution to the VBM differences, a large proportion of the group difference observed using VBM is not explained by the individual surface anatomical properties. While VBM may be more sensitive in identifying the regions with gray matter abnormalities, studies investigating the pathophysiology of illnesses such as schizophrenia are better informed when both SBM and VBM analyses are performed concurrently. PMID:22227049

  12. A Voxel Based Morphometry Study of Brain Gray Matter Volumes in Juvenile Obsessive Compulsive Disorder

    PubMed Central

    Jayarajan, Rajan Nishanth; Agarwal, Sri Mahavir; Viswanath, Biju; Kalmady, Sunil V.; Venkatasubramanian, Ganesan; Srinath, Shoba; Chandrashekar, C.R.; Janardhan Reddy, Y.C.

    2015-01-01

    Introduction: Adult patients with Obsessive Compulsive Disorder (OCD) have been shown to have gray matter (GM) volume differences from healthy controls in multiple regions – the orbitofrontal cortex (OFC), anterior cingulate cortex (ACC), medial frontal gyri (MFG), striatum, thalamus, and superior parietal lobule. However, there is paucity of data with regard to juvenile OCD. Hence, we examined GM volume differences between juvenile OCD patients and matched healthy controls using voxel based morphometry (VBM) with the above apriori regions of interest. Method: Fifteen right handed juvenile patients with OCD and age- sex- handedness- matched healthy controls were recruited after administering the Mini International Neuropsychiatric Interview-KID and the Children’s Yale-Brown Obsessive Compulsive Scale, and scanned using a 3 Tesla magnetic resonance imaging scanner. VBM methodology was followed. Results: In comparison with healthy controls, patients had significantly smaller GM volumes in left ACC. YBOCS total score (current) showed significant negative correlation with GM volumes in bilateral OFC, and left superior parietal lobule. Conclusion: These findings while reiterating the important role of the orbito-fronto-striatal circuitry, also implicate in the parietal lobe – especially the superior parietal lobule as an important structure involved in the pathogenesis of OCD. PMID:26379719

  13. The relationship between inflammatory markers and voxel-based gray matter volumes in nondemented older adults.

    PubMed

    Zhang, Haobo; Sachdev, Perminder S; Wen, Wei; Crawford, John D; Brodaty, Henry; Baune, Bernard T; Kochan, Nicole A; Slavin, Melissa J; Reppermund, Simone; Kang, Kristan; Trollor, Julian N

    2016-01-01

    Ageing is characterized by chronically elevated inflammatory markers (IMs). Peripheral IM levels have been found in negative correlations with brain structural measures including global and lobar volumes and the hippocampus. This study investigated the relationship between 10 peripheral IMs and voxel-based gray matter (GM) volumes in nondemented older adults (n = 463). Two proinflammatory cytokines (tumor necrosis factor-α [TNF-α] and interleukin-1β) and 2 vascular IMs (vascular cellular adhesion molecule-1 and plasminogen activator inhibitor-1) were negatively correlated with regional GM volumes. TNF-α and interleukin-1β were both significantly correlated with GM volumes in the left occipitotemporal area, left superior occipital gyrus, and left inferior parietal lobule; TNF-α was also significantly correlated with the bilateral medial prefrontal cortices and approached significance for the correlations with the bilateral hippocampi. Significant GM correlations with vascular cellular adhesion molecule-1 were located in the bilateral anterior cingulate cortices, and with plasminogen activator inhibitor-1 in the cerebellum and right hippocampus. The neuroanatomical correlation patterns of 2 proinflammatory cytokines and 2 vascular IMs might be reflective of the effects of neurodegenerative and vascular pathological processes in the ageing brain.

  14. The correlation between gray matter volume and perceived social support: a voxel-based morphometry study.

    PubMed

    Che, XianWei; Wei, DongTao; Li, WenFu; Li, HaiJiang; Qiao, Lei; Qiu, Jiang; Zhang, QingLin; Liu, YiJun

    2014-01-01

    Social support refers to interpersonal exchanges that include the combinations of aid, affirmation and affection. Perceived social support is a kind of subjective judgment of one's availability of social support. In spite of the importance of perceived social support to health, however, its neural substrate remains unknown. To address this question, voxel-based morphometry was employed to investigate the neural bases of individual differences in responses to the Perceived Social Support Scale (PSSS) in healthy volunteers (144 men and 203 women; mean age = 19.9; SD = 1.33, age range : 17-27). As a result, multiple regression analysis revealed that the PSSS scores were significantly and positively correlated with gray matter volume in a cluster that mainly included areas in posterior parts of posterior cingulate cortex, bilateral lingual cortex, left occipital lobe and cuneus. Highly-supported individuals had larger gray matter volume in these brain regions, implying a relatively high level of ability to engage in self-referential processes and social cognition. Our results provide a biological basis for exploring perceived social support particularly in relationship to various health parameters and outcomes.

  15. Grey matter alterations in patients with depersonalization disorder: a voxel-based morphometry study

    PubMed Central

    Daniels, Judith K.; Gaebler, Michael; Lamke, Jan-Peter; Walter, Henrik

    2015-01-01

    Background To our knowledge, no whole brain investigation of morphological aberrations in dissociative disorder is available to date. Previous region-of-interest studies focused exclusively on amygdalar, hippocampal and parahippocampal grey matter volumes and did not include patients with depersonalization disorder (DPD). We therefore carried out an explorative whole brain study on structural brain aberrations in patients with DPD. Methods We acquired whole brain, structural MRI data for patients with DPD and healthy controls. Voxel-based morphometry was carried out to test for group differences, and correlations with symptom severity scores were computed for grey matter volume. Results Our study included 25 patients with DPD and 23 controls. Patients exhibited volume reductions in the right caudate, right thalamus and right cuneus as well as volume increases in the left dorsomedial prefrontal cortex and right somatosensory region that are not a direct function of anxiety or depression symptoms. Limitations To ensure ecological validity, we included patients with comorbid disorders and patients taking psychotropic medication. Conclusion The results of this first whole brain investigation of grey matter volume in patients with a dissociative disorder indentified structural alterations in regions subserving the emergence of conscious perception. It remains unknown if these alterations are best understood as risk factors for or results of the disorder. PMID:25285875

  16. Social cognition and frontal lobe pathology in schizophrenia: a voxel-based morphometric study.

    PubMed

    Yamada, Makiko; Hirao, Kazuyuki; Namiki, Chihiro; Hanakawa, Takashi; Fukuyama, Hidenao; Hayashi, Takuji; Murai, Toshiya

    2007-03-01

    Impaired social cognition in schizophrenia is considered as the core contributor in the poor psychosocial functioning of schizophrenic patients. In this study, in order to better understand the neurobiological processes underlying social dysfunction in schizophrenia, we investigated regional structural brain abnormalities and emotion-attribution abilities in these patients. Twenty schizophrenic patients and 20 group-matched healthy comparison participants underwent magnetic resonance imaging (MRI) and were examined for emotion-attribution abilities by using the Perception of Affect Task (PAT). Voxel-based morphometry (VBM) was applied to investigate regional brain structural alterations. Relative to the healthy participants, the schizophrenic patients exhibited reduced gray matter concentrations in the left superior temporal gyrus, the medial prefrontal cortex (MPFC), right anterior cingulate gyrus, bilateral ventrolateral prefrontal cortex, and right insula. The schizophrenic patients performed poorly on emotion-attribution tasks. Importantly, poor performance on emotion attribution to protagonists in social situations was found to be associated with reductions in gray matter in the MPFC of the patient group. This preliminary result suggests that in schizophrenia, difficulties in understanding the emotional experiences of others are possible manifestations of structural abnormalities in the MPFC. This study provides the neurobiological correlates of social dysfunction in schizophrenia and links structural abnormalities with impaired social cognitive abilities. PMID:17240165

  17. Whole-brain voxel-based morphometry study of children and adolescents with Down syndrome

    PubMed Central

    Carducci, Filippo; Onorati, Paolo; Condoluci, Claudia; Di Gennaro, Giancarlo; Quarato, Pier Paolo; Pierallini, Alberto; Sarà, Marco; Miano, Silvia; Cornia, Riccardo; Albertini, Giorgio

    2013-01-01

    Summary In order to investigate alterations in brain morphology and a possible temporal pattern of neuroanatomical abnormalities in the gray matter (GM), white matter (WM) and cerebrospinal fluid (CSF) of young patients with Down syndrome (DS), high-resolution magnetic resonance imaging (MRI) voxel-based morphometry (VBM) was performed on 21 children and adolescents with this chromosomal aberration and 27 age-matched participants as controls. In comparison with control subjects, children and adolescents with DS showed not only an overall smaller whole-brain volume, but also volume reductions of the GM in the cerebellum, frontal lobes, frontal region of the limbic lobe, parahippocampal gyri and hippocampi and of the WM in the cerebellum, frontal and parietal lobes, sub-lobar regions and brainstem. By contrast, volume preservation was observed in the GM of the parietal lobes, temporal lobe and sub-lobar regions and in the WM of the temporal lobe and temporal regions of the limbic lobe. A lower volume of CSF was also detected in the frontal lobes. This study is the first to use the high-resolution MRI VBM method to describe a whole-brain pattern of abnormalities in young DS patients falling within such a narrow age range and it provides new information on the neuroanatomically specific regional changes that occur during development in these patients. PMID:23731912

  18. Voxel-based morphometry with templates and validation in a mouse model of Huntington's disease.

    PubMed

    Sawiak, Stephen J; Wood, Nigel I; Williams, Guy B; Morton, A Jennifer; Carpenter, T Adrian

    2013-11-01

    Despite widespread application to human imaging, voxel-based morphometry (VBM), where images are compared following grey matter (GM) segmentation, is seldom used in mice. Here VBM is performed for the R6/2 model of Huntington's disease, a progressive neurological disorder. This article discusses issues in translating the methods to mice and shows that its statistical basis is sound in mice as it is in human studies. Whole brain images from live transgenic and control mice are segmented into GM maps after processing and compared to produce statistical parametric maps of likely differences. To assess whether false positives were likely to occur, a large cohort of ex vivo magnetic resonance brain images were sampled with permutation testing. Differences were seen particularly in the striatum and cortex, in line with studies performed ex vivo and as seen in human patients. In validation, the rate of false positives is as expected and these have no discernible distribution through the brain. The study shows that VBM successfully detects differences in the Huntington's disease mouse brain. The method is rapid compared to manual delineation and reliable. The templates created here for the mouse brain are freely released for other users in addition to an open-source software toolbox for performing mouse VBM.

  19. Neural Correlates of Post-Conventional Moral Reasoning: A Voxel-Based Morphometry Study

    PubMed Central

    Prehn, Kristin; Korczykowski, Marc; Rao, Hengyi; Fang, Zhuo; Detre, John A.; Robertson, Diana C.

    2015-01-01

    Going back to Kohlberg, moral development research affirms that people progress through different stages of moral reasoning as cognitive abilities mature. Individuals at a lower level of moral reasoning judge moral issues mainly based on self-interest (personal interests schema) or based on adherence to laws and rules (maintaining norms schema), whereas individuals at the post-conventional level judge moral issues based on deeper principles and shared ideals. However, the extent to which moral development is reflected in structural brain architecture remains unknown. To investigate this question, we used voxel-based morphometry and examined the brain structure in a sample of 67 Master of Business Administration (MBA) students. Subjects completed the Defining Issues Test (DIT-2) which measures moral development in terms of cognitive schema preference. Results demonstrate that subjects at the post-conventional level of moral reasoning were characterized by increased gray matter volume in the ventromedial prefrontal cortex and subgenual anterior cingulate cortex, compared with subjects at a lower level of moral reasoning. Our findings support an important role for both cognitive and emotional processes in moral reasoning and provide first evidence for individual differences in brain structure according to the stages of moral reasoning first proposed by Kohlberg decades ago. PMID:26039547

  20. Multimodal voxel-based meta-analysis of white matter abnormalities in obsessive-compulsive disorder.

    PubMed

    Radua, Joaquim; Grau, Mar; van den Heuvel, Odile A; Thiebaut de Schotten, Michel; Stein, Dan J; Canales-Rodríguez, Erick J; Catani, Marco; Mataix-Cols, David

    2014-06-01

    White matter (WM) abnormalities have long been suspected in obsessive-compulsive disorder (OCD) but the available evidence has been inconsistent. We conducted the first multimodal meta-analysis of WM volume (WMV) and fractional anisotropy (FA) studies in OCD. All voxel-wise studies comparing WMV or FA between patients with OCD and healthy controls in the PubMed, ScienceDirect, Google Scholar, Web of Knowledge and Scopus databases were retrieved. Manual searches were also conducted and authors were contacted soliciting additional data. Thirty-four data sets were identified, of which 22 met inclusion criteria (five of them unpublished; comprising 537 adult and pediatric patients with OCD and 575 matched healthy controls). Whenever possible, raw statistical parametric maps were also obtained from the authors. Peak and raw WMV and FA data were combined using novel multimodal meta-analytic methods implemented in effect-size signed differential mapping. Patients with OCD showed widespread WM abnormalities, but findings were particularly robust in the anterior midline tracts (crossing between anterior parts of cingulum bundle and body of corpus callosum), which showed both increased WMV and decreased FA, possibly suggesting an increase of fiber crossing in these regions. This finding was also observed when the analysis was limited to adult participants, and especially pronounced in samples with a higher proportion of medicated patients. Therefore, patients with OCD may have widespread WM abnormalities, particularly evident in anterior midline tracts, although these changes might be, at least in part, attributable to the effects of therapeutic drugs.

  1. Estabilidad de los modelos de Heggie y Ramamani

    NASA Astrophysics Data System (ADS)

    Muzzio, J. C.; Vergne, M. M.; Wachlin, F. C.; Carpintero, D. D.

    Los modelos de Heggie y Ramamani de satélites galácticos en órbitas circulares se basan en una teoría aproximada, por lo que es importante verificar su estabilidad mediante simulaciones numéricas. En esta forma, hemos logrado mostrar que son estables sobre intervalos de tiempo mucho mayores que los que lograron los propios autores de los modelos. Por otra parte, dado que hemos mostrado que el caos es significativo en estos modelos, son un sistema ideal para investigar si, pese a ello, se mantienen estacionarios. Nuestras simulaciones numéricas muestran que, pese al caos, la estacionariedad se mantiene sobre intervalos de centenares de tiempos de cruce del sistema, mucho mayores que los tiempos de Liapunov característicos de sus movimientos caóticos.

  2. A convenient scheme for coupling a finite element curvilinear mesh to a finite element voxel mesh: application to the heart

    PubMed Central

    Hopenfeld, Bruce

    2006-01-01

    Background In some cases, it may be necessary to combine distinct finite element meshes into a single system. The present work describes a scheme for coupling a finite element mesh, which may have curvilinear elements, to a voxel based finite element mesh. Methods The method is described with reference to a sample problem that involves combining a heart, which is defined by a curvilinear mesh, with a voxel based torso mesh. The method involves the creation of a temporary (scaffolding) mesh that couples the outer surface of the heart mesh to a voxel based torso mesh. The inner surface of the scaffolding mesh is the outer heart surface, and the outer surface of the scaffolding mesh is defined by the nodes in the torso mesh that are nearest (but outside of) the heart. The finite element stiffness matrix for the scaffolding mesh is then computed. This stiffness matrix includes extraneous nodes that are then removed, leaving a coupling matrix that couples the original outer heart surface nodes to adjacent nodes in the torso voxel mesh. Finally, a complete system matrix is assembled from the pre-existing heart stiffness matrix, the heart/torso coupling matrix, and the torso stiffness matrix. Results Realistic body surface electrocardiograms were generated. In a test involving a dipole embedded in a spherical shell, relative error of the scheme rapidly converged to slightly over 4%, although convergence thereafter was relatively slow. Conclusion The described method produces reasonably accurate results and may be best suited for problems where computational speed and convenience have a higher priority than very high levels of accuracy. PMID:17112373

  3. Resonance behaviour of whole-body averaged specific energy absorption rate (SAR) in the female voxel model, NAOMI

    NASA Astrophysics Data System (ADS)

    Dimbylow, Peter

    2005-09-01

    Finite-difference time-domain (FDTD) calculations have been performed of the whole-body averaged specific energy absorption rate (SAR) in a female voxel model, NAOMI, under isolated and grounded conditions from 10 MHz to 3 GHz. The 2 mm resolution voxel model, NAOMI, was scaled to a height of 1.63 m and a mass of 60 kg, the dimensions of the ICRP reference adult female. Comparison was made with SAR values from a reference male voxel model, NORMAN. A broad SAR resonance in the NAOMI values was found around 900 MHz and a resulting enhancement, up to 25%, over the values for the male voxel model, NORMAN. This latter result confirmed previously reported higher values in a female model. The effect of differences in anatomy was investigated by comparing values for 10-, 5- and 1-year-old phantoms rescaled to the ICRP reference values of height and mass which are the same for both sexes. The broad resonance in the NAOMI child values around 1 GHz is still a strong feature. A comparison has been made with ICNIRP guidelines. The ICNIRP occupational reference level provides a conservative estimate of the whole-body averaged SAR restriction. The linear scaling of the adult phantom using different factors in longitudinal and transverse directions, in order to match the ICRP stature and weight, does not exactly reproduce the anatomy of children. However, for public exposure the calculations with scaled child models indicate that the ICNIRP reference level may not provide a conservative estimate of the whole-body averaged SAR restriction, above 1.2 GHz for scaled 5- and 1-year-old female models, although any underestimate is by less than 20%.

  4. An EGS4 based Monte Carlo code for the calculation of organ equivalent dose to a modified Yale voxel phantom.

    PubMed

    Kramer, R; Vieira, J W; Lima, F R A; Fuelle, D

    2002-07-01

    Organ or tissue equivalent dose, the most important quantity in radiation protection, cannot be measured directly. Therefore it became common practice to calculate the quantity of interest with Monte Carlo methods applied to so-called human phantoms, which are virtual representations of the human body. The Monte Carlo computer code determines conversion coefficients, which are ratios between organ or tissue equivalent dose and measurable quantities. Conversion coefficients have been published by the ICRP (Report No. 74) for various types of radiation, energies and fields, which have been calculated, among others, with the mathematical phantoms ADAM and EVA. Since then progress of image processing, and of clock speed and memory capacity of computers made it possible to create so-called voxel phantoms, which are a far more realistic representation of the human body. Voxel (Volume pixel) phantoms are built from segmented CT and/or MRI images of real persons. A complete set of such images can be joined to a 3-dimensional representation of the human body, which can be linked to a Monte Carlo code allowing for particle transport calculations. A modified version of the VOX_TISS8 human voxel phantom (Yale University) has been connected to the EGS4 Monte Carlo code. The paper explains the modifications, which have been made, the method of coupling the voxel phantom with the code, and presents results as conversion coefficients between organ equivalent dose and kerma in air for external photon radiation. A comparison of the results with published data shows good agreement. PMID:12146699

  5. Association between lesion location and language function in adult glioma using voxel-based lesion-symptom mapping

    PubMed Central

    Banerjee, Pia; Leu, Kevin; Harris, Robert J.; Cloughesy, Timothy F.; Lai, Albert; Nghiemphu, Phioanh L.; Pope, Whitney B.; Bookheimer, Susan Y.; Ellingson, Benjamin M.

    2015-01-01

    Background Management of language difficulties is an important aspect of clinical care for glioma patients, and accurately identifying the possible language deficits in patients based on lesion location would be beneficial to clinicians. To that end, we examined the relationship between lesion presence and language performance on tests of receptive language and expressive language using a highly specific voxel-based lesion–symptom mapping (VLSM) approach in glioma patients. Methods 98 adults with primary glioma, who were pre-surgical candidates, were administered seven neurocognitive tests within the domains of receptive language and expressive language. The association between language performance and lesion presence was examined using VLSM. Statistical parametric maps were created for each test, and composite maps for both receptive language and expressive language were created to display the significant voxels common to all tests within these language domains. Results We identified clusters of voxels with a significant relationship between lesion presence and language performance. All tasks were associated with several white matter pathways. The receptive language tasks were additionally all associated with regions primarily within the lateral temporal lobe and medial temporal lobe. In contrast, the expressive language tasks shared little overlap, despite each task being independently associated with large anatomic areas. Conclusions Our findings identify the key anatomic structures involved in language functioning in adult glioma patients using an innovative lesion analysis technique and suggest that expressive language abilities may be more task-dependent and distributed than receptive language abilities. PMID:26740915

  6. Voxel-Based Lesion Symptom Mapping of Coarse Coding and Suppression Deficits in Patients With Right Hemisphere Damage

    PubMed Central

    Tompkins, Connie A.; Meigh, Kimberly M.; Prat, Chantel S.

    2015-01-01

    Purpose This study examined right hemisphere (RH) neuroanatomical correlates of lexical–semantic deficits that predict narrative comprehension in adults with RH brain damage. Coarse semantic coding and suppression deficits were related to lesions by voxel-based lesion symptom mapping. Method Participants were 20 adults with RH cerebrovascular accidents. Measures of coarse coding and suppression deficits were computed from lexical decision reaction times at short (175 ms) and long (1000 ms) prime-target intervals. Lesions were drawn on magnetic resonance imaging images and through normalization were registered on an age-matched brain template. Voxel-based lesion symptom mapping analysis was applied to build a general linear model at each voxel. Z score maps were generated for each deficit, and results were interpreted using automated anatomical labeling procedures. Results A deficit in coarse semantic activation was associated with lesions to the RH posterior middle temporal gyrus, dorsolateral prefrontal cortex, and lenticular nuclei. A maintenance deficit for coarsely coded representations involved the RH temporal pole and dorsolateral prefrontal cortex more medially. Ineffective suppression implicated lesions to the RH inferior frontal gyrus and subcortical regions, as hypothesized, along with the rostral temporal pole. Conclusion Beyond their scientific implications, these lesion–deficit correspondences may help inform the clinical diagnosis and enhance decisions about candidacy for deficit-focused treatment to improve narrative comprehension in individuals with RH damage. PMID:26425785

  7. Regional and tissue-specific differences in brain glutamate concentration measured by in vivo single voxel MRS

    PubMed Central

    Zhang, Yan; Shen, Jun

    2015-01-01

    Background There is growing interest in characterizing spatial distribution of glutamate (Glu) in brain disorders. Comparing differences in Glu concentration using magnetic resonance spectroscopy (MRS) is hampered by the confounding effects of different anatomical regions and tissue composition. New Method Effect of tissue composition on Glu concentrations was studied by selecting closely adjacent voxels within a designated cortical region. Glu regional differences were assessed using voxels comprising essentially the same tissue composition from different cortical regions. Results Using point-resolved-spectroscopy (PRESS)-based averaged echo time method, Glu concentration in the anterior cingulate cortex (ACC) was found to correlate strongly with tissue gray matter (GM) fraction (r = 0.87, p = 10−5). No significant regional difference in Glu concentration was found between frontal and occipital lobes (p = 0.23) when the two measured voxels had essentially the same tissue composition. Comparison with Existing Methods The method of the current study is aimed to circumvent the difficulties in differentiating anatomical region from tissue composition, given that both can lead to Glu variations in brain. Glu concentration versus tissue composition was measured in the same anatomical region, while the comparison of regional differences was performed with the two regions that had essentially the same tissue composition. Conclusions In brain cortices, Glu level is significantly higher in GM than in WM. Glu level difference between frontal lobe and occipital lobe is insignificant. PMID:25261738

  8. False positive control of activated voxels in single fMRI analysis using bootstrap resampling in comparison to spatial smoothing.

    PubMed

    Darki, Fahimeh; Oghabian, Mohammad Ali

    2013-10-01

    Functional magnetic resonance imaging (fMRI) is an effective tool for the measurement of brain neuronal activities. To date, several statistical methods have been proposed for analyzing fMRI datasets to select true active voxels among all the voxels appear to be positively activated. Finding a reliable and valid activation map is very important and becomes more crucial in clinical and neurosurgical investigations of single fMRI data, especially when pre-surgical planning requires accurate lateralization index as well as a precise localization of activation map. Defining a proper threshold to determine true activated regions, using common statistical processes, is a challenging task. This is due to a number of variation sources such as noise, artifacts, and physiological fluctuations in time series of fMRI data which affect spatial distribution of noise in an expected uniform activated region. Spatial smoothing methods are frequently used as a preprocessing step to reduce the effect of noise and artifacts. The smoothing may lead to a shift and enlargement of activation regions, and in some extend, unification of distinct regions. In this article, we propose a bootstrap resampling technique for analyzing single fMRI dataset with the aim of finding more accurate and reliable activated regions. This method can remove false positive voxels and present high localization accuracy in activation map without any spatial smoothing and statistical threshold setting.

  9. Abnormal functional specialization within medial prefrontal cortex in high-functioning autism: a multi-voxel similarity analysis

    PubMed Central

    Meuwese, Julia D.I.; Towgood, Karren J.; Frith, Christopher D.; Burgess, Paul W.

    2009-01-01

    Multi-voxel pattern analyses have proved successful in ‘decoding’ mental states from fMRI data, but have not been used to examine brain differences associated with atypical populations. We investigated a group of 16 (14 males) high-functioning participants with autism spectrum disorder (ASD) and 16 non-autistic control participants (12 males) performing two tasks (spatial/verbal) previously shown to activate medial rostral prefrontal cortex (mrPFC). Each task manipulated: (i) attention towards perceptual versus self-generated information and (ii) reflection on another person's mental state (‘mentalizing'versus ‘non-mentalizing’) in a 2 × 2 design. Behavioral performance and group-level fMRI results were similar between groups. However, multi-voxel similarity analyses revealed strong differences. In control participants, the spatial distribution of activity generalized significantly between task contexts (spatial/verbal) when examining the same function (attention/mentalizing) but not when comparing different functions. This pattern was disrupted in the ASD group, indicating abnormal functional specialization within mrPFC, and demonstrating the applicability of multi-voxel pattern analysis to investigations of atypical populations. PMID:19174370

  10. An ICRP-based Chinese adult male voxel model and its absorbed dose for idealized photon exposures--the skeleton.

    PubMed

    Liu, Liye; Zeng, Zhi; Li, Junli; Zhang, Binquan; Qiu, Rui; Ma, Jizeng

    2009-11-01

    A site-specific skeleton voxel model for a Chinese adult male was constructed in this paper upon a previous Chinese individual voxel model. The whole skeleton was divided into 19 site-specific bones and bone groups; the mass of various skeleton tissues at each bone site, e.g. red bone marrow, was specified according to Asian reference data and the distribution data from ICRP Publication 70. The resultant voxel model (called CAM) has a resolution of 1.741 mm x 1.741 mm in plane, and the total bone mass is 8397.8 g which is almost equal to the Asian reference value. Dose coefficients for the red bone marrow and bone surface in CAM were calculated, and then compared with those from Rex, CMP and ICRP 74. It shows that the dose to RBM in Rex is generally 12% lower than that to CAM in low-energy range (30-150 keV) for AP, LAT, ROT and ISO geometries. It is also found that the RBM dose from mathematical models, i.e. CMP and ICRP 74, is underestimated by -30% in AP geometry and overestimated by 30% in PA geometry for low-energy photons. Meanwhile, the bone surface dose in the low-energy range is overestimated by 150% and 75% in CMP and ICRP 74, respectively, if compared with that from CAM. PMID:19841519

  11. Organ dose conversion coefficients on an ICRP-based Chinese adult male voxel model from idealized external photons exposures

    NASA Astrophysics Data System (ADS)

    Liu, Liye; Zeng, Zhi; Li, Junli; Qiu, Rui; Zhang, Binquan; Ma, Jizeng; Li, Ren; Li, Wenqian; Bi, Lei

    2009-11-01

    A high-resolution whole-body voxel model called CAM representing the Chinese adult male was constructed in this paper based on a previous individual voxel model. There are more than 80 tissues and organs in CAM, including almost all organs required in the ICRP new recommendation. The mass of individual organs has been adjusted to the Chinese reference data. Special considerations were given to representing the gross spatial distribution of various bone constituents as realistically as possible during the construction of the site-specific skeleton. Organ dose conversion coefficients were calculated for six idealized external photon exposures from 10 keV to 10 MeV by using Monte Carlo simulation. The resulting dose coefficients were then compared with those from other models, e.g. CMP, ICRP 74, Rex, HDRK-man and VIP-man. Old and new effective male doses of CAM were calculated by using the tissue weighting factors from ICRP 60 and 103 Publications, respectively. Dosimetric differences between mathematical and voxel models, and the differences between Asian and Caucasian models are also discussed in this paper.

  12. Organ dose conversion coefficients on an ICRP-based Chinese adult male voxel model from idealized external photons exposures.

    PubMed

    Liu, Liye; Zeng, Zhi; Li, Junli; Qiu, Rui; Zhang, Binquan; Ma, Jizeng; Li, Ren; Li, Wenqian; Bi, Lei

    2009-11-01

    A high-resolution whole-body voxel model called CAM representing the Chinese adult male was constructed in this paper based on a previous individual voxel model. There are more than 80 tissues and organs in CAM, including almost all organs required in the ICRP new recommendation. The mass of individual organs has been adjusted to the Chinese reference data. Special considerations were given to representing the gross spatial distribution of various bone constituents as realistically as possible during the construction of the site-specific skeleton. Organ dose conversion coefficients were calculated for six idealized external photon exposures from 10 keV to 10 MeV by using Monte Carlo simulation. The resulting dose coefficients were then compared with those from other models, e.g. CMP, ICRP 74, Rex, HDRK-man and VIP-man. Old and new effective male doses of CAM were calculated by using the tissue weighting factors from ICRP 60 and 103 Publications, respectively. Dosimetric differences between mathematical and voxel models, and the differences between Asian and Caucasian models are also discussed in this paper. PMID:19841518

  13. Selected organ dose conversion coefficients for external photons calculated using ICRP adult voxel phantoms and Monte Carlo code FLUKA.

    PubMed

    Patni, H K; Nadar, M Y; Akar, D K; Bhati, S; Sarkar, P K

    2011-11-01

    The adult reference male and female computational voxel phantoms recommended by ICRP are adapted into the Monte Carlo transport code FLUKA. The FLUKA code is then utilised for computation of dose conversion coefficients (DCCs) expressed in absorbed dose per air kerma free-in-air for colon, lungs, stomach wall, breast, gonads, urinary bladder, oesophagus, liver and thyroid due to a broad parallel beam of mono-energetic photons impinging in anterior-posterior and posterior-anterior directions in the energy range of 15 keV-10 MeV. The computed DCCs of colon, lungs, stomach wall and breast are found to be in good agreement with the results published in ICRP publication 110. The present work thus validates the use of FLUKA code in computation of organ DCCs for photons using ICRP adult voxel phantoms. Further, the DCCs for gonads, urinary bladder, oesophagus, liver and thyroid are evaluated and compared with results published in ICRP 74 in the above-mentioned energy range and geometries. Significant differences in DCCs are observed for breast, testis and thyroid above 1 MeV, and for most of the organs at energies below 60 keV in comparison with the results published in ICRP 74. The DCCs of female voxel phantom were found to be higher in comparison with male phantom for almost all organs in both the geometries. PMID:21147784

  14. An ICRP-based Chinese adult male voxel model and its absorbed dose for idealized photon exposures—the skeleton

    NASA Astrophysics Data System (ADS)

    Liu, Liye; Zeng, Zhi; Li, Junli; Zhang, Binquan; Qiu, Rui; Ma, Jizeng

    2009-11-01

    A site-specific skeleton voxel model for a Chinese adult male was constructed in this paper upon a previous Chinese individual voxel model. The whole skeleton was divided into 19 site-specific bones and bone groups; the mass of various skeleton tissues at each bone site, e.g. red bone marrow, was specified according to Asian reference data and the distribution data from ICRP Publication 70. The resultant voxel model (called CAM) has a resolution of 1.741 mm × 1.741 mm in plane, and the total bone mass is 8397.8 g which is almost equal to the Asian reference value. Dose coefficients for the red bone marrow and bone surface in CAM were calculated, and then compared with those from Rex, CMP and ICRP 74. It shows that the dose to RBM in Rex is generally 12% lower than that to CAM in low-energy range (30-150 keV) for AP, LAT, ROT and ISO geometries. It is also found that the RBM dose from mathematical models, i.e. CMP and ICRP 74, is underestimated by -30% in AP geometry and overestimated by 30% in PA geometry for low-energy photons. Meanwhile, the bone surface dose in the low-energy range is overestimated by 150% and 75% in CMP and ICRP 74, respectively, if compared with that from CAM.

  15. The effect of in situ/in vitro three-dimensional quantitative computed tomography image voxel size on the finite element model of human vertebral cancellous bone.

    PubMed

    Lu, Yongtao; Engelke, Klaus; Glueer, Claus-C; Morlock, Michael M; Huber, Gerd

    2014-11-01

    Quantitative computed tomography-based finite element modeling technique is a promising clinical tool for the prediction of bone strength. However, quantitative computed tomography-based finite element models were created from image datasets with different image voxel sizes. The aim of this study was to investigate whether there is an influence of image voxel size on the finite element models. In all 12 thoracolumbar vertebrae were scanned prior to autopsy (in situ) using two different quantitative computed tomography scan protocols, which resulted in image datasets with two different voxel sizes (0.29 × 0.29 × 1.3 mm(3) vs 0.18 × 0.18 × 0.6 mm(3)). Eight of them were scanned after autopsy (in vitro) and the datasets were reconstructed with two voxel sizes (0.32 × 0.32 × 0.6 mm(3) vs. 0.18 × 0.18 × 0.3 mm(3)). Finite element models with cuboid volume of interest extracted from the vertebral cancellous part were created and inhomogeneous bilinear bone properties were defined. Axial compression was simulated. No effect of voxel size was detected on the apparent bone mineral density for both the in situ and in vitro cases. However, the apparent modulus and yield strength showed significant differences in the two voxel size group pairs (in situ and in vitro). In conclusion, the image voxel size may have to be considered when the finite element voxel modeling technique is used in clinical applications.

  16. The SENSE-Isomorphism Theoretical Image Voxel Estimation (SENSE-ITIVE) model for reconstruction and observing statistical properties of reconstruction operators.

    PubMed

    Bruce, Iain P; Karaman, M Muge; Rowe, Daniel B

    2012-10-01

    The acquisition of sub-sampled data from an array of receiver coils has become a common means of reducing data acquisition time in MRI. Of the various techniques used in parallel MRI, SENSitivity Encoding (SENSE) is one of the most common, making use of a complex-valued weighted least squares estimation to unfold the aliased images. It was recently shown in Bruce et al. [Magn. Reson. Imag. 29(2011):1267-1287] that when the SENSE model is represented in terms of a real-valued isomorphism,it assumes a skew-symmetric covariance between receiver coils, as well as an identity covariance structure between voxels. In this manuscript, we show that not only is the skew-symmetric coil covariance unlike that of real data, but the estimated covariance structure between voxels over a time series of experimental data is not an identity matrix. As such, a new model, entitled SENSE-ITIVE, is described with both revised coil and voxel covariance structures. Both the SENSE and SENSE-ITIVE models are represented in terms of real-valued isomorphisms, allowing for a statistical analysis of reconstructed voxel means, variances, and correlations resulting from the use of different coil and voxel covariance structures used in the reconstruction processes to be conducted. It is shown through both theoretical and experimental illustrations that the miss-specification of the coil and voxel covariance structures in the SENSE model results in a lower standard deviation in each voxel of the reconstructed images, and thus an artificial increase in SNR, compared to the standard deviation and SNR of the SENSE-ITIVE model where both the coil and voxel covariances are appropriately accounted for. It is also shown that there are differences in the correlations induced by the reconstruction operations of both models, and consequently there are differences in the correlations estimated throughout the course of reconstructed time series. These differences in correlations could result in meaningful

  17. Development of a voxel-matching technique for substantial reduction of subtraction artifacts in temporal subtraction images obtained from thoracic MDCT.

    PubMed

    Itai, Yoshinori; Kim, Hyoungseop; Ishikawa, Seiji; Katsuragawa, Shigehiko; Doi, Kunio

    2010-02-01

    A temporal subtraction image, which is obtained by subtraction of a previous image from a current one, can be used for enhancing interval changes (such as formation of new lesions and changes in existing abnormalities) on medical images by removing most of the normal structures. However, subtraction artifacts are commonly included in temporal subtraction images obtained from thoracic computed tomography and thus tend to reduce its effectiveness in the detection of pulmonary nodules. In this study, we developed a new method for substantially removing the artifacts on temporal subtraction images of lungs obtained from multiple-detector computed tomography (MDCT) by using a voxel-matching technique. Our new method was examined on 20 clinical cases with MDCT images. With this technique, the voxel value in a warped (or nonwarped) previous image is replaced by a voxel value within a kernel, such as a small cube centered at a given location, which would be closest (identical or nearly equal) to the voxel value in the corresponding location in the current image. With the voxel-matching technique, the correspondence not only between the structures but also between the voxel values in the current and the previous images is determined. To evaluate the usefulness of the voxel-matching technique for removal of subtraction artifacts, the magnitude of artifacts remaining in the temporal subtraction images was examined by use of the full width at half maximum and the sum of a histogram of voxel values, which may indicate the average contrast and the total amount, respectively, of subtraction artifacts. With our new method, subtraction artifacts due to normal structures such as blood vessels were substantially removed on temporal subtraction images. This computerized method can enhance lung nodules on chest MDCT images without disturbing misregistration artifacts.

  18. A voxel-based investigation for MRI-only radiotherapy of the brain using ultra short echo times

    NASA Astrophysics Data System (ADS)

    Edmund, Jens M.; Kjer, Hans M.; Van Leemput, Koen; Hansen, Rasmus H.; Andersen, Jon AL; Andreasen, Daniel

    2014-12-01

    Radiotherapy (RT) based on magnetic resonance imaging (MRI) as the only modality, so-called MRI-only RT, would remove the systematic registration error between MR and computed tomography (CT), and provide co-registered MRI for assessment of treatment response and adaptive RT. Electron densities, however, need to be assigned to the MRI images for dose calculation and patient setup based on digitally reconstructed radiographs (DRRs). Here, we investigate the geometric and dosimetric performance for a number of popular voxel-based methods to generate a so-called pseudo CT (pCT). Five patients receiving cranial irradiation, each containing a co-registered MRI and CT scan, were included. An ultra short echo time MRI sequence for bone visualization was used. Six methods were investigated for three popular types of voxel-based approaches; (1) threshold-based segmentation, (2) Bayesian segmentation and (3) statistical regression. Each approach contained two methods. Approach 1 used bulk density assignment of MRI voxels into air, soft tissue and bone based on logical masks and the transverse relaxation time T2 of the bone. Approach 2 used similar bulk density assignments with Bayesian statistics including or excluding additional spatial information. Approach 3 used a statistical regression correlating MRI voxels with their corresponding CT voxels. A similar photon and proton treatment plan was generated for a target positioned between the nasal cavity and the brainstem for all patients. The CT agreement with the pCT of each method was quantified and compared with the other methods geometrically and dosimetrically using both a number of reported metrics and introducing some novel metrics. The best geometrical agreement with CT was obtained with the statistical regression methods which performed significantly better than the threshold and Bayesian segmentation methods (excluding spatial information). All methods agreed significantly better with CT than a reference water MRI

  19. Voxel-based clustered imaging by multiparameter diffusion tensor images for glioma grading.

    PubMed

    Inano, Rika; Oishi, Naoya; Kunieda, Takeharu; Arakawa, Yoshiki; Yamao, Yukihiro; Shibata, Sumiya; Kikuchi, Takayuki; Fukuyama, Hidenao; Miyamoto, Susumu

    2014-01-01

    Gliomas are the most common intra-axial primary brain tumour; therefore, predicting glioma grade would influence therapeutic strategies. Although several methods based on single or multiple parameters from diagnostic images exist, a definitive method for pre-operatively determining glioma grade remains unknown. We aimed to develop an unsupervised method using multiple parameters from pre-operative diffusion tensor images for obtaining a clustered image that could enable visual grading of gliomas. Fourteen patients with low-grade gliomas and 19 with high-grade gliomas underwent diffusion tensor imaging and three-dimensional T1-weighted magnetic resonance imaging before tumour resection. Seven features including diffusion-weighted imaging, fractional anisotropy, first eigenvalue, second eigenvalue, third eigenvalue, mean diffusivity and raw T2 signal with no diffusion weighting, were extracted as multiple parameters from diffusion tensor imaging. We developed a two-level clustering approach for a self-organizing map followed by the K-means algorithm to enable unsupervised clustering of a large number of input vectors with the seven features for the whole brain. The vectors were grouped by the self-organizing map as protoclusters, which were classified into the smaller number of clusters by K-means to make a voxel-based diffusion tensor-based clustered image. Furthermore, we also determined if the diffusion tensor-based clustered image was really helpful for predicting pre-operative glioma grade in a supervised manner. The ratio of each class in the diffusion tensor-based clustered images was calculated from the regions of interest manually traced on the diffusion tensor imaging space, and the common logarithmic ratio scales were calculated. We then applied support vector machine as a classifier for distinguishing between low- and high-grade gliomas. Consequently, the sensitivity, specificity, accuracy and area under the curve of receiver operating characteristic

  20. Multi-voxel Patterns Reveal Functionally Differentiated Networks Underlying Auditory Feedback Processing of Speech

    PubMed Central

    Zheng, Zane Z.; Vicente-Grabovetsky, Alejandro; MacDonald, Ewen N.; Munhall, Kevin G.; Cusack, Rhodri; Johnsrude, Ingrid S.

    2013-01-01

    The everyday act of speaking involves the complex processes of speech motor control. An important component of control is monitoring, detection and processing of errors when auditory feedback does not correspond to the intended motor gesture. Here we show, using fMRI and converging operations within a multi-voxel pattern analysis framework, that this sensorimotor process is supported by functionally differentiated brain networks. During scanning, a real-time speech-tracking system was employed to deliver two acoustically different types of distorted auditory feedback or unaltered feedback while human participants were vocalizing monosyllabic words, and to present the same auditory stimuli while participants were passively listening. Whole-brain analysis of neural-pattern similarity revealed three functional networks that were differentially sensitive to distorted auditory feedback during vocalization, compared to during passive listening. One network of regions appears to encode an ‘error signal’ irrespective of acoustic features of the error: this network, including right angular gyrus, right supplementary motor area, and bilateral cerebellum, yielded consistent neural patterns across acoustically different, distorted feedback types, only during articulation (not during passive listening). In contrast, a fronto-temporal network appears sensitive to the speech features of auditory stimuli during passive listening; this preference for speech features was diminished when the same stimuli were presented as auditory concomitants of vocalization. A third network, showing a distinct functional pattern from the other two, appears to capture aspects of both neural response profiles. Taken together, our findings suggest that auditory feedback processing during speech motor control may rely on multiple, interactive, functionally differentiated neural systems. PMID:23467350

  1. Sports and brain morphology - a voxel-based morphometry study with endurance athletes and martial artists.

    PubMed

    Schlaffke, L; Lissek, S; Lenz, M; Brüne, M; Juckel, G; Hinrichs, T; Platen, P; Tegenthoff, M; Schmidt-Wilcke, T

    2014-02-14

    Physical exercises and motor skill learning have been shown to induce changes in regional brain morphology, this has been demonstrated for various activities and tasks. Also individuals with special skills show differences in regional brain morphology. This has been indicated for professional musicians, London taxi drivers, as well as for athletes like dancers, golfers and judokas. However little is known about whether sports with different metabolic profiles (aerobic vs. anaerobic) are associated with different patterns of altered brain morphology. In this cross-sectional study we investigated two groups of high-performance athletes, one group performing sports that are thought to be mainly aerobic, and one group performing sports known to have intermittent phases of anaerobic metabolism. Using high-resolution structural imaging and voxel-based morphometry (VBM), we investigated a group of 26 male athletes consisting of 13 martial artists and 13 endurance athletes as well as a group of non-exercising men (n=13). VBM analyses revealed higher gray matter (GM) volumes in the supplementary motor area/dorsal premotor cortex (BA 6) in both athlete groups as compared to the control group. In addition, endurance athletes showed significantly higher GM volume in the medial temporal lobe (MTL), specifically in the hippocampus and parahippocampal gyrus, which was not seen in the martial arts group. Our data suggest that high-performance sports are associated with changes in regional brain morphology in areas implicated in motor planning and motor learning. In addition high-level endurance sports seem to affect MTL structures, areas that have previously been shown to be modulated by aerobic exercise. PMID:24291669

  2. Regional Grey Matter Structure Differences between Transsexuals and Healthy Controls—A Voxel Based Morphometry Study

    PubMed Central

    Simon, Lajos; Kozák, Lajos R.; Simon, Viktória; Czobor, Pál; Unoka, Zsolt; Szabó, Ádám; Csukly, Gábor

    2013-01-01

    Gender identity disorder (GID) refers to transsexual individuals who feel that their assigned biological gender is incongruent with their gender identity and this cannot be explained by any physical intersex condition. There is growing scientific interest in the last decades in studying the neuroanatomy and brain functions of transsexual individuals to better understand both the neuroanatomical features of transsexualism and the background of gender identity. So far, results are inconclusive but in general, transsexualism has been associated with a distinct neuroanatomical pattern. Studies mainly focused on male to female (MTF) transsexuals and there is scarcity of data acquired on female to male (FTM) transsexuals. Thus, our aim was to analyze structural MRI data with voxel based morphometry (VBM) obtained from both FTM and MTF transsexuals (n = 17) and compare them to the data of 18 age matched healthy control subjects (both males and females). We found differences in the regional grey matter (GM) structure of transsexual compared with control subjects, independent from their biological gender, in the cerebellum, the left angular gyrus and in the left inferior parietal lobule. Additionally, our findings showed that in several brain areas, regarding their GM volume, transsexual subjects did not differ significantly from controls sharing their gender identity but were different from those sharing their biological gender (areas in the left and right precentral gyri, the left postcentral gyrus, the left posterior cingulate, precuneus and calcarinus, the right cuneus, the right fusiform, lingual, middle and inferior occipital, and inferior temporal gyri). These results support the notion that structural brain differences exist between transsexual and healthy control subjects and that majority of these structural differences are dependent on the biological gender. PMID:24391851

  3. Current smoking and reduced gray matter volume-a voxel-based morphometry study.

    PubMed

    Fritz, Hans-Christian; Wittfeld, Katrin; Schmidt, Carsten O; Domin, Martin; Grabe, Hans J; Hegenscheid, Katrin; Hosten, Norbert; Lotze, Martin

    2014-10-01

    Nicotine modulates prefrontal processing when tested with functional imaging. Previous studies on changes in regional brain volumes in small samples, reporting different life-time exposure to nicotine, identified reduced volume in smokers in prefrontal areas but reported controversial results for other areas. We investigated the association of cigarette smoking and regional gray and white matter volume by using voxel-based morphometry (VBM) for T1-weighted high-resolution magnetic resonance imaging in 315 current-smokers and 659 never-smokers from the representative Study of Health in Pomerania (SHIP). Our study showed that in current-smokers smoking is significantly associated with gray matter volume loss in the prefrontal cortex, the anterior cingulate cortex, the insula, and the olfactory gyrus. White matter volumes were not relevantly reduced in current-smokers. In current-smokers, we found associations of gray matter loss and smoking exposure (pack-years) in the prefrontal cortex, the anterior and middle cingulate cortex, and the superior temporal and angular gyrus, which however did not stand corrections for multiple testing. We confirmed associations between smoking and gray matter differences in the prefrontal cortex, the anterior cingulate cortex and the insula in the general population of Pomerania (Germany). For the first time, we identified differences in brain volumes in the olfactory gyrus. Other cerebral regions did not show significant differences when correcting for multiple comparisons within the whole brain. The regions of structural deficits might be involved in addictive behavior and withdrawal symptoms, whereas further investigations have to show if the observed atrophies were caused by smoking itself or are preexisting differences between smoking and non-smoking individuals.

  4. A Voxel-Based Morphometric MRI Study in Young Adults with Borderline Personality Disorder

    PubMed Central

    Jin, Xinhu; Zhong, Mingtian; Yao, Shuqiao; Cao, Xiyu; Tan, Changlian; Gan, Jun; Zhu, Xiongzhao; Yi, Jinyao

    2016-01-01

    Background Increasing evidence has documented subtle changes in brain morphology and function in patients with borderline personality disorder (BPD). However, results of magnetic resonance imaging volumetry in patients with BPD are inconsistent. In addition, few researchers using voxel-based morphometry (VBM) have focused on attachment and childhood trauma in BPD. This preliminary study was performed to investigate structural brain changes and their relationships to attachment and childhood trauma in a homogenous sample of young adults with BPD. Method We examined 34 young adults with BPD and 34 healthy controls (HCs) to assess regionally specific differences in gray matter volume (GMV) and gray matter concentration (GMC). Multiple regressions between brain volumes measured by VBM and attachment style questionnaire (ASQ) and childhood trauma questionnaire (CTQ) scores were performed. Results Compared with HCs, subjects with BPD showed significant bilateral increases in GMV in the middle cingulate cortex (MCC)/posterior cingulate cortex (PCC)/precuneus. GMC did not differ significantly between groups. In multiple regression models, ASQ insecure attachment scores were correlated negatively with GMV in the precuneus/MCC and middle occipital gyrus in HCs, HCs with more severe insecure attachment showed smaller volumes in precuneus/MCC and middle occipital gyrus, whereas no negative correlations between insecure attachment and GMV in any region were found in BPD group. In addition, CTQ total scores were not correlated with GMV in any region in the two groups respectively. Conclusions Our findings fit with those of previous reports of larger precuneus GMV in patients with BPD, and suggest that GMV in the precuneus/MCC and middle occipital gyrus is associated inversely with insecure attachment style in HCs. Our finding of increased GMV in the MCC and PCC in patients with BPD compared with HCs has not been reported in previous VBM studies. PMID:26808504

  5. Analytical calculation of proton linear energy transfer in voxelized geometries including secondary protons.

    PubMed

    Sanchez-Parcerisa, D; Cortés-Giraldo, M A; Dolney, D; Kondrla, M; Fager, M; Carabe, A

    2016-02-21

    In order to integrate radiobiological modelling with clinical treatment planning for proton radiotherapy, we extended our in-house treatment planning system FoCa with a 3D analytical algorithm to calculate linear energy transfer (LET) in voxelized patient geometries. Both active scanning and passive scattering delivery modalities are supported. The analytical calculation is much faster than the Monte-Carlo (MC) method and it can be implemented in the inverse treatment planning optimization suite, allowing us to create LET-based objectives in inverse planning. The LET was calculated by combining a 1D analytical approach including a novel correction for secondary protons with pencil-beam type LET-kernels. Then, these LET kernels were inserted into the proton-convolution-superposition algorithm in FoCa. The analytical LET distributions were benchmarked against MC simulations carried out in Geant4. A cohort of simple phantom and patient plans representing a wide variety of sites (prostate, lung, brain, head and neck) was selected. The calculation algorithm was able to reproduce the MC LET to within 6% (1 standard deviation) for low-LET areas (under 1.7 keV μm(-1)) and within 22% for the high-LET areas above that threshold. The dose and LET distributions can be further extended, using radiobiological models, to include radiobiological effectiveness (RBE) calculations in the treatment planning system. This implementation also allows for radiobiological optimization of treatments by including RBE-weighted dose constraints in the inverse treatment planning process. PMID:26840945

  6. Medical staff extremity dosimetry in CT fluoroscopy: an anthropomorphic hand voxel phantom study

    NASA Astrophysics Data System (ADS)

    Figueira, C.; Becker, F.; Blunck, C.; DiMaria, S.; Baptista, M.; Esteves, B.; Paulo, G.; Santos, J.; Teles, P.; Vaz, P.

    2013-08-01

    This work aims to contribute to the study of the radiation dose distribution delivered to the hands of medical staff members during a general computed tomographic (CT) fluoroscopic guided procedure. In this study, both Monte Carlo simulations and measurements were performed. For free-in-air and computed tomography dose index (CTDI) body phantom measurements, a standard pencil ionization chamber (IC) 100 mm long was used. The CT scanner model was implemented using MCNPX (Monte Carlo N-Particle eXtended) and was successfully validated by comparing the simulated results with measurements. Subsequently, CT images of a hand, together with an anthropomorphic phantom, were voxelized and used with the MCNPX code for dose calculations. The hand dose distribution study was performed both by using thermo-luminescent detector measurements and Monte Carlo simulations. The validated simulation tool provides a new perspective for detailed investigations of CT-irradiation scenarios. Simulations show that there is a strong dose gradient, namely the even zones of the hand that are in precise vicinity to the x-ray beam only receive about 4% of the maximum dose delivered to adjacent areas which are directly exposed to the primary x-ray beam. Finally, the scatter contribution of the patient was also studied through MC simulations. The results show that for directly exposed parts of the hand surface, the dose is reduced by the body of the patient (due to the shielding), whereas the dose is increased by scattered radiation from the patient for parts of the skin that receive scattered radiation only.

  7. Structural Abnormalities in Childhood Absence Epilepsy: Voxel-Based Analysis Using Diffusion Tensor Imaging

    PubMed Central

    Qiu, Wenchao; Gao, Yuan; Yu, Chuanyong; Miao, Ailiang; Tang, Lu; Huang, Shuyang; Hu, Zheng; Xiang, Jing; Wang, Xiaoshan

    2016-01-01

    Purpose: Childhood absence epilepsy (CAE) is a common syndrome of idiopathic generalized epilepsy. However, little is known about the brain structural changes in this type of epilepsy, especially in the default mode network (DMN) regions. This study aims at using the diffusion tensor imaging (DTI) technique to quantify structural abnormalities of DMN nodes in CAE patients. Method: DTI data were acquired in 14 CAE patients (aged 8.64 ± 2.59 years, seven females and seven males) and 16 age- and sex-matched healthy controls. The data were analyzed using voxel-based analysis (VBA) and statistically compared between patients and controls. Pearson correlation was explored between altered DTI metrics and clinical parameters. The difference of brain volumes between patients and controls were also tested using unpaired t-test. Results: Patients showed significant increase of mean diffusivity (MD) and radial diffusivity (RD) in left medial prefrontal cortex (MPFC), and decrease of fractional anisotropy (FA) in left precuneus and axial diffusivity (AD) in both left MPFC and precuneus. In correlation analysis, MD value from left MPFC was positively associated with duration of epilepsy. Neither the disease duration nor the seizure frequency showed significant correlation with FA values. Between-group comparison of brain volumes got no significant difference. Conclusion: The findings indicate that structural impairments exist in DMN regions in children suffering from absence epilepsy and MD values positively correlate with epilepsy duration. This may contribute to understanding the pathological mechanisms of chronic neurological deficits and promote the development of new therapies for this disorder. PMID:27733824

  8. Brain volumetric abnormalities in patients with anorexia and bulimia nervosa: a voxel-based morphometry study.

    PubMed

    Amianto, Federico; Caroppo, Paola; D'Agata, Federico; Spalatro, Angela; Lavagnino, Luca; Caglio, Marcella; Righi, Dorico; Bergui, Mauro; Abbate-Daga, Giovanni; Rigardetto, Roberto; Mortara, Paolo; Fassino, Secondo

    2013-09-30

    Recent studies focussing on neuroimaging features of eating disorders have observed that anorexia nervosa (AN) is characterized by significant grey matter (GM) atrophy in many brain regions, especially in the cerebellum and anterior cingulate cortex. To date, no studies have found GM atrophy in bulimia nervosa (BN) or have directly compared patients with AN and BN. We used voxel-based morphometry (VBM) to characterize brain abnormalities in AN and BN patients, comparing them with each other and with a control group, and correlating brain volume with clinical features. We recruited 17 AN, 13 BN and 14 healthy controls. All subjects underwent high-resolution magnetic resonance imaging (MRI) with a T1-weighted 3D image. VBM analysis was carried out with the FSL-VBM 4.1 tool. We found no global atrophy, but regional GM reduction in AN with respect to controls and BN in the cerebellum, fusiform area, supplementary motor area, and occipital cortex, and in the caudate in BN compared to AN and controls. Both groups of patients had a volumetric increase bilaterally in somatosensory regions with respect to controls, in areas that are typically involved in the sensory-motor integration of body stimuli and in mental representation of the body image. Our VBM study documented, for the first time in BN patients, the presence of volumetric alterations and replicated previous findings in AN patients. We evidenced morphological differences between AN and BN, demonstrating in the latter atrophy of the caudate nucleus, a region involved in reward mechanisms and processes of self-regulation, perhaps involved in the genesis of the binge-eating behaviors of this disorder.

  9. Rapid registration of multimodal images using a reduced number of voxels

    NASA Astrophysics Data System (ADS)

    Huang, Xishi; Hill, Nicholas A.; Ren, Jing; Peters, Terry M.

    2006-03-01

    Rapid registration of multimodal cardiac images can improve image-guided cardiac surgeries and cardiac disease diagnosis. While mutual information (MI) is arguably the most suitable registration technique, this method is too slow to converge for real time cardiac image registration; moreover, correct registration may not coincide with a global or even local maximum of MI. These limitations become quite evident when registering three-dimensional (3D) ultrasound (US) images and dynamic 3D magnetic resonance (MR) images of the beating heart. To overcome these issues, we present a registration method that uses a reduced number of voxels, while retaining adequate registration accuracy. Prior to registration we preprocess the images such that only the most representative anatomical features are depicted. By selecting samples from preprocessed images, our method dramatically speeds up the registration process, as well as ensuring correct registration. We validated this registration method for registering dynamic US and MR images of the beating heart of a volunteer. Experimental results on in vivo cardiac images demonstrate significant improvements in registration speed without compromising registration accuracy. A second validation study was performed registering US and computed tomography (CT) images of a rib cage phantom. Two similarity metrics, MI and normalized crosscorrelation (NCC) were used to register the image sets. Experimental results on the rib cage phantom indicate that our method can achieve adequate registration accuracy within 10% of the computation time of conventional registration methods. We believe this method has the potential to facilitate intra-operative image fusion for minimally invasive cardio-thoracic surgical navigation.

  10. Sports and brain morphology - a voxel-based morphometry study with endurance athletes and martial artists.

    PubMed

    Schlaffke, L; Lissek, S; Lenz, M; Brüne, M; Juckel, G; Hinrichs, T; Platen, P; Tegenthoff, M; Schmidt-Wilcke, T

    2014-02-14

    Physical exercises and motor skill learning have been shown to induce changes in regional brain morphology, this has been demonstrated for various activities and tasks. Also individuals with special skills show differences in regional brain morphology. This has been indicated for professional musicians, London taxi drivers, as well as for athletes like dancers, golfers and judokas. However little is known about whether sports with different metabolic profiles (aerobic vs. anaerobic) are associated with different patterns of altered brain morphology. In this cross-sectional study we investigated two groups of high-performance athletes, one group performing sports that are thought to be mainly aerobic, and one group performing sports known to have intermittent phases of anaerobic metabolism. Using high-resolution structural imaging and voxel-based morphometry (VBM), we investigated a group of 26 male athletes consisting of 13 martial artists and 13 endurance athletes as well as a group of non-exercising men (n=13). VBM analyses revealed higher gray matter (GM) volumes in the supplementary motor area/dorsal premotor cortex (BA 6) in both athlete groups as compared to the control group. In addition, endurance athletes showed significantly higher GM volume in the medial temporal lobe (MTL), specifically in the hippocampus and parahippocampal gyrus, which was not seen in the martial arts group. Our data suggest that high-performance sports are associated with changes in regional brain morphology in areas implicated in motor planning and motor learning. In addition high-level endurance sports seem to affect MTL structures, areas that have previously been shown to be modulated by aerobic exercise.

  11. Do we need a voxel-based approach for LiDAR data in geomorphology?

    NASA Astrophysics Data System (ADS)

    Székely, Balázs; Dorninger, Peter; Faber, Robert; Nothegger, Clemens

    2010-05-01

    to store, process and visualize the results. To reduce the amount of originally collected data for further applications, in general, continuous model surfaces are derived from the point clouds using interpolation approaches. Commonly, grid-based or triangulation models are used for that purpose. Typical models are Digital Surface Models (DSM) representing the whole topography including all natural (e.g. vegetation) and artificial (e.g. buildings) objects and Digital Terrain Models (DTM) representing the topography only. In the visual computing industry the voxel-based approach is quite common for various purposes. Although this technology is quite straightforward concerning the data reduction, it is hardly applied in the geomorphic context. An argument can be against its application that mostly we are interested in a surface, not a volume. Of course in the strict sense it is true, however, if we consider the technology itself how the data, especially the ground data are derived, it turns out that actually it is a volume with a certain accuracy that we are sampling of. The position of this "relatively thin" volume also varies, especially in mountainous areas. Here, depending on the slope angles, the accuracy also varies, especially for the integrated data set consisting of a multitude of sources, e.g. mixing conventional (first echo/last echo) and full-waveform data. These point clouds also contain attributes that otherwise could be very valuable, but during the integration, their meaning may be lost, or it cannot be integrated to the data set. A large scale application of such approaches is mainly prevented by the problems introduced by the high amount of data, making on-the-fly processing a challenging task. To overcome these restrictions and to enable taking advantage of the new possibilities provided by the waveform analysis, we propose a voxel-based data representation approach. The multichannel/multilayer design with an a priori unlimited number of layers

  12. A Fully GPU-Based Ray-Driven Backprojector via a Ray-Culling Scheme with Voxel-Level Parallelization for Cone-Beam CT Reconstruction.

    PubMed

    Park, Hyeong-Gyu; Shin, Yeong-Gil; Lee, Ho

    2015-12-01

    A ray-driven backprojector is based on ray-tracing, which computes the length of the intersection between the ray paths and each voxel to be reconstructed. To reduce the computational burden caused by these exhaustive intersection tests, we propose a fully graphics processing unit (GPU)-based ray-driven backprojector in conjunction with a ray-culling scheme that enables straightforward parallelization without compromising the high computing performance of a GPU. The purpose of the ray-culling scheme is to reduce the number of ray-voxel intersection tests by excluding rays irrelevant to a specific voxel computation. This rejection step is based on an axis-aligned bounding box (AABB) enclosing a region of voxel projection, where eight vertices of each voxel are projected onto the detector plane. The range of the rectangular-shaped AABB is determined by min/max operations on the coordinates in the region. Using the indices of pixels inside the AABB, the rays passing through the voxel can be identified and the voxel is weighted as the length of intersection between the voxel and the ray. This procedure makes it possible to reflect voxel-level parallelization, allowing an independent calculation at each voxel, which is feasible for a GPU implementation. To eliminate redundant calculations during ray-culling, a shared-memory optimization is applied to exploit the GPU memory hierarchy. In experimental results using real measurement data with phantoms, the proposed GPU-based ray-culling scheme reconstructed a volume of resolution 28032803176 in 77 seconds from 680 projections of resolution 10243768 , which is 26 times and 7.5 times faster than standard CPU-based and GPU-based ray-driven backprojectors, respectively. Qualitative and quantitative analyses showed that the ray-driven backprojector provides high-quality reconstruction images when compared with those generated by the Feldkamp-Davis-Kress algorithm using a pixel-driven backprojector, with an average of 2.5 times

  13. A DOS Primer for Librarians: Part II.

    ERIC Educational Resources Information Center

    Beecher, Henry

    1990-01-01

    Provides an introduction to DOS commands and strategies for the effective organization and use of hard disks. Functions discussed include the creation of directories and subdirectories, enhanced copying, the assignment of disk drives, and backing up the hard disk. (CLB)

  14. DOS Batch Files As Control Programs

    NASA Technical Reports Server (NTRS)

    Van Dyk, David A.

    1991-01-01

    Computer-programming technique circumvents maximum of 640K imposed on random-access memory (RAM) by DOS (Disk Operating System) software. Involves breaking application program into smaller programs. Each resulting subprogram, when compiled and linked, must be small enough to fit within 640K of RAM. Retrieved from storage on disk as needed. In terms of DOS software, each subprogram ".EXE" file executed in "stand-alone" manner.

  15. Creation of two tomographic voxel models of paediatric patients in the first year of life

    NASA Astrophysics Data System (ADS)

    Nipper, J. C.; Williams, J. L.; Bolch, W. E.

    2002-09-01

    Tomographic computational models, based on regional segmentation of CT or MRI medical images, have increasingly been proposed as replacements for current stylized mathematical models of human anatomy used in radiation dosimetry studies. While much effort has been devoted towards the creation of adult models, few research studies have been initiated to address the need for models supporting paediatric radiology dosimetry. In this study, two tomographic models were created using a combination of automatic and manual segmentation via a program created in-house using IDL version 5.5. The first model is of a normal 6 day female newborn, and consists of a 512 × 512 × 485 data array. The CT slices of this model were obtained every 1 mm, and 66 different anatomic regions were defined. The second model is of a patient developmentally equivalent to a 2 month male, and was saved as a 512 × 512 × 438 data array. This subject had severe tissue oedema within the gut, kidneys, liver and spleen. The model is thus considered representative of a critically ill child, from a patient subpopulation expected to receive a larger than normal number of diagnostic x-ray exams. The voxel volumes for the two models are 0.35 mm3 and 0.30 mm3, respectively, thus making these models the most detailed in existence for paediatric dosimetry applications. Ratios of organ masses for the UF newborn model to those within the reference ORNL/MIRD model range from highs of 1.2 to 1.7 for the oesophagus and small intestine/colon, respectively, to lows of 0.18 to 0.27 for the mandible and humeri, respectively. For the UF 2 month model, ratios of organ masses in the UF model to those in the 8 week GSF BABY model ranged from highs of 3.7 to 5.2 for the clavicles and spleen, respectively, to lows of 0.2 to 0.3 for the adrenals and scapulae, respectively.

  16. Voxel-based morphometry in epileptic baboons: Parallels to human juvenile myoclonic epilepsy.

    PubMed

    Szabó, C Ákos; Salinas, Felipe S

    2016-08-01

    The epileptic baboon represents a natural model for genetic generalized epilepsy (GGE), closely resembling juvenile myoclonic epilepsy (JME). Due to functional neuroimaging and pathological differences between epileptic (SZ+) and asymptomatic control (CTL) baboons, we expected structural differences in gray matter concentration (GMC) using voxel-based morphometry (VBM). Standard anatomical (MP-RAGE) MRI scans using a 3T Siemens TIM Trio (Siemens, Erlangen, Germany) were available in 107 baboons (67 females; mean age 16±6years) with documented clinical histories and scalp-electroencephalography (EEG) results. For neuroimaging, baboons were anesthetized with isoflurane 1% (1-1.5 MAC) and paralyzed with vecuronium (0.1-0.3mg/kg). Data processing and analysis were performed using FSL's VBM toolbox. GMC was compared between CTL and SZ+ baboons, epileptic baboons with interictal epileptic discharges on scalp EEG (SZ+/IED+), asymptomatic baboons with abnormal EEGs (SZ-/IED+), and IED+ baboons with (IED+/PS+) and without (IED+/PS-) photosensitivity, and the subgroups amongst themselves. Age and gender related changes in gray matter volumes were also included as confound regressors in the VBM analyses of each animal group. Significant increases in GMC were noted in the SZ+/IED+ subgroup compared to the CTL group, including bilaterally in the frontopolar, orbitofrontal and anterolateral temporal cortices, while decreases in GMC were noted in the right more than left primary visual cortices and in the specific nuclei of the thalamus, including reticular, anterior and medial dorsal nuclei. No significant differences were noted otherwise, except that SZ+/IED+ baboons demonstrated increased GMC in the globus pallidae bilaterally compared to the SZ-/IED+ group. Similar to human studies of JME, the epileptic baboons demonstrated GMC decreases in the thalami and occipital cortices, suggesting secondary injury due to chronic epilepsy. Cortical GMC, on the other hand, was increased

  17. Voxel-based morphometry in epileptic baboons: Parallels to human juvenile myoclonic epilepsy.

    PubMed

    Szabó, C Ákos; Salinas, Felipe S

    2016-08-01

    The epileptic baboon represents a natural model for genetic generalized epilepsy (GGE), closely resembling juvenile myoclonic epilepsy (JME). Due to functional neuroimaging and pathological differences between epileptic (SZ+) and asymptomatic control (CTL) baboons, we expected structural differences in gray matter concentration (GMC) using voxel-based morphometry (VBM). Standard anatomical (MP-RAGE) MRI scans using a 3T Siemens TIM Trio (Siemens, Erlangen, Germany) were available in 107 baboons (67 females; mean age 16±6years) with documented clinical histories and scalp-electroencephalography (EEG) results. For neuroimaging, baboons were anesthetized with isoflurane 1% (1-1.5 MAC) and paralyzed with vecuronium (0.1-0.3mg/kg). Data processing and analysis were performed using FSL's VBM toolbox. GMC was compared between CTL and SZ+ baboons, epileptic baboons with interictal epileptic discharges on scalp EEG (SZ+/IED+), asymptomatic baboons with abnormal EEGs (SZ-/IED+), and IED+ baboons with (IED+/PS+) and without (IED+/PS-) photosensitivity, and the subgroups amongst themselves. Age and gender related changes in gray matter volumes were also included as confound regressors in the VBM analyses of each animal group. Significant increases in GMC were noted in the SZ+/IED+ subgroup compared to the CTL group, including bilaterally in the frontopolar, orbitofrontal and anterolateral temporal cortices, while decreases in GMC were noted in the right more than left primary visual cortices and in the specific nuclei of the thalamus, including reticular, anterior and medial dorsal nuclei. No significant differences were noted otherwise, except that SZ+/IED+ baboons demonstrated increased GMC in the globus pallidae bilaterally compared to the SZ-/IED+ group. Similar to human studies of JME, the epileptic baboons demonstrated GMC decreases in the thalami and occipital cortices, suggesting secondary injury due to chronic epilepsy. Cortical GMC, on the other hand, was increased

  18. Spatial distribution of lacunarity of voxelized airborne LiDAR point clouds in various forest assemblages

    NASA Astrophysics Data System (ADS)

    Székely, Balázs; Kania, Adam; Standovár, Tibor; Heilmeier, Hermann

    2015-04-01

    Forest ecosystems have characteristic structure of features defined by various structural elements of different scales and vertical positions: shrub layers, understory vegetation, tree trunks, and branches. Furthermore in most of the cases there are superimposed structures in distributions (mosaic or island patterns) due to topography, soil variability, or even anthropogenic factors like past/present forest management activity. This multifaceted spatial context of the forests is relevant for many ecological issues, especially for maintaining forest biodiversity. Our aim in this study is twofold: (1) to quantify this structural variability laterally and vertically using lacunarity, and (2) to relate these results to relevant ecological features, i.e quantitatively described forest properties. Airborne LiDAR data of various quality and point density have been used for our study including a number of forested sites in Central and East Europe (partly Natura 2000 sites). The point clouds have been converted to voxel format and then converted to horizontal layers as images. These images were processed further for the lacunarity calculation. Areas of interest (AOIs) have been selected based on evaluation of the forested areas and auxiliary field information. The calculation has been performed for the AOIs for all available vertical data slices. The lacunarity function referring to a certain point and given vicinity varies horizontally and vertically, depending on the vegetation structure. Furthermore, the topography may also influence this property as the growth of plants, especially spacing and size of trees are influenced by the local topography and relief (e.g., slope, aspect). The comparisons of the flatland and hilly settings show interesting differences and the spatial patterns also vary differently. Because of the large amount of data resulting from these calculations, sophisticated methods are required to analyse the results. The large data amount then has been

  19. Motion as a perturbation: Measurement-guided dose estimates to moving patient voxels during modulated arc deliveries

    SciTech Connect

    Feygelman, Vladimir; Zhang, Geoffrey; Hunt, Dylan; Opp, Daniel; Stambaugh, Cassandra; Wolf, Theresa K.; Nelms, Benjamin E.

    2013-02-15

    Purpose: To present a framework for measurement-guided VMAT dose reconstruction to moving patient voxels from a known motion kernel and the static phantom data, and to validate this perturbation-based approach with the proof-of-principle experiments. Methods: As described previously, the VMAT 3D dose to a static patient can be estimated by applying a phantom measurement-guided perturbation to the treatment planning system (TPS)-calculated dose grid. The fraction dose to any voxel in the presence of motion, assuming the motion kernel is known, can be derived in a similar fashion by applying a measurement-guided motion perturbation. The dose to the diodes in a helical phantom is recorded at 50 ms intervals and is transformed into a series of time-resolved high-density volumetric dose grids. A moving voxel is propagated through this 4D dose space and the fraction dose to that voxel in the phantom is accumulated. The ratio of this motion-perturbed, reconstructed dose to the TPS dose in the phantom serves as a perturbation factor, applied to the TPS fraction dose to the similarly situated voxel in the patient. This approach was validated by the ion chamber and film measurements on four phantoms of different shape and structure: homogeneous and inhomogeneous cylinders, a homogeneous cube, and an anthropomorphic thoracic phantom. A 2D motion stage was used to simulate the motion. The stage position was synchronized with the beam start time with the respiratory gating simulator. The motion patterns were designed such that the motion speed was in the upper range of the expected tumor motion (1-1.4 cm/s) and the range exceeded the normally observed limits (up to 5.7 cm). The conformal arc plans for X or Y motion (in the IEC 61217 coordinate system) consisted of manually created narrow (3 cm) rectangular strips moving in-phase (tracking) or phase-shifted by 90 Degree-Sign (crossing) with respect to the phantom motion. The XY motion was tested with the computer-derived VMAT

  20. Voxel-Wise Perfusion Assessment in Cerebral White Matter with PCASL at 3T; Is It Possible and How Long Does It Take?

    PubMed Central

    Skurdal, Mikjel Johannes; Bjørnerud, Atle; van Osch, Matthias J. P.; Nordhøy, Wibeke; Lagopoulos, Jim; Groote, Inge Rasmus

    2015-01-01

    Purpose To establish whether reliable voxel-wise assessment of perfusion in cerebral white matter (WM) is possible using arterial spin labeling (ASL) at 3T in a cohort of healthy subjects. Materials and Methods Pseudo-continuous ASL (PCASL) with background suppression (BS) optimized for WM measurements was performed at 3T in eight healthy male volunteers aged 25–41. Four different labeling schemes were evaluated by varying the labeling duration (LD) and post-labeling delay (PLD). Eight slices with voxel dimension 3.75x3.75x5 mm3 were acquired from the anterosuperior aspect of the brain, and 400 image/control pairs were collected for each run. Rigid head immobilization was applied using individually fitted thermoplastic masks. For each voxel in the resulting ASL time series, the time needed to reach a 95% significance level for the ASL signal to be higher than zero (paired t-test), was estimated. Results The four protocols detected between 88% and 95% (after Bonferroni correction: 75% and 88%) of WM voxels at 95% significance level. In the most efficient sequence, 80% was reached after 5 min and 95% after 53 min (after Bonferroni correction 40% and 88% respectively). For all protocols, the fraction of significant WM voxels increased in an asymptotic fashion with increasing scan time. A small subgroup of voxels was shown to not benefit at all from prolonged measurement. Conclusion Acquisition of a significant ASL signal from a majority of WM voxels is possible within clinically acceptable scan times, whereas full coverage needs prohibitively long scan times, as a result of the asymptotic trajectory. PMID:26267661

  1. Clusters of Low (18)F-Fluorodeoxyglucose Uptake Voxels in Combat Veterans with Traumatic Brain Injury and Post-Traumatic Stress Disorder.

    PubMed

    Buchsbaum, Monte S; Simmons, Alan N; DeCastro, Alex; Farid, Nikdokht; Matthews, Scott C

    2015-11-15

    Individuals with mild traumatic brain injury (TBI) show diminished metabolic activity when studied with positron emission tomography (PET) with (18)F-fluorodeoxyglucose (FDG). Since blast injury may not be localized in the same specific anatomical areas in every patient or may be diffuse, significance probability mapping may be vulnerable to false-negative detection of abnormalities. To address this problem, we used an anatomically independent measure to assess PET scans: increased numbers of contiguous voxels that are 2 standard deviations below values found in an uninjured control group. We examined this in three age-matched groups of male patients: 16 veterans with a history of mild TBI, 17 veterans with both mild TBI and post-traumatic stress disorder (PTSD), and 15 veterans without either condition. After FDG administration, subjects performed a modified version of the California Verbal Learning Task. Clusters of low uptake voxels were identified by computing the mean and standard deviation for each voxel in the healthy combat veteran group and then determining the voxel-based z-score for the patient groups. Abnormal clusters were defined as those that contained contiguous voxels with a z-score <-2. Patients with mild TBI alone and patients with TBI+PTSD had larger clusters of low uptake voxels, and cluster size significantly differentiated the mild TBI groups from combat controls. Clusters were more irregular in shape in patients, and patients also had a larger number of low-activity voxels throughout the brain. In mild TBI and TBI+PTSD patients, but not healthy subjects, cluster volume was significantly correlated with verbal learning during FDG uptake.

  2. Measuring Complete 3D Vegetation Structure With Airborne Waveform Lidar: A Calibration and Validation With Terrestrial Lidar Derived Voxels

    NASA Astrophysics Data System (ADS)

    Hancock, S.; Anderson, K.; Disney, M.; Gaston, K. J.

    2015-12-01

    Accurate measurements of vegetation are vital to understand habitats and their provision of ecosystem services as well as having applications in satellite calibration, weather modelling and forestry. The majority of humans now live in urban areas and so understanding vegetation structure in these very heterogeneous areas is of importance. A number of previous studies have used airborne lidar (ALS) to characterise canopy height and canopy cover, but very few have fully characterised 3D vegetation, including understorey. Those that have either relied on leaf-off scans to allow unattenuated measurement of understorey or else did not validate. A method for creating a detailed voxel map of urban vegetation, in which the surface area of vegetation within a grid of cuboids (1.5m by 1.5m by 25 cm) is defined, from full-waveform ALS is presented. The ALS was processed with deconvolution and attenuation correction methods. The signal processing was calibrated and validated against synthetic waveforms generated from terrestrial laser scanning (TLS) data, taken as "truth". The TLS data was corrected for partial hits and attenuation using a voxel approach and these steps were validated and found to be accurate. The ALS results were benchmarked against the more common discrete return ALS products (produced automatically by the lidar manufacturer's algorithms) and Gaussian decomposition of full-waveform ALS. The true vegetation profile was accurately recreated by deconvolution. Far more detail was captured by the deconvolved waveform than either the discrete return or Gaussian decomposed ALS, particularly detail within the canopy; vital information for understanding habitats. In the paper, we will present the results with a focus on the methodological steps towards generating the voxel model, and the subsequent quantitative calibration and validation of the modelling approach using TLS. We will discuss the implications of the work for complete vegetation canopy descriptions in

  3. Towards biologically relevant indicators of forest structure using lacunarity approach based on voxelized LiDAR data

    NASA Astrophysics Data System (ADS)

    Székely, Balázs; Kania, Adam; Standovár, Tibor; Heilmeier, Hermann

    2014-05-01

    Considering the forest as a porous material that consists of the trees and other vegetation (representing the grains or aggregated grain groups) and the empty space between the plants (as the porous space in the analogy) this geometrical model provides a new approach to study the structure of the vegetation. Lacunarity, defined by Mandelbrot (1982), is a straightforward measure of structured empty space divided by the vegetation. This approach may allow the application of various concepts developed for porous media like tortuosity, percolation, directed percolation, anisotropic behaviour etc. The original LiDAR point cloud is voxelized using a voxel size determined by the point density. Our approach considers 2D and 3D lacunarities derived from the voxels; in 2D approach the topography-parallel and topography-perpendicular cross-sections are considered. In the latter case anisotropic behaviour can also be analysed. The lacunarity curves are evaluated in order to quantify the structural diversity that is positively related to species diversity. The relationship of vertical profile structural diversity to the richness of bird community has been widely shown in a wide range of forest types. The proposed method is able to characterize the structural differences that later can be related to the recognized relationships. Lacunarity curves can be further analysed to focus on both fine-scale (<10 m) and coarse-scale (100 ha) behaviour; comparison and categorization of lacunarity curve sections may reveal hidden spatial structural context. Application of the technology on multitemporal LiDAR surveys allows to detect the structural development after natural and human disturbances. BS contributed as Alexander von Humboldt Research Fellow, some of the used data have been acquired in the framework of the ChangeHabitats2 project, an IAPP project of the Marie Curie Actions of the European Commission. Mandelbrot, B. (1982): The fractal geometry of nature. Freeman, San Francisco.

  4. A voxel based comparative analysis using magnetization transfer imaging and T1-weighted magnetic resonance imaging in progressive supranuclear palsy

    PubMed Central

    Sandhya, Mangalore; Saini, Jitender; Pasha, Shaik Afsar; Yadav, Ravi; Pal, Pramod Kumar

    2014-01-01

    Aims: In progressive supranuclear palsy (PSP) tissue damage occurs in specific cortical and subcortical regions. Voxel based analysis using T1-weighted images depict quantitative gray matter (GM) atrophy changes. Magnetization transfer (MT) imaging depicts qualitative changes in the brain parenchyma. The purpose of our study was to investigate whether MT imaging could indicate abnormalities in PSP. Settings and Design: A total of 10 patients with PSP (9 men and 1 woman) and 8 controls (5 men and 3 women) were studied with T1-weighted magnetic resonance imaging (MRI) and 3DMT imaging. Voxel based analysis of T1-weighted MRI was performed to investigate brain atrophy while MT was used to study qualitative abnormalities in the brain tissue. We used SPM8 to investigate group differences (with two sample t-test) using the GM and white matter (WM) segmented data. Results: T1-weighted imaging and MT are equally sensitive to detect changes in GM and WM in PSP. Magnetization transfer ratio images and magnetization-prepared rapid acquisition of gradient echo revealed extensive bilateral volume and qualitative changes in the orbitofrontal, prefrontal cortex and limbic lobe and sub cortical GM. The prefrontal structures involved were the rectal gyrus, medial, inferior frontal gyrus (IFG) and middle frontal gyrus (MFG). The anterior cingulate, cingulate gyrus and lingual gyrus of limbic lobe and subcortical structures such as caudate, thalamus, insula and claustrum were also involved. Cerebellar involvement mainly of anterior lobe was also noted. Conclusions: The findings suggest that voxel based MT imaging permits a whole brain unbiased investigation of central nervous system structural integrity in PSP. PMID:25024571

  5. The influence of lithium on hippocampal volume in elderly bipolar patients: a study using voxel-based morphometry

    PubMed Central

    Zung, S; Souza-Duran, F L; Soeiro-de-Souza, M G; Uchida, R; Bottino, C M; Busatto, G F; Vallada, H

    2016-01-01

    Recent studies have demonstrated that lithium (Li) exerts neuronal protective and regenerative effects both in vitro and in vivo. However, the effects of long-term Li treatment in the brain areas associated with memory impairment of elderly bipolar patients are still unknown. The aim of this study was to compare the hippocampal volumes of elderly bipolar patients using Li, elderly bipolar patients not using Li and healthy controls. Sociodemographic, clinical and magnetic resonance imaging data from 30 elderly euthymic bipolar patients who had been using Li for an average of >61 months; 27 elderly euthymic bipolar patients not taking Li for an average of 45 months; and 22 elderly healthy controls were analyzed. Volumetric differences in the hippocampus between groups were investigated with voxel-based morphometry (VBM) based on the Statistical Parametric Mapping technique. No statistical differences in sociodemographic and clinical characteristics and course of bipolar disorder between the two bipolar groups were observed. Using small volume correction in the VBM analysis (analysis of variance (ANOVA)), one voxel cluster of statistical significance was detected in the left hippocampus (P<0.05 corrected for multiple comparisons, extent threshold >10 voxels). Post hoc unpaired t-tests revealed increased left hippocampal volume in the Li-treated group compared with the non-Li-treated group, and decreased left hippocampal volume in the non-Li group relative to controls. Additional exploratory two-group comparisons indicated trends toward reduced right-hippocampal volumes in the non-Li-treated group relative to both the Li-treated group and controls. The findings suggested that the use of Li may influence the volume of the hippocampus, possibly due to its neuroprotective effects. PMID:27351600

  6. Looking for Neuroimaging Markers in Frontotemporal Lobar Degeneration Clinical Trials: A Multi-Voxel Pattern Analysis Study in Granulin Disease.

    PubMed

    Premi, Enrico; Cauda, Franco; Costa, Tommaso; Diano, Matteo; Gazzina, Stefano; Gualeni, Vera; Alberici, Antonella; Archetti, Silvana; Magoni, Mauro; Gasparotti, Roberto; Padovani, Alessandro; Borroni, Barbara

    2016-01-01

    In light of future pharmacological interventions, neuroimaging markers able to assess the response to treatment would be crucial. In Granulin (GRN) disease, preclinical data will prompt pharmacological trials in the future. Two main points need to be assessed: (1) to identify target regions in different disease stages and (2) to determine the most accurate functional and structural neuroimaging index to be used. To this aim, we have taken advantage of the multivariate approach of multi-voxel pattern analysis (MVPA) to explore the information of brain activity patterns in a cohort of GRN Thr272fs carriers at different disease stages (14 frontotemporal dementia (FTD) patients and 17 asymptomatic carriers) and a group of 33 healthy controls. We studied structural changes by voxel-based morphometry (VBM), functional connectivity by assessing salience, default mode, fronto-parietal, dorsal attentional, executive networks, and local connectivity by regional homogeneity, amplitude of low frequency fluctuations (ALFF), fractional ALFF (fALFF), degree centrality, and voxel-mirrored homotopic connectivity. In FTD patients with GRN mutation, the most predictive measure was VBM structural analysis, while in asymptomatic carriers the best predictor marker was the local connectivity measure (fALFF). Altogether, all indexes demonstrated fronto-temporo-parietal damage in GRN pathology, with widespread structural damage of fronto-parietal and temporal regions when disease is overt. MVPA could be of aid in identifying the most accurate neuroimaging marker for clinical trials. This approach was able to identify both the target region and the best neuroimaging approach, which would be specific in the different disease stages. Further studies are needed to simultaneously integrate multimodal indexes in a classifier able to trace the disease progression moving from preclinical to clinical stage of the disease.

  7. Exploratory analysis of voxel size effects on CT measurements of situation characteristics of type point-to-point distance

    NASA Astrophysics Data System (ADS)

    Fernandes, T. L.; Donatelli, G. D.; Baldo, C. R.

    2016-07-01

    In recent years, computed tomography (CT) has been applied as an industrial metrology tool for the dimensional evaluation of visible and even hidden features of production parts in a non-destructive manner. Considering the experimental findings of a recent work of the authors, this paper deals with the effect of voxel size on measuring distances between feature-of-size centers, which would be less sensitive to edge offset errors. Particular attention is given to the design of experiment and to the measurement uncertainty sources. The most significant experimental findings are outlined and discussed in this paper.

  8. Modelling shallow urban geology using reservoir modelling techniques: voxel-based lithology and physical properties of the greater Glasgow area

    NASA Astrophysics Data System (ADS)

    Kingdon, Andrew; Williams, John D. O.; Williamson, J. Paul; Lark, R. Murray; Dobbs, Marcus R.; Kearsey, Timothy; Finlayson, Andrew; Campbell, S. Diarmad G.

    2013-04-01

    Conventional 3D geological models of lithostratigraphy undertaken by BGS have facilitated a significant step forward in understanding of the 3D sedimentological and structural controls in the subsurface of the UK. However, when lithostratigraphic units are mapped or modelled in 3D, intra-unit variability is often not recognized and may be substantial, particularly in sedimentologically heterogeneous successions. Because of this BGS has been testing voxel grid-based approaches in urban areas with high borehole density. A city-scale lithology model of shallow, unconsolidated sediments in Glasgow, Scotland has been developed as a test of the applicability of these techniques to aid geological understanding and possible future applications. This is of particular significance in this location due to the complex fluvial and glacial history of the superficial geology which alternates between inter-fingering sedimentary packages and short-scale variability of subsurface materials. The model has been created by developing a stochastic model of clastic geology on a voxel support, based on upscaling of observed borehole lithology, independent of lithostratigraphy. Multiple realisations of lithology were generated, each honouring the borehole observations. Lithology information has therefore been used to both develop a model of the distribution of lithology throughout the grid, but also to develop an understanding of the associated uncertainty by providing estimates of the probability with which a particular lithology occurs at a given node. This lithological model compares well with 'traditional' deterministic lithostratigraphic 3D models created in the same area, and with field-based geological maps. This lithological voxel model has been used as a matrix through which physical property data can be attributed within the grid by stochastic modelling and simulation of the variability of properties within the lithological units. Several different property datasets have been

  9. Structural Differences in Gray Matter between Glider Pilots and Non-Pilots. A Voxel-Based Morphometry Study

    PubMed Central

    Ahamed, Tosif; Kawanabe, Motoaki; Ishii, Shin; Callan, Daniel E.

    2014-01-01

    Glider flying is a unique skill that requires pilots to control an aircraft at high speeds in three dimensions and amidst frequent full-body rotations. In the present study, we investigated the neural correlates of flying a glider using voxel-based morphometry. The comparison between gray matter densities of 15 glider pilots and a control group of 15 non-pilots exhibited significant gray matter density increases in left ventral premotor cortex, anterior cingulate cortex, and the supplementary eye field. We posit that the identified regions might be associated with cognitive and motor processes related to flying, such as joystick control, visuo-vestibular interaction, and oculomotor control. PMID:25506339

  10. Shallow subsurface control on earthquake damage patterns: first results from a 3D geological voxel model study (Tokyo Lowland, Japan)

    NASA Astrophysics Data System (ADS)

    Stafleu, Jan; Busschers, Freek; Tanabe, Susumu

    2016-04-01

    The Tokyo Lowland is situated in a Neogene sedimentary basin near the triple junction of the North American, Pacific, and Philippine tectonic plates. The basin is filled with Neogene and Quaternary sediments up to a thickness of 3 km. In the upper 70 m of the basin, thick sequences of soft Holocene sediments occur which are assumed to have played a key role in the spatial variation of damage intensity during the 1923 Kanto earthquake (Magnitude 7.9 to 8.3). Historical records show this earthquake destroyed large parts of the Tokyo urban area which in that time was largely made up by wooden houses. Although the epicentre was 70 km to the southwest of Tokyo, severe damage occurred north of the city centre, presumably due to ground motion amplification in the soft Holocene sediments in the shallow subsurface. In order to assess the presumed relation between the damage pattern of the 1923 earthquake and the occurrence of soft Holocene sediments in the shallow subsurface, we constructed a 3D geological voxel model of the central part of the Tokyo Lowland. The model was constructed using a methodology originally developed for the lowlands of the Netherlands. The modelling workflow basically consists of three steps. First, some 10,000 borehole descriptions (gathered for geomechanical purposes), were subdivided into geological units that have uniform sediment characteristics, using both lithological and geomechanical (N-value) criteria. Second, 2D bounding surfaces were constructed, representing tops and bases of the geological units. These surfaces were used to place each voxel (100 by 100 by 1 m) within the correct geological unit. The N-values and lithological units in the borehole descriptions were subsequently used to perform a 3D stochastic interpolation of N-value and lithological class within each geological unit. Using a vertical voxel stack analysis, we were able to create a map showing the accumulated thickness of soft muds in the Holocene succession. A

  11. The effect of voxel size on dose distribution in Varian Clinac iX 6 MV photon beam using Monte Carlo simulation

    SciTech Connect

    Yani, Sitti; Dirgayussa, I Gde E.; Haryanto, Freddy; Arif, Idam; Rhani, Moh. Fadhillah

    2015-09-30

    Recently, Monte Carlo (MC) calculation method has reported as the most accurate method of predicting dose distributions in radiotherapy. The MC code system (especially DOSXYZnrc) has been used to investigate the different voxel (volume elements) sizes effect on the accuracy of dose distributions. To investigate this effect on dosimetry parameters, calculations were made with three different voxel sizes. The effects were investigated with dose distribution calculations for seven voxel sizes: 1 × 1 × 0.1 cm{sup 3}, 1 × 1 × 0.5 cm{sup 3}, and 1 × 1 × 0.8 cm{sup 3}. The 1 × 10{sup 9} histories were simulated in order to get statistical uncertainties of 2%. This simulation takes about 9-10 hours to complete. Measurements are made with field sizes 10 × 10 cm2 for the 6 MV photon beams with Gaussian intensity distribution FWHM 0.1 cm and SSD 100.1 cm. MC simulated and measured dose distributions in a water phantom. The output of this simulation i.e. the percent depth dose and dose profile in d{sub max} from the three sets of calculations are presented and comparisons are made with the experiment data from TTSH (Tan Tock Seng Hospital, Singapore) in 0-5 cm depth. Dose that scored in voxels is a volume averaged estimate of the dose at the center of a voxel. The results in this study show that the difference between Monte Carlo simulation and experiment data depend on the voxel size both for percent depth dose (PDD) and profile dose. PDD scan on Z axis (depth) of water phantom, the big difference obtain in the voxel size 1 × 1 × 0.8 cm{sup 3} about 17%. In this study, the profile dose focused on high gradient dose area. Profile dose scan on Y axis and the big difference get in the voxel size 1 × 1 × 0.1 cm{sup 3} about 12%. This study demonstrated that the arrange voxel in Monte Carlo simulation becomes important.

  12. The effect of voxel size on dose distribution in Varian Clinac iX 6 MV photon beam using Monte Carlo simulation

    NASA Astrophysics Data System (ADS)

    Yani, Sitti; Dirgayussa, I. Gde E.; Rhani, Moh. Fadhillah; Haryanto, Freddy; Arif, Idam

    2015-09-01

    Recently, Monte Carlo (MC) calculation method has reported as the most accurate method of predicting dose distributions in radiotherapy. The MC code system (especially DOSXYZnrc) has been used to investigate the different voxel (volume elements) sizes effect on the accuracy of dose distributions. To investigate this effect on dosimetry parameters, calculations were made with three different voxel sizes. The effects were investigated with dose distribution calculations for seven voxel sizes: 1 × 1 × 0.1 cm3, 1 × 1 × 0.5 cm3, and 1 × 1 × 0.8 cm3. The 1 × 109 histories were simulated in order to get statistical uncertainties of 2%. This simulation takes about 9-10 hours to complete. Measurements are made with field sizes 10 × 10 cm2 for the 6 MV photon beams with Gaussian intensity distribution FWHM 0.1 cm and SSD 100.1 cm. MC simulated and measured dose distributions in a water phantom. The output of this simulation i.e. the percent depth dose and dose profile in dmax from the three sets of calculations are presented and comparisons are made with the experiment data from TTSH (Tan Tock Seng Hospital, Singapore) in 0-5 cm depth. Dose that scored in voxels is a volume averaged estimate of the dose at the center of a voxel. The results in this study show that the difference between Monte Carlo simulation and experiment data depend on the voxel size both for percent depth dose (PDD) and profile dose. PDD scan on Z axis (depth) of water phantom, the big difference obtain in the voxel size 1 × 1 × 0.8 cm3 about 17%. In this study, the profile dose focused on high gradient dose area. Profile dose scan on Y axis and the big difference get in the voxel size 1 × 1 × 0.1 cm3 about 12%. This study demonstrated that the arrange voxel in Monte Carlo simulation becomes important.

  13. Two-voxel spectroscopy with dynamic B0 shimming and flip angle adjustment at 7 T in the human motor cortex.

    PubMed

    Lemke, Clark; Hess, Aaron; Clare, Stuart; Bachtiar, Velicia; Stagg, Charlotte; Jezzard, Peter; Emir, Uzay

    2015-07-01

    The aim of this study was to acquire high-quality in vivo (1) H spectra concurrently from two voxels at ultra-high field (7 T) without specialized hardware. To this end, an acquisition scheme was developed in which first-order shims and flip angles are dynamically updated to acquire spectra from both of the brain's motor cortices in an alternating fashion. To validate this acquisition scheme, separate, static, single-voxel acquisitions were also performed for comparison. Six subjects were examined using semi-LASER spectroscopy at 7 T. Barium titanate pads were used to increase the extent of the effective transmit field (B1 (+) ). Spectra were obtained from the hand area of both motor cortices for both acquisition schemes. LCModel was used to determine neurochemical profiles in order to examine variations between acquisition schemes and volumes of interest. The dynamic two-voxel acquisition protocol produced water linewidths (full width at half-maximum between 11.6 and 12.8 Hz) and signal-to-noise ratios similar to those from static single-voxel measurements. The concentrations of 13 individual and 3 combined metabolites with Cramér-Rao lower bounds below 30% were reliably detected for both acquisition schemes, and agreed well with previous postmortem assay and spectroscopy studies. The results show that high spectral quality from two voxels can be acquired concurrently without specialized hardware. This practical technique can be applied to many neuroscience applications.

  14. Improvements in the Quantitative Assessment of Cerebral Blood Volume and Flow with the Removal of Vessel Voxels from MR Perfusion Images

    PubMed Central

    Teng, Michael Mu Huo; Cho, I-Chieh; Kao, Yi-Hsuan; Chuang, Chi-Shuo; Chiu, Fang-Ying; Chang, Feng-Chi

    2013-01-01

    Objective. To improve the quantitative assessment of cerebral blood volume (CBV) and flow (CBF) in the brain voxels from MR perfusion images. Materials and Methods. Normal brain parenchyma was automatically segmented with the time-to-peak criteria after cerebrospinal fluid removal and preliminary vessel voxel removal. Two scaling factors were calculated by comparing the relative CBV and CBF of the segmented normal brain parenchyma with the absolute values in the literature. Using the scaling factors, the relative values were converted to the absolute CBV and CBF. Voxels with either CBV > 8 mL/100 g or CBF > 100 mL/100 g/min were characterized as vessel voxels and were excluded from the quantitative measurements. Results. The segmented brain parenchyma with normal perfusion was consistent with the angiographic findings for each patient. We confirmed the necessity of dual thresholds including CBF and CBV for proper removal of vessel voxels. The scaling factors were 0.208 ± 0.041 for CBV, and 0.168 ± 0.037, 0.172 ± 0.037 for CBF calculated using standard and circulant singular value decomposition techniques, respectively. Conclusion. The automatic scaling and vessel removal techniques provide an alternative method for obtaining improved quantitative assessment of CBV and CBF in patients with thromboembolic cerebral arterial disease. PMID:23586033

  15. Fast voxel-level dosimetry for (177)Lu labelled peptide treatments.

    PubMed

    Hippeläinen, E; Tenhunen, M; Sohlberg, A

    2015-09-01

    In peptide receptor radionuclide therapy (PRRT), voxel-level radiation absorbed dose calculations can be performed using several different methods. Each method has it strengths and weaknesses; however, Monte Carlo (MC) simulation is presently considered the most accurate method at providing absorbed dose distributions. Unfortunately MC simulation is time-consuming and often impractical to carry out in a clinical practice. In this work, a fast semi-Monte Carlo (sMC) absorbed dose calculation method for (177)Lu PRRT dosimetry is presented. The sMC method is based on a local electron absorption assumption and fast photon MC simulations. The sMC method is compared against full MC simulation code built on PENELOPE (vxlPen) using digital phantoms to assess the accuracy of these assumptions.Due to the local electron absorption assumption of sMC, the potential errors in cross-fire dose from electrons and photons emitted by (177)Lu were first evaluated using an ellipsoidal kidney model by comparing vxlPen and sMC. The photon cross-fire dose from background to kidney and kidney to background with varying kidney-to-background activity concentration ratios were calculated. In addition, kidney to kidney photon and electron cross-dose with different kidney to kidney distances were studied. Second, extended cardiac-torso (XCAT) phantoms were created with liver lesions and with realistic activity distributions and tissue densities. The XCAT phantoms were used to simulate SPECT projections and 3D activity distribution images were reconstructed using an OSEM algorithm. Image-based dose rate distributions were calculated using vxlPen and sMC. Total doses and dose rate volume histograms (DrVH) produced by the two methods were compared.The photon cross-fire dose from the kidney increased the background's absorbed dose by 5% or more up to 5.8 cm distance with 20 : 1 kidney to background activity concentration ratio. On the other hand, the photon cross-fire dose from the background to

  16. Fast voxel-level dosimetry for 177Lu labelled peptide treatments

    NASA Astrophysics Data System (ADS)

    Hippeläinen, E.; Tenhunen, M.; Sohlberg, A.

    2015-09-01

    In peptide receptor radionuclide therapy (PRRT), voxel-level radiation absorbed dose calculations can be performed using several different methods. Each method has it strengths and weaknesses; however, Monte Carlo (MC) simulation is presently considered the most accurate method at providing absorbed dose distributions. Unfortunately MC simulation is time-consuming and often impractical to carry out in a clinical practice. In this work, a fast semi-Monte Carlo (sMC) absorbed dose calculation method for 177Lu PRRT dosimetry is presented. The sMC method is based on a local electron absorption assumption and fast photon MC simulations. The sMC method is compared against full MC simulation code built on PENELOPE (vxlPen) using digital phantoms to assess the accuracy of these assumptions. Due to the local electron absorption assumption of sMC, the potential errors in cross-fire dose from electrons and photons emitted by 177Lu were first evaluated using an ellipsoidal kidney model by comparing vxlPen and sMC. The photon cross-fire dose from background to kidney and kidney to background with varying kidney-to-background activity concentration ratios were calculated. In addition, kidney to kidney photon and electron cross-dose with different kidney to kidney distances were studied. Second, extended cardiac-torso (XCAT) phantoms were created with liver lesions and with realistic activity distributions and tissue densities. The XCAT phantoms were used to simulate SPECT projections and 3D activity distribution images were reconstructed using an OSEM algorithm. Image-based dose rate distributions were calculated using vxlPen and sMC. Total doses and dose rate volume histograms (DrVH) produced by the two methods were compared. The photon cross-fire dose from the kidney increased the background’s absorbed dose by 5% or more up to 5.8 cm distance with 20 : 1 kidney to background activity concentration ratio. On the other hand, the photon cross-fire dose from the background to

  17. Fast voxel-level dosimetry for (177)Lu labelled peptide treatments.

    PubMed

    Hippeläinen, E; Tenhunen, M; Sohlberg, A

    2015-09-01

    In peptide receptor radionuclide therapy (PRRT), voxel-level radiation absorbed dose calculations can be performed using several different methods. Each method has it strengths and weaknesses; however, Monte Carlo (MC) simulation is presently considered the most accurate method at providing absorbed dose distributions. Unfortunately MC simulation is time-consuming and often impractical to carry out in a clinical practice. In this work, a fast semi-Monte Carlo (sMC) absorbed dose calculation method for (177)Lu PRRT dosimetry is presented. The sMC method is based on a local electron absorption assumption and fast photon MC simulations. The sMC method is compared against full MC simulation code built on PENELOPE (vxlPen) using digital phantoms to assess the accuracy of these assumptions.Due to the local electron absorption assumption of sMC, the potential errors in cross-fire dose from electrons and photons emitted by (177)Lu were first evaluated using an ellipsoidal kidney model by comparing vxlPen and sMC. The photon cross-fire dose from background to kidney and kidney to background with varying kidney-to-background activity concentration ratios were calculated. In addition, kidney to kidney photon and electron cross-dose with different kidney to kidney distances were studied. Second, extended cardiac-torso (XCAT) phantoms were created with liver lesions and with realistic activity distributions and tissue densities. The XCAT phantoms were used to simulate SPECT projections and 3D activity distribution images were reconstructed using an OSEM algorithm. Image-based dose rate distributions were calculated using vxlPen and sMC. Total doses and dose rate volume histograms (DrVH) produced by the two methods were compared.The photon cross-fire dose from the kidney increased the background's absorbed dose by 5% or more up to 5.8 cm distance with 20 : 1 kidney to background activity concentration ratio. On the other hand, the photon cross-fire dose from the background to

  18. Combining terrestrial stereophotogrammetry, DGPS and GIS-based 3D voxel modelling in the volumetric recording of archaeological features

    NASA Astrophysics Data System (ADS)

    Orengo, Hector A.

    2013-02-01

    Archaeological recording of structures and excavations in high mountain areas is greatly hindered by the scarce availability of both space, to transport material, and time. The Madriu-Perafita-Claror, InterAmbAr and PCR Mont Lozère high mountain projects have documented hundreds of archaeological structures and carried out many archaeological excavations. These projects required the development of a technique which could record both structures and the process of an archaeological excavation in a fast and reliable manner. The combination of DGPS, close-range terrestrial stereophotogrammetry and voxel based GIS modelling offered a perfect solution since it helped in developing a strategy which would obtain all the required data on-site fast and with a high degree of precision. These data are treated off-site to obtain georeferenced orthoimages covering both the structures and the excavation process from which site and excavation plans can be created. The proposed workflow outputs also include digital surface models and volumetric models of the excavated areas from which topography and archaeological profiles were obtained by voxel-based GIS procedures. In this way, all the graphic recording required by standard archaeological practices was met.

  19. Usefulness of voxel-based lesion mapping for predicting motor recovery in subjects with basal ganglia hemorrhage

    PubMed Central

    Kim, Dae Hyun; Kyeong, Sunghyon; Cho, Yoona; Jung, Tae-min; Ahn, Sung Jun; Park, Yoon Ghil

    2016-01-01

    Abstract It is important to estimate motor recovery in the early phase after stroke. Many studies have demonstrated that both diffusion tensor tractography (DTT) and motor-evoked potentials (MEP) are valuable predictors of motor recovery, but these modalities do not directly reflect the status of the injured gray matter. We report on 2 subjects with basal ganglia hemorrhage who showed similar DTT and MEP findings, but had markedly different clinical outcomes. Specifically, Subject 1 showed no improvement in motor function, whereas Subject 2 exhibited substantial improvement 7 weeks after onset. To determine if differences in gray matter might lend insight into these different outcomes, we analyzed gray matter lesions of the 2 subjects using a novel voxel-based lesion mapping method. The lesion of Subject 1 mainly included the putamen, thalamus, and Heschl's gyri, indicating extension of the hemorrhage in the posterior direction. In contrast, the lesion of Subject 2 mainly included the putamen, insula, and pallidum, indicating that the hemorrhage extended anterior laterally. These differential findings suggest that voxel-based gray matter lesion mapping may help to predict differential motor recovery in subjects with basal ganglia hemorrhage with similar DTT and MEP findings. PMID:27281090

  20. FDTD calculations of SAR for child voxel models in different postures between 10 MHz and 3 GHz.

    PubMed

    Findlay, R P; Lee, A-K; Dimbylow, P J

    2009-08-01

    Calculations of specific energy absorption rate (SAR) have been performed on the rescaled NORMAN 7-y-old voxel model and the Electronics and Telecommunications Research Institute (ETRI) child 7-y-old voxel model in the standing arms down, arms up and sitting postures. These calculations were for plane-wave exposure under isolated and grounded conditions between 10 MHz and 3 GHz. It was found that there was little difference at each resonant frequency between the whole-body averaged SAR values calculated for the NORMAN and ETRI 7-y-old models for each of the postures studied. However, when compared with the arms down posture, raising the arms increased the SAR by up to 25%. Electric field values required to produce the International Commission on Non-Ionizing Radiation Protection and Institute of Electrical and Electronic Engineers public basic restriction were calculated, and compared with reference levels for the different child models and postures. These showed that, under certain worst-case exposure conditions, the reference levels may not be conservative.

  1. Grey matter damage in progressive multiple sclerosis versus amyotrophic lateral sclerosis: a voxel-based morphometry MRI study.

    PubMed

    Tavazzi, Eleonora; Laganà, Maria Marcella; Bergsland, Niels; Tortorella, Paola; Pinardi, Giovanna; Lunetta, Christian; Corbo, Massimo; Rovaris, Marco

    2015-03-01

    Primary progressive multiple sclerosis (PPMS) and amyotrophic lateral sclerosis (ALS) seem to share some clinical and pathological features. MRI studies revealed the presence of grey matter (GM) atrophy in both diseases, but no comparative data are available. The objective was to compare the regional patterns of GM tissue loss in PPMS and ALS with voxel-based morphometry (VBM). Eighteen PPMS patients, 20 ALS patients, and 31 healthy controls (HC) were studied with a 1.5 Tesla scanner. VBM was performed to assess volumetric GM differences with age and sex as covariates. Threshold-free cluster enhancement analysis was used to obtain significant clusters. Group comparisons were tested with family-wise error correction for multiple comparisons (p < 0.05) except for HC versus MND which was tested at a level of p < 0.001 uncorrected and a cluster threshold of 20 contiguous voxels. Compared to HC, ALS patients showed GM tissue reduction in selected frontal and temporal areas, while PPMS patients showed a widespread bilateral GM volume decrease, involving both deep and cortical regions. Compared to ALS, PPMS patients showed tissue volume reductions in both deep and cortical GM areas. This preliminary study confirms that PPMS is characterized by a more diffuse cortical and subcortical GM atrophy than ALS and that, in the latter condition, brain damage is present outside the motor system. These results suggest that PPMS and ALS may share pathological features leading to GM tissue loss.

  2. Sparse reduced-rank regression detects genetic associations with voxel-wise longitudinal phenotypes in Alzheimer’s disease

    PubMed Central

    Vounou, Maria; Janousova, Eva; Wolz, Robin; Stein, Jason L.; Thompson, Paul M.; Rueckert, Daniel; Montana, Giovanni

    2012-01-01

    Scanning the entire genome in search of variants related to imaging phenotypes holds great promise in elucidating the genetic etiology of neurodegenerative disorders. Here we discuss the application of a penalized multivariate model, sparse reduced-rank regression (sRRR), for the genome-wide detection of markers associated with voxel-wise longitudinal changes in the brain caused by Alzheimer’s disease (AD). Using a sample from the Alzheimer’s Disease Neuroimaging Initiative database, we performed three separate studies that each compared two groups of individuals to identify genes associated with disease development and progression. For each comparison we took a two-step approach: initially, using penalized linear discriminant analysis, we identified voxels that provide an imaging signature of the disease with high classification accuracy; then we used this multivariate biomarker as a phenotype in a genome-wide association study, carried out using sRRR. The genetic markers were ranked in order of importance of association to the phenotypes using a data re-sampling approach. Our findings confirmed the key role of the APOE and TOMM40 genes but also highlighted some novel potential associations with AD. PMID:22209813

  3. Structural brain abnormalities in patients with Parkinson's disease with visual hallucinations: a comparative voxel-based analysis.

    PubMed

    Gama, Romulo Lopes; Bruin, Veralice Meireles Sales; Távora, Daniel Gurgel Fernandes; Duran, Fábio L S; Bittencourt, Lia; Tufik, Sergio

    2014-06-01

    The objective is to evaluate clinical characteristics and cerebral alterations in Parkinson's disease (PD) patients with diurnal visual hallucinations (VHs). Assessment was performed using magnetic resonance image (MRI) and voxel-based morphometry (VBM). Thirty-nine patients with PD (53.8%) and ten controls were studied. Voxel based morphology analysis was performed. Eleven patients presented diurnal VHs and among these, six had cognitive dysfunction. Patients with VHs performed worse in the mentation-related UPDRS I (p=0.005) and motor-related UPDRS III (p=0.02). Patients with VHs showed significant clusters of reduced grey matter volume compared to controls in the left opercula frontal gyrus and left superior frontal gyrus. PD without hallucinations demonstrated reduced grey matter volume in the left superior frontal gyrus compared to controls. Comparisons between patients with VHs regarding the presence of cognitive dysfunction showed that cases with cognitive dysfunction as compared to those without cognitive dysfunction showed significant clusters of reduced grey matter volume in the left opercular frontal gyrus. Cases without cognitive dysfunction had reduced grey matter substance in the left insula and left trigonal frontal gyrus. Judging from our findings, an abnormal frontal cortex, particularly left sided insula, frontal opercular, trigonal frontal gyrus and orbital frontal would make PD patients vulnerable to hallucinations. Compromise of the left operculum distinguished cases with VHs and cognitive dysfunction. Our findings reinforce the theoretical concept of a top-down visual processing in the genesis of VHs in PD.

  4. Spatial Mapping of Protein Abundances in the Mouse Brain by Voxelation Integrated with High-Throughput Liquid Chromatography - Mass Spectrometry

    SciTech Connect

    Petyuk, Vladislav A; Qian, Weijun; Chin, Mark H; Wang, Haixing H; Livesay, Eric A; Monroe, Matthew E; Adkins, Joshua N; Jaitly, Navdeep; Anderson, David J; Camp, David G; Smith, Desmond J; Smith, Richard D

    2007-01-25

    Temporally and spatially resolved mapping of protein abundance patterns within the mammalian brain is of significant interest for understanding brain function and molecular etiologies of neurodegenerative diseases; however, such imaging efforts have been greatly challenged by complexity of the proteome, throughput and sensitivity of applied analytical methodologies, and accurate quantitation of protein abundances across the brain. Here, we describe a methodology for comprehensive spatial proteome mapping that addresses these challenges by employing voxelation integrated with automated microscale sample processing, high-throughput LC system coupled with high resolution Fourier transform ion cyclotron mass spectrometer and a “universal” stable isotope labeled reference sample approach for robust quantitation. We applied this methodology as a proof-of-concept trial for the analysis of protein distribution within a single coronal slice of a C57BL/6J mouse brain. For relative quantitation of the protein abundances across the slice, an 18O-isotopically labeled reference sample, derived from a whole control coronal slice from another mouse, was spiked into each voxel sample and stable isotopic intensity ratios were used to obtain measures of relative protein abundances. In total, we generated maps of protein abundance patterns for 1,028 proteins. The significant agreement of the protein distributions with previously reported data supports the validity of this methodology, which opens new opportunities for studying the spatial brain proteome and its dynamics during the course of disease progression and other important biological and associated health aspects in a discovery-driven fashion.

  5. Multi-voxel magnetic resonance spectroscopy of cerebral metabolites in healthy dogs at 1.5 Tesla

    PubMed Central

    Choi, Sooyoung; Song, Yumi; Lee, Kija; Lee, Youngwon

    2016-01-01

    This study was conducted to measure the difference in levels of cerebral metabolites in the right and left hemispheres, gray (GM) and white matter (WM), imaging planes, and anatomical regions of healthy dogs to establish normal variations. Eight male Beagle dogs (1 to 4 years of age; mean age, 2 years) with no evidence of neurologic disease were studied. Using the multi-voxel technique on a 1.5 Tesla magnetic resonance imaging scanner, metabolite values (N-acetyl aspartate [NAA], choline [Cho], creatine [Cr]) were obtained from the frontoparietal WM, parietal GM, temporal GM, occipital GM, thalamus, cerebellum, mid-brain, and pons. There was no significant difference in levels of these metabolites between the right and left in any locations or between the GM and WM in the cerebral hemispheres. However, there were significant differences in metabolite ratios within imaging planes. The NAA/Cr was lower in the cerebellum than other regions and the thalamus had a higher Cho/Cr and lower NAA/Cho ratio than in other regions. The spectral and metabolic values will provide a useful internal reference for clinical practice and research involving multi-voxel magnetic resonance spectroscopy. Measurement of metabolite values in the transverse plane is recommended for comparing levels of regional metabolites. PMID:26645339

  6. Cognitive 3D geological voxel modelling based on AEM and seismic data - a case from the southern part of Denmark

    NASA Astrophysics Data System (ADS)

    Jørgensen, Flemming; Møller, Rasmus R.; Sandersen, Peter B. E.; Høyer, Anne-Sophie

    2013-04-01

    high quality sediment samples and down-hole geophysical logs. A comprehensive geological overview and understanding of the area is gained by integrated and cognitive interpretation of the geophysical and geological data enabling a detailed and reliable 3D geological model to be built. The model covers the area on the Danish side of the border. In order to address the detailed information from the SkyTEM data, the model has been constructed as a voxel model combined with surfaces representing layer boundaries and unconformities. Lithofacies and interpretation uncertainty attributes have been added to each voxel. Geostatistic inversion has been used to distribute lithological parameters to voxels in the most complicated areas of the model (areas with glaciotectonism). Experiments with octree modelling giving a high resolution with a limited number of voxels have also been performed. The final 3D model is primarily intended to serve as an input for groundwater flow modelling. The voxel model will therefore be supplemented by another attribute, hydraulic conductivity.

  7. Organ Dose-Rate Calculations for Small Mammals at Maralinga, the Nevada Test Site, Hanford and Fukushima: A Comparison of Ellipsoidal and Voxelized Dosimetric Methodologies.

    PubMed

    Caffrey, Emily A; Johansen, Mathew P; Higley, Kathryn A

    2015-10-01

    Radiological dosimetry for nonhuman biota typically relies on calculations that utilize the Monte Carlo simulations of simple, ellipsoidal geometries with internal radioactivity distributed homogeneously throughout. In this manner it is quick and easy to estimate whole-body dose rates to biota. Voxel models are detailed anatomical phantoms that were first used for calculating radiation dose to humans, which are now being extended to nonhuman biota dose calculations. However, if simple ellipsoidal models provide conservative dose-rate estimates, then the additional labor involved in creating voxel models may be unnecessary for most scenarios. Here we show that the ellipsoidal method provides conservative estimates of organ dose rates to small mammals. Organ dose rates were calculated for environmental source terms from Maralinga, the Nevada Test Site, Hanford and Fukushima using both the ellipsoidal and voxel techniques, and in all cases the ellipsoidal method yielded more conservative dose rates by factors of 1.2-1.4 for photons and 5.3 for beta particles. Dose rates for alpha-emitting radionuclides are identical for each method as full energy absorption in source tissue is assumed. The voxel procedure includes contributions to dose from organ-to-organ irradiation (shown here to comprise 2-50% of total dose from photons and 0-93% of total dose from beta particles) that is not specifically quantified in the ellipsoidal approach. Overall, the voxel models provide robust dosimetry for the nonhuman mammals considered in this study, and though the level of detail is likely extraneous to demonstrating regulatory compliance today, voxel models may nevertheless be advantageous in resolving ongoing questions regarding the effects of ionizing radiation on wildlife.

  8. Skeletal dosimetry for external exposures to photons based on {mu}CT images of spongiosa: Consideration of voxel resolution, cluster size, and medullary bone surfaces

    SciTech Connect

    Kramer, R.; Khoury, H. J.; Vieira, J. W.; Brown, K. A. Robson

    2009-11-15

    Skeletal dosimetry based on {mu}CT images of trabecular bone has recently been introduced to calculate the red bone marrow (RBM) and the bone surface cell (BSC) equivalent doses in human phantoms for external exposure to photons. In order to use the {mu}CT images for skeletal dosimetry, spongiosa voxels in the skeletons were replaced at run time by so-called micromatrices, which have exactly the size of a spongiosa voxel and contain segmented trabecular bone and marrow microvoxels. A cluster (=parallelepiped) of 2x2x2=8 micromatrices was used systematically and periodically throughout the spongiosa volume during the radiation transport calculation. Systematic means that when a particle leaves a spongiosa voxel to enter into a neighboring spongiosa voxel, then the next micromatrix in the cluster will be used. Periodical means that if the particle travels through more than two spongiosa voxels in a row, then the cluster will be repeated. Based on the bone samples available at the time, clusters of up to 3x3x3=27 micromatrices were studied. While for a given trabecular bone volume fraction the whole-body RBM equivalent dose showed converging results for cluster sizes between 8 and 27 micromatrices, this was not the case for the BSC equivalent dose. The BSC equivalent dose seemed to be very sensitive to the number, form, and thickness of the trabeculae. In addition, the cluster size and/or the microvoxel resolution were considered to be possible causes for the differences observed. In order to resolve this problem, this study used a bone sample large enough to extract clusters containing up to 8x8x8=512 micromatrices and which was scanned with two different voxel resolutions. Taking into account a recent proposal, this investigation also calculated the BSC equivalent dose on medullary surfaces of cortical bone in the arm and leg bones. The results showed (1) that different voxel resolutions have no effect on the RBM equivalent dose but do influence the BSC equivalent

  9. 27 CFR 9.175 - Dos Rios.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... TREASURY LIQUORS AMERICAN VITICULTURAL AREAS Approved American Viticultural Areas § 9.175 Dos Rios. (a... is located in northern Mendocino County, California, at the confluence of the Eel River and the Middle Fork of the Eel River. The area's boundaries are defined as follows— (1) Beginning in...

  10. "DOS for Managers." Management Training Series.

    ERIC Educational Resources Information Center

    Marion County Schools, Fairmont, WV.

    A plan is provided for a lesson on disk operating systems (DOS) for managers. Twenty-five lesson objectives are listed, followed by suggestions for learning activities and special resources. In the presentation section, key points and content are provided for 25 instructional topics that correspond to the 25 lesson objectives. The topics are as…

  11. Uso de modelos mecânicos em curso informal de astronomia para deficientes visuais. Resgate de uma experiência

    NASA Astrophysics Data System (ADS)

    Tavares, E. T., Jr.; Klafke, J. C.

    2003-08-01

    O presente trabalho propõe-se a resgatar uma experiência que teve lugar no Planetário de São Paulo nos anos 60. Em 1962, o Sr. Acácio, então com 37 anos, deficiente visual desde os 27, passou a assistir às aulas ministradas pelo Prof. Aristóteles Orsini aos integrantes do corpo de servidores do Planetário. O Sr. Acácio era o único deficiente da turma e, embora possuísse conhecimentos básicos e relativamente avançados de matemática, enfrentava dificuldades na compreensão e acompanhamento da exposição, como também em estudos posteriores. Com o intuito de auxiliá-lo na superação desses problemas, o Prof. Orsini solicitou a construção de modelos mecânicos que, através do sentido do tato, permitissem o acompanhamento das aulas e a transposição do modelo para o "constructo" mental. Essa prática mostrou-se tão eficaz que facilitou sobejamente o aprendizado da matéria pelo sujeito. O Sr. Acácio passou a integrar o corpo de professores do Planetário/Escola Municipal de Astrofísica, tendo ficado responsável pelo curso de "Introdução à Astronomia" por vários anos. Além disso, a experiência foi tão bem sucedida que alguns dos modelos tiveram seus elementos constitutivos pintados diferencialmente para serem utilizados em cursos regulares do Planetário, tornando-se parte integrante do conjunto de recursos didáticos da instituição. É pensando nessa eficácia, tanto em seu objetivo original permitir o aprendizado de um deficiente visual quanto no subsidiário recurso didático sistemático da instituição que decidimos resgatar essa experiência. Estribados nela, acreditamos ser extremamente produtivo, em termos educacionais, o aperfeiçoamento dos modelos originais, agora resgatados e restaurados, e a criação de outros que pudessem ser utilizados no ensino dessa ciência a deficientes visuais.

  12. Compositionality and the angular gyrus: A multi-voxel similarity analysis of the semantic composition of nouns and verbs.

    PubMed

    Boylan, Christine; Trueswell, John C; Thompson-Schill, Sharon L

    2015-11-01

    The cognitive and neural systems that enable conceptual processing must support the ability to combine (and recombine) concepts to form an infinite number of ideas. Two candidate neural systems for conceptual combination-the left anterior temporal lobe (ATL) and the left angular gyrus (AG)-have been characterized as "semantic hubs" due to both functional and anatomical properties; however, these two regions likely support different aspects of composition. Here we consider two hypotheses for the role of AG in conceptual combination, both of which differ from a putative role for the ATL in "feature-based" combinatorics (i.e., meaning derived by combining concepts' features). Firstly, we examine whether AG is more sensitive to function-argument relations of the sort that arise when a predicate is combined with its arguments. Secondly, we examine the non-mutually exclusive possibility that AG represents information carried on a verb in particular, whether this be information about event composition or about thematic relations denoted uniquely by verbs. We identified voxels that respond differentially to two-word versus one-word stimuli, and we measured the similarity of the patterns in these voxels evoked by (1) pairs of two-word phrases that shared a noun that was an argument, thus sharing function-argument composition (e.g. eats meat and with meat), in comparison with two-word phrases that shared only a noun, not an argument (e.g., eats meat and tasty meat); and (2) stimulus pairs that shared only an event (operationalized here as sharing a verb; e.g. eats meat and eats quickly), in comparison to both of the above. We found that activity patterns in left AG tracked information relating to the presence of an event-denoting verb in a pair of two-word phrases. We also found that the neural similarity in AG voxel patterns between two phrases sharing a verb correlated with subjects' ratings of how similar the meanings of those two verb phrases were. These findings

  13. Single-shot single-voxel lactate measurements using FOCI-LASER and a multiple-quantum filter.

    PubMed

    Payne, Geoffrey S; deSouza, Nandita M; Messiou, Christina; Leach, Martin O

    2015-04-01

    Measurement of tissue lactate using (1) H MRS is often confounded by overlap with intense lipid signals at 1.3 ppm. Single-voxel localization using PRESS is also compromised by the large chemical shift displacement between voxels for the 4.1 ppm (-CH) resonance and the 1.3 ppm -CH3 resonance, leading to subvoxels with signals of opposite phase and hence partial signal cancellation. To reduce the chemical shift displacement to negligible proportions, a modified semi-LASER sequence was written ("FOCI-LASER", abbreviated as fLASER) using FOCI pulses to permit high RF bandwidth even with the limited RF amplitude characteristic of clinical MRI scanners. A further modification, MQF-fLASER, includes a selective multiple-quantum filter to detect lactate and reject lipid signals. The sequences were implemented on a Philips 3 T Achieva TX system. In a solution of brain metabolites fLASER lactate signals were 2.7 times those of PRESS. MQF-fLASER lactate was 47% of fLASER (the theoretical maximum is 50%) but still larger than PRESS lactate. In oil, the main 1.3 ppm lipid peak was suppressed to less than 1%. Enhanced suppression was possible using increased gradient durations. The minimum detectable lactate concentration was approximately 0.5 mM. Coherence selection gradients needed to be at the magic angle to avoid large water signals derived from intermolecular multiple-quantum coherences. In pilot patient measurements, lactate peaks were often observed in brain tumours, but not in cervix tumours; lipids were effectively suppressed. In summary, compared with PRESS, the fLASER sequence yields greatly superior sensitivity for direct detection of lactate (and equivalent sensitivity for other metabolites), while the single-voxel single-shot MQF-fLASER sequence surpasses PRESS for lactate detection while eliminating substantial signals from lipids. This sequence will increase the potential for in vivo lactate measurement as a biomarker in targeted anti-cancer treatments as well as

  14. Compositionality and the angular gyrus: A multi-voxel similarity analysis of the semantic composition of nouns and verbs.

    PubMed

    Boylan, Christine; Trueswell, John C; Thompson-Schill, Sharon L

    2015-11-01

    The cognitive and neural systems that enable conceptual processing must support the ability to combine (and recombine) concepts to form an infinite number of ideas. Two candidate neural systems for conceptual combination-the left anterior temporal lobe (ATL) and the left angular gyrus (AG)-have been characterized as "semantic hubs" due to both functional and anatomical properties; however, these two regions likely support different aspects of composition. Here we consider two hypotheses for the role of AG in conceptual combination, both of which differ from a putative role for the ATL in "feature-based" combinatorics (i.e., meaning derived by combining concepts' features). Firstly, we examine whether AG is more sensitive to function-argument relations of the sort that arise when a predicate is combined with its arguments. Secondly, we examine the non-mutually exclusive possibility that AG represents information carried on a verb in particular, whether this be information about event composition or about thematic relations denoted uniquely by verbs. We identified voxels that respond differentially to two-word versus one-word stimuli, and we measured the similarity of the patterns in these voxels evoked by (1) pairs of two-word phrases that shared a noun that was an argument, thus sharing function-argument composition (e.g. eats meat and with meat), in comparison with two-word phrases that shared only a noun, not an argument (e.g., eats meat and tasty meat); and (2) stimulus pairs that shared only an event (operationalized here as sharing a verb; e.g. eats meat and eats quickly), in comparison to both of the above. We found that activity patterns in left AG tracked information relating to the presence of an event-denoting verb in a pair of two-word phrases. We also found that the neural similarity in AG voxel patterns between two phrases sharing a verb correlated with subjects' ratings of how similar the meanings of those two verb phrases were. These findings

  15. Micro-computed tomography pore-scale study of flow in porous media: Effect of voxel resolution

    NASA Astrophysics Data System (ADS)

    Shah, S. M.; Gray, F.; Crawshaw, J. P.; Boek, E. S.

    2016-09-01

    A fundamental understanding of flow in porous media at the pore-scale is necessary to be able to upscale average displacement processes from core to reservoir scale. The study of fluid flow in porous media at the pore-scale consists of two key procedures: Imaging - reconstruction of three-dimensional (3D) pore space images; and modelling such as with single and two-phase flow simulations with Lattice-Boltzmann (LB) or Pore-Network (PN) Modelling. Here we analyse pore-scale results to predict petrophysical properties such as porosity, single-phase permeability and multi-phase properties at different length scales. The fundamental issue is to understand the image resolution dependency of transport properties, in order to up-scale the flow physics from pore to core scale. In this work, we use a high resolution micro-computed tomography (micro-CT) scanner to image and reconstruct three dimensional pore-scale images of five sandstones (Bentheimer, Berea, Clashach, Doddington and Stainton) and five complex carbonates (Ketton, Estaillades, Middle Eastern sample 3, Middle Eastern sample 5 and Indiana Limestone 1) at four different voxel resolutions (4.4 μm, 6.2 μm, 8.3 μm and 10.2 μm), scanning the same physical field of view. Implementing three phase segmentation (macro-pore phase, intermediate phase and grain phase) on pore-scale images helps to understand the importance of connected macro-porosity in the fluid flow for the samples studied. We then compute the petrophysical properties for all the samples using PN and LB simulations in order to study the influence of voxel resolution on petrophysical properties. We then introduce a numerical coarsening scheme which is used to coarsen a high voxel resolution image (4.4 μm) to lower resolutions (6.2 μm, 8.3 μm and 10.2 μm) and study the impact of coarsening data on macroscopic and multi-phase properties. Numerical coarsening of high resolution data is found to be superior to using a lower resolution scan because it

  16. TH-A-9A-01: Active Optical Flow Model: Predicting Voxel-Level Dose Prediction in Spine SBRT

    SciTech Connect

    Liu, J; Wu, Q.J.; Yin, F; Kirkpatrick, J; Cabrera, A; Ge, Y

    2014-06-15

    Purpose: To predict voxel-level dose distribution and enable effective evaluation of cord dose sparing in spine SBRT. Methods: We present an active optical flow model (AOFM) to statistically describe cord dose variations and train a predictive model to represent correlations between AOFM and PTV contours. Thirty clinically accepted spine SBRT plans are evenly divided into training and testing datasets. The development of predictive model consists of 1) collecting a sequence of dose maps including PTV and OAR (spinal cord) as well as a set of associated PTV contours adjacent to OAR from the training dataset, 2) classifying data into five groups based on PTV's locations relative to OAR, two “Top”s, “Left”, “Right”, and “Bottom”, 3) randomly selecting a dose map as the reference in each group and applying rigid registration and optical flow deformation to match all other maps to the reference, 4) building AOFM by importing optical flow vectors and dose values into the principal component analysis (PCA), 5) applying another PCA to features of PTV and OAR contours to generate an active shape model (ASM), and 6) computing a linear regression model of correlations between AOFM and ASM.When predicting dose distribution of a new case in the testing dataset, the PTV is first assigned to a group based on its contour characteristics. Contour features are then transformed into ASM's principal coordinates of the selected group. Finally, voxel-level dose distribution is determined by mapping from the ASM space to the AOFM space using the predictive model. Results: The DVHs predicted by the AOFM-based model and those in clinical plans are comparable in training and testing datasets. At 2% volume the dose difference between predicted and clinical plans is 4.2±4.4% and 3.3±3.5% in the training and testing datasets, respectively. Conclusion: The AOFM is effective in predicting voxel-level dose distribution for spine SBRT. Partially supported by NIH/NCI under grant

  17. Visual Exploration of Genetic Association with Voxel-based Imaging Phenotypes in an MCI/AD Study

    PubMed Central

    Kim, Sungeun; Shen, Li; Saykin, Andrew J.; West, John D.

    2010-01-01

    Neuroimaging genomics is a new transdisciplinary research field, which aims to examine genetic effects on brain via integrated analyses of high throughput neuroimaging and genomic data. We report our recent work on (1) developing an imaging genomic browsing system that allows for whole genome and entire brain analyses based on visual exploration and (2) applying the system to the imaging genomic analysis of an existing MCI/AD cohort. Voxel-based morphometry is used to define imaging phenotypes. ANCOVA is employed to evaluate the effect of the interaction of genotypes and diagnosis in relation to imaging phenotypes while controlling for relevant covariates. Encouraging experimental results suggest that the proposed system has substantial potential for enabling discovery of imaging genomic associations through visual evaluation and for localizing candidate imaging regions and genomic regions for refined statistical modeling. PMID:19963597

  18. Larger right posterior parietal volume in action video game experts: a behavioral and voxel-based morphometry (VBM) study.

    PubMed

    Tanaka, Satoshi; Ikeda, Hanako; Kasahara, Kazumi; Kato, Ryo; Tsubomi, Hiroyuki; Sugawara, Sho K; Mori, Makoto; Hanakawa, Takashi; Sadato, Norihiro; Honda, Manabu; Watanabe, Katsumi

    2013-01-01

    Recent studies suggest that action video game players exhibit superior performance in visuospatial cognitive tasks compared with non-game players. However, the neural basis underlying this visuospatial cognitive performance advantage remains largely unknown. The present human behavioral and imaging study compared gray matter volume in action video game experts and non-experts using structural magnetic resonance imaging and voxel-based morphometry analysis. The results revealed significantly larger gray matter volume in the right posterior parietal cortex in experts compared with non-experts. Furthermore, the larger gray matter volume in the right posterior parietal cortex significantly correlated with individual performance in a visual working memory task in experts. These results suggest that differences in brain structure may be linked to extensive video game play, leading to superior visuospatial cognitive performance in action video game experts.

  19. An accelerator-based epithermal neutron beam design for BNCT and dosimetric evaluation using a voxel head phantom.

    PubMed

    Lee, Deok-jae; Han, Chi Young; Park, Sung Ho; Kim, Jong Kyung

    2004-01-01

    The beam shaping assembly design has been investigated in order to improve the epithermal neutron beam for accelerator-based boron neutron capture therapy in intensity and quality, and dosimetric evaluation for the beams has been performed using both mathematical and voxel head phantoms with MCNP runs. The neutron source was assumed to be produced from a conventional 2.5 MeV proton accelerator with a thick (7)Li target. The results indicate that it is possible to enhance epithermal neutron flux remarkably as well as to embody a good spectrum shaping to epithermal neutrons only with the proper combination of moderator and reflector. It is also found that a larger number of thermal neutrons can reach deeply into the brain and, therefore, can reduce considerably the treatment time for brain tumours. Consequently, the epithermal neutron beams designed in this study can treat more effectively deep-seated brain tumours.

  20. Incorporando a variabilidade no processo de identificação do modelo de máximo global no Grade of Membership (GoM): considerações metodológicas

    PubMed Central

    Guedes, Gilvan Ramalho; Siviero, Pamila Cristina Lima; Caetano, André Junqueira; Machado, Carla Jorge; Brondízio, Eduardo

    2012-01-01

    A disponibilidade de bases de dados cada vez mais complexas e multidimensionais é um dos principais motivadores para o aumento do número de estudos que utilizam análises multivariadas baseadas em lógica de conjuntos nebulosos. Apesar da disseminação do método Grade of Membership nos trabalhos empíricos brasileiros da área de ciências sociais e saúde, questões relativas à identificabilidade e estabilidade dos parâmetros finais estimados pelo programa GoM 3.4 não foram suficientemente aprofundadas. Dada a relevância de se obterem parâmetros únicos e estáveis, Guedes et al. (2010) propuseram um procedimento empírico para localizar um modelo de máximo global (MG) com parâmetros estáveis. Entretanto, seu localizador de MG não incorpora qualquer medida de variabilidade. Neste artigo, tal limitação é contornada por meio da utilização de uma estatística de ponderação – Máximo Global Ponderado (MGP) – semelhante ao coeficiente de variação. Esse indicador busca não penalizar de forma desproporcional situações nas quais os desvios médios, apesar de diferentes de zero, são muito pequenos. Apresentam-se evidências de que o localizador MGP reduz a distância do modelo identificado à real estrutura latente dos dados em análise, quando comparados ao modelo identificado pelo localizador não ponderado, MG. PMID:23293402

  1. Dyslexia and voxel-based morphometry: correlations between five behavioural measures of dyslexia and gray and white matter volumes.

    PubMed

    Tamboer, Peter; Scholte, H Steven; Vorst, Harrie C M

    2015-10-01

    In voxel-based morphometry studies of dyslexia, the relation between causal theories of dyslexia and gray matter (GM) and white matter (WM) volume alterations is still under debate. Some alterations are consistently reported, but others failed to reach significance. We investigated GM alterations in a large sample of Dutch students (37 dyslexics and 57 non-dyslexics) with two analyses: group differences in local GM and total GM and WM volume and correlations between GM and WM volumes and five behavioural measures. We found no significant group differences after corrections for multiple comparisons although total WM volume was lower in the group of dyslexics when age was partialled out. We presented an overview of uncorrected clusters of voxels (p < 0.05, cluster size k > 200) with reduced or increased GM volume. We found four significant correlations between factors of dyslexia representing various behavioural measures and the clusters found in the first analysis. In the whole sample, a factor related to performances in spelling correlated negatively with GM volume in the left posterior cerebellum. Within the group of dyslexics, a factor related to performances in Dutch-English rhyme words correlated positively with GM volume in the left and right caudate nucleus and negatively with increased total WM volume. Most of our findings were in accordance with previous reports. A relatively new finding was the involvement of the caudate nucleus. We confirmed the multiple cognitive nature of dyslexia and suggested that experience greatly influences anatomical alterations depending on various subtypes of dyslexia, especially in a student sample.

  2. Altered Brain Network in Amyotrophic Lateral Sclerosis: A Resting Graph Theory-Based Network Study at Voxel-Wise Level.

    PubMed

    Zhou, Chaoyang; Hu, Xiaofei; Hu, Jun; Liang, Minglong; Yin, Xuntao; Chen, Lin; Zhang, Jiuquan; Wang, Jian

    2016-01-01

    Amyotrophic lateral sclerosis (ALS) is a rare degenerative disorder characterized by loss of upper and lower motor neurons. Neuroimaging has provided noticeable evidence that ALS is a complex disease, and shown that anatomical and functional lesions extend beyond precentral cortices and corticospinal tracts, to include the corpus callosum; frontal, sensory, and premotor cortices; thalamus; and midbrain. The aim of this study is to investigate graph theory-based functional network abnormalities at voxel-wise level in ALS patients on a whole brain scale. Forty-three ALS patients and 44 age- and sex-matched healthy volunteers were enrolled. The voxel-wise network degree centrality (DC), a commonly employed graph-based measure of network organization, was used to characterize the alteration of whole brain functional network. Compared with the controls, the ALS patients showed significant increase of DC in the left cerebellum posterior lobes, bilateral cerebellum crus, bilateral occipital poles, right orbital frontal lobe, and bilateral prefrontal lobes; significant decrease of DC in the bilateral primary motor cortex, bilateral sensory motor region, right prefrontal lobe, left bilateral precuneus, bilateral lateral temporal lobes, left cingulate cortex, and bilateral visual processing cortex. The DC's z-scores of right inferior occipital gyrus were significant negative correlated with the ALSFRS-r scores. Our findings confirm that the regions with abnormal network DC in ALS patients were located in multiple brain regions including primary motor, somatosensory and extra-motor areas, supporting the concept that ALS is a multisystem disorder. Specifically, our study found that DC in the visual areas was altered and ALS patients with higher DC in right inferior occipital gyrus have more severity of disease. The result demonstrated that the altered DC value in this region can probably be used to assess severity of ALS. PMID:27242409

  3. A Voxel-Based Morphometry Study Reveals Local Brain Structural Alterations Associated with Ambient Fine Particles in Older Women

    PubMed Central

    Casanova, Ramon; Wang, Xinhui; Reyes, Jeanette; Akita, Yasuyuki; Serre, Marc L.; Vizuete, William; Chui, Helena C.; Driscoll, Ira; Resnick, Susan M.; Espeland, Mark A.; Chen, Jiu-Chiuan; Wassertheil-Smoller, Sylvia; Goodwin, Mimi; DeNise, Richard; Lipton, Michael; Hannigan, James; Carpini, Anthony; Noble, David; Guzman, Wilton; Kotchen, Jane Morley; Goveas, Joseph; Kerwin, Diana; Ulmer, John; Censky, Steve; Flinton, Troy; Matusewic, Tracy; Prost, Robert; Stefanick, Marcia L.; Swope, Sue; Sawyer-Glover, Anne Marie; Hartley, Susan; Jackson, Rebecca; Hallarn, Rose; Kennedy, Bonnie; Bolognone, Jill; Casimir, Lindsay; Kochis, Amanda; Robbins, John; Zaragoza, Sophia; Carter, Cameron; Ryan, John; Macias, Denise; Sonico, Jerry; Nathan, Lauren; Voigt, Barbara; Villablanca, Pablo; Nyborg, Glen; Godinez, Sergio; Perrymann, Adele; Limacher, Marian; Anderson, Sheila; Toombs, Mary Ellen; Bennett, Jeffrey; Jones, Kevin; Brum, Sandy; Chatfield, Shane; Vantrees, Kevin; Robinson, Jennifer; Wilson, Candy; Koch, Kevin; Hart, Suzette; Carroll, Jennifer; Cherrico, Mary; Ockene, Judith; Churchill, Linda; Fellows, Douglas; Serio, Anthony; Jackson, Sharon; Spavich, Deidre; Margolis, Karen; Bjerk, Cindy; Truwitt, Chip; Peitso, Margaret; Camcrena, Alexa; Grim, Richard; Levin, Julie; Perron, Mary; Brunner, Robert; Golding, Ross; Pansky, Leslie; Arguello, Sandie; Hammons, Jane; Peterson, Nikki; Murphy, Carol; Morgan, Maggie; Castillo, Mauricio; Beckman, Thomas; Huang, Benjamin; Kuller, Lewis; McHugh, Pat; Meltzer, Carolyn; Davis, Denise; Davis, Joyce; Kost, Piera; Lucas, Kim; Potter, Tom; Tarr, Lee; Shumaker, Sally; Espeland, Mark; Coker, Laura; Williamson, Jeff; Felton, Debbie; Gleiser, LeeAnn; Rapp, Steve; Legault, Claudine; Dailey, Maggie; Casanova, Ramon; Robertson, Julia; Hogan, Patricia; Gaussoin, Sarah; Nance, Pam; Summerville, Cheryl; Peral, Ricardo; Tan, Josh; Bryan, Nick; Davatzikos, Christos; Desiderio, Lisa; Buckholtz, Neil; Molchan, Susan; Resnick, Susan; Rossouw, Jacques; Pottern, Linda

    2016-01-01

    Objective: Exposure to ambient fine particulate matter (PM2.5: PM with aerodynamic diameters < 2.5 μm) has been linked with cognitive deficits in older adults. Using fine-grained voxel-wise analyses, we examined whether PM2.5 exposure also affects brain structure. Methods: Brain MRI data were obtained from 1365 women (aged 71–89) in the Women's Health Initiative Memory Study and local brain volumes were estimated using RAVENS (regional analysis of volumes in normalized space). Based on geocoded residential locations and air monitoring data from the U.S. Environmental Protection Agency, we employed a spatiotemporal model to estimate long-term (3-year average) exposure to ambient PM2.5 preceding MRI scans. Voxel-wise linear regression models were fit separately to gray matter (GM) and white matter (WM) maps to analyze associations between brain structure and PM2.5 exposure, with adjustment for potential confounders. Results: Increased PM2.5 exposure was associated with smaller volumes in both cortical GM and subcortical WM areas. For GM, associations were clustered in the bilateral superior, middle, and medial frontal gyri. For WM, the largest clusters were in the frontal lobe, with smaller clusters in the temporal, parietal, and occipital lobes. No statistically significant associations were observed between PM2.5 exposure and hippocampal volumes. Conclusions: Long-term PM2.5 exposures may accelerate loss of both GM and WM in older women. While our previous work linked smaller WM volumes to PM2.5, this is the first neuroimaging study reporting associations between air pollution exposure and smaller volumes of cortical GM. Our data support the hypothesized synaptic neurotoxicity of airborne particles. PMID:27790103

  4. Using voxel-based morphometry to map the structural changes associated with rapid conversion in MCI: a longitudinal MRI study.

    PubMed

    Chételat, G; Landeau, B; Eustache, F; Mézenge, F; Viader, F; de la Sayette, V; Desgranges, B; Baron, J-C

    2005-10-01

    Capturing the dynamics of gray matter (GM) atrophy in relation to the conversion from mild cognitive impairment (MCI) to clinically probable Alzheimer's disease (AD) would be of considerable interest. In this prospective study we have used a novel longitudinal voxel-based method to map the progression of GM loss in MCI patients over time and compared converters to non-converters. Eighteen amnestic MCI patients were followed-up for a predefined fixed period of 18 months and conversion was judged according to NINCDS-ADRDA criteria for probable AD. Each patient underwent a high-resolution T1-weighted volume MRI scan both at entry in the study and 18 months later. We used an optimal VBM protocol to compare baseline imaging data of converters to those of non-converters. Moreover, to map GM loss from baseline to follow-up assessment, we used a modified voxel-based morphometry (VBM) procedure specially designed for longitudinal studies. At the end of the follow-up period, seven patients had converted to probable AD. Areas of lower baseline GM value in converters mainly included the hippocampus, parahippocampal cortex, and lingual and fusiform gyri. Regions of significant GM loss over the 18-month follow-up period common to both converters and non-converters included the temporal neocortex, parahippocampal cortex, orbitofrontal and inferior parietal areas, and the left thalamus. However, there was significantly greater GM loss in converters relative to non-converters in the hippocampal area, inferior and middle temporal gyrus, posterior cingulate, and precuneus. This accelerated atrophy may result from both neurofibrillary tangles accumulation and parallel pathological processes such as functional alteration in the posterior cingulate. The ability to longitudinally assess GM changes in MCI offers new perspectives to better understand the pathological processes underlying AD and to monitor the effects of treatment on brain structure.

  5. Age-related differences in regional brain volumes: A comparison of optimized voxel-based morphometry to manual volumetry

    PubMed Central

    Kennedy, Kristen M.; Erickson, Kirk I.; Rodrigue, Karen M.; Voss, Michelle W.; Colcombe, Stan J.; Kramer, Arthur F.; Acker, James D.; Raz, Naftali

    2009-01-01

    Regional manual volumetry is the gold standard of in vivo neuroanatomy, but is labor-intensive, can be imperfectly reliable, and allows for measuring limited number of regions. Voxel-based morphometry (VBM) has perfect repeatability and assesses local structure across the whole brain. However, its anatomic validity is unclear, and with its increasing popularity, a systematic comparison of VBM to manual volumetry is necessary. The few existing comparison studies are limited by small samples, qualitative comparisons, and limited selection and modest reliability of manual measures. Our goal was to overcome those limitations by quantitatively comparing optimized VBM findings with highly reliable multiple regional measures in a large sample (N = 200) across a wide agespan (18–81). We report a complex pattern of similarities and differences. Peak values of VBM volume estimates (modulated density) produced stronger age differences and a different spatial distribution from manual measures. However, when we aggregated VBM-derived information across voxels contained in specific anatomically defined regions (masks), the patterns of age differences became more similar, although important discrepancies emerged. Notably, VBM revealed stronger age differences in the regions bordering CSF and white matter areas prone to leukoaraiosis, and VBM was more likely to report nonlinearities in age-volume relationships. In the white matter regions, manual measures showed stronger negative associations with age than the corresponding VBM-based masks. We conclude that VBM provides realistic estimates of age differences in the regional gray matter only when applied to anatomically defined regions, but overestimates effects when individual peaks are interpreted. It may be beneficial to use VBM as a first-pass strategy, followed by manual measurement of anatomically-defined regions. PMID:18276037

  6. SU-E-T-169: Evaluation of Oncentra TPS for Nasopharynx Brachy Using Patient Specific Voxel Phantom and EGSnrc

    SciTech Connect

    Hadad, K; Zoherhvand, M; Faghihi, R

    2014-06-01

    Purpose: Nasopharnx carcinoma (NPC) treatment is being carried out using Ir-192 HDR seeds in Mehdieh Hospital in Hamadan, Iran. The Oncentra™ TPS is based on optimized TG-43 formalism which disregards heterogeneity in the treatment area. Due to abundant heterogeneity in head and neck, comparison of the Oncentra™ TPS dose evaluation and an accurate dose calculation method in NPC brachytherapy is the objective of this study. Methods: CT DICOMs of a patient with NPC obtained from Mehdieh Hospital used to create 3D voxel phantom with CTCREATE utility of EGSnrc code package. The voxel phantom together with Ir-192 HDR brachytherapy source were the input to DOSXYZnrc to calculate the 3D dose distribution. The sources were incorporate with type 6 source in DOSXYZnrc and their dwell times were taken into account in final dose calculations. Results: The direct comparison between isodoses as well as DVHs for the GTV, PTV and CTV obtained by Oncentra™ and EGSnrc Monte Carlo code are made. EGSnrc results are obtained using 5×10{sup 9} histories to reduce the statistical error below 1% in GTV and 5% in 5% dose areas. The standard ICRP700 cross section library is employed in DOSXYZnrc dose calculation. Conclusion: A direct relationship between increased dose differences and increased material density (hence heterogeneity) is observed when isodoses contours of the TPS and DOSXYZnrc are compared. Regarding the point dose calculations, the differences range from 1.2% in PTV to 5.6% for cavity region and 7.8% for bone regions. While Oncentra™ TPS overestimates the dose in cavities, it tends to underestimate dose depositions within bones.

  7. From Cortical and Subcortical Grey Matter Abnormalities to Neurobehavioral Phenotype of Angelman Syndrome: A Voxel-Based Morphometry Study

    PubMed Central

    Aghakhanyan, Gayane; Bonanni, Paolo; Randazzo, Giovanna; Nappi, Sara; Tessarotto, Federica; De Martin, Lara; Frijia, Francesca; De Marchi, Daniele; De Masi, Francesco; Kuppers, Beate; Lombardo, Francesco; Caramella, Davide; Montanaro, Domenico

    2016-01-01

    Angelman syndrome (AS) is a rare neurogenetic disorder due to loss of expression of maternal ubiquitin-protein ligase E3A (UBE3A) gene. It is characterized by severe developmental delay, speech impairment, movement or balance disorder and typical behavioral uniqueness. Affected individuals show normal magnetic resonance imaging (MRI) findings, although mild dysmyelination may be observed. In this study, we adopted a quantitative MRI analysis with voxel-based morphometry (FSL-VBM) method to investigate disease-related changes in the cortical/subcortical grey matter (GM) structures. Since 2006 to 2013 twenty-six AS patients were assessed by our multidisciplinary team. From those, sixteen AS children with confirmed maternal 15q11-q13 deletions (mean age 7.7 ± 3.6 years) and twenty-one age-matched controls were recruited. The developmental delay and motor dysfunction were assessed using Bayley III and Gross Motor Function Measure (GMFM). Principal component analysis (PCA) was applied to the clinical and neuropsychological datasets. High-resolution T1-weighted images were acquired and FSL-VBM approach was applied to investigate differences in the local GM volume and to correlate clinical and neuropsychological changes in the regional distribution of GM. We found bilateral GM volume loss in AS compared to control children in the striatum, limbic structures, insular and orbitofrontal cortices. Voxel-wise correlation analysis with the principal components of the PCA output revealed a strong relationship with GM volume in the superior parietal lobule and precuneus on the left hemisphere. The anatomical distribution of cortical/subcortical GM changes plausibly related to several clinical features of the disease and may provide an important morphological underpinning for clinical and neurobehavioral symptoms in children with AS. PMID:27626634

  8. Approach to voxel-based carbon stock quanticiation using LiDAR data in tropical rainforest, Brunei

    NASA Astrophysics Data System (ADS)

    Kim, Eunji; Piao, Dongfan; Lee, Jongyeol; Lee, Woo-Kyun; Yoon, Mihae; Moon, Jooyeon

    2016-04-01

    Forest is an important means to adapt climate change as the only carbon sink recognized by the international community (KFS 2009). According to the Intergovernmental Panel on Climate Change (IPCC) 5th Assessment Report (AR5), Agriculture, Forestry, and Other Land Use (AFOLU) sectors including forestry contributed 24% of total anthropogenic emissions in 2010 (IPCC 2014; Tubiello et al. 2015). While all sectors excluding AFOLU have increased Greenhouse Gas (GHG) emissions, land use sectors including forestry remains similar level as before due to decreasing deforestation and increasing reforestation. In earlier researches, optical imagery has been applied for analysis (Jakubowski et al. 2013). Optical imagery collects spectral information in 2D. It is difficult to effectively quantify forest stocks, especially in dense forest (Cui et al. 2012). To detect individual trees information from remotely sensed data, Light detection and ranging (LiDAR) has been used (Hyyppäet al. 2001; Persson et al. 2002; Chen et al. 2006). Moreover, LiDAR has the ability to actively acquire vertical tree information such as tree height using geo-registered 3D points (Kwak et al. 2007). In general, however, geo-register 3D point was used with a raster format which contains only 2D information by missing all the 3D data. Therefore, this research aimed to use the volumetric pixel (referred as "voxel") approach using LiDAR data in tropical rainforest, Brunei. By comparing the parameters derived from voxel based LiDAR data and field measured data, we examined the relationships between them for the quantification of forest carbon. This study expects to be more helpful to take advantage of the strategic application of climate change adaption.

  9. From Cortical and Subcortical Grey Matter Abnormalities to Neurobehavioral Phenotype of Angelman Syndrome: A Voxel-Based Morphometry Study.

    PubMed

    Aghakhanyan, Gayane; Bonanni, Paolo; Randazzo, Giovanna; Nappi, Sara; Tessarotto, Federica; De Martin, Lara; Frijia, Francesca; De Marchi, Daniele; De Masi, Francesco; Kuppers, Beate; Lombardo, Francesco; Caramella, Davide; Montanaro, Domenico

    2016-01-01

    Angelman syndrome (AS) is a rare neurogenetic disorder due to loss of expression of maternal ubiquitin-protein ligase E3A (UBE3A) gene. It is characterized by severe developmental delay, speech impairment, movement or balance disorder and typical behavioral uniqueness. Affected individuals show normal magnetic resonance imaging (MRI) findings, although mild dysmyelination may be observed. In this study, we adopted a quantitative MRI analysis with voxel-based morphometry (FSL-VBM) method to investigate disease-related changes in the cortical/subcortical grey matter (GM) structures. Since 2006 to 2013 twenty-six AS patients were assessed by our multidisciplinary team. From those, sixteen AS children with confirmed maternal 15q11-q13 deletions (mean age 7.7 ± 3.6 years) and twenty-one age-matched controls were recruited. The developmental delay and motor dysfunction were assessed using Bayley III and Gross Motor Function Measure (GMFM). Principal component analysis (PCA) was applied to the clinical and neuropsychological datasets. High-resolution T1-weighted images were acquired and FSL-VBM approach was applied to investigate differences in the local GM volume and to correlate clinical and neuropsychological changes in the regional distribution of GM. We found bilateral GM volume loss in AS compared to control children in the striatum, limbic structures, insular and orbitofrontal cortices. Voxel-wise correlation analysis with the principal components of the PCA output revealed a strong relationship with GM volume in the superior parietal lobule and precuneus on the left hemisphere. The anatomical distribution of cortical/subcortical GM changes plausibly related to several clinical features of the disease and may provide an important morphological underpinning for clinical and neurobehavioral symptoms in children with AS. PMID:27626634

  10. Altered Brain Network in Amyotrophic Lateral Sclerosis: A Resting Graph Theory-Based Network Study at Voxel-Wise Level

    PubMed Central

    Zhou, Chaoyang; Hu, Xiaofei; Hu, Jun; Liang, Minglong; Yin, Xuntao; Chen, Lin; Zhang, Jiuquan; Wang, Jian

    2016-01-01

    Amyotrophic lateral sclerosis (ALS) is a rare degenerative disorder characterized by loss of upper and lower motor neurons. Neuroimaging has provided noticeable evidence that ALS is a complex disease, and shown that anatomical and functional lesions extend beyond precentral cortices and corticospinal tracts, to include the corpus callosum; frontal, sensory, and premotor cortices; thalamus; and midbrain. The aim of this study is to investigate graph theory-based functional network abnormalities at voxel-wise level in ALS patients on a whole brain scale. Forty-three ALS patients and 44 age- and sex-matched healthy volunteers were enrolled. The voxel-wise network degree centrality (DC), a commonly employed graph-based measure of network organization, was used to characterize the alteration of whole brain functional network. Compared with the controls, the ALS patients showed significant increase of DC in the left cerebellum posterior lobes, bilateral cerebellum crus, bilateral occipital poles, right orbital frontal lobe, and bilateral prefrontal lobes; significant decrease of DC in the bilateral primary motor cortex, bilateral sensory motor region, right prefrontal lobe, left bilateral precuneus, bilateral lateral temporal lobes, left cingulate cortex, and bilateral visual processing cortex. The DC's z-scores of right inferior occipital gyrus were significant negative correlated with the ALSFRS-r scores. Our findings confirm that the regions with abnormal network DC in ALS patients were located in multiple brain regions including primary motor, somatosensory and extra-motor areas, supporting the concept that ALS is a multisystem disorder. Specifically, our study found that DC in the visual areas was altered and ALS patients with higher DC in right inferior occipital gyrus have more severity of disease. The result demonstrated that the altered DC value in this region can probably be used to assess severity of ALS. PMID:27242409

  11. From Particles and Point Clouds to Voxel Models: High Resolution Modeling of Dynamic Landscapes in Open Source GIS

    NASA Astrophysics Data System (ADS)

    Mitasova, H.; Hardin, E. J.; Kratochvilova, A.; Landa, M.

    2012-12-01

    Multitemporal data acquired by modern mapping technologies provide unique insights into processes driving land surface dynamics. These high resolution data also offer an opportunity to improve the theoretical foundations and accuracy of process-based simulations of evolving landforms. We discuss development of new generation of visualization and analytics tools for GRASS GIS designed for 3D multitemporal data from repeated lidar surveys and from landscape process simulations. We focus on data and simulation methods that are based on point sampling of continuous fields and lead to representation of evolving surfaces as series of raster map layers or voxel models. For multitemporal lidar data we present workflows that combine open source point cloud processing tools with GRASS GIS and custom python scripts to model and analyze dynamics of coastal topography (Figure 1) and we outline development of coastal analysis toolbox. The simulations focus on particle sampling method for solving continuity equations and its application for geospatial modeling of landscape processes. In addition to water and sediment transport models, already implemented in GIS, the new capabilities under development combine OpenFOAM for wind shear stress simulation with a new module for aeolian sand transport and dune evolution simulations. Comparison of observed dynamics with the results of simulations is supported by a new, integrated 2D and 3D visualization interface that provides highly interactive and intuitive access to the redesigned and enhanced visualization tools. Several case studies will be used to illustrate the presented methods and tools and demonstrate the power of workflows built with FOSS and highlight their interoperability.Figure 1. Isosurfaces representing evolution of shoreline and a z=4.5m contour between the years 1997-2011at Cape Hatteras, NC extracted from a voxel model derived from series of lidar-based DEMs.

  12. Organ dose conversion coefficients for voxel models of the reference male and female from idealized photon exposures

    NASA Astrophysics Data System (ADS)

    Schlattl, H.; Zankl, M.; Petoussi-Henss, N.

    2007-04-01

    A new series of organ equivalent dose conversion coefficients for whole body external photon exposure is presented for a standardized couple of human voxel models, called Rex and Regina. Irradiations from broad parallel beams in antero-posterior, postero-anterior, left- and right-side lateral directions as well as from a 360° rotational source have been performed numerically by the Monte Carlo transport code EGSnrc. Dose conversion coefficients from an isotropically distributed source were computed, too. The voxel models Rex and Regina originating from real patient CT data comply in body and organ dimensions with the currently valid reference values given by the International Commission on Radiological Protection (ICRP) for the average Caucasian man and woman, respectively. While the equivalent dose conversion coefficients of many organs are in quite good agreement with the reference values of ICRP Publication 74, for some organs and certain geometries the discrepancies amount to 30% or more. Differences between the sexes are of the same order with mostly higher dose conversion coefficients in the smaller female model. However, much smaller deviations from the ICRP values are observed for the resulting effective dose conversion coefficients. With the still valid definition for the effective dose (ICRP Publication 60), the greatest change appears in lateral exposures with a decrease in the new models of at most 9%. However, when the modified definition of the effective dose as suggested by an ICRP draft is applied, the largest deviation from the current reference values is obtained in postero-anterior geometry with a reduction of the effective dose conversion coefficient by at most 12%.

  13. Organ dose conversion coefficients for voxel models of the reference male and female from idealized photon exposures.

    PubMed

    Schlattl, H; Zankl, M; Petoussi-Henss, N

    2007-04-21

    A new series of organ equivalent dose conversion coefficients for whole body external photon exposure is presented for a standardized couple of human voxel models, called Rex and Regina. Irradiations from broad parallel beams in antero-posterior, postero-anterior, left- and right-side lateral directions as well as from a 360 degrees rotational source have been performed numerically by the Monte Carlo transport code EGSnrc. Dose conversion coefficients from an isotropically distributed source were computed, too. The voxel models Rex and Regina originating from real patient CT data comply in body and organ dimensions with the currently valid reference values given by the International Commission on Radiological Protection (ICRP) for the average Caucasian man and woman, respectively. While the equivalent dose conversion coefficients of many organs are in quite good agreement with the reference values of ICRP Publication 74, for some organs and certain geometries the discrepancies amount to 30% or more. Differences between the sexes are of the same order with mostly higher dose conversion coefficients in the smaller female model. However, much smaller deviations from the ICRP values are observed for the resulting effective dose conversion coefficients. With the still valid definition for the effective dose (ICRP Publication 60), the greatest change appears in lateral exposures with a decrease in the new models of at most 9%. However, when the modified definition of the effective dose as suggested by an ICRP draft is applied, the largest deviation from the current reference values is obtained in postero-anterior geometry with a reduction of the effective dose conversion coefficient by at most 12%. PMID:17404459

  14. Altered Brain Network in Amyotrophic Lateral Sclerosis: A Resting Graph Theory-Based Network Study at Voxel-Wise Level.

    PubMed

    Zhou, Chaoyang; Hu, Xiaofei; Hu, Jun; Liang, Minglong; Yin, Xuntao; Chen, Lin; Zhang, Jiuquan; Wang, Jian

    2016-01-01

    Amyotrophic lateral sclerosis (ALS) is a rare degenerative disorder characterized by loss of upper and lower motor neurons. Neuroimaging has provided noticeable evidence that ALS is a complex disease, and shown that anatomical and functional lesions extend beyond precentral cortices and corticospinal tracts, to include the corpus callosum; frontal, sensory, and premotor cortices; thalamus; and midbrain. The aim of this study is to investigate graph theory-based functional network abnormalities at voxel-wise level in ALS patients on a whole brain scale. Forty-three ALS patients and 44 age- and sex-matched healthy volunteers were enrolled. The voxel-wise network degree centrality (DC), a commonly employed graph-based measure of network organization, was used to characterize the alteration of whole brain functional network. Compared with the controls, the ALS patients showed significant increase of DC in the left cerebellum posterior lobes, bilateral cerebellum crus, bilateral occipital poles, right orbital frontal lobe, and bilateral prefrontal lobes; significant decrease of DC in the bilateral primary motor cortex, bilateral sensory motor region, right prefrontal lobe, left bilateral precuneus, bilateral lateral temporal lobes, left cingulate cortex, and bilateral visual processing cortex. The DC's z-scores of right inferior occipital gyrus were significant negative correlated with the ALSFRS-r scores. Our findings confirm that the regions with abnormal network DC in ALS patients were located in multiple brain regions including primary motor, somatosensory and extra-motor areas, supporting the concept that ALS is a multisystem disorder. Specifically, our study found that DC in the visual areas was altered and ALS patients with higher DC in right inferior occipital gyrus have more severity of disease. The result demonstrated that the altered DC value in this region can probably be used to assess severity of ALS.

  15. Modeling the Effect of Intra-Voxel Diffusion of Contrast Agent on the Quantitative Analysis of Dynamic Contrast Enhanced Magnetic Resonance Imaging

    PubMed Central

    Barnes, Stephanie L.; Quarles, C. Chad; Yankeelov, Thomas E.

    2014-01-01

    Quantitative dynamic contrast enhanced magnetic resonance imaging (DCE-MRI) provides estimates of physiologically relevant parameters related to tissue blood flow, vascular permeability, and tissue volume fractions which can then be used for prognostic and diagnostic reasons. However, standard techniques for DCE-MRI analysis ignore intra-voxel diffusion, which may play an important role in contrast agent distribution and voxel signal intensity and, thus, will affect quantification of the aforementioned parameters. To investigate the effect of intra-voxel diffusion on quantitative DCE-MRI, we developed a finite element model of contrast enhancement at the voxel level. For diffusion in the range of that expected for gadolinium chelates in tissue (i.e., 1×10−4 to 4×10−4 mm2/s), parameterization errors range from −58% to 12% for Ktrans, −9% to 8% for ve, and −60% to 213% for vp over the range of Ktrans, ve, vp, and temporal resolutions investigated. Thus the results show that diffusion has a significant effect on parameterization using standard techniques. PMID:25275536

  16. Early Gray-Matter and White-Matter Concentration in Infancy Predict Later Language Skills: A Whole Brain Voxel-Based Morphometry Study

    ERIC Educational Resources Information Center

    Can, Dilara Deniz; Richards, Todd; Kuhl, Patricia K.

    2013-01-01

    Magnetic Resonance Imaging (MRI) brain scans were obtained from 19 infants at 7 months. Expressive and receptive language performance was assessed at 12 months. Voxel-based morphometry (VBM) identified brain regions where gray-matter and white-matter concentrations at 7 months correlated significantly with children's language scores at 12 months.…

  17. Stimulus-related independent component and voxel-wise analysis of human brain activity during free viewing of a feature film.

    PubMed

    Lahnakoski, Juha M; Salmi, Juha; Jääskeläinen, Iiro P; Lampinen, Jouko; Glerean, Enrico; Tikka, Pia; Sams, Mikko

    2012-01-01

    Understanding how the brain processes stimuli in a rich natural environment is a fundamental goal of neuroscience. Here, we showed a feature film to 10 healthy volunteers during functional magnetic resonance imaging (fMRI) of hemodynamic brain activity. We then annotated auditory and visual features of the motion picture to inform analysis of the hemodynamic data. The annotations were fitted to both voxel-wise data and brain network time courses extracted by independent component analysis (ICA). Auditory annotations correlated with two independent components (IC) disclosing two functional networks, one responding to variety of auditory stimulation and another responding preferentially to speech but parts of the network also responding to non-verbal communication. Visual feature annotations correlated with four ICs delineating visual areas according to their sensitivity to different visual stimulus features. In comparison, a separate voxel-wise general linear model based analysis disclosed brain areas preferentially responding to sound energy, speech, music, visual contrast edges, body motion and hand motion which largely overlapped the results revealed by ICA. Differences between the results of IC- and voxel-based analyses demonstrate that thorough analysis of voxel time courses is important for understanding the activity of specific sub-areas of the functional networks, while ICA is a valuable tool for revealing novel information about functional connectivity which need not be explained by the predefined model. Our results encourage the use of naturalistic stimuli and tasks in cognitive neuroimaging to study how the brain processes stimuli in rich natural environments. PMID:22496909

  18. Voxel-Based Morphometry for Separation of Schizophrenia From Other Types of Psychosis in First-Episode Psychosis: Diagnostic Test Review.

    PubMed

    Palaniyappan, Lena; Maayan, Nicola; Bergman, Hanna; Davenport, Clare; Adams, Clive E; Soares-Weiser, Karla

    2016-03-01

    Subtle but widespread deficit in the cortical and subcortical grey matter is a consistent neuroimaging observation in schizophrenia. Several studies have used voxel based morphometry (VBM) to investigate the nature of this structural deficit. We conducted a diagnostic test review to explore the diagnostic potential of VBM in differentiating schizophrenia from other types of first-episode psychoses. PMID:26738529

  19. Stimulus-Related Independent Component and Voxel-Wise Analysis of Human Brain Activity during Free Viewing of a Feature Film

    PubMed Central

    Lahnakoski, Juha M.; Salmi, Juha; Jääskeläinen, Iiro P.; Lampinen, Jouko; Glerean, Enrico; Tikka, Pia; Sams, Mikko

    2012-01-01

    Understanding how the brain processes stimuli in a rich natural environment is a fundamental goal of neuroscience. Here, we showed a feature film to 10 healthy volunteers during functional magnetic resonance imaging (fMRI) of hemodynamic brain activity. We then annotated auditory and visual features of the motion picture to inform analysis of the hemodynamic data. The annotations were fitted to both voxel-wise data and brain network time courses extracted by independent component analysis (ICA). Auditory annotations correlated with two independent components (IC) disclosing two functional networks, one responding to variety of auditory stimulation and another responding preferentially to speech but parts of the network also responding to non-verbal communication. Visual feature annotations correlated with four ICs delineating visual areas according to their sensitivity to different visual stimulus features. In comparison, a separate voxel-wise general linear model based analysis disclosed brain areas preferentially responding to sound energy, speech, music, visual contrast edges, body motion and hand motion which largely overlapped the results revealed by ICA. Differences between the results of IC- and voxel-based analyses demonstrate that thorough analysis of voxel time courses is important for understanding the activity of specific sub-areas of the functional networks, while ICA is a valuable tool for revealing novel information about functional connectivity which need not be explained by the predefined model. Our results encourage the use of naturalistic stimuli and tasks in cognitive neuroimaging to study how the brain processes stimuli in rich natural environments. PMID:22496909

  20. DOS: the discrete-ordinates system. [LMFBR

    SciTech Connect

    Rhoades, W. A.; Emmett, M. B.

    1982-09-01

    The Discrete Ordinates System determines the flux of neutrons or photons due either to fixed sources specified by the user or to sources generated by particle interaction with the problem materials. It also determines numerous secondary results which depend upon flux. Criticality searches can be performed. Numerous input, output, and file manipulation facilities are provided. The DOS driver program reads the problem specification from an input file and calls various program modules into execution as specified by the input file.

  1. DIGLIB. PC-DOS Graphics Subroutine Library

    SciTech Connect

    Brand, H.R.

    1989-02-01

    DIGLIB is a collection of general graphics subroutines. It was designed to be small, reasonably fast, device-independent, and compatible with DEC-supplied operating systems for VAXes, PDP-11s, and LSI-11s, and the DOS operating system for IBM PCs and IBM-compatible machines. DIGLIB/VMS runs on the VAX and MicroVAX series of computers under VMS. The software is readily usable by casual programmers for two-dimensional plotting.

  2. From DOS to UNIX: An independent's experience

    SciTech Connect

    Hepguler, G.; Meehan, D.N.

    1993-06-01

    Union Pacific Resources Co. (UPRC) is a large independent operator with about 100 petroleum engineers. UPRC has a reasonably sophisticated PC network with many hundreds of PC's connected by several local area network (LAN) servers. Essentially all engineers have a 386-based PC on their desks with access to a host of software packages, peripheral devices, and mainframe computers, Many engineers have acquired 486-based PC's. UPRC's solution has involved migrating from a DOS-based platform on individual users' desks to UNIX workstations. Dozens of UNIX workstations are networked; some are on the desk', while others are located in central locations. Reservoir simulation, geostatistical modeling, image processing, and log analysis are now done exclusively on the UNIX workstations. Numerous DOS-based programs, however, have not yet been migrated into the UNIX environment. This paper describes the topography of both PC DOS and UNIX workstations networks in UPRC and examines the flow of information in each network configuration to identify differences. The successes and failures of various techniques for providing access to both platforms are presented.

  3. Novas determinações dos parâmetros atmosféricos das estrelas anãs brancas DA

    NASA Astrophysics Data System (ADS)

    Giovannini, O.; Costa, A. F. M.; Kepler, S. O.

    2003-08-01

    Nós temos selecionado uma amostra de estrelas anãs brancas DA (atmosfera de hidrogênio) a partir dos índices de Strömgren cujos valores estão próximos a região de instabilidade das estrelas anãs brancas DA variáveis, as chamadas estrelas DAV ou ZZ Ceti. O objetivo é determinar os parâmetros fundamentais (temperatura efetiva, Teff, aceleração da gravidade, log g, e massa) destas estrelas para verificar quais os parâmetros estelares estão envolvidos com o mecanismo de pulsação das estrelas DAV. Nós obtemos, até agora, mais de 120 espectros óticos de estrelas DA. Entre as estrelas selecionadas há 20 estrelas variáveis (DAV). Assim, podemos verificar se existem ou não estrelas não variáveis dentro da faixa de instabilidade das estrelas ZZ Ceti. Neste trabalho nós apresentamos a determinação dos parâmetros atmosféricos (temperatura efetiva, Teff, e aceleração da gravidade, log g) das estrelas anãs brancas DA usando os novos modelos de atmosfera ML2/a = 0.6. Estes modelos têm sido utilizados recentemente por fornecerem uma excelente consistência interna na determinação das temperaturas nas regiões do ultra-violeta e ótico. Os parâmetros atmosféricos são determinados espectroscopicamente através da comparação do fluxo de energia das linhas de Balmer (Hb à H9) entre os espectros observados e sintéticos (gerados pelos modelos de atmosfera). As temperaturas obtidas com os novos modelos são, em geral, menores (~ 1000 K menos) que as temperaturas determinadas anteriormente, com modelos ML1. Os valores de log g não mudaram significativamente (menos de 10%). A faixa de instabilidade das DAVs está entre 11000 e 13000 K, consistente com dados de outros autores.

  4. Prediction of plasma-induced damage distribution during silicon nitride etching using advanced three-dimensional voxel model

    SciTech Connect

    Kuboi, Nobuyuki Tatsumi, Tetsuya; Kinoshita, Takashi; Shigetoshi, Takushi; Fukasawa, Masanaga; Komachi, Jun; Ansai, Hisahiro

    2015-11-15

    The authors modeled SiN film etching with hydrofluorocarbon (CH{sub x}F{sub y}/Ar/O{sub 2}) plasma considering physical (ion bombardment) and chemical reactions in detail, including the reactivity of radicals (C, F, O, N, and H), the area ratio of Si dangling bonds, the outflux of N and H, the dependence of the H/N ratio on the polymer layer, and generation of by-products (HCN, C{sub 2}N{sub 2}, NH, HF, OH, and CH, in addition to CO, CF{sub 2}, SiF{sub 2}, and SiF{sub 4}) as ion assistance process parameters for the first time. The model was consistent with the measured C-F polymer layer thickness, etch rate, and selectivity dependence on process variation for SiN, SiO{sub 2}, and Si film etching. To analyze the three-dimensional (3D) damage distribution affected by the etched profile, the authors developed an advanced 3D voxel model that can predict the time-evolution of the etched profile and damage distribution. The model includes some new concepts for gas transportation in the pattern using a fluid model and the property of voxels called “smart voxels,” which contain details of the history of the etching situation. Using this 3D model, the authors demonstrated metal–oxide–semiconductor field-effect transistor SiN side-wall etching that consisted of the main-etch step with CF{sub 4}/Ar/O{sub 2} plasma and an over-etch step with CH{sub 3}F/Ar/O{sub 2} plasma under the assumption of a realistic process and pattern size. A large amount of Si damage induced by irradiated hydrogen occurred in the source/drain region, a Si recess depth of 5 nm was generated, and the dislocated Si was distributed in a 10 nm deeper region than the Si recess, which was consistent with experimental data for a capacitively coupled plasma. An especially large amount of Si damage was also found at the bottom edge region of the metal–oxide–semiconductor field-effect transistors. Furthermore, our simulation results for bulk fin-type field-effect transistor side-wall etching

  5. 3-D ion distribution and evolution in storm-time RC Retrieved from TWINS ENA by differential voxel CT technique

    NASA Astrophysics Data System (ADS)

    Ma, S.; Yan, W.; Xu, L.

    2013-12-01

    The quantitative retrieval of the 3-D spatial distribution of the parent energetic ions of ENA from a 2-D ENA image is a quite challenge task. The Two Wide-angle Imaging Neutral-atom Spectrometers (TWINS) mission of NASA is the first constellation to perform stereoscopic magnetospheric imaging of energetic neutral atoms (ENA) from a pair of spacecraft flying on two widely-separated Molniya orbits. TWINS provides a unique opportunity to retrieve the 3-D distribution of ions in the ring current (RC) by using a volumetric pixel (voxel) CT inversion method. In this study the voxel CT method is implemented for a series of differential ENA fluxes averaged over about 6 to 7 sweeps (corresponding to a time period of about 9 min.) at different energy levels ranging from 5 to 100 keV, obtained simultaneously by the two satellites during the main phase of a great magnetic storm with minimum Sym-H of -156 nT on 24-25 October 2011. The data were selected to span a period about 50 minutes during which a large substorm was undergoing its expansion phase first and then recovery. The ENA species of O and H are distinguished for some time-segments by analyzing the signals of pulse heights of second electrons emitted from the carbon foil and impacted on the MCP detector in the TWINS sensors. In order to eliminate the possible influence on retrieval induced by instrument bias error, a differential voxel CT technique is applied. The flux intensity of the ENAs' parent ions in the RC has been obtained as a function of energy, L value, MLT sector and latitude, along with their time evolution during the storm-time substorm expansion phase. Forward calculations proved the reliability of the retrieved results. It shows that the RC is highly asymmetric, with a major concentration in the midnight to dawn sector for equatorial latitudes. Halfway through the substorm expansion there occurred a large enhancement of equatorial ion flux at lower energy (5 keV) in the dusk sector, with narrow extent

  6. Storm-time RC ion distribution and evolution retrieved from TWINS ENA by differential voxel CT technique

    NASA Astrophysics Data System (ADS)

    Yan, Wei-Nan; Ma, Shu-Ying; Xu, Liang

    2014-05-01

    The quantitative retrieval of the 3-D spatial distribution of the parent energetic ions of ENA from a 2-D ENA image is a challenge task. The Two Wide-angle Imaging Neutral-atom Spectrometers (TWINS) mission of NASA provides an unique opportunity to retrieve the 3-D distribution of ions in the ring current (RC) by using a volumetric pixel (voxel) CT inversion method. In this study the voxel CT method is implemented for a series of differential ENA fluxes at different energy levels ranging from 5 to 80 keV obtained simultaneously by the two satellites of TWINS flying on two widely-separated Molniya orbits during the main phase of the magnetic storm of 24-25 October 2011 with minimum Sym-H index of -160 nT. The data were selected to span a period of about 50 minutes during which a large substorm was undergoing its expansion phase first and then recovery. The ENA species of O and H are distinguished for lower energy-mass ratio in some time- segments by analyzing the signals of pulse heights of second electrons emitted from the carbon foil and impacted on the MCP detector in the TWINS sensors. In order to eliminate the possible influence on retrieval caused by instrument bias error, a differential voxel CT technique is applied. To weaken the influence of low altitude emission (LAE) produced by ion precipitation, a correction is made for the ENA intensity along the line-of-sight that run deep into the high latitude atmosphere, invoking the so called thick-target approximation. The flux intensity of the ENAs' parent ions in the RC has been obtained as a function of energy, L value, MLT sector and latitude, along with their time evolution during the storm-time substorm expansion phase. Forward calculations proved the reliability of the retrieved results. It shows that the RC is highly asymmetric with a major concentration in the midnight to dawn sector for equatorial latitudes. The ion flux spectra undergo dramatic changes from pre-storm to the main phase. Besides, halfway

  7. Storm-time RC ion distribution and evolution retrieved from TWINS ENA by differential voxel CT technique

    NASA Astrophysics Data System (ADS)

    Ma, S. Y.; Xu, Liang; Yan, Wei-Nan

    The quantitative retrieval of the 3-D spatial distribution of the parent energetic ions of ENA from a 2-D ENA image is a challenge task. The Two Wide-angle Imaging Neutral-atom Spectrometers (TWINS) mission of NASA provides an unique opportunity to retrieve the 3-D distribution of ions in the ring current (RC) by using a volumetric pixel (voxel) CT inversion method. In this study the voxel CT method is implemented for a series of differential ENA fluxes at different energy levels ranging from 5 to 80 keV obtained simultaneously by the two satellites of TWINS flying on two widely-separated Molniya orbits during the main phase of the magnetic storm of 24-25 October 2011 with minimum Sym-H index of -160 nT. The data were selected to span a period of about 50 minutes during which a large substorm was undergoing its expansion phase first and then recovery. The ENA species of O and H are distinguished for lower energy-mass ratio in some time- segments by analyzing the signals of pulse heights of second electrons emitted from the carbon foil and impacted on the MCP detector in the TWINS sensors. In order to eliminate the possible influence on retrieval caused by instrument bias error, a differential voxel CT technique is applied. To weaken the influence of low altitude emission (LAE) produced by ion precipitation, a correction is made for the ENA intensity along the line-of-sight that run deep into the high latitude atmosphere, invoking the so called thick-target approximation. The flux intensity of the ENAs’ parent ions in the RC has been obtained as a function of energy, L value, MLT sector and latitude, along with their time evolution during the storm-time substorm expansion phase. Forward calculations proved the reliability of the retrieved results. It shows that the RC is highly asymmetric with a major concentration in the midnight to dawn sector for equatorial latitudes. The ion flux spectra undergo dramatic changes from pre-storm to the main phase. Besides

  8. Functional atlas of emotional faces processing: a voxel-based meta-analysis of 105 functional magnetic resonance imaging studies

    PubMed Central

    Fusar-Poli, Paolo; Placentino, Anna; Carletti, Francesco; Landi, Paola; Allen, Paul; Surguladze, Simon; Benedetti, Francesco; Abbamonte, Marta; Gasparotti, Roberto; Barale, Francesco; Perez, Jorge; McGuire, Philip; Politi, Pierluigi

    2009-01-01

    Background Most of our social interactions involve perception of emotional information from the faces of other people. Furthermore, such emotional processes are thought to be aberrant in a range of clinical disorders, including psychosis and depression. However, the exact neurofunctional maps underlying emotional facial processing are not well defined. Methods Two independent researchers conducted separate comprehensive PubMed (1990 to May 2008) searches to find all functional magnetic resonance imaging (fMRI) studies using a variant of the emotional faces paradigm in healthy participants. The search terms were: “fMRI AND happy faces,” “fMRI AND sad faces,” “fMRI AND fearful faces,” “fMRI AND angry faces,” “fMRI AND disgusted faces” and “fMRI AND neutral faces.” We extracted spatial coordinates and inserted them in an electronic database. We performed activation likelihood estimation analysis for voxel-based meta-analyses. Results Of the originally identified studies, 105 met our inclusion criteria. The overall database consisted of 1785 brain coordinates that yielded an overall sample of 1600 healthy participants. Quantitative voxel-based meta-analysis of brain activation provided neurofunctional maps for 1) main effect of human faces; 2) main effect of emotional valence; and 3) modulatory effect of age, sex, explicit versus implicit processing and magnetic field strength. Processing of emotional faces was associated with increased activation in a number of visual, limbic, temporoparietal and prefrontal areas; the putamen; and the cerebellum. Happy, fearful and sad faces specifically activated the amygdala, whereas angry or disgusted faces had no effect on this brain region. Furthermore, amygdala sensitivity was greater for fearful than for happy or sad faces. Insular activation was selectively reported during processing of disgusted and angry faces. However, insular sensitivity was greater for disgusted than for angry faces. Conversely

  9. Is there more valuable information in PWI datasets for a voxel-wise acute ischemic stroke tissue outcome prediction than what is represented by typical perfusion maps?

    NASA Astrophysics Data System (ADS)

    Forkert, Nils Daniel; Siemonsen, Susanne; Dalski, Michael; Verleger, Tobias; Kemmling, Andre; Fiehler, Jens

    2014-03-01

    The acute ischemic stroke is a leading cause for death and disability in the industry nations. In case of a present acute ischemic stroke, the prediction of the future tissue outcome is of high interest for the clinicians as it can be used to support therapy decision making. Within this context, it has already been shown that the voxel-wise multi-parametric tissue outcome prediction leads to more promising results compared to single channel perfusion map thresholding. Most previously published multi-parametric predictions employ information from perfusion maps derived from perfusion-weighted MRI together with other image sequences such as diffusion-weighted MRI. However, it remains unclear if the typically calculated perfusion maps used for this purpose really include all valuable information from the PWI dataset for an optimal tissue outcome prediction. To investigate this problem in more detail, two different methods to predict tissue outcome using a k-nearest-neighbor approach were developed in this work and evaluated based on 18 datasets of acute stroke patients with known tissue outcome. The first method integrates apparent diffusion coefficient and perfusion parameter (Tmax, MTT, CBV, CBF) information for the voxel-wise prediction, while the second method employs also apparent diffusion coefficient information but the complete perfusion information in terms of the voxel-wise residue functions instead of the perfusion parameter maps for the voxel-wise prediction. Overall, the comparison of the results of the two prediction methods for the 18 patients using a leave-one-out cross validation revealed no considerable differences. Quantitatively, the parameter-based prediction of tissue outcome led to a mean Dice coefficient of 0.474, while the prediction using the residue functions led to a mean Dice coefficient of 0.461. Thus, it may be concluded from the results of this study that the perfusion parameter maps typically derived from PWI datasets include all

  10. CT-Based Attenuation Correction in Brain SPECT/CT Can Improve the Lesion Detectability of Voxel-Based Statistical Analyses

    PubMed Central

    Kato, Hiroki; Shimosegawa, Eku; Fujino, Koichi; Hatazawa, Jun

    2016-01-01

    Background Integrated SPECT/CT enables non-uniform attenuation correction (AC) using built-in CT instead of the conventional uniform AC. The effect of CT-based AC on voxel-based statistical analyses of brain SPECT findings has not yet been clarified. Here, we assessed differences in the detectability of regional cerebral blood flow (CBF) reduction using SPECT voxel-based statistical analyses based on the two types of AC methods. Subjects and Methods N-isopropyl-p-[123I]iodoamphetamine (IMP) CBF SPECT images were acquired for all the subjects and were reconstructed using 3D-OSEM with two different AC methods: Chang’s method (Chang’s AC) and the CT-based AC method. A normal database was constructed for the analysis using SPECT findings obtained for 25 healthy normal volunteers. Voxel-based Z-statistics were also calculated for SPECT findings obtained for 15 patients with chronic cerebral infarctions and 10 normal subjects. We assumed that an analysis with a higher specificity would likely produce a lower mean absolute Z-score for normal brain tissue, and a more sensitive voxel-based statistical analysis would likely produce a higher absolute Z-score for in old infarct lesions, where the CBF was severely decreased. Results The inter-subject variation in the voxel values in the normal database was lower using CT-based AC, compared with Chang’s AC, for most of the brain regions. The absolute Z-score indicating a SPECT count reduction in infarct lesions was also significantly higher in the images reconstructed using CT-based AC, compared with Chang’s AC (P = 0.003). The mean absolute value of the Z-score in the 10 intact brains was significantly lower in the images reconstructed using CT-based AC than in those reconstructed using Chang’s AC (P = 0.005). Conclusions Non-uniform CT-based AC by integrated SPECT/CT significantly improved sensitivity and the specificity of the voxel-based statistical analyses for regional SPECT count reductions, compared with

  11. Modelo de atmosfera solar ajustado às observações do raio solar em 17GHz

    NASA Astrophysics Data System (ADS)

    Selhorst, C. L.; Silva, A. V. R.; Costa, J. E. R.

    2003-08-01

    O estudo das variações do raio solar durante o ciclo de atividades do Sol e das diferenças em relação à sua distribuição angular nos fornece informações importantes sobre as mudanças na estrutura da atmosfera solar. Neste trabalho foram analisados mais de 3600 mapas do Sol em 17 GHz obtidos pelo Rádio Heliógrafo de Nobeyama (NoRH), durante 1 ciclo de atividade solar (1992-2003). O raio solar foi definido no ponto onde a temperatura de brilho do mapa era equivalente à metade da temperatura do Sol calmo (temperatura mais comum no mapa).Em relação à sua variação ao longo do ciclo solar, o estudo foi dividido em duas partes: a) ajuste de uma circunferência a pontos distribuídos ao redor do Sol todo. Este estudo mostrou uma variação correlacionada com o ciclo de atividade do Sol. b) ajuste da circunferência a pontos situados somente nas regiões polares. Neste caso os resultados mostraram que o raio polar sofre pouca variação durante o ciclo, com tendência à anticorrelação com este. Além disto, a média do raio polar, durante o período analisado, foi 1" menor que o raio medido no Sol todo. Para estudar a distribuição angular do raio solar, comparamos a média da distribuição de 10 mapas no período de mínima atividade solar com a média de 10 mapas no período de máximo, este estudo mostrou um grande aumento do raio na região equatorial no período de máxima atividade solar. As medidas do raio foram usadas como um dos parâmetros para a criação de um modelo atmosférico (além da temperatura de brilho do Sol e do abrilhantamento do limbo observado), onde mostramos que um modelo atmosférico com a região de transição situada a 3500 km fornece um raio 5" menor que as medidas observacionais. Esta incompatibilidade do modelo com os dados observacionais foi contornada com a inclusão de espículas, estas fazem com que o raio solar aumente proporcionalmente à altura que estas atingem na atmosfera solar. A anticorrelação do raio

  12. Performance of the moving voxel image reconstruction (MVIR) method in the fixed site detection system (FSDS) prototype

    SciTech Connect

    Estep, Robert J.

    2012-05-31

    We have developed a dynamic image reconstruction method called MVIR (Moving Voxel Image Reconstruction) for lane detection in multilane portal monitor systems. MVIR was evaluated for use in the Fixed Site Detection System, a prototype three-lane portal monitor system for EZ-pass toll plazas. As a baseline, we compared MVIR with a static image reconstruction method in analyzing the same real and simulated data sets. Performance was judged by the distributions of image intensities for source and no-source vehicles over many trials as a function of source strength. We found that MVIR produced significantly better results in all cases. The performance difference was greatest at low count rates, where source/no-source distributions were well separated with the MVIR method, allowing reliable source vehicle identification with a low probability of false positive identifications. Static reconstruction of the same data produced overlapping distributions that made source vehicle identification unreliable. The performance of the static method was acceptable at high count rates. Both algorithms reliably identified two strong sources passing through at nearly the same time.

  13. A Voxel-Based Morphometry Study of the Brain of University Students Majoring in Music and Nonmusic Disciplines.

    PubMed

    Sato, Kanako; Kirino, Eiji; Tanaka, Shoji

    2015-01-01

    The brain changes flexibly due to various experiences during the developmental stages of life. Previous voxel-based morphometry (VBM) studies have shown volumetric differences between musicians and nonmusicians in several brain regions including the superior temporal gyrus, sensorimotor areas, and superior parietal cortex. However, the reported brain regions depend on the study and are not necessarily consistent. By VBM, we investigated the effect of musical training on the brain structure by comparing university students majoring in music with those majoring in nonmusic disciplines. All participants were right-handed healthy Japanese females. We divided the nonmusic students into two groups and therefore examined three groups: music expert (ME), music hobby (MH), and nonmusic (NM) group. VBM showed that the ME group had the largest gray matter volumes in the right inferior frontal gyrus (IFG; BA 44), left middle occipital gyrus (BA 18), and bilateral lingual gyrus. These differences are considered to be caused by neuroplasticity during long and continuous musical training periods because the MH group showed intermediate volumes in these regions. PMID:26494943

  14. Increased Grey Matter Associated with Long-Term Sahaja Yoga Meditation: A Voxel-Based Morphometry Study

    PubMed Central

    Hernández, Sergio Elías; Suero, José; Barros, Alfonso; González-Mora, José Luis; Rubia, Katya

    2016-01-01

    Objectives To investigate regional differences in grey matter volume associated with the practice of Sahaja Yoga Meditation. Design Twenty three experienced practitioners of Sahaja Yoga Meditation and twenty three non-meditators matched on age, gender and education level, were scanned using structural Magnetic Resonance Imaging and their grey matter volume were compared using Voxel-Based Morphometry. Results Grey matter volume was larger in meditators relative to non-meditators across the whole brain. In addition, grey matter volume was larger in several predominantly right hemispheric regions: in insula, ventromedial orbitofrontal cortex, inferior temporal and parietal cortices as well as in left ventrolateral prefrontal cortex and left insula. No areas with larger grey matter volume were found in non-meditators relative to meditators. Conclusions The study shows that long-term practice of Sahaja Yoga Meditation is associated with larger grey matter volume overall, and with regional enlargement in several right hemispheric cortical and subcortical brain regions that are associated with sustained attention, self-control, compassion and interoceptive perception. The increased grey matter volume in these attention and self-control mediating regions suggests use-dependent enlargement with regular practice of this meditation. PMID:26938433

  15. Surface errors without semantic impairment in acquired dyslexia: a voxel-based lesion-symptom mapping study.

    PubMed

    Binder, Jeffrey R; Pillay, Sara B; Humphries, Colin J; Gross, William L; Graves, William W; Book, Diane S

    2016-05-01

    Patients with surface dyslexia have disproportionate difficulty pronouncing irregularly spelled words (e.g. pint), suggesting impaired use of lexical-semantic information to mediate phonological retrieval. Patients with this deficit also make characteristic 'regularization' errors, in which an irregularly spelled word is mispronounced by incorrect application of regular spelling-sound correspondences (e.g. reading plaid as 'played'), indicating over-reliance on sublexical grapheme-phoneme correspondences. We examined the neuroanatomical correlates of this specific error type in 45 patients with left hemisphere chronic stroke. Voxel-based lesion-symptom mapping showed a strong positive relationship between the rate of regularization errors and damage to the posterior half of the left middle temporal gyrus. Semantic deficits on tests of single-word comprehension were generally mild, and these deficits were not correlated with the rate of regularization errors. Furthermore, the deep occipital-temporal white matter locus associated with these mild semantic deficits was distinct from the lesion site associated with regularization errors. Thus, in contrast to patients with surface dyslexia and semantic impairment from anterior temporal lobe degeneration, surface errors in our patients were not related to a semantic deficit. We propose that these patients have an inability to link intact semantic representations with phonological representations. The data provide novel evidence for a post-semantic mechanism mediating the production of surface errors, and suggest that the posterior middle temporal gyrus may compute an intermediate representation linking semantics with phonology. PMID:26966139

  16. Subcortical and cortical gray matter differences between Kraepelinian and non-Kraepelinian schizophrenia patients identified using voxel-based morphometry.

    PubMed

    Molina, Vicente; Hernández, Juan A; Sanz, Javier; Paniagua, Juan C; Hernández, Ana I; Martín, Carmen; Matías, Juan; Calama, Julia; Bote, Berta

    2010-10-30

    The long-term outcome of schizophrenia patients may differ depending on their brain structure. This would be reflected in significant structural differences between poor-outcome (i.e., Kraepelinian) and non-Kraepelinian patients. To assess this possibility, we have evaluated the degree of deviation in brain structure in Kraepelinian patients with respect to controls and non-Kraepelinian schizophrenia patients. We used voxel-brain morphometry (VBM) to assess the differences in gray matter volume across the brain in the Kraepelinian group with respect to the healthy controls and non-Kraepelinian patients. Twenty-six Kraepelinian and 18 non-Kraepelinian schizophrenia patients and 41 healthy controls were included. With respect to the healthy controls, the Kraepelinian patients showed a very significant decrease in gray matter in the frontal, occipital, and limbic cortices, and, at a subcortical level, bilaterally in the striatum and thalamus. In comparison with the non-Kraepelinian patients, the Kraepelinian individuals continued to show a similar subcortical decrease. Thus, Kraepelinian patients may be characterized by a distinct pattern of brain abnormalities, in particular, in subcortical regions.

  17. Relationship between personality and gray matter volume in healthy young adults: a voxel-based morphometric study.

    PubMed

    Lu, Fengmei; Huo, Yajun; Li, Meiling; Chen, Heng; Liu, Feng; Wang, Yifeng; Long, Zhiliang; Duan, Xujun; Zhang, Jiang; Zeng, Ling; Chen, Huafu

    2014-01-01

    This study aims to investigate the neurostructural foundations of the human personality in young adults. High-resolution structural T1-weighted MR images of 71 healthy young individuals were processed using voxel-based morphometric (VBM) approach. Multiple regression analyses were performed to identify the associations between personality traits and gray matter volume (GMV). The Eysenck Personality Questionnaire-Revised, Short Scale for Chinese was chosen to assess the personality traits. This scale includes four dimensions, namely, extraversion, neuroticism, psychoticism, and lie. Particularly, we studied on two dimensions (extraversion and neuroticism) of Eysenck's personality. Our results showed that extraversion was negatively correlated with GMV of the bilateral amygdala, the bilateral parahippocampal gyrus, the right middle temporal gyrus, and the left superior frontal gyrus, all of which are involved in emotional and social cognitive processes. These results might suggest an association between extraversion and affective processing. In addition, a positive correlation was detected between neuroticism and GMV of the right cerebellum, a key brain region for negative affect coordination. Meanwhile, a negative association was revealed between GMV of the left superior frontal gyrus and neuroticism. These results may prove that neuroticism is related to several brain regions involved in regulating negative emotions. Based on those findings, we concluded that brain regions involved in social cognition and affective process accounted for modulation and shaping of personality traits among young individuals. Results of this study may serve as a basis for elucidating the anatomical factors of personality.

  18. Grey matter, an endophenotype for schizophrenia? A voxel-based morphometry study in siblings of patients with schizophrenia

    PubMed Central

    van der Velde, Jorien; Gromann, Paula M.; Swart, Marte; de Haan, Lieuwe; Wiersma, Durk; Bruggeman, Richard; Krabbendam, Lydia; Aleman, André

    2015-01-01

    Background Grey matter, both volume and concentration, has been proposed as an endophenotype for schizophrenia given a number of reports of grey matter abnormalities in relatives of patients with schizophrenia. However, previous studies on grey matter abnormalities in relatives have produced inconsistent results. The aim of the present study was to examine grey matter differences between controls and siblings of patients with schizophrenia and to examine whether the age, genetic loading or subclinical psychotic symptoms of selected individuals could explain the previously reported inconsistencies. Methods We compared the grey matter volume and grey matter concentration of healthy siblings of patients with schizophrenia and healthy controls matched for age, sex and education using voxel-based morphometry (VBM). Furthermore, we selected subsamples based on age (< 30 yr), genetic loading and subclinical psychotic symptoms to examine whether this would lead to different results. Results We included 89 siblings and 69 controls in our study. The results showed that siblings and controls did not differ significantly on grey matter volume or concentration. Furthermore, specifically selecting participants based on age, genetic loading or subclinical psychotic symptoms did not alter these findings. Limitations The main limitation was that subdividing the sample resulted in smaller samples for the subanalyses. Furthermore, we used MRI data from 2 different scanner sites. Conclusion These results indicate that grey matter measured through VBM might not be a suitable endophenotype for schizophrenia. PMID:25768029

  19. Voxel-based morphometry in opera singers: Increased gray-matter volume in right somatosensory and auditory cortices.

    PubMed

    Kleber, Boris; Veit, Ralf; Moll, Christina Valérie; Gaser, Christian; Birbaumer, Niels; Lotze, Martin

    2016-06-01

    In contrast to instrumental musicians, professional singers do not train on a specific instrument but perfect a motor system that has already been extensively trained during speech motor development. Previous functional imaging studies suggest that experience with singing is associated with enhanced somatosensory-based vocal motor control. However, experience-dependent structural plasticity in vocal musicians has rarely been studied. We investigated voxel-based morphometry (VBM) in 27 professional classical singers and compared gray matter volume in regions of the "singing-network" to an age-matched group of 28 healthy volunteers with no special singing experience. We found right hemispheric volume increases in professional singers in ventral primary somatosensory cortex (larynx S1) and adjacent rostral supramarginal gyrus (BA40), as well as in secondary somatosensory (S2) and primary auditory cortices (A1). Moreover, we found that earlier commencement with vocal training correlated with increased gray-matter volume in S1. However, in contrast to studies with instrumental musicians, this correlation only emerged in singers who began their formal training after the age of 14years, when speech motor development has reached its first plateau. Structural data thus confirm and extend previous functional reports suggesting a pivotal role of somatosensation in vocal motor control with increased experience in singing. Results furthermore indicate a sensitive period for developing additional vocal skills after speech motor coordination has matured.

  20. Cerebral gray matter volume variation in female-to-male transsexuals: a voxel-based morphometric study.

    PubMed

    Kim, Tae-Hoon; Kim, Seok-Kwun; Jeong, Gwang-Woo

    2015-12-16

    Several studies seem to support the hypothesis that brain anatomy is associated with transsexualism. However, these studies were still limited because few neuroanatomical findings have been obtained from female-to-male (FtM) transsexuals. This study compared the cerebral regional volumes of gray matter (GM) between FtM transsexuals and female controls using a voxel-based morphometry. Twelve FtM transsexuals who had undergone sex-reassignment surgery and 15 female controls participated in this study. Both groups were age matched and right-handed, with no history of neurological illness. Fifteen female controls were recruited to determine whether GM volumes in FtM transsexuals more closely resembled individuals who shared their biological sex. MRI data were processed using SPM 8 with the diffeomorphic anatomical registration through exponentiated Lie algebra (DARTEL). FtM transsexuals showed significantly larger volumes of the thalamus, hypothalamus, midbrain, gyrus rectus, head of caudate nucleus, precentral gyrus, and subcallosal area compared with the female controls. However, the female controls showed a significantly larger volume in the superior temporal gyrus including Heschl's gyrus and Rolandic operculum. These findings confirm that the volume difference in brain substructures in FtM transsexuals is likely to be associated with transsexualism and that transsexualism is probably associated with distinct cerebral structures, determining gender identity. PMID:26559725

  1. Concordance of white matter and gray matter abnormalities in autism spectrum disorders: a voxel-based meta-analysis study.

    PubMed

    Cauda, Franco; Costa, Tommaso; Palermo, Sara; D'Agata, Federico; Diano, Matteo; Bianco, Francesca; Duca, Sergio; Keller, Roberto

    2014-05-01

    There are at least two fundamental unanswered questions in the literature on autism spectrum disorders (ASD): Are abnormalities in white (WM) and gray matter (GM) consistent with one another? Are WM morphometric alterations consistent with alterations in the GM of regions connected by these abnormal WM bundles and vice versa? The aim of this work is to bridge this gap. After selecting voxel-based morphometry and diffusion tensor imaging studies comparing autistic and normally developing groups of subjects, we conducted an activation likelihood estimation (ALE) meta-analysis to estimate consistent brain alterations in ASD. Multidimensional scaling was used to test the similarity of the results. The ALE results were then analyzed to identify the regions of concordance between GM and WM areas. We found statistically significant topological relationships between GM and WM abnormalities in ASD. The most numerous were negative concordances, found bilaterally but with a higher prevalence in the right hemisphere. Positive concordances were found in the left hemisphere. Discordances reflected the spatial distribution of negative concordances. Thus, a different hemispheric contribution emerged, possibly related to pathogenetic factors affecting the right hemisphere during early developmental stages. Besides, WM fiber tracts linking the brain structures involved in social cognition showed abnormalities, and most of them had a negative concordance with the connected GM regions. We interpreted the results in terms of altered brain networks and their role in the pervasive symptoms dramatically impairing communication and social skills in ASD patients.

  2. Damage to Fronto-Parietal Networks Impairs Motor Imagery Ability after Stroke: A Voxel-Based Lesion Symptom Mapping Study

    PubMed Central

    Oostra, Kristine M.; Van Bladel, Anke; Vanhoonacker, Ann C. L.; Vingerhoets, Guy

    2016-01-01

    Background: Mental practice with motor imagery has been shown to promote motor skill acquisition in healthy subjects and patients. Although lesions of the common motor imagery and motor execution neural network are expected to impair motor imagery ability, functional equivalence appears to be at least partially preserved in stroke patients. Aim: To identify brain regions that are mandatory for preserved motor imagery ability after stroke. Method: Thirty-seven patients with hemiplegia after a first time stroke participated. Motor imagery ability was measured using a Motor Imagery questionnaire and temporal congruence test. A voxelwise lesion symptom mapping approach was used to identify neural correlates of motor imagery in this cohort within the first year post-stroke. Results: Poor motor imagery vividness was associated with lesions in the left putamen, left ventral premotor cortex and long association fibers linking parieto-occipital regions with the dorsolateral premotor and prefrontal areas. Poor temporal congruence was otherwise linked to lesions in the more rostrally located white matter of the superior corona radiata. Conclusion: This voxel-based lesion symptom mapping study confirms the association between white matter tract lesions and impaired motor imagery ability, thus emphasizing the importance of an intact fronto-parietal network for motor imagery. Our results further highlight the crucial role of the basal ganglia and premotor cortex when performing motor imagery tasks. PMID:26869894

  3. Contralesional Cortical Structural Reorganization Contributes to Motor Recovery after Sub-Cortical Stroke: A Longitudinal Voxel-Based Morphometry Study

    PubMed Central

    Cai, Jianxin; Ji, Qiling; Xin, Ruiqiang; Zhang, Dianping; Na, Xu; Peng, Ruchen; Li, Kuncheng

    2016-01-01

    Although changes in brain gray matter after stroke have been identified in some neuroimaging studies, lesion heterogeneity and individual variability make the detection of potential neuronal reorganization difficult. This study attempted to investigate the potential structural cortical reorganization after sub-cortical stroke using a longitudinal voxel-based gray matter volume (GMV) analysis. Eleven right-handed patients with first-onset, subcortical, ischemic infarctions involving the basal ganglia regions underwent structural magnetic resonance imaging in addition to National Institutes of Health Stroke Scale (NIHSS) and Motricity Index (MI) assessments in the acute (<5 days) and chronic stages (1 year later). The GMVs were calculated and compared between the two stages using nonparametric permutation paired t-tests. Moreover, the Spearman correlations between the GMV changes and clinical recoveries were analyzed. Compared with the acute stage, significant decreases in GMV were observed in the ipsilesional (IL) precentral gyrus (PreCG), paracentral gyrus (ParaCG), and contralesional (CL) cerebellar lobule VII in the chronic stage. Additionally, significant increases in GMV were found in the CL orbitofrontal cortex (OFC) and middle (MFG) and inferior frontal gyri (IFG). Furthermore, severe GMV atrophy in the IL PreCG predicted poorer clinical recovery, and greater GMV increases in the CL OFG and MFG predicted better clinical recovery. Our findings suggest that structural reorganization of the CL “cognitive” cortices might contribute to motor recovery after sub-cortical stroke. PMID:27536229

  4. Development of a Multiparametric Voxel-Based Magnetic Resonance Imaging Biomarker for Early Cancer Therapeutic Response Assessment

    PubMed Central

    Galbán, Craig J.; Lemasson, Benjamin; Hoff, Benjamin A.; Johnson, Timothy D.; Sundgren, Pia C.; Tsien, Christina; Chenevert, Thomas L.; Ross, Brian D.

    2015-01-01

    Quantitative magnetic resonance imaging (MRI)-based biomarkers, which capture physiological and functional tumor processes, were evaluated as imaging surrogates of early tumor response following chemoradiotherapy in glioma patients. A multiparametric extension of a voxel-based analysis, referred as the parametric response map (PRM), was applied to quantitative MRI maps to test the predictive potential of this metric for detecting response. Fifty-six subjects with newly diagnosed high-grade gliomas treated with radiation and concurrent temozolomide were enrolled in a single-site prospective institutional review board-approved MRI study. Apparent diffusion coefficient (ADC) and relative cerebral blood volume (rCBV) maps were acquired before therapy and 3 weeks after therapy was initiated. Multiparametric PRM (mPRM) was applied to both physiological MRI maps and evaluated as an imaging biomarker of patient survival. For comparison, single-biomarker PRMs were also evaluated in this study. The simultaneous analysis of ADC and rCBV by the mPRM approach was found to improve the predictive potential for patient survival over single PRM measures. With an array of quantitative imaging parameters being evaluated as biomarkers of therapeutic response, mPRM shows promise as a new methodology for consolidating physiologically distinct imaging parameters into a single interpretable and quantitative metric. PMID:26568982

  5. Brain Gray Matter Changes Associated with Mindfulness Meditation in Older Adults: An Exploratory Pilot Study using Voxel-based Morphometry

    PubMed Central

    Kurth, Florian; Luders, Eileen; Wu, Brian; Black, David S.

    2015-01-01

    Background Mindfulness-based interventions (MBIs) have previously been associated with structural gray matter changes in normal healthy adults. However, it remains unknown if standardized MBIs can induce similar changes in older adults and those with health complaints as well. The objective of this investigation was to examine the effect of a standardized MBI on the gray matter tissue of older adults with sleep disturbances. Methods This exploratory single-group pilot longitudinal study examined local gray matter changes over a six-week MBI period. Participants included six older adult community volunteers (M=66.5 years of age, SD=5.5, range=58–75; 66% female) with sleep disturbances recruited through advertisement in local newspapers/flyers posted at a university medical center and affiliated clinics in Los Angeles, CA. The MBI was delivered as a weekly, two-hour, six-session, group-based course in mindfulness meditation. Gray matter was measured voxel-wise pre- and post-intervention. Results A significant gray matter increase was identified within the precuneus, possibly implicating meditation-induced changes of the default mode network. In contrast, observed significant gray matter decreases may have been driven by MBI-related remediation of brain architecture subserving sleep complaints. Conclusions Exploratory findings suggest that mindfulness meditation practice is associated with a detectable alteration of cerebral gray matter in older adults. PMID:25632405

  6. A Voxel-Based Morphometry Study of the Brain of University Students Majoring in Music and Nonmusic Disciplines

    PubMed Central

    Sato, Kanako; Kirino, Eiji; Tanaka, Shoji

    2015-01-01

    The brain changes flexibly due to various experiences during the developmental stages of life. Previous voxel-based morphometry (VBM) studies have shown volumetric differences between musicians and nonmusicians in several brain regions including the superior temporal gyrus, sensorimotor areas, and superior parietal cortex. However, the reported brain regions depend on the study and are not necessarily consistent. By VBM, we investigated the effect of musical training on the brain structure by comparing university students majoring in music with those majoring in nonmusic disciplines. All participants were right-handed healthy Japanese females. We divided the nonmusic students into two groups and therefore examined three groups: music expert (ME), music hobby (MH), and nonmusic (NM) group. VBM showed that the ME group had the largest gray matter volumes in the right inferior frontal gyrus (IFG; BA 44), left middle occipital gyrus (BA 18), and bilateral lingual gyrus. These differences are considered to be caused by neuroplasticity during long and continuous musical training periods because the MH group showed intermediate volumes in these regions. PMID:26494943

  7. False positive rates in Voxel-based Morphometry studies of the human brain: should we be worried?

    PubMed

    Scarpazza, Cristina; Tognin, Stefania; Frisciata, Silvia; Sartori, Giuseppe; Mechelli, Andrea

    2015-05-01

    Voxel-based Morphometry (VBM) is a widely used automated technique for the analysis of neuroanatomical images. Despite its popularity within the neuroimaging community, there are outstanding concerns about its potential susceptibility to false positive findings. Here we review the main methodological factors that are known to influence the results of VBM studies comparing two groups of subjects. We then use two large, open-access data sets to empirically estimate false positive rates and how these depend on sample size, degree of smoothing and modulation. Our review and investigation provide three main results: (i) when groups of equal size are compared false positive rate is not higher than expected, i.e. about 5%; (ii) the sample size, degree of smoothing and modulation do not appear to influence false positive rate; (iii) when they exist, false positive findings are randomly distributed across the brain. These results provide reassurance that VBM studies comparing groups are not vulnerable to the higher than expected false positive rates that are evident in single case VBM.

  8. The association between the brain and mind pops: a voxel-based morphometry study in 256 Chinese college students.

    PubMed

    Zhang, Lei; Li, Wenfu; Wei, Dongtao; Yang, Wenjing; Yang, Ning; Qiao, Lei; Qiu, Jiang; Zuo, Xi-Nian; Zhang, Qinglin

    2016-06-01

    Mind pops or involuntary semantic memories refer to words, phrases, images, or melodies that suddenly pop into one's mind without any deliberate attempt to recall them. Despite their prevalence in everyday life, research on mind pops has started only recently. Notably, mind pops are very similar to clinical involuntary phenomena such as hallucinations in schizophrenia, suggesting their potential role in pathology. The present study aimed to investigate the relationship between mind pops and the brain morphometry measured in 302 healthy young adults; after exclusions, 256 participants were included in our analyses. Specifically, the Mind Popping Questionnaire (MPQ) was employed to measure the degree of individual mind pops, whereas the Voxel-Based Morphometry (VBM) was used to compute the volumes of both gray and white matter tissues. Multiple regression analyses on MPQ and VBM metrics indicated that high-frequency mind pops were significantly associated with smaller gray matter volume in the left middle temporal gyrus as well as with larger gray and white matter volume in the right medial prefrontal cortex. This increase in mind pops is also linked to higher creativity and the personality trait of 'openness'. These data not only suggest a key role of the two regions in generating self-related thoughts, but also open a possible link between brain and creativity or personality.

  9. Voxelized computational model for convection-enhanced delivery in the rat ventral hippocampus: comparison with in vivo MR experimental studies.

    PubMed

    Kim, Jung Hwan; Astary, Garrett W; Kantorovich, Svetlana; Mareci, Thomas H; Carney, Paul R; Sarntinoranont, Malisa

    2012-09-01

    Convection-enhanced delivery (CED) is a promising local delivery technique for overcoming the blood-brain barrier (BBB) and treating diseases of the central nervous system (CNS). For CED, therapeutics are infused directly into brain tissue and the drug agent is spread through the extracellular space, considered to be highly tortuous porous media. In this study, 3D computational models developed using magnetic resonance (MR) diffusion tensor imaging data sets were used to predict CED transport in the rat ventral hippocampus using a voxelized modeling previously developed by our group. Predicted albumin tracer distributions were compared with MR-measured distributions from in vivo CED in the ventral hippocampus up to 10 μL of Gd-DTPA albumin tracer infusion. Predicted and measured tissue distribution volumes and distribution patterns after 5 and 10 μL infusions were found to be comparable. Tracers were found to occupy the underlying landmark structures with preferential transport found in regions with less fluid resistance such as the molecular layer of the dentate gyrus. Also, tracer spread was bounded by high fluid resistance layers such as the granular cell layer and pyramidal cell layer of dentate gyrus. Leakage of tracers into adjacent CSF spaces was observed towards the end of infusions.

  10. Relating inter-individual differences in verbal creative thinking to cerebral structures: an optimal voxel-based morphometry study.

    PubMed

    Zhu, Feifei; Zhang, Qinglin; Qiu, Jiang

    2013-01-01

    Creativity can be defined the capacity of an individual to produce something original and useful. An important measurable component of creativity is divergent thinking. Despite existing studies on creativity-related cerebral structural basis, no study has used a large sample to investigate the relationship between individual verbal creativity and regional gray matter volumes (GMVs) and white matter volumes (WMVs). In the present work, optimal voxel-based morphometry (VBM) was employed to identify the structure that correlates verbal creativity (measured by the verbal form of Torrance Tests of Creative Thinking) across the brain in young healthy subjects. Verbal creativity was found to be significantly positively correlated with regional GMV in the left inferior frontal gyrus (IFG), which is believed to be responsible for language production and comprehension, new semantic representation, and memory retrieval, and in the right IFG, which may involve inhibitory control and attention switching. A relationship between verbal creativity and regional WMV in the left and right IFG was also observed. Overall, a highly verbal creative individual with superior verbal skills may demonstrate a greater computational efficiency in the brain areas involved in high-level cognitive processes including language production, semantic representation and cognitive control.

  11. Voxel-based morphometric analysis in hypothyroidism using diffeomorphic anatomic registration via an exponentiated lie algebra algorithm approach.

    PubMed

    Singh, S; Modi, S; Bagga, D; Kaur, P; Shankar, L R; Khushu, S

    2013-03-01

    The present study aimed to investigate whether brain morphological differences exist between adult hypothyroid subjects and age-matched controls using voxel-based morphometry (VBM) with diffeomorphic anatomic registration via an exponentiated lie algebra algorithm (DARTEL) approach. High-resolution structural magnetic resonance images were taken in ten healthy controls and ten hypothyroid subjects. The analysis was conducted using statistical parametric mapping. The VBM study revealed a reduction in grey matter volume in the left postcentral gyrus and cerebellum of hypothyroid subjects compared to controls. A significant reduction in white matter volume was also found in the cerebellum, right inferior and middle frontal gyrus, right precentral gyrus, right inferior occipital gyrus and right temporal gyrus of hypothyroid patients compared to healthy controls. Moreover, no meaningful cluster for greater grey or white matter volume was obtained in hypothyroid subjects compared to controls. Our study is the first VBM study of hypothyroidism in an adult population and suggests that, compared to controls, this disorder is associated with differences in brain morphology in areas corresponding to known functional deficits in attention, language, motor speed, visuospatial processing and memory in hypothyroidism.

  12. Surface errors without semantic impairment in acquired dyslexia: a voxel-based lesion-symptom mapping study.

    PubMed

    Binder, Jeffrey R; Pillay, Sara B; Humphries, Colin J; Gross, William L; Graves, William W; Book, Diane S

    2016-05-01

    Patients with surface dyslexia have disproportionate difficulty pronouncing irregularly spelled words (e.g. pint), suggesting impaired use of lexical-semantic information to mediate phonological retrieval. Patients with this deficit also make characteristic 'regularization' errors, in which an irregularly spelled word is mispronounced by incorrect application of regular spelling-sound correspondences (e.g. reading plaid as 'played'), indicating over-reliance on sublexical grapheme-phoneme correspondences. We examined the neuroanatomical correlates of this specific error type in 45 patients with left hemisphere chronic stroke. Voxel-based lesion-symptom mapping showed a strong positive relationship between the rate of regularization errors and damage to the posterior half of the left middle temporal gyrus. Semantic deficits on tests of single-word comprehension were generally mild, and these deficits were not correlated with the rate of regularization errors. Furthermore, the deep occipital-temporal white matter locus associated with these mild semantic deficits was distinct from the lesion site associated with regularization errors. Thus, in contrast to patients with surface dyslexia and semantic impairment from anterior temporal lobe degeneration, surface errors in our patients were not related to a semantic deficit. We propose that these patients have an inability to link intact semantic representations with phonological representations. The data provide novel evidence for a post-semantic mechanism mediating the production of surface errors, and suggest that the posterior middle temporal gyrus may compute an intermediate representation linking semantics with phonology.

  13. Cortical and subcortical gray matter shrinkage in alcohol-use disorders: a voxel-based meta-analysis.

    PubMed

    Yang, Xun; Tian, Fangfang; Zhang, Handi; Zeng, Jianguang; Chen, Taolin; Wang, Song; Jia, Zhiyun; Gong, Qiyong

    2016-07-01

    Although gray matter (GM) damages caused by long term and excessive alcohol consumption have long been reported, the structural neuroimaging findings on alcohol-use disorders (AUD) are inconsistent. The aim of this study was to conduct a meta-analysis, using a novel voxel-based meta-analytic method effect-size signed differential mapping (ES-SDM), to characterize GM changes in AUD patients. Twelve studies including 433 AUD patients and 498 healthy controls (HCs) were retrieved. The AUD group demonstrated significant GM reductions in the corticostriatal-limbic circuits, including bilateral insula, superior temporal gyrus, striatum, dorsal lateral prefrontal cortex (DLPFC), precentral gyrus, anterior cingulate cortex (ACC), left thalamus and right hippocampus compared to HCs. GM reduction in the right striatum is significantly negatively related to duration of alcohol dependence, while GM shrinkage of the left superior, middle frontal gyrus, and left thalamus is related to lifetime alcohol consumption. The findings demonstrate that the GM abnormalities caused by AUD are in corticostriatal-limbic circuits whose dysfunctions may involve in craving and observed functional deficits. PMID:27108216

  14. Brain glucose metabolism is associated with hormone level in Cushing's disease: A voxel-based study using FDG-PET.

    PubMed

    Liu, Shuai; Wang, Yinyan; Xu, Kaibin; Ping, Fan; Wang, Renzhi; Li, Fang; Cheng, Xin

    2016-01-01

    Chronic exposure to elevated levels of glucocorticoids can exert a neurotoxic effect in patients, possibly manifesting as molecular imaging alterations in patients. The aim of this study was to investigate the potential association between brain metabolism and elevated hormone level using (18)F-fluorodeoxyglucose positron emission tomography. We retrospectively enrolled 92 consecutive patients with confirmed diagnosis of Cushing's disease. A voxel-based analysis was performed to investigate the association between cerebral (18)F-fluorodeoxyglucose uptake and serum cortisol level. Relatively impaired metabolism of specific brain regions correlated with serum cortisol level was found. Specifically, notable correlations were found in the hippocampus, amygdala, and cerebellum, regions considered to be involved in the regulation and central action of glucocorticoids. Moreover, some hormone-associated regions were found in the frontal and occipital cortex, possibly mediating the cognitive changes seen in Cushing's disease. Our findings link patterns of perturbed brain metabolism relates to individual hormone level, thus presenting a substrate for cognitive disturbances seen in Cushing's disease patients, as well as in other conditions with abnormal cortisol levels.

  15. A voxel-based morphometry study of gray matter correlates of facial emotion recognition in bipolar disorder.

    PubMed

    Neves, Maila de Castro L; Albuquerque, Maicon Rodrigues; Malloy-Diniz, Leandro; Nicolato, Rodrigo; Silva Neves, Fernando; de Souza-Duran, Fábio Luis; Busatto, Geraldo; Corrêa, Humberto

    2015-08-30

    Facial emotion recognition (FER) is one of the many cognitive deficits reported in bipolar disorder (BD) patients. The aim of this study was to investigate neuroanatomical correlates of FER impairments in BD type I (BD-I). Participants comprised 21 euthymic BD-I patients without Axis I DSM IV-TR comorbidities and 21 healthy controls who were assessed using magnetic resonance imaging and the Penn Emotion Recognition Test (ER40). Preprocessing of images used DARTEL (diffeomorphic anatomical registration through exponentiated Lie algebra) for optimized voxel-based morphometry in SPM8. Compared with healthy subjects, BD-I patients performed poorly in on the ER40 and had reduced gray matter volume (GMV) in the left orbitofrontal cortex, superior portion of the temporal pole and insula. In the BD-I group, the statistical maps indicated a direct correlation between FER on the ER40 and right middle cingulate gyrus GMV. Our findings are consistent with the previous studies regarding the overlap of multiple brain networks of social cognition and BD neurobiology, particularly components of the anterior-limbic neural network.

  16. A Voxel-Based Morphometry Study of the Brain of University Students Majoring in Music and Nonmusic Disciplines.

    PubMed

    Sato, Kanako; Kirino, Eiji; Tanaka, Shoji

    2015-01-01

    The brain changes flexibly due to various experiences during the developmental stages of life. Previous voxel-based morphometry (VBM) studies have shown volumetric differences between musicians and nonmusicians in several brain regions including the superior temporal gyrus, sensorimotor areas, and superior parietal cortex. However, the reported brain regions depend on the study and are not necessarily consistent. By VBM, we investigated the effect of musical training on the brain structure by comparing university students majoring in music with those majoring in nonmusic disciplines. All participants were right-handed healthy Japanese females. We divided the nonmusic students into two groups and therefore examined three groups: music expert (ME), music hobby (MH), and nonmusic (NM) group. VBM showed that the ME group had the largest gray matter volumes in the right inferior frontal gyrus (IFG; BA 44), left middle occipital gyrus (BA 18), and bilateral lingual gyrus. These differences are considered to be caused by neuroplasticity during long and continuous musical training periods because the MH group showed intermediate volumes in these regions.

  17. Entorhinal volume, aerobic fitness, and recognition memory in healthy young adults: A voxel-based morphometry study.

    PubMed

    Whiteman, Andrew S; Young, Daniel E; Budson, Andrew E; Stern, Chantal E; Schon, Karin

    2016-02-01

    Converging evidence supports the hypothesis effects of aerobic exercise and environmental enrichment are beneficial for cognition, in particular for hippocampus-supported learning and memory. Recent work in humans suggests that exercise training induces changes in hippocampal volume, but it is not known if aerobic exercise and fitness also impact the entorhinal cortex. In animal models, aerobic exercise increases expression of growth factors, including brain derived neurotrophic factor (BDNF). This exercise-enhanced expression of growth hormones may boost synaptic plasticity, and neuronal survival and differentiation, potentially supporting function and structure in brain areas including but not limited to the hippocampus. Here, using voxel based morphometry and a standard graded treadmill test to determine cardio-respiratory fitness (Bruce protocol; ·VO2 max), we examined if entorhinal and hippocampal volumes were associated with cardio-respiratory fitness in healthy young adults (N=33). In addition, we examined if volumes were modulated by recognition memory performance and by serum BDNF, a putative marker of synaptic plasticity. Our results show a positive association between volume in right entorhinal cortex and cardio-respiratory fitness. In addition, average gray matter volume in the entorhinal cortex, bilaterally, was positively associated with memory performance. These data extend prior work on the cerebral effects of aerobic exercise and fitness to the entorhinal cortex in healthy young adults thus providing compelling evidence for a relationship between aerobic fitness and structure of the medial temporal lobe memory system.

  18. A Large Scale (N=400) Investigation of Gray Matter Differences in Schizophrenia Using Optimized Voxel-based Morphometry

    PubMed Central

    Meda, Shashwath A.; Giuliani, Nicole R.; Calhoun, Vince D.; Jagannathan, Kanchana; Schretlen, David J.; Pulver, Anne; Cascella, Nicola; Keshavan, Matcheri; Kates, Wendy; Buchanan, Robert; Sharma, Tonmoy; Pearlson, Godfrey D.

    2008-01-01

    Background Many studies have employed voxel-based morphometry (VBM) of MRI images as an automated method of investigating cortical gray matter differences in schizophrenia. However, results from these studies vary widely, likely due to different methodological or statistical approaches. Objective To use VBM to investigate gray matter differences in schizophrenia in a sample significantly larger than any published to date, and to increase statistical power sufficiently to reveal differences missed in smaller analyses. Methods Magnetic resonance whole brain images were acquired from four geographic sites, all using the same model 1.5T scanner and software version, and combined to form a sample of 200 patients with both first episode and chronic schizophrenia and 200 healthy controls, matched for age, gender and scanner location. Gray matter concentration was assessed and compared using optimized VBM. Results Compared to the healthy controls, schizophrenia patients showed significantly less gray matter concentration in multiple cortical and subcortical regions, some previously unreported. Overall, we found lower concentrations of gray matter in regions identified in prior studies, most of which reported only subsets of the affected areas. Conclusions Gray matter differences in schizophrenia are most comprehensively elucidated using a large, diverse and representative sample. PMID:18378428

  19. Brain glucose metabolism is associated with hormone level in Cushing's disease: A voxel-based study using FDG-PET.

    PubMed

    Liu, Shuai; Wang, Yinyan; Xu, Kaibin; Ping, Fan; Wang, Renzhi; Li, Fang; Cheng, Xin

    2016-01-01

    Chronic exposure to elevated levels of glucocorticoids can exert a neurotoxic effect in patients, possibly manifesting as molecular imaging alterations in patients. The aim of this study was to investigate the potential association between brain metabolism and elevated hormone level using (18)F-fluorodeoxyglucose positron emission tomography. We retrospectively enrolled 92 consecutive patients with confirmed diagnosis of Cushing's disease. A voxel-based analysis was performed to investigate the association between cerebral (18)F-fluorodeoxyglucose uptake and serum cortisol level. Relatively impaired metabolism of specific brain regions correlated with serum cortisol level was found. Specifically, notable correlations were found in the hippocampus, amygdala, and cerebellum, regions considered to be involved in the regulation and central action of glucocorticoids. Moreover, some hormone-associated regions were found in the frontal and occipital cortex, possibly mediating the cognitive changes seen in Cushing's disease. Our findings link patterns of perturbed brain metabolism relates to individual hormone level, thus presenting a substrate for cognitive disturbances seen in Cushing's disease patients, as well as in other conditions with abnormal cortisol levels. PMID:27622138

  20. Retrieving Leaf Area Index and Foliage Profiles Through Voxelized 3-D Forest Reconstruction Using Terrestrial Full-Waveform and Dual-Wavelength Echidna Lidars

    NASA Astrophysics Data System (ADS)

    Strahler, A. H.; Yang, X.; Li, Z.; Schaaf, C.; Wang, Z.; Yao, T.; Zhao, F.; Saenz, E.; Paynter, I.; Douglas, E. S.; Chakrabarti, S.; Cook, T.; Martel, J.; Howe, G.; Hewawasam, K.; Jupp, D.; Culvenor, D.; Newnham, G.; Lowell, J.

    2013-12-01

    Measuring and monitoring canopy biophysical parameters provide a baseline for carbon flux studies related to deforestation and disturbance in forest ecosystems. Terrestrial full-waveform lidar systems, such as the Echidna Validation Instrument (EVI) and its successor Dual-Wavelength Echidna Lidar (DWEL), offer rapid, accurate, and automated characterization of forest structure. In this study, we apply a methodology based on voxelized 3-D forest reconstructions built from EVI and DWEL scans to directly estimate two important biophysical parameters: Leaf Area Index (LAI) and foliage profile. Gap probability, apparent reflectance, and volume associated with the laser pulse footprint at the observed range are assigned to the foliage scattering events in the reconstructed point cloud. Leaf angle distribution is accommodated with a simple model based on gap probability with zenith angle as observed in individual scans of the stand. The DWEL instrument, which emits simultaneous laser pulses at 1064 nm and 1548 nm wavelengths, provides a better capability to separate trunk and branch hits from foliage hits due to water absorption by leaf cellular contents at 1548 nm band. We generate voxel datasets of foliage points using a classification methodology solely based on pulse shape for scans collected by EVI and with pulse shape and band ratio for scans collected by DWEL. We then compare the LAIs and foliage profiles retrieved from the voxel datasets of the two instruments at the same red fir site in Sierra National Forest, CA, with each other and with observations from airborne and field measurements. This study further tests the voxelization methodology in obtaining LAI and foliage profiles that are largely free of clumping effects and returns from woody materials in the canopy. These retrievals can provide a valuable 'ground-truth' validation data source for large-footprint spaceborne or airborne lidar systems retrievals.

  1. Wavelet-based cluster analysis: data-driven grouping of voxel time courses with application to perfusion-weighted and pharmacological MRI of the rat brain.

    PubMed

    Whitcher, Brandon; Schwarz, Adam J; Barjat, Hervé; Smart, Sean C; Grundy, Robert I; James, Michael F

    2005-01-15

    MRI time series experiments produce a wealth of information contained in two or three spatial dimensions that evolve over time. Such experiments can, for example, localize brain response to pharmacological stimuli, but frequently the spatiotemporal characteristics of the cerebral response are unknown a priori and variable, and thus difficult to evaluate using hypothesis-based methods alone. Here we used features in the temporal dimension to group voxels with similar time courses based on a nonparametric discrete wavelet transform (DWT) representation of each time course. Applying the DWT to each voxel decomposes its temporal information into coefficients associated with both time and scale. Discarding scales in the DWT that are associated with high-frequency oscillations (noise) provided a straight-forward data reduction step and decreased the computational burden. Optimization-based clustering was then applied to the remaining wavelet coefficients in order to produce a finite number of voxel clusters. This wavelet-based cluster analysis (WCA) was evaluated using two representative classes of MRI neuroimaging experiments. In perfusion-weighted MRI, following occlusion of the middle cerebral artery (MCAO), WCA differentiated healthy tissue and different regions within the ischemic hemisphere. Following an acute cocaine challenge, WCA localized subtle differences in the pharmacokinetic profile of the cerebral response. We conclude that WCA provides a robust method for blind analysis of time series image data.

  2. Comparison of Organ Dose and Dose Equivalent Using Ray Tracing of Male and Female Voxel Phantoms to Space Flight Phantom Torso Data

    NASA Technical Reports Server (NTRS)

    Kim, Myung-Hee Y.; Qualls, Garry D.; Cucinotta, Francis A.

    2008-01-01

    Phantom torso experiments have been flown on the space shuttle and International Space Station (ISS) providing validation data for radiation transport models of organ dose and dose equivalents. We describe results for space radiation organ doses using a new human geometry model based on detailed Voxel phantoms models denoted for males and females as MAX (Male Adult voXel) and Fax (Female Adult voXel), respectively. These models represent the human body with much higher fidelity than the CAMERA model currently used at NASA. The MAX and FAX models were implemented for the evaluation of directional body shielding mass for over 1500 target points of major organs. Radiation exposure to solar particle events (SPE), trapped protons, and galactic cosmic rays (GCR) were assessed at each specific site in the human body by coupling space radiation transport models with the detailed body shielding mass of MAX/FAX phantom. The development of multiple-point body-shielding distributions at each organ site made it possible to estimate the mean and variance of space dose equivalents at the specific organ. For the estimate of doses to the blood forming organs (BFOs), active marrow distributions in adult were accounted at bone marrow sites over the human body. We compared the current model results to space shuttle and ISS phantom torso experiments and to calculations using the CAMERA model.

  3. Regional and voxel-wise comparisons of blood flow measurements between dynamic susceptibility contrast magnetic resonance imaging (DSC-MRI) and arterial spin labeling (ASL) in brain tumors.

    PubMed

    White, Carissa M; Pope, Whitney B; Zaw, Taryar; Qiao, Joe; Naeini, Kourosh M; Lai, Albert; Nghiemphu, Phioanh L; Wang, J J; Cloughesy, Timothy F; Ellingson, Benjamin M

    2014-01-01

    The objective of the current study was to evaluate the regional and voxel-wise correlation between dynamic susceptibility contrast (DSC) and arterial spin labeling (ASL) perfusion magnetic resonance imaging (MRI) measurement of cerebral blood flow (CBF) in patients with brain tumors. Thirty patients with histologically verified brain tumors were evaluated in the current study. DSC-MRI was performed by first using a preload dose of gadolinium contrast, then collecting a dynamic image acquisition during a bolus of contrast, followed by posthoc contrast agent leakage correction. Pseudocontinuous ASL was collected using 30 pairs of tag and control acquisition using a 3-dimensional gradient-echo spin-echo (GRASE) acquisition. All images were registered to a high-resolution anatomical atlas. Average CBF measurements within regions of contrast-enhancement and T2 hyperintensity were evaluated between the two modalities. Additionally, voxel-wise correlation between CBF measurements obtained with DSC and ASL were assessed. Results demonstrated a positive linear correlation between DSC and ASL measurements of CBF when regional average values were compared; however, a statistically significant voxel-wise correlation was only observed in around 30-40% of patients. These results suggest DSC and ASL may provide regionally similar, but spatially different measurements of CBF.

  4. Comparison of organ dose and dose equivalent using ray tracing of male and female Voxel phantoms to space flight phantom torso data

    NASA Astrophysics Data System (ADS)

    Kim, Myung-Hee; Qualls, Garry; Slaba, Tony; Cucinotta, Francis A.

    Phantom torso experiments have been flown on the space shuttle and International Space Station (ISS) providing validation data for radiation transport models of organ dose and dose equivalents. We describe results for space radiation organ doses using a new human geometry model based on detailed Voxel phantoms models denoted for males and females as MAX (Male Adult voXel) and Fax (Female Adult voXel), respectively. These models represent the human body with much higher fidelity than the CAMERA model currently used at NASA. The MAX and FAX models were implemented for the evaluation of directional body shielding mass for over 1500 target points of major organs. Radiation exposure to solar particle events (SPE), trapped protons, and galactic cosmic rays (GCR) were assessed at each specific site in the human body by coupling space radiation transport models with the detailed body shielding mass of MAX/FAX phantom. The development of multiple-point body-shielding distributions at each organ site made it possible to estimate the mean and variance of space dose equivalents at the specific organ. For the estimate of doses to the blood forming organs (BFOs), active marrow distributions in adult were accounted at bone marrow sites over the human body. We compared the current model results to space shuttle and ISS phantom torso experiments and to calculations using the CAMERA model.

  5. Transferências orbitais dentro do modelo quase bicircular no sistema Terra-Lua-Sol

    NASA Astrophysics Data System (ADS)

    Corrêa, A. A.; de Almeida Prado, A. F. B.; Stuchi, T. J.; Beaugé, C.

    2003-08-01

    O problema quase bicircular planar consiste na determinação da dinâmica de um corpo, de massa desprezível, que se move sob o campo gravitacional de três corpos. No caso estudado, o quarto corpo é considerado um satélite artificial e os demais são a Terra, a Lua e o Sol, formando o sistema de três corpos. Este modelo permite a construção de uma hamiltoniana similar a do problema restrito de três corpos (PRTC), incluindo termos periódicos não autônomos, provenientes da presença do Sol, portanto pode ser entendido como uma perturbação ao PRTC. Suas órbitas periódicas aparecem isoladas e possuem o mesmo período solar. Os pontos de equilíbrio colineares possuem o mesmo caráter de estabilidade linear dos pontos lagrangianos (L1, L2 e L3) do PRTC, sendo do tipo sela x centro x centro, instável na direção x e estáveis nas direções y e z. As órbitas periódicas tridimensionais ao redor do ponto colinear é chamada órbita Halo. O objetivo deste trabalho é determinar órbitas de transferências de baixo consumo de combustível para um veículo espacial partindo de uma órbita de estacionamento ao redor da Terra em direção a uma órbita Halo do ponto L1, situado entre a Terra e Lua. Esta tarefa pode ser transformada no problema de valor de contorno: dado um ponto inicial na órbita de estacionamento, um ponto final na órbita halo e o tempo de transferência, deseja-se obter a trajetória que liga estes dois pontos e que minimize os incrementos de velocidade do veículo. Essas transferências são realizadas baseadas no método de Lambert e analisadas de modo a fornecer um baixo consumo. Posteriormente, é feita uma comparação de consumo com as órbitas de transferência equivalentes do PRTC.

  6. Perfil de temperatura dos funis magnetosféricos de estrelas T Tauri com aquecimento alfvênico

    NASA Astrophysics Data System (ADS)

    Vasconcelos, M. J.

    2003-08-01

    Estrelas T Tauri Clássicas são objetos jovens circundados por discos de gás e poeira e que apresentam uma intensa atividade magnética. Seu espectro mostra linhas de emissão alargadas que são razoavelmente reproduzidas nos modelos de acresção magnetosférica. No entanto, o perfil de temperatura dos funis magnéticos é desconhecido. Aquecimento magnético compressional e difusão ambipolar foram considerados para estas estruturas, porém as temperaturas obtidas não são suficientes para explicar as observações. Neste trabalho, examinamos o aquecimento gerado pelo amortecimento de ondas Alfvén através de quatro mecanismos, os amortecimentos não-linear, turbulento, viscoso-resistivo e colisional como função da freqüência da onda. Inicialmente, a temperatura é ajustada para reproduzir as observações e o grau de turbulência requerido para que o mecanismo seja viável é calculado. Os resultados mostram que este é compatível com os dados observacionais. Apresentam-se, também, resultados preliminares do cálculo auto-consistente do perfil de temperatura dos funis, levando-se em conta fontes de aquecimento Alfvênica e fontes de resfriamento.

  7. A critical study of different Monte Carlo scoring methods of dose average linear-energy-transfer maps calculated in voxelized geometries irradiated with clinical proton beams.

    PubMed

    Cortés-Giraldo, M A; Carabe, A

    2015-04-01

    We compare unrestricted dose average linear energy transfer (LET) maps calculated with three different Monte Carlo scoring methods in voxelized geometries irradiated with proton therapy beams with three different Monte Carlo scoring methods. Simulations were done with the Geant4 (Geometry ANd Tracking) toolkit. The first method corresponds to a step-by-step computation of LET which has been reported previously in the literature. We found that this scoring strategy is influenced by spurious high LET components, which relative contribution in the dose average LET calculations significantly increases as the voxel size becomes smaller. Dose average LET values calculated for primary protons in water with voxel size of 0.2 mm were a factor ~1.8 higher than those obtained with a size of 2.0 mm at the plateau region for a 160 MeV beam. Such high LET components are a consequence of proton steps in which the condensed-history algorithm determines an energy transfer to an electron of the material close to the maximum value, while the step length remains limited due to voxel boundary crossing. Two alternative methods were derived to overcome this problem. The second scores LET along the entire path described by each proton within the voxel. The third followed the same approach of the first method, but the LET was evaluated at each step from stopping power tables according to the proton kinetic energy value. We carried out microdosimetry calculations with the aim of deriving reference dose average LET values from microdosimetric quantities. Significant differences between the methods were reported either with pristine or spread-out Bragg peaks (SOBPs). The first method reported values systematically higher than the other two at depths proximal to SOBP by about 15% for a 5.9 cm wide SOBP and about 30% for a 11.0 cm one. At distal SOBP, the second method gave values about 15% lower than the others. Overall, we found that the third method gave the most consistent

  8. Voxel-based evidence of perfusion normalization in glioblastoma patients included in a phase I-II trial of radiotherapy/tipifarnib combination.

    PubMed

    Ken, Soléakhéna; Deviers, Alexandra; Filleron, Thomas; Catalaa, Isabelle; Lotterie, Jean-Albert; Khalifa, Jonathan; Lubrano, Vincent; Berry, Isabelle; Péran, Patrice; Celsis, Pierre; Moyal, Elizabeth Cohen-Jonathan; Laprie, Anne

    2015-09-01

    We previously showed that the farnesyl transferase inihibitor, Tipifarnib induced vascularization normalization, oxygenation and radiosensitization in a pre-clinical glioblastoma (GBM) model. The aim of this study was to assess by dynamic-susceptibility-contrast MRI (DSC-MRI) the effect of radiotherapy (RT) and Tipifarnib combination on tumor perfusion in GBM patients. Eighteen patients with newly diagnosed GBM, enrolled in a phase I-II clinical trial associating RT with Tipifarnib, underwent anatomical MR imaging and DSC-MRI before (M0) and two months after treatment (M2). Anatomic volumes of interest (VOIs) were delineated according to contrast-enhanced and hyper-intense signal areas on T1-Gd and T2 images, respectively. Perfusion variations between M0 and M2 were assessed with median relative cerebral blood volume (rCBV) inside these VOIs. Another voxel by voxel analysis of CBV values classified 405,117 tumor voxels into High_, Normal_ and Low_CBVTUMOR according to the distribution of CBV in the contralateral normal tissue. These three categories of CBVTUMOR voxels were color-coded over anatomical MRI. Variations of median rCBV were significantly different for two groups of patients (P < 0.013): rCBV decreased when initial rCBV was ≥ 1.0 (Group_rCBV_M0 > 1) and rCBV increased when initial rCBV was < 1.0 (Group_rCBV_M0 < 1). Mapping of color-coded voxels provided additional spatial and quantitative information about tumor perfusion: Group_rCBV_M0 > 1 presented a significant decrease of High_CBVTUMOR volume (P = 0.015) simultaneously with a significant increase of Normal_CBVTUMOR volume (P = 0.009) after treatment. Group_rCBV_M0 < 1 presented a decrease of Low_CBVTUMOR volume with an increase of Normal_ and High_CBV TUMOR volume after treatment. Pre and post-treatment CBV measurements with DSC-MRI characterized tumor perfusion evolution in GBM patients treated with RT combined to Tipifarnib; showing variations in favour of tumor perfusion

  9. Alpha image reconstruction (AIR): A new iterative CT image reconstruction approach using voxel-wise alpha blending

    SciTech Connect

    Hofmann, Christian; Sawall, Stefan; Knaup, Michael; Kachelrieß, Marc

    2014-06-15

    Purpose: Iterative image reconstruction gains more and more interest in clinical routine, as it promises to reduce image noise (and thereby patient dose), to reduce artifacts, or to improve spatial resolution. Among vendors and researchers, however, there is no consensus of how to best achieve these aims. The general approach is to incorporatea priori knowledge into iterative image reconstruction, for example, by adding additional constraints to the cost function, which penalize variations between neighboring voxels. However, this approach to regularization in general poses a resolution noise trade-off because the stronger the regularization, and thus the noise reduction, the stronger the loss of spatial resolution and thus loss of anatomical detail. The authors propose a method which tries to improve this trade-off. The proposed reconstruction algorithm is called alpha image reconstruction (AIR). One starts with generating basis images, which emphasize certain desired image properties, like high resolution or low noise. The AIR algorithm reconstructs voxel-specific weighting coefficients that are applied to combine the basis images. By combining the desired properties of each basis image, one can generate an image with lower noise and maintained high contrast resolution thus improving the resolution noise trade-off. Methods: All simulations and reconstructions are performed in native fan-beam geometry. A water phantom with resolution bar patterns and low contrast disks is simulated. A filtered backprojection (FBP) reconstruction with a Ram-Lak kernel is used as a reference reconstruction. The results of AIR are compared against the FBP results and against a penalized weighted least squares reconstruction which uses total variation as regularization. The simulations are based on the geometry of the Siemens Somatom Definition Flash scanner. To quantitatively assess image quality, the authors analyze line profiles through resolution patterns to define a contrast

  10. GATA4 variant interaction with brain limbic structure and relapse risk: A voxel-based morphometry study.

    PubMed

    Zois, Evangelos; Vollstädt-Klein, Sabine; Hoffmann, Sabine; Reinhard, Iris; Bach, Patrick; Charlet, Katrin; Beck, Anne; Treutlein, Jens; Frank, Josef; Jorde, Anne; Kirsch, Martina; Degenhardt, Franziska; Walter, Henrik; Heinz, Andreas; Kiefer, Falk

    2016-09-01

    Atrial natriuretic peptide (ANP) receptors are highly expressed in the amygdala, caudate and hypothalamus. GATA4 gene encodes a transcription factor of ANP associated with the pathophysiology of alcohol dependence. We have previously demonstrated that the GATA4 single nucleotide polymorphism (SNP) rs13273672 revealed stronger alcohol-specific amygdala activation associated with lowered relapse risk to heavy drinking at 90 days in the AA-homozygotes. Our understanding however with respect to GATA4 variation on gray matter (GM) regional amygdala, caudate and hypothalamus volume is limited. We investigated GM differences specific to GATA4 and hypothesized that GM alterations will be predictive of heavy relapse. Eighty-three recently detoxified alcohol dependent patients were included. Neuroimaging data was analyzed using Voxel Based Morphometry (VBM). The main effects of GM volume and genotype as well as their interaction effect on time to heavy relapse (60 and 90 days) were analyzed using cox regression. Significant higher GM volume was found for the AA-genotype group compared with AG/GG-genotype in the hypothalamus and caudate. A significant interaction was revealed between caudate and amygdala GM volume and GATA4 genotype on time to heavy relapse. The interaction was expressed by means of higher GM in the AA genotype group to be associated with reduced risk to relapse whereas in the AG/GG group higher GM was associated with increased risk to relapse. This is the first report on GM regional volume alterations specific to GATA4 genotype [(SNP) rs13273672] and its association with relapse in alcohol dependence. Current findings further support the role of GATA4 in alcoholism. PMID:27397865

  11. Abnormal Intrinsic Functional Hubs in Severe Male Obstructive Sleep Apnea: Evidence from a Voxel-Wise Degree Centrality Analysis

    PubMed Central

    Shao, Yi; Gong, Honghan; Zhang, Wei; Zeng, Xianjun; Ye, Chenglong; Nie, Si; Chen, Liting; Peng, Dechang

    2016-01-01

    Purpose Obstructive sleep apnea (OSA) has been associated with changes in brain structure and regional function in certain brain areas. However, the functional features of network organization in the whole brain remain largely uncertain. The purpose of this study was to identify the OSA-related spatial centrality distribution of the whole brain functional network and to investigate the potential altered intrinsic functional hubs. Methods Forty male patients with newly confirmed severe OSA on polysomnography, and well-matched good sleepers, participated in this study. All participants underwent a resting-state functional MRI scan and clinical and cognitive evaluation. Voxel-wise degree centrality (DC) was measured across the whole brain, and group difference in DC was compared. The relationship between the abnormal DC value and clinical variables was assessed using a linear correlation analysis. Results Remarkably similar spatial distributions of the functional hubs (high DC) were found in both groups. However, OSA patients exhibited a pattern of significantly reduced regional DC in the left middle occipital gyrus, posterior cingulate cortex, left superior frontal gyrus, and bilateral inferior parietal lobule, and DC was increased in the right orbital frontal cortex, bilateral cerebellum posterior lobes, and bilateral lentiform nucleus, including the putamen, extending to the hippocampus, and the inferior temporal gyrus, which overlapped with the functional hubs. Furthermore, a linear correlation analysis revealed that the DC value in the posterior cingulate cortex and left superior frontal gyrus were positively correlated with Montreal cognitive assessment scores, The DC value in the left middle occipital gyrus and bilateral inferior parietal lobule were negatively correlated with apnea-hypopnea index and arousal index in OSA patients. Conclusion Our findings suggest that OSA patients exhibited specific abnormal intrinsic functional hubs including relatively

  12. Voxel-based morphometry and automated lobar volumetry: The trade-off between spatial scale and statistical correction

    PubMed Central

    Voormolen, Eduard H.J.; Wei, Corie; Chow, Eva W.C.; Bassett, Anne S.; Mikulis, David J.; Crawley, Adrian P.

    2011-01-01

    Voxel-based morphometry (VBM) and automated lobar region of interest (ROI) volumetry are comprehensive and fast methods to detect differences in overall brain anatomy on magnetic resonance images. However, VBM and automated lobar ROI volumetry have detected dissimilar gray matter differences within identical image sets in our own experience and in previous reports. To gain more insight into how diverging results arise and to attempt to establish whether one method is superior to the other, we investigated how differences in spatial scale and in the need to statistically correct for multiple spatial comparisons influence the relative sensitivity of either technique to group differences in gray matter volumes. We assessed the performance of both techniques on a small dataset containing simulated gray matter deficits and additionally on a dataset of 22q11-deletion syndrome patients with schizophrenia (22q11DS-SZ) vs. matched controls. VBM was more sensitive to simulated focal deficits compared to automated ROI volumetry, and could detect global cortical deficits equally well. Moreover, theoretical calculations of VBM and ROI detection sensitivities to focal deficits showed that at increasing ROI size, ROI volumetry suffers more from loss in sensitivity than VBM. Furthermore, VBM and automated ROI found corresponding GM deficits in 22q11DS-SZ patients, except in the parietal lobe. Here, automated lobar ROI volumetry found a significant deficit only after a smaller subregion of interest was employed. Thus, sensitivity to focal differences is impaired relatively more by averaging over larger volumes in automated ROI methods than by the correction for multiple comparisons in VBM. These findings indicate that VBM is to be preferred over automated lobar-scale ROI volumetry for assessing gray matter volume differences between groups. PMID:19619660

  13. Voxel-based magnetic resonance imaging investigation of poor and preserved clinical insight in people with schizophrenia

    PubMed Central

    Sapara, Adegboyega; Ffytche, Dominic H; Cooke, Michael A; Williams, Steven CR; Kumari, Veena

    2016-01-01

    AIM To define regional grey-matter abnormalities in schizophrenia patients with poor insight (Insight-), relative to patients with preserved clinical insight (Insight+), and healthy controls. METHODS Forty stable schizophrenia outpatients (20 Insight- and 20 Insight+) and 20 healthy controls underwent whole brain magnetic resonance imaging (MRI). Insight in all patients was assessed using the Birchwood Insight Scale (BIS; a self-report measure). The two patient groups were pre-selected to match on most clinical and demographic parameters but, by design, they had markedly distinct BIS scores. Voxel-based morphometry employed in SPM8 was used to examine group differences in grey matter volumes across the whole brain. RESULTS The three participant groups were comparable in age [F(2,57) = 0.34, P = 0.71] and the patient groups did not differ in age at illness onset [t(38) = 0.87, P = 0.39]. Insight- and Insight+ patient groups also did not differ in symptoms on the Positive and Negative Syndromes scale (PANSS): Positive symptoms [t(38) = 0.58, P = 0.57], negative symptoms [t(38) = 0.61, P = 0.55], general psychopathology [t(38) = 1.30, P = 0.20] and total PANSS scores [t(38) = 0.21, P = 0.84]. The two patient groups, as expected, varied significantly in the level of BIS-assessed insight [t(38) = 12.11, P < 0.001]. MRI results revealed lower fronto-temporal, parahippocampal, occipital and cerebellar grey matter volumes in Insight- patients, relative to Insight+ patients and healthy controls (for all clusters, family-wise error corrected P < 0.05). Insight+ patient and healthy controls did not differ significantly (P > 0.20) from each other. CONCLUSION Our findings demonstrate a clear association between poor clinical insight and smaller fronto-temporal, occipital and cerebellar grey matter volumes in stable long-term schizophrenia patients.

  14. First Steps in Using Multi-Voxel Pattern Analysis to Disentangle Neural Processes Underlying Generalization of Spider Fear

    PubMed Central

    Visser, Renée M.; Haver, Pia; Zwitser, Robert J.; Scholte, H. Steven; Kindt, Merel

    2016-01-01

    A core symptom of anxiety disorders is the tendency to interpret ambiguous information as threatening. Using electroencephalography and blood oxygenation level dependent magnetic resonance imaging (BOLD-MRI), several studies have begun to elucidate brain processes involved in fear-related perceptual biases, but thus far mainly found evidence for general hypervigilance in high fearful individuals. Recently, multi-voxel pattern analysis (MVPA) has become popular for decoding cognitive states from distributed patterns of neural activation. Here, we used this technique to assess whether biased fear generalization, characteristic of clinical fear, is already present during the initial perception and categorization of a stimulus, or emerges during the subsequent interpretation of a stimulus. Individuals with low spider fear (n = 20) and high spider fear (n = 18) underwent functional MRI scanning while viewing series of schematic flowers morphing to spiders. In line with previous studies, individuals with high fear of spiders were behaviorally more likely to classify ambiguous morphs as spiders than individuals with low fear of spiders. Univariate analyses of BOLD-MRI data revealed stronger activation toward spider pictures in high fearful individuals compared to low fearful individuals in numerous areas. Yet, neither average activation, nor support vector machine classification (i.e., a form of MVPA) matched the behavioral results – i.e., a biased response toward ambiguous stimuli – in any of the regions of interest. This may point to limitations of the current design, and to challenges associated with classifying emotional and neutral stimuli in groups that differ in their judgment of emotionality. Improvements for future research are suggested. PMID:27303278

  15. Voxel-based magnetic resonance imaging investigation of poor and preserved clinical insight in people with schizophrenia

    PubMed Central

    Sapara, Adegboyega; Ffytche, Dominic H; Cooke, Michael A; Williams, Steven CR; Kumari, Veena

    2016-01-01

    AIM To define regional grey-matter abnormalities in schizophrenia patients with poor insight (Insight-), relative to patients with preserved clinical insight (Insight+), and healthy controls. METHODS Forty stable schizophrenia outpatients (20 Insight- and 20 Insight+) and 20 healthy controls underwent whole brain magnetic resonance imaging (MRI). Insight in all patients was assessed using the Birchwood Insight Scale (BIS; a self-report measure). The two patient groups were pre-selected to match on most clinical and demographic parameters but, by design, they had markedly distinct BIS scores. Voxel-based morphometry employed in SPM8 was used to examine group differences in grey matter volumes across the whole brain. RESULTS The three participant groups were comparable in age [F(2,57) = 0.34, P = 0.71] and the patient groups did not differ in age at illness onset [t(38) = 0.87, P = 0.39]. Insight- and Insight+ patient groups also did not differ in symptoms on the Positive and Negative Syndromes scale (PANSS): Positive symptoms [t(38) = 0.58, P = 0.57], negative symptoms [t(38) = 0.61, P = 0.55], general psychopathology [t(38) = 1.30, P = 0.20] and total PANSS scores [t(38) = 0.21, P = 0.84]. The two patient groups, as expected, varied significantly in the level of BIS-assessed insight [t(38) = 12.11, P < 0.001]. MRI results revealed lower fronto-temporal, parahippocampal, occipital and cerebellar grey matter volumes in Insight- patients, relative to Insight+ patients and healthy controls (for all clusters, family-wise error corrected P < 0.05). Insight+ patient and healthy controls did not differ significantly (P > 0.20) from each other. CONCLUSION Our findings demonstrate a clear association between poor clinical insight and smaller fronto-temporal, occipital and cerebellar grey matter volumes in stable long-term schizophrenia patients. PMID:27679770

  16. First Steps in Using Multi-Voxel Pattern Analysis to Disentangle Neural Processes Underlying Generalization of Spider Fear.

    PubMed

    Visser, Renée M; Haver, Pia; Zwitser, Robert J; Scholte, H Steven; Kindt, Merel

    2016-01-01

    A core symptom of anxiety disorders is the tendency to interpret ambiguous information as threatening. Using electroencephalography and blood oxygenation level dependent magnetic resonance imaging (BOLD-MRI), several studies have begun to elucidate brain processes involved in fear-related perceptual biases, but thus far mainly found evidence for general hypervigilance in high fearful individuals. Recently, multi-voxel pattern analysis (MVPA) has become popular for decoding cognitive states from distributed patterns of neural activation. Here, we used this technique to assess whether biased fear generalization, characteristic of clinical fear, is already present during the initial perception and categorization of a stimulus, or emerges during the subsequent interpretation of a stimulus. Individuals with low spider fear (n = 20) and high spider fear (n = 18) underwent functional MRI scanning while viewing series of schematic flowers morphing to spiders. In line with previous studies, individuals with high fear of spiders were behaviorally more likely to classify ambiguous morphs as spiders than individuals with low fear of spiders. Univariate analyses of BOLD-MRI data revealed stronger activation toward spider pictures in high fearful individuals compared to low fearful individuals in numerous areas. Yet, neither average activation, nor support vector machine classification (i.e., a form of MVPA) matched the behavioral results - i.e., a biased response toward ambiguous stimuli - in any of the regions of interest. This may point to limitations of the current design, and to challenges associated with classifying emotional and neutral stimuli in groups that differ in their judgment of emotionality. Improvements for future research are suggested. PMID:27303278

  17. Voxel-based meta-analysis of gray matter volume reductions associated with cognitive impairment in Parkinson's disease.

    PubMed

    Xu, Yaqian; Yang, Jing; Hu, Xinyu; Shang, Huifang

    2016-06-01

    Brain gray matter volume (GMV) reduction has been reported in Parkinson's disease (PD) with mild cognitive impairment (PD-MCI) and in PD patients with dementia (PDD) with cumulative evidence using voxel-based morphometry (VBM). However, the findings of these studies have not been entirely concordant. Whole-brain VBM studies comparing PD-MCI with PD patients without cognitive impairment (PD-NCI) and comparing PDD with PD patients without dementia (PDND) were systematically searched in PubMed and EMBASE databases from January 1995 to December 2015. Coordinates with significant differences were extracted from each cluster. Meta-analysis was performed using AES-SDM to quantitatively evaluate the GMV changes. Five studies comparing 92 PD-MCI with 192 PD-NCI patients were included in the PD-MCI vs. PD-NCI meta-analysis. Ten studies with 168 PDD and 233 PDND patients were included in the PDD vs. PDND meta-analysis. Compared with PD-NCI, GMV reductions were observed in left superior temporal lobe, left insula and left superior frontal lobe in PD-MCI patients. Significant GMV reduction were found in bilateral superior temporal lobe extending to hippocampus, and left superior frontal lobe in PDD patients comparing with PDND. Meta-regression of PDD studies showed that disease duration was negatively correlated with GMV in the left superior frontal lobe. GMV reductions in the frontal-limbic-temporal regions were main features of cognitive decline in PD. Unilateral-to-bilateral development of GMV reduction in the frontal-limbic-temporal regions is a possible indicator for PD-MCI to PDD progression, whereas significant hippocampal GMV reduction may not be a marker for early cognitive decline in PD. PMID:27113603

  18. Voxel-based morphometry analysis reveals frontal brain differences in participants with ADHD and their unaffected siblings

    PubMed Central

    Bralten, Janita; Greven, Corina U.; Franke, Barbara; Mennes, Maarten; Zwiers, Marcel P.; Rommelse, Nanda N.J.; Hartman, Catharina; van der Meer, Dennis; O’Dwyer, Laurence; Oosterlaan, Jaap; Hoekstra, Pieter J.; Heslenfeld, Dirk; Arias-Vasquez, Alejandro; Buitelaar, Jan K.

    2016-01-01

    Background Data on structural brain alterations in patients with attention-deficit/hyperactivity disorder (ADHD) have been inconsistent. Both ADHD and brain volumes have a strong genetic loading, but whether brain alterations in patients with ADHD are familial has been underexplored. We aimed to detect structural brain alterations in adolescents and young adults with ADHD compared with healthy controls. We examined whether these alterations were also found in their unaffected siblings, using a uniquely large sample. Methods We performed voxel-based morphometry analyses on MRI scans of patients with ADHD, their unaffected siblings and typically developing controls. We identified brain areas that differed between participants with ADHD and controls and investigated whether these areas were different in unaffected siblings. Influences of medication use, age, sex and IQ were considered. Results Our sample included 307 patients with ADHD, 169 unaffected siblings and 196 typically developing controls (mean age 17.2 [range 8–30] yr). Compared with controls, participants with ADHD had significantly smaller grey matter volume in 5 clusters located in the precentral gyrus, medial and orbitofrontal cortex, and (para)cingulate cortices. Unaffected siblings showed intermediate volumes significantly different from controls in 4 of these clusters (all except the precentral gyrus). Medication use, age, sex and IQ did not have an undue influence on the results. Limitations Our sample was heterogeneous, most participants with ADHD were taking medication, and the comparison was cross-sectional. Conclusion Brain areas involved in decision making, motivation, cognitive control and motor functioning were smaller in participants with ADHD than in controls. Investigation of unaffected siblings indicated familiality of 4 of the structural brain differences, supporting their potential in molecular genetic analyses in ADHD research. PMID:26679925

  19. Specific regions display altered grey matter volume in μ-opioid receptor knockout mice: MRI voxel-based morphometry

    PubMed Central

    Sasaki, Kazumasu; Sumiyoshi, Akira; Nonaka, Hiroi; Kasahara, Yoshiyuki; Ikeda, Kazutaka; Hall, F Scott; Uhl, George R; Watanabe, Masahiko; Kawashima, Ryuta; Sora, Ichiro

    2015-01-01

    BACKGROUND AND PURPOSE μ Opioid receptor knockout (MOP-KO) mice display several behavioural differences from wild-type (WT) littermates including differential responses to nociceptive stimuli. Brain structural changes have been tied to behavioural alterations noted in transgenic mice with targeting of different genes. Hence, we assess the brain structure of MOP-KO mice. EXPERIMENTAL APPROACH Magnetic resonance imaging (MRI) voxel-based morphometry (VBM) and histological methods were used to identify structural differences between extensively backcrossed MOP-KO mice and WT mice. KEY RESULTS MOP-KO mice displayed robust increases in regional grey matter volume in olfactory bulb, several hypothalamic nuclei, periaqueductal grey (PAG) and several cerebellar areas, most confirmed by VBM analysis. The largest increases in grey matter volume were detected in the glomerular layer of the olfactory bulb, arcuate nucleus of hypothalamus, ventrolateral PAG (VLPAG) and cerebellar regions including paramedian and cerebellar lobules. Histological analyses confirm several of these results, with increased VLPAG cell numbers and increased thickness of the olfactory bulb granule cell layer and cerebellar molecular and granular cell layers. CONCLUSIONS AND IMPLICATIONS MOP deletion causes previously undescribed structural changes in specific brain regions, but not in all regions with high MOP receptor densities (e.g. thalamus, nucleus accumbens) or that exhibit adult neurogenesis (e.g. hippocampus). Volume differences in hypothalamus and PAG may reflect behavioural changes including hyperalgesia. Although the precise relationship between volume change and MOP receptor deletion was not determined from this study alone, these findings suggest that levels of MOP receptor expression may influence a broader range of neural structure and function in humans than previously supposed. LINKED ARTICLES This article is part of a themed section on Opioids: New Pathways to Functional Selectivity

  20. Analysis of the VAV3 as candidate gene for schizophrenia: evidences from voxel-based morphometry and mutation screening.

    PubMed

    Aleksic, Branko; Kushima, Itaru; Hashimoto, Ryota; Ohi, Kazutaka; Ikeda, Masashi; Yoshimi, Akira; Nakamura, Yukako; Ito, Yoshihito; Okochi, Tomo; Fukuo, Yasuhisa; Yasuda, Yuka; Fukumoto, Motoyuki; Yamamori, Hidenaga; Ujike, Hiroshi; Suzuki, Michio; Inada, Toshiya; Takeda, Masatoshi; Kaibuchi, Kozo; Iwata, Nakao; Ozaki, Norio

    2013-05-01

    In recently completed Japanese genome-wide association studies (GWAS) of schizophrenia (JPN_GWAS) one of the top association signals was detected in the region of VAV3, a gene that maps to the chromosome 1p13.3. In order to complement JPN_GWAS findings, we tested the association of rs1410403 with brain structure in healthy individuals and schizophrenic patients and performed exon resequencing of VAV3. We performed voxel-based morphometry (VBM) and mutation screening of VAV3. Four independent samples were used in the present study: (1) for VBM analysis, we used case-control sample comprising 100 patients with schizophrenia and 264 healthy controls, (2) mutation analysis was performed on a total of 321 patients suffering from schizophrenia, and 2 case-control samples (3) 729 unrelated patients with schizophrenia and 564 healthy comparison subjects, and (4) sample comprising 1511 cases and 1517 healthy comparison subjects and were used for genetic association analysis of novel coding variants with schizophrenia. The VBM analysis suggests that rs1410403 might affect the volume of the left superior and middle temporal gyri (P=.011 and P=.013, respectively), which were reduced in patients with schizophrenia compared with healthy subjects. Moreover, 4 rare novel missense variants were detected. The mutations were followed-up in large independent sample, and one of the novel variants (Glu741Gly) was associated with schizophrenia (P=.02). These findings demonstrate that VAV3 can be seen as novel candidate gene for schizophrenia in which both rare and common variants may be related to increased genetic risk for schizophrenia in Japanese population.

  1. Voxel-based registration of simulated and real patient CBCT data for accurate dental implant pose estimation

    NASA Astrophysics Data System (ADS)

    Moreira, António H. J.; Queirós, Sandro; Morais, Pedro; Rodrigues, Nuno F.; Correia, André Ricardo; Fernandes, Valter; Pinho, A. C. M.; Fonseca, Jaime C.; Vilaça, João. L.

    2015-03-01

    The success of dental implant-supported prosthesis is directly linked to the accuracy obtained during implant's pose estimation (position and orientation). Although traditional impression techniques and recent digital acquisition methods are acceptably accurate, a simultaneously fast, accurate and operator-independent methodology is still lacking. Hereto, an image-based framework is proposed to estimate the patient-specific implant's pose using cone-beam computed tomography (CBCT) and prior knowledge of implanted model. The pose estimation is accomplished in a threestep approach: (1) a region-of-interest is extracted from the CBCT data using 2 operator-defined points at the implant's main axis; (2) a simulated CBCT volume of the known implanted model is generated through Feldkamp-Davis-Kress reconstruction and coarsely aligned to the defined axis; and (3) a voxel-based rigid registration is performed to optimally align both patient and simulated CBCT data, extracting the implant's pose from the optimal transformation. Three experiments were performed to evaluate the framework: (1) an in silico study using 48 implants distributed through 12 tridimensional synthetic mandibular models; (2) an in vitro study using an artificial mandible with 2 dental implants acquired with an i-CAT system; and (3) two clinical case studies. The results shown positional errors of 67+/-34μm and 108μm, and angular misfits of 0.15+/-0.08° and 1.4°, for experiment 1 and 2, respectively. Moreover, in experiment 3, visual assessment of clinical data results shown a coherent alignment of the reference implant. Overall, a novel image-based framework for implants' pose estimation from CBCT data was proposed, showing accurate results in agreement with dental prosthesis modelling requirements.

  2. A primitive study of voxel feature generation by multiple stacked denoising autoencoders for detecting cerebral aneurysms on MRA

    NASA Astrophysics Data System (ADS)

    Nemoto, Mitsutaka; Hayashi, Naoto; Hanaoka, Shouhei; Nomura, Yukihiro; Miki, Soichiro; Yoshikawa, Takeharu; Ohtomo, Kuni

    2016-03-01

    The purpose of this study is to evaluate the feasibility of a novel feature generation, which is based on multiple deep neural networks (DNNs) with boosting, for computer-assisted detection (CADe). It is hard and time-consuming to optimize the hyperparameters for DNNs such as stacked denoising autoencoder (SdA). The proposed method allows using SdA based features without the burden of the hyperparameter setting. The proposed method was evaluated by an application for detecting cerebral aneurysms on magnetic resonance angiogram (MRA). A baseline CADe process included four components; scaling, candidate area limitation, candidate detection, and candidate classification. Proposed feature generation method was applied to extract the optimal features for candidate classification. Proposed method only required setting range of the hyperparameters for SdA. The optimal feature set was selected from a large quantity of SdA based features by multiple SdAs, each of which was trained using different hyperparameter set. The feature selection was operated through ada-boost ensemble learning method. Training of the baseline CADe process and proposed feature generation were operated with 200 MRA cases, and the evaluation was performed with 100 MRA cases. Proposed method successfully provided SdA based features just setting the range of some hyperparameters for SdA. The CADe process by using both previous voxel features and SdA based features had the best performance with 0.838 of an area under ROC curve and 0.312 of ANODE score. The results showed that proposed method was effective in the application for detecting cerebral aneurysms on MRA.

  3. Effects of Hormone Therapy on Brain Volumes Changes of Postmenopausal Women Revealed by Optimally-Discriminative Voxel-Based Morphometry

    PubMed Central

    Zhang, Tianhao; Casanova, Ramon; Resnick, Susan M.; Manson, JoAnn E.; Baker, Laura D.; Padual, Claudia B.; Kuller, Lewis H.; Bryan, R. Nick; Espeland, Mark A.; Davatzikos, Christos

    2016-01-01

    Backgrounds The Women's Health Initiative Memory Study Magnetic Resonance Imaging (WHIMS-MRI) provides an opportunity to evaluate how menopausal hormone therapy (HT) affects the structure of older women’s brains. Our earlier work based on region of interest (ROI) analysis demonstrated potential structural changes underlying adverse effects of HT on cognition. However, the ROI-based analysis is limited in statistical power and precision, and cannot provide fine-grained mapping of whole-brain changes. Methods We aimed to identify local structural differences between HT and placebo groups from WHIMS-MRI in a whole-brain refined level, by using a novel method, named Optimally-Discriminative Voxel-Based Analysis (ODVBA). ODVBA is a recently proposed imaging pattern analysis approach for group comparisons utilizing a spatially adaptive analysis scheme to accurately locate areas of group differences, thereby providing superior sensitivity and specificity to detect the structural brain changes over conventional methods. Results Women assigned to HT treatments had significant Gray Matter (GM) losses compared to the placebo groups in the anterior cingulate and the adjacent medial frontal gyrus, and the orbitofrontal cortex, which persisted after multiple comparison corrections. There were no regions where HT was significantly associated with larger volumes compared to placebo, although a trend of marginal significance was found in the posterior cingulate cortical area. The CEE-Alone and CEE+MPA groups, although compared with different placebo controls, demonstrated similar effects according to the spatial patterns of structural changes. Conclusions HT had adverse effects on GM volumes and risk for cognitive impairment and dementia in older women. These findings advanced our understanding of the neurobiological underpinnings of HT effects. PMID:26974440

  4. Motor versus body awareness: Voxel-based lesion analysis in anosognosia for hemiplegia and somatoparaphrenia following right hemisphere stroke.

    PubMed

    Moro, Valentina; Pernigo, Simone; Tsakiris, Manos; Avesani, Renato; Edelstyn, Nicola M J; Jenkinson, Paul M; Fotopoulou, Aikaterini

    2016-10-01

    Anosognosia for hemiplegia (AHP) is informative about the neurocognitive basis of motor awareness. However, it is frequently associated with concomitant symptoms, such as hemispatial neglect and disturbances in the sense of body ownership (DSO). Although double dissociations between these symptoms have been reported, there is ongoing debate about whether they are manifestations of independent abnormalities, or a single neurocognitive deficit. We aimed to investigate the specificity of lesions associated with AHP by surpassing four, existing methodological limitations: (a) recruit a relatively large sample of patients (total N = 70) in a multi-centre study; (b) identify lesions associated with AHP in grey and white matter using voxel-based methods; (c) take into account the duration of AHP and concomitant neglect symptoms; and (d) compare lesions against a control hemiplegic group, patients suffering from AHP and DSO, and a few, rare patients with selective DSO. Results indicated that acute AHP is associated with a wide network, mainly including: (1) the Rolandic operculum, (2) the insula and (3) the superior temporal gyri. Subcortically, damage mainly involved the basal ganglia and white matter, mostly the superior corona radiate, arcuate fasciculus and the part of the ventral, superior longitudinal fasciculus. Persistent symptoms were linked with wider damage involving fronto-temporal cortex and long white matter tracts. A shift in the latero-medial direction (mainly involving the basal ganglia and surrounding white matter) emerged when DSO was taken accounted for. These results suggest that while bodily awareness is processed by areas widely distributed across the brain, intact subcortical structures and white matter tracts may be necessary to support basic feelings of owning and controlling contralateral body parts. An accurate and 'up-to-date' awareness of our motor abilities, however, may rely also on intact processing in cortical areas which presumably

  5. Shear wave velocity for the upper 30 m: Combining a 3D voxel model and seismic CPTS for the Groningen gas field, the Netherlands.

    NASA Astrophysics Data System (ADS)

    Dambrink, Roula; Gunnink, Jan; Stafleu, Jan; de Lange, Ger; Kruiver, Pauline

    2016-04-01

    The Groningen gas field in the Netherlands is one of the largest gas fields of Europe and has been in production since the 1960's. Due to the progressive depletion of the reservoir, induced seismic activity has increased in recent years. In 2012, an earthquake of magnitude 3.6 initiated further research in prediction and management of risks related to man-induced earthquakes. Last year the government decided to reduce the gas extraction for this reason. One of the topics of concern is the large difference in earthquake-related damage to buildings which, in addition to the distance to the epicenter, appears to be also related to the composition of the shallow subsurface. To improve the spatial distribution of Shear Wave Velocities (Vs) in the shallow subsurface, used for hazard prediction, the Geological Survey of the Netherlands and Deltares constructed a Vs30 map of the upper 30 m of the gas field. In this map a high-resolution geological model (GeoTOP) is combined with seismic cone penetration tests (SCPT) from the area. The GeoTOP model is a 3D voxel model of the upper 50 m, in which each voxel (100x100x0.5 m) is attributed with lithostratigraphy and the most likely lithological class (peat, clay, fine sand, etc.). To obtain statistical distributions (with mean and standard deviation) of Vs for each combination of lithostratigraphical unit and lithoclass, 60 SCPTs were analyzed. In this way, it was possible to assign a specific Vs to each voxel in the model. For each voxel in the stack of voxels that covers the upper 30 m (i.e. 60 voxels), a Vs value was randomly drawn from the statistical distribution of the lithostratigraphical - lithoclass combination it belongs to. The Vs30 for each voxelstack is then calculated using the harmonic mean of the Vs of the 60 voxels. By repeating this procedure 100 times, an (average) Vs30 map and the uncertainty in Vs30 has been constructed. Using the procedure described above we were able to delineate zones with distinct Vs30

  6. Fast interrupt platform for extended DOS

    NASA Technical Reports Server (NTRS)

    Duryea, T. W.

    1995-01-01

    Extended DOS offers the unique combination of a simple operating system which allows direct access to the interrupt tables, 32 bit protected mode access to 4096 MByte address space, and the use of industry standard C compilers. The drawback is that fast interrupt handling requires both 32 bit and 16 bit versions of each real-time process interrupt handler to avoid mode switches on the interrupts. A set of tools has been developed which automates the process of transforming the output of a standard 32 bit C compiler to 16 bit interrupt code which directly handles the real mode interrupts. The entire process compiles one set of source code via a make file, which boosts productivity by making the management of the compile-link cycle very simple. The software components are in the form of classes written mostly in C. A foreground process written as a conventional application which can use the standard C libraries can communicate with the background real-time classes via a message passing mechanism. The platform thus enables the integration of high performance real-time processing into a conventional application framework.

  7. Teaching Bibliometric Analysis and MS/DOS Commands.

    ERIC Educational Resources Information Center

    Dou, Henri; And Others

    1988-01-01

    Outlines the steps involved in bibliometric studies, and demonstrates the ability to execute simple studies on microcomputers by downloading files using only the capability of MS/DOS. Detailed illustrations of the MS/DOS commands used are provided. (eight references) (CLB)

  8. Application of Three-Dimensional Models for the Teaching of Time Zones. (Breton Title: Aplicação de Modelos Tridimensionais Para o Ensino de Fusos Horários.) Aplicación de Modelos Tridimensionales Para la Enseñanza de Husos Horarios

    NASA Astrophysics Data System (ADS)

    Azevedo Sobreira, Paulo Henrique

    2012-07-01

    There are several interesting astronomical topics that must be addressed in the High School and Elementary/Middle School in the disciplines of Geography and of Sciences. Among them, the topic of time zones which is one of the most important to understand the correlation of the Earth's rotation and its implications on daily activities of citizens in local scale, regional and global scales which involve problems of time differences. For the teaching of time zones in the lessons of Geography, for example, there are bi-dimensional representations of thematic maps of world time zones, textbooks and atlas. It happens that teachers face some difficulties to permit its students to view three-dimensionally this astronomical phenomenon from the textbooks available in schools. The aim of this paper is to present two proposals with low-cost materials, which allow the preparation of three-dimensional models for the teaching of time zones. Há vários temas astronômicos interessantes que devem ser trabalhados nos Ensinos Médio e Fundamental, nas disciplinas de Geografia e de Ciências. Entre eles, o tema dos fusos horários que é um dos mais importantes para se correlacionar a rotação da Terra e suas implicações nas atividades cotidianas dos cidadãos em escala local, regional e global, que envolvem problemas de diferenças horárias. Para o ensino dos fusos horários nas aulas de Geografia, por exemplo, há representações bidimensionais de mapas temáticos de fusos horários mundiais, nos livros didáticos e nos atlas. Ocorre que os professores enfrentam algumas dificuldades para possibilitar aos seus alunos a visão tridimensional deste fenômeno astronômico, a partir dos materiais didáticos disponíveis nas escolas. O objetivo deste trabalho é apresentar duas propostas para a confecção de materiais de baixo custo, que possibilitem a elaboração de modelos tridimensionais para o ensino dos fusos horários. Hay algunos temas astronómicos interesantes que se

  9. The Voxel-Wise Functional Connectome Can Be Efficiently Derived from Co-activations in a Sparse Spatio-Temporal Point-Process

    PubMed Central

    Tagliazucchi, Enzo; Siniatchkin, Michael; Laufs, Helmut; Chialvo, Dante R.

    2016-01-01

    Large efforts are currently under way to systematically map functional connectivity between all pairs of millimeter-scale brain regions based on large neuroimaging databases. The exploratory unraveling of this “functional connectome” based on functional Magnetic Resonance Imaging (fMRI) can benefit from a better understanding of the contributors to resting state functional connectivity. In this work, we introduce a sparse representation of fMRI data in the form of a discrete point-process encoding high-amplitude events in the blood oxygenation level-dependent (BOLD) signal and we show it contains sufficient information for the estimation of functional connectivity between all pairs of voxels. We validate this method by replicating results obtained with standard whole-brain voxel-wise linear correlation matrices in two datasets. In the first one (n = 71), we study the changes in node strength (a measure of network centrality) during deep sleep. The second is a large database (n = 1147) of subjects in which we look at the age-related reorganization of the voxel-wise network of functional connections. In both cases it is shown that the proposed method compares well with standard techniques, despite requiring only data on the order of 1% of the original BOLD signal time series. Furthermore, we establish that the point-process approach does not reduce (and in one case increases) classification accuracy compared to standard linear correlations. Our results show how large fMRI datasets can be drastically simplified to include only the timings of large-amplitude events, while still allowing the recovery of all pair-wise interactions between voxels. The practical importance of this dimensionality reduction is manifest in the increasing number of collaborative efforts aiming to study large cohorts of healthy subjects as well as patients suffering from brain disease. Our method also suggests that the electrophysiological signals underlying the dynamics of fMRI time series

  10. Electromagnetic analysis of an RF rectangular resonant cavity applicator for hyperthermic treatment using whole-body voxel human model of Japanese adult male.

    PubMed

    Tange, Yutaka; Yabumoto, Kosuke; Kanai, Yasushi

    2011-01-01

    The numerical whole-body voxel human model (numerical model) developed by National Institute of Information and Communications Technology (NICT) was assumed and hyperthemic treatment using radio-frequency wave was investigated. We assumed 51 different human tissues and organs with 2-mm spatial resolution in the numerical model, inserted it into the resonant cavity applicator, and Maxwell's equations were solved by FDTD method with variable mesh. We obtained the realistic energy patterns for a deep-seated tumor as compared to those obtained in our previous studies.

  11. The Voxel-Wise Functional Connectome Can Be Efficiently Derived from Co-activations in a Sparse Spatio-Temporal Point-Process.

    PubMed

    Tagliazucchi, Enzo; Siniatchkin, Michael; Laufs, Helmut; Chialvo, Dante R

    2016-01-01

    Large efforts are currently under way to systematically map functional connectivity between all pairs of millimeter-scale brain regions based on large neuroimaging databases. The exploratory unraveling of this "functional connectome" based on functional Magnetic Resonance Imaging (fMRI) can benefit from a better understanding of the contributors to resting state functional connectivity. In this work, we introduce a sparse representation of fMRI data in the form of a discrete point-process encoding high-amplitude events in the blood oxygenation level-dependent (BOLD) signal and we show it contains sufficient information for the estimation of functional connectivity between all pairs of voxels. We validate this method by replicating results obtained with standard whole-brain voxel-wise linear correlation matrices in two datasets. In the first one (n = 71), we study the changes in node strength (a measure of network centrality) during deep sleep. The second is a large database (n = 1147) of subjects in which we look at the age-related reorganization of the voxel-wise network of functional connections. In both cases it is shown that the proposed method compares well with standard techniques, despite requiring only data on the order of 1% of the original BOLD signal time series. Furthermore, we establish that the point-process approach does not reduce (and in one case increases) classification accuracy compared to standard linear correlations. Our results show how large fMRI datasets can be drastically simplified to include only the timings of large-amplitude events, while still allowing the recovery of all pair-wise interactions between voxels. The practical importance of this dimensionality reduction is manifest in the increasing number of collaborative efforts aiming to study large cohorts of healthy subjects as well as patients suffering from brain disease. Our method also suggests that the electrophysiological signals underlying the dynamics of fMRI time series

  12. The Voxel-Wise Functional Connectome Can Be Efficiently Derived from Co-activations in a Sparse Spatio-Temporal Point-Process

    PubMed Central

    Tagliazucchi, Enzo; Siniatchkin, Michael; Laufs, Helmut; Chialvo, Dante R.

    2016-01-01

    Large efforts are currently under way to systematically map functional connectivity between all pairs of millimeter-scale brain regions based on large neuroimaging databases. The exploratory unraveling of this “functional connectome” based on functional Magnetic Resonance Imaging (fMRI) can benefit from a better understanding of the contributors to resting state functional connectivity. In this work, we introduce a sparse representation of fMRI data in the form of a discrete point-process encoding high-amplitude events in the blood oxygenation level-dependent (BOLD) signal and we show it contains sufficient information for the estimation of functional connectivity between all pairs of voxels. We validate this method by replicating results obtained with standard whole-brain voxel-wise linear correlation matrices in two datasets. In the first one (n = 71), we study the changes in node strength (a measure of network centrality) during deep sleep. The second is a large database (n = 1147) of subjects in which we look at the age-related reorganization of the voxel-wise network of functional connections. In both cases it is shown that the proposed method compares well with standard techniques, despite requiring only data on the order of 1% of the original BOLD signal time series. Furthermore, we establish that the point-process approach does not reduce (and in one case increases) classification accuracy compared to standard linear correlations. Our results show how large fMRI datasets can be drastically simplified to include only the timings of large-amplitude events, while still allowing the recovery of all pair-wise interactions between voxels. The practical importance of this dimensionality reduction is manifest in the increasing number of collaborative efforts aiming to study large cohorts of healthy subjects as well as patients suffering from brain disease. Our method also suggests that the electrophysiological signals underlying the dynamics of fMRI time series

  13. The Heme-Based Oxygen-Sensor Phosphodiesterase Ec DOS (DosP): Structure-Function Relationships

    PubMed Central

    Shimizu, Toru

    2013-01-01

    Escherichia coli Direct Oxygen Sensor (Ec DOS, also known as Ec DosP) is a heme-based O2-sensing phosphodiesterase from Escherichia coli that catalyzes the conversion of cyclic-di-GMP to linear di-GMP. Cyclic-di-GMP is an important second messenger in bacteria, highlighting the importance of understanding structure-function relationships of Ec DOS. Ec DOS is composed of an N-terminal heme-bound O2-sensing PAS domain and a C-terminal phosphodiesterase catalytic domain. Notably, its activity is markedly enhanced by O2 binding to the heme Fe(II) complex in the PAS sensor domain. X-ray crystal structures and spectroscopic and catalytic characterization of the wild-type and mutant proteins have provided important structural and functional clues to understanding the molecular mechanism of intramolecular catalytic regulation by O2 binding. This review summarizes the intriguing findings that have obtained for Ec DOS. PMID:25586128

  14. Espectro de radiación derivado de un modelo de colapso protoestelar

    NASA Astrophysics Data System (ADS)

    Coca, S.; Rohrmann, R.

    El exceso de emisión infrarroja en objetos protoestelares es atribuido usualmente a un disco de material en torno al cuerpo central. A pesar del avance alcanzado en la elaboración de modelos, aún existen dificultades para explicar la ley de temperatura del disco necesaria para reproducir las luminosidades y perfiles de energía observados. Nuestra propuesta consiste en determinar la distribución espectral de la radiación derivada de un particular modelo de colapso protoestelar, y estudiar la evolución del espectro desde estadíos tempranos de la contracción gravitatoria. Este plan es orientado a evaluar las propiedades del modelo (distribuciones de masa y temperatura del material circunestelar) por comparación con datos observacionales, a fin de inferir de ello los posibles ajustes requeridos en la teoría actualmente empleada.

  15. Dosimetric characterization and organ dose assessment in digital breast tomosynthesis: Measurements and Monte Carlo simulations using voxel phantoms

    SciTech Connect

    Baptista, Mariana Di Maria, Salvatore; Barros, Sílvia; Vaz, Pedro; Figueira, Catarina; Sarmento, Marta; Orvalho, Lurdes

    2015-07-15

    Purpose: Due to its capability to more accurately detect deep lesions inside the breast by removing the effect of overlying anatomy, digital breast tomosynthesis (DBT) has the potential to replace the standard mammography technique in clinical screening exams. However, the European Guidelines for DBT dosimetry are still a work in progress and there are little data available on organ doses other than to the breast. It is, therefore, of great importance to assess the dosimetric performance of DBT with respect to the one obtained with standard digital mammography (DM) systems. The aim of this work is twofold: (i) to study the dosimetric properties of a combined DBT/DM system (MAMMOMAT Inspiration Siemens{sup ®}) for a tungsten/rhodium (W/Rh) anode/filter combination and (ii) to evaluate organs doses during a DBT examination. Methods: For the first task, measurements were performed in manual and automatic exposure control (AEC) modes, using two homogeneous breast phantoms: a PMMA slab phantom and a 4 cm thick breast-shaped rigid phantom, with 50% of glandular tissue in its composition. Monte Carlo (MC) simulations were performed using Monte Carlo N-Particle eXtended v.2.7.0. A MC model was implemented to mimic DM and DBT acquisitions for a wide range of x-ray spectra (24 –34 kV). This was used to calculate mean glandular dose (MGD) and to compute series of backscatter factors (BSFs) that could be inserted into the DBT dosimetric formalism proposed by Dance et al. Regarding the second aim of the study, the implemented MC model of the clinical equipment, together with a female voxel phantom (“Laura”), was used to calculate organ doses considering a typical DBT acquisition. Results were compared with a standard two-view mammography craniocaudal (CC) acquisition. Results: Considering the AEC mode, the acquisition of a single CC view results in a MGD ranging from 0.53 ± 0.07 mGy to 2.41 ± 0.31 mGy in DM mode and from 0.77 ± 0.11 mGy to 2.28 ± 0.32 mGy in DBT mode

  16. Voxel-based analysis of the immediate early gene, c-jun, in the honey bee brain after a sucrose stimulus.

    PubMed

    McNeill, M S; Robinson, G E

    2015-06-01

    Immediate early genes (IEGs) have served as useful markers of brain neuronal activity in mammals, and more recently in insects. The mammalian canonical IEG, c-jun, is part of regulatory pathways conserved in insects and has been shown to be responsive to alarm pheromone in honey bees. We tested whether c-jun was responsive in honey bees to another behaviourally relevant stimulus, sucrose, in order to further identify the brain regions involved in sucrose processing. To identify responsive regions, we developed a new method of voxel-based analysis of c-jun mRNA expression. We found that c-jun is expressed in somata throughout the brain. It was rapidly induced in response to sucrose stimuli, and it responded in somata near the antennal and mechanosensory motor centre, mushroom body calices and lateral protocerebrum, which are known to be involved in sucrose processing. c-jun also responded to sucrose in somata near the lateral suboesophageal ganglion, dorsal optic lobe, ventral optic lobe and dorsal posterior protocerebrum, which had not been previously identified by other methods. These results demonstrate the utility of voxel-based analysis of mRNA expression in the insect brain.

  17. The Observation and Execution of Actions Share Motor and Somatosensory Voxels in all Tested Subjects: Single-Subject Analyses of Unsmoothed fMRI Data

    PubMed Central

    Keysers, Christian

    2009-01-01

    Many neuroimaging studies of the mirror neuron system (MNS) examine if certain voxels in the brain are shared between action observation and execution (shared voxels, sVx). Unfortunately, finding sVx in standard group analyses is not a guarantee that sVx exist in individual subjects. Using unsmoothed, single-subject analyses we show sVx can be reliably found in all 16 investigated participants. Beside the ventral premotor (BA6/44) and inferior parietal cortex (area PF) where mirror neurons (MNs) have been found in monkeys, sVx were reliably observed in dorsal premotor, supplementary motor, middle cingulate, somatosensory (BA3, BA2, and OP1), superior parietal, middle temporal cortex and cerebellum. For the premotor, somatosensory and parietal areas, sVx were more numerous in the left hemisphere. The hand representation of the primary motor cortex showed a reduced BOLD during hand action observation, possibly preventing undesired overt imitation. This study provides a more detailed description of the location and reliability of sVx and proposes a model that extends the original idea of the MNS to include forward and inverse internal models and motor and sensory simulation, distinguishing the MNS from a more general concept of sVx. PMID:19020203

  18. Two-photon excited fluorescence in the LYB:Eu monoclinic crystal: towards a new scheme of single-beam dual-voxel direct laser writing in crystals.

    PubMed

    Petit, Y; Royon, A; Marquestaut, N; Dussauze, M; Fargues, A; Veber, P; Jubera, V; Cardinal, T; Canioni, L

    2013-01-14

    We report on two-photon excited fluorescence in the oriented Eu(3+)doped LYB monoclinic crystal under femtosecond laser tight focusing. Due to spatial walk-off, the two polarization modes of the incident femtosecond beam simultaneously provide the independent excitation of two distinct focuses, leading to a single-beam dual-voxel nonlinear excitation of fluorescence below material modification threshold. These observations emphasize on the anisotropy of both two-photon absorption as well as fluorescence emission. They demonstrate the localized control of the nonlinear energy deposit, thanks to the adjustment of both the input power and polarization, by properly balancing the injected energy in each voxel. Such approach should be considered for future direct laser writing of waveguides in propagation directions out of the dielectric axes, so as to optimally cope with the highly probable anisotropy of laser-induced material modification thresholds in these crystals. These results open new ways for further potential developments in direct laser writing as the simultaneous inscription of double-line structures for original waveguides processes.

  19. HDRK-Man: a whole-body voxel model based on high-resolution color slice images of a Korean adult male cadaver.

    PubMed

    Kim, Chan Hyeong; Choi, Sang Hyoun; Jeong, Jong Hwi; Lee, Choonsik; Chung, Min Suk

    2008-08-01

    A Korean voxel model, named 'High-Definition Reference Korean-Man (HDRK-Man)', was constructed using high-resolution color photographic images that were obtained by serially sectioning the cadaver of a 33-year-old Korean adult male. The body height and weight, the skeletal mass and the dimensions of the individual organs and tissues were adjusted to the reference Korean data. The resulting model was then implemented into a Monte Carlo particle transport code, MCNPX, to calculate the dose conversion coefficients for the internal organs and tissues. The calculated values, overall, were reasonable in comparison with the values from other adult voxel models. HDRK-Man showed higher dose conversion coefficients than other models, due to the facts that HDRK-Man has a smaller torso and that the arms of HDRK-Man are shifted backward. The developed model is believed to adequately represent average Korean radiation workers and thus can be used for more accurate calculation of dose conversion coefficients for Korean radiation workers in the future. PMID:18612173

  20. Two-photon excited fluorescence in the LYB:Eu monoclinic crystal: new scheme for single-beam dual-voxel direct laser writing in crystals

    NASA Astrophysics Data System (ADS)

    Petit, Y.; Royon, A.; Marquestaut, N.; Dussauze, M.; Fargues, A.; Veber, P.; Jubera, V.; Cardinal, T.; Canioni, L.

    2013-03-01

    We report on two-photon excited fluorescence in the oriented Eu3+-doped LYB monoclinic crystal under femtosecond laser tight focusing. Due to spatial walk-off, the two polarization modes of the incident femtosecond beam simultaneously provide the independent excitation of two distinct focuses, leading to a single-beam dual-voxel nonlinear excitation of fluorescence below material modification threshold. These observations emphasize on the anisotropy of both two-photon absorption as well as fluorescence emission. They demonstrate the localized control of the nonlinear energy deposit, thanks to the adjustment of both the input power and polarization, by properly balancing the injected energy in each voxel. Such approach should be considered for future direct laser writing of waveguides in propagation directions out of the dielectric axes, so as to optimally cope with the highly probable anisotropy of laser-induced material modification thresholds in these crystals. These results open new ways for further potential developments in direct laser writing as the simultaneous inscription of double-line structures for original waveguides processes.

  1. Single-voxel (1)H spectroscopy in the human hippocampus at 3 T using the LASER sequence: characterization of neurochemical profile and reproducibility.

    PubMed

    Allaïli, Najib; Valabrègue, Romain; Auerbach, Edward J; Guillemot, Vincent; Yahia-Cherif, Lydia; Bardinet, Eric; Jabourian, Maritza; Fossati, Philippe; Lehéricy, Stéphane; Marjańska, Małgorzata

    2015-10-01

    The hippocampus is crucial for long-term episodic memory and learning. It undergoes structural change in aging and is sensitive to neurodegenerative and psychiatric diseases. MRS studies have seldom been performed in the hippocampus due to technical challenges. The reproducibility of MRS in the hippocampus has not been evaluated at 3 T. The purpose of the present study was to quantify the concentration of metabolites in a small voxel placed in the hippocampus and evaluate the reproducibility of the quantification. Spectra were measured in a 2.4 mL voxel placed in the left hippocampus covering the body and most of the tail of the structure in 10 healthy subjects across three different sessions and quantified using LCModel. High-quality spectra were obtained, which allowed a reliable quantification of 10 metabolites including glutamate and glutamine. Reproducibility of MRS was evaluated with coefficient of variation, standard errors of measurement, and intraclass correlation coefficients. All of these measures showed improvement with increased number of averages. Changes of less than 5% in concentration of N-acetylaspartate, choline-containing compounds, and total creatine and of less than 10% in concentration of myo-inositol and the sum of glutamate and glutamine can be confidently detected between two measurements in a group of 20 subjects. A reliable and reproducible neurochemical profile of the human hippocampus was obtained using MRS at 3 T in a small hippocampal volume. PMID:26282328

  2. Simultaneous two-voxel localized 1H-observed 13C-edited spectroscopy for in vivo MRS on rat brain at 9.4 T: Application to the investigation of excitotoxic lesions

    NASA Astrophysics Data System (ADS)

    Doan, Bich-Thuy; Autret, Gwennhael; Mispelter, Joël; Méric, Philippe; Même, William; Montécot-Dubourg, Céline; Corrèze, Jean-Loup; Szeremeta, Frédéric; Gillet, Brigitte; Beloeil, Jean-Claude

    2009-05-01

    13C spectroscopy combined with the injection of 13C-labeled substrates is a powerful method for the study of brain metabolism in vivo. Since highly localized measurements are required in a heterogeneous organ such as the brain, it is of interest to augment the sensitivity of 13C spectroscopy by proton acquisition. Furthermore, as focal cerebral lesions are often encountered in animal models of disorders in which the two brain hemispheres are compared, we wished to develop a bi-voxel localized sequence for the simultaneous bilateral investigation of rat brain metabolism, with no need for external additional references. Two sequences were developed at 9.4 T: a bi-voxel 1H-( 13C) STEAM-POCE (Proton Observed Carbon Edited) sequence and a bi-voxel 1H-( 13C) PRESS-POCE adiabatically decoupled sequence with Hadamard encoding. Hadamard encoding allows both voxels to be recorded simultaneously, with the same acquisition time as that required for a single voxel. The method was validated in a biological investigation into the neuronal damage and the effect on the Tri Carboxylic Acid cycle in localized excitotoxic lesions. Following an excitotoxic quinolinate-induced localized lesion in the rat cortex and the infusion of U- 13C glucose, two 1H-( 13C) spectra of distinct (4 × 4 × 4 mm 3) voxels, one centred on the injured hemisphere and the other on the contralateral hemisphere, were recorded simultaneously. Two 1H bi-voxel spectra were also recorded and showed a significant decrease in N-acetyl aspartate, and an accumulation of lactate in the ipsilateral hemisphere. The 1H-( 13C) spectra could be recorded dynamically as a function of time, and showed a fall in the glutamate/glutamine ratio and the presence of a stable glutamine pool, with a permanent increase of lactate in the ipsilateral hemisphere. This bi-voxel 1H-( 13C) method can be used to investigate simultaneously both brain hemispheres, and to perform dynamic studies. We report here the neuronal damage and the

  3. Discos de acreción circumplanares: Modelo de Co-acreción

    NASA Astrophysics Data System (ADS)

    Parisi, M. G.; de Elía, G.

    Los discos de acreción circumplanetarios precursores de los satélites regulares de los planetas gigantes, se pueden formar por cuatro mecanismos (Pollack y otros, 1991, In Uranus, Bergtralh, Miner y Mattews, Eds., p. 469, Univ. de Arizona Press, Tucson). En este trabajo estudiamos uno de tales mecanismos: el Modelo de Co-acreción. En dicho modelo, el disco circumplanetario se forma a partir de las colisiones mutuas entre planetesimales dentro de la esfera de Hill del planeta durante el proceso de formación planetaria. Realizamos un modelo semi-analítico para calcular la masa del disco y compararla con la masa requerida para formar los satélites regulares de los planetas gigantes. Hemos obtenido una cota superior para la masa del disco que resulta inferior a la masa de los satélites más grandes de los planetas gigantes. En principio, estos resultados permitirían descartar el modelo de co-acreción como uno de los procesos que podrían dar lugar a la formación de los satélites regulares. Estos resultados permiten obtener restricciones en el escenario de formación planetaria y en los mecanismos de formación de sistemas de satélites.

  4. Service-Learning in Physical Education Teacher Training. Physical Education in the Modelo Prison, Barcelona

    ERIC Educational Resources Information Center

    Lleixà, Teresa; Ríos, Merche

    2015-01-01

    In the Psychiatric Unit of the Modelo Prison, Barcelona, a physical education programme is carried out annually with the participation of University of Barcelona (UB) students. In this context, we carried out a study based on service-learning parameters. The aim of the study was twofold: to determine the impact on inmates of the physical education…

  5. Modelo B/Dual Language Programmes in the Basque Country and the USA

    ERIC Educational Resources Information Center

    Torres-Guzman, Maria E.; Etxeberria, Feli

    2005-01-01

    In this paper, we undertake a cross-national comparison of early partial immersion programmes, known as dual language or Modelo B programmes, in the USA and the Basque Country in Spain, respectively. We attempt to make sense of their growth, the expanded social uses of the minority languages, and address seemingly contradictory pedagogical…

  6. 68Ga-HBED-CC-PSMA PET/CT Versus Histopathology in Primary Localized Prostate Cancer: A Voxel-Wise Comparison

    PubMed Central

    Zamboglou, Constantinos; Schiller, Florian; Fechter, Tobias; Wieser, Gesche; Jilg, Cordula Annette; Chirindel, Alin; Salman, Nasr; Drendel, Vanessa; Werner, Martin; Mix, Michael; Meyer, Philipp Tobias; Grosu, Anca Ligia

    2016-01-01

    Purpose: We performed a voxel-wise comparison of 68Ga-HBED-CC-PSMA PET/CT with prostate histopathology to evaluate the performance of 68Ga-HBED-CC-PSMA for the detection and delineation of primary prostate cancer (PCa). Methodology: Nine patients with histopathological proven primary PCa underwent 68Ga-HBED-CC-PSMA PET/CT followed by radical prostatectomy. Resected prostates were scanned by ex-vivo CT in a special localizer and histopathologically prepared. Histopathological information was matched to ex-vivo CT. PCa volume (PCa-histo) and non-PCa tissue in the prostate (NPCa-histo) were processed to obtain a PCa-model, which was adjusted to PET-resolution (histo-PET). Each histo-PET was coregistered to in-vivo PSMA-PET/CT data. Results: Analysis of spatial overlap between histo-PET and PSMA PET revealed highly significant correlations (p < 10-5) in nine patients and moderate to high coefficients of determination (R²) from 42 to 82 % with an average of 60 ± 14 % in eight patients (in one patient R2 = 7 %). Mean SUVmean in PCa-histo and NPCa-histo was 5.6 ± 6.1 and 3.3 ± 2.5 (p = 0.012). Voxel-wise receiver-operating characteristic (ROC) analyses comparing the prediction by PSMA-PET with the non-smoothed tumor distribution from histopathology yielded an average area under the curve of 0.83 ± 0.12. Absolute and relative SUV (normalized to SUVmax) thresholds for achieving at least 90 % sensitivity were 3.19 ± 3.35 and 0.28 ± 0.09, respectively. Conclusions: Voxel-wise analyses revealed good correlations of 68Ga-HBED-CC-PSMA PET/CT and histopathology in eight out of nine patients. Thus, PSMA-PET allows a reliable detection and delineation of PCa as basis for PET-guided focal therapies. PMID:27446496

  7. Using Voxelized Point-Cloud Forest Reconstructions from Ground-Based Full-Waveform Lidar to Retrieve Leaf Area Index and Foliage Profiles

    NASA Astrophysics Data System (ADS)

    Yang, X.; Strahler, A. H.; Schaaf, C.; Li, Z.; Yao, T.; Zhao, F.; Wang, Z.; Woodcock, C. E.; Jupp, D.; Culvenor, D.; Newnham, G.; Lovell, J.

    2012-12-01

    This study presents a new methodology to directly retrieve two important biophysical parameters, Leaf Area Index (LAI; m^2) and Foliage Area Volume Density (FAVD; m^2 LAI/m^3 volume) profiles through the voxelization of point-cloud forest reconstructions from multiple ground-based full-waveform Echidna® lidar scans. Previous studies have verified that estimates of LAI and FAVD made from single EVI scans, using azimuth-averaged gap probability with zenith angle (Jupp et al. 2009; Zhao et al. 2011), agree well with those of traditional hemispherical photos and LAI-2000 measurements. Strahler et al. (2008) and Yang et al. (2012) established a paradigm for the 3-D reconstruction of forest stands using a full-waveform, ground-based, scanning lidar by merging point clouds constructed from overlapping EVI scans, thereby allowing virtual direct representation of forest biomass. Classification procedures (Yang et al. 2012), based on the shape of the laser pulse returned to the instrument, can separate trunk from foliage scattering events. Volumetric datasets are produced by properly assigning attributes, such as gap probability, apparent reflectance, and volume associated with the laser pulse footprint at the observed range, to the foliage scattering events in the reconstructed point cloud. Leaf angle distribution is accommodated with a simple model based on gap probability with zenith angle as observed in individual scans of the stand. Clumping occurring at scales coarser than elemental volumes associated with scattering events is observed directly and therefore does not require parametric correction. For validation, comparisons are made between LAI and FAVD profiles retrieved directly from the voxelized 3-D forest reconstructions and those observed from airborne and field measurements. The voxelized 3-D forest reconstructions derived from EVI point clouds provide a pathway to estimate "ground truth" FAVD, LAI, and above-ground biomass without destructive sampling. These

  8. Design, fabrication, and implementation of voxel-based 3D printed textured phantoms for task-based image quality assessment in CT

    NASA Astrophysics Data System (ADS)

    Solomon, Justin; Ba, Alexandre; Diao, Andrew; Lo, Joseph; Bier, Elianna; Bochud, François; Gehm, Michael; Samei, Ehsan

    2016-03-01

    In x-ray computed tomography (CT), task-based image quality studies are typically performed using uniform background phantoms with low-contrast signals. Such studies may have limited clinical relevancy for modern non-linear CT systems due to possible influence of background texture on image quality. The purpose of this study was to design and implement anatomically informed textured phantoms for task-based assessment of low-contrast detection. Liver volumes were segmented from 23 abdominal CT cases. The volumes were characterized in terms of texture features from gray-level co-occurrence and run-length matrices. Using a 3D clustered lumpy background (CLB) model, a fitting technique based on a genetic optimization algorithm was used to find the CLB parameters that were most reflective of the liver textures, accounting for CT system factors of spatial blurring and noise. With the modeled background texture as a guide, a cylinder phantom (165 mm in diameter and 30 mm height) was designed, containing 20 low-contrast spherical signals (6 mm in diameter at targeted contrast levels of ~3.2, 5.2, 7.2, 10, and 14 HU, 4 repeats per signal). The phantom was voxelized and input into a commercial multi-material 3D printer (Object Connex 350), with custom software for voxel-based printing. Using principles of digital half-toning and dithering, the 3D printer was programmed to distribute two base materials (VeroWhite and TangoPlus, nominal voxel size of 42x84x30 microns) to achieve the targeted spatial distribution of x-ray attenuation properties. The phantom was used for task-based image quality assessment of a clinically available iterative reconstruction algorithm (Sinogram Affirmed Iterative Reconstruction, SAFIRE) using a channelized Hotelling observer paradigm. Images of the textured phantom and a corresponding uniform phantom were acquired at six dose levels and observer model performance was estimated for each condition (5 contrasts x 6 doses x 2 reconstructions x 2

  9. Numerical Transcoding Proficiency in 10-Year-Old Schoolchildren is Associated with Gray Matter Inter-Individual Differences: A Voxel-Based Morphometry Study

    PubMed Central

    Lubin, Amélie; Rossi, Sandrine; Simon, Grégory; Lanoë, Céline; Leroux, Gaëlle; Poirel, Nicolas; Pineau, Arlette; Houdé, Olivier

    2013-01-01

    Are individual differences in numerical performance sustained by variations in gray matter volume in schoolchildren? To our knowledge, this challenging question for neuroeducation has not yet been investigated in typical development. We used the Voxel-Based Morphometry method to search for possible structural brain differences between two groups of 10-year-old schoolchildren (N = 22) whose performance differed only in numerical transcoding between analog and symbolic systems. The results indicated that children with low numerical proficiency have less gray matter volume in the parietal (particularly in the left intraparietal sulcus and the bilateral angular gyri) and occipito-temporal areas. All the identified regions have previously been shown to be functionally involved in transcoding between analog and symbolic numerical systems. Our data contribute to a better understanding of the intertwined relationships between mathematics learning and brain structure in healthy schoolchildren. PMID:23630510

  10. Numerical Transcoding Proficiency in 10-Year-Old Schoolchildren is Associated with Gray Matter Inter-Individual Differences: A Voxel-Based Morphometry Study.

    PubMed

    Lubin, Amélie; Rossi, Sandrine; Simon, Grégory; Lanoë, Céline; Leroux, Gaëlle; Poirel, Nicolas; Pineau, Arlette; Houdé, Olivier

    2013-01-01

    Are individual differences in numerical performance sustained by variations in gray matter volume in schoolchildren? To our knowledge, this challenging question for neuroeducation has not yet been investigated in typical development. We used the Voxel-Based Morphometry method to search for possible structural brain differences between two groups of 10-year-old schoolchildren (N = 22) whose performance differed only in numerical transcoding between analog and symbolic systems. The results indicated that children with low numerical proficiency have less gray matter volume in the parietal (particularly in the left intraparietal sulcus and the bilateral angular gyri) and occipito-temporal areas. All the identified regions have previously been shown to be functionally involved in transcoding between analog and symbolic numerical systems. Our data contribute to a better understanding of the intertwined relationships between mathematics learning and brain structure in healthy schoolchildren.

  11. Early gray-matter and white-matter concentration in infancy predict later language skills: A whole brain voxel-based morphometry study

    PubMed Central

    Can, Dilara Deniz; Richards, Todd; Kuhl, Patricia

    2012-01-01

    Magnetic Resonance Imaging (MRI) brain scans were obtained from 19 infants at 7 months. Expressive and receptive language performance was assessed at 12 months. Voxel-based morphometry (VBM) identified brain regions where gray-matter and white-matter concentrations at 7 months correlated significantly with children’s language scores at 12 months. Early gray-matter concentration in the right cerebellum, early white-matter concentration in the right cerebellum, and early white-matter concentration in the left posterior limb of the internal capsule (PLIC)/cerebral peduncle were positively and strongly associated with infants’ receptive language ability at 12 months. Early gray-matter concentration in the right hippocampus was positively and strongly correlated with infants’ expressive language ability at 12 months. Our results suggest that the cerebellum, PLIC/cerebral peduncle, and the hippocampus may be associated with early language development. Potential links between these structural predictors and infants’ linguistic functions are discussed. PMID:23274797

  12. Grey matter volume differences associated with gender in children with attention-deficit/hyperactivity disorder: A voxel-based morphometry study.

    PubMed

    Villemonteix, Thomas; De Brito, Stéphane A; Slama, Hichem; Kavec, Martin; Balériaux, Danielle; Metens, Thierry; Baijot, Simon; Mary, Alison; Peigneux, Philippe; Massat, Isabelle

    2015-08-01

    Female participants have been underrepresented in previous structural magnetic resonance imaging reports on attention-deficit/hyperactivity disorder (ADHD). In this study, we used optimized voxel-based morphometry to examine grey matter volumes in a sample of 33 never-medicated children with combined-type ADHD and 27 typically developing (TD) children. We found a gender-by-diagnosis interaction effect in the ventral anterior cingulate cortex (ACC), whereby boys with ADHD exhibited reduced volumes compared with TD boys, while girls with ADHD showed increased volumes when compared with TD girls. Considering the key role played by the ventral ACC in emotional regulation, we discuss the potential contribution of these alterations to gender-specific symptoms' profiles in ADHD.

  13. The reduction in Monte Carlo calculated organ doses from CT with tube current modulation using WILLIAM, a voxel model of seven year-old anatomy.

    PubMed

    Caon, Martin

    2014-12-01

    The construction of a voxel model of seven year-old male anatomy from a low resolution whole body CT scan acquired with a PET-CT scanner is described. The model is referred to as WILLIAM. The model was used to compare the Monte Carlo calculated relative organ doses with and without tube current modulation from simulated CAP and chest CT examinations. Tube current modulation was simulated in both the angular (x-y plane) and axial (along the z axis) senses. For organs that are located wholly within the scanned anatomy, significant relative dose reductions of approximately 43 to 62 % were calculated when tube current modulation was simulated compared to Monte Carlo calculations that did not include tube current modulation. Organs located outside of the directly irradiated anatomy, experienced a decrease in their relative dose of between 33 and 38 % when tube current modulation was simulated.