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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. 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

  3. Voxelated liquid crystal elastomers

    NASA Astrophysics Data System (ADS)

    Ware, Taylor H.; McConney, Michael E.; Wie, Jeong Jae; Tondiglia, Vincent P.; White, Timothy J.

    2015-02-01

    Dynamic control of shape can bring multifunctionality to devices. Soft materials capable of programmable shape change require localized control of the magnitude and directionality of a mechanical response. We report the preparation of soft, ordered materials referred to as liquid crystal elastomers. The direction of molecular order, known as the director, is written within local volume elements (voxels) as small as 0.0005 cubic millimeters. Locally, the director controls the inherent mechanical response (55% strain) within the material. In monoliths with spatially patterned director, thermal or chemical stimuli transform flat sheets into three-dimensional objects through controlled bending and stretching. The programmable mechanical response of these materials could yield monolithic multifunctional devices or serve as reconfigurable substrates for flexible devices in aerospace, medicine, or consumer goods.

  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 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

  6. 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

  7. The GSF family of voxel phantoms

    NASA Astrophysics Data System (ADS)

    Petoussi-Henss, Nina; Zankl, Maria; Fill, Ute; Regulla, Dieter

    2002-01-01

    Voxel phantoms are human models based on computed tomographic or magnetic resonance images obtained from high-resolution scans of a single individual. They consist of a huge number of volume elements (voxels) and are at the moment the most precise representation of the human anatomy. The purpose of this paper is to introduce the GSF voxel phantoms, with emphasis on the new ones and highlight their characteristics and limitations. The GSF voxel family includes at the moment two paediatric and five adult phantoms of both sexes, different ages and stature and several others are under construction. Two phantoms made of physical calibration phantoms are also available to be used for validation purposes. The GSF voxel phantoms tend to cover persons of individual anatomy and were developed to be used for numerical dosimetry of radiation transport but other applications are also possible. Examples of applications in patient dosimetry in diagnostic radiology and in nuclear medicine as well as for whole-body irradiations from idealized external exposures are given and discussed.

  8. VOXEL-WISE GROUP ANALYSIS OF DTI

    PubMed Central

    Liu, Zhexing; Zhu, Hongtu; Marks, Bonita L.; Katz, Laurence M.; Goodlett, Casey B.; Gerig, Guido; Styner, Martin

    2013-01-01

    Diffusion tensor MRI (DTI) is now a widely used modality to investigate the fiber tissues in vivo, especially the white matter in brain. An automatic pipeline is described in this paper to conduct a localized voxel-wise multiple-subject group comparison study of DTI. The pipeline consists of 3 steps: 1) Preprocessing, including image format converting, image quality check, eddy-current and motion artifact correction, skull stripping and tensor image estimation, 2) study-specific unbiased DTI atlas computation via affine followed by fluid nonlinear registration and warping of all individual DTI images into the common atlas space to achieve voxel-wise correspondence, 3) voxelwise statistical analysis via heterogeneous linear regression and wild bootstrap technique for correcting for multiple comparisons. This pipeline was applied to process data from a fitness and aging study and preliminary results are presented. The results show that this fully automatic pipeline is suitable for voxel-wise group DTI analysis. PMID:23703686

  9. VOXEL-WISE GROUP ANALYSIS OF DTI.

    PubMed

    Liu, Zhexing; Zhu, Hongtu; Marks, Bonita L; Katz, Laurence M; Goodlett, Casey B; Gerig, Guido; Styner, Martin

    2009-01-01

    Diffusion tensor MRI (DTI) is now a widely used modality to investigate the fiber tissues in vivo, especially the white matter in brain. An automatic pipeline is described in this paper to conduct a localized voxel-wise multiple-subject group comparison study of DTI. The pipeline consists of 3 steps: 1) Preprocessing, including image format converting, image quality check, eddy-current and motion artifact correction, skull stripping and tensor image estimation, 2) study-specific unbiased DTI atlas computation via affine followed by fluid nonlinear registration and warping of all individual DTI images into the common atlas space to achieve voxel-wise correspondence, 3) voxelwise statistical analysis via heterogeneous linear regression and wild bootstrap technique for correcting for multiple comparisons. This pipeline was applied to process data from a fitness and aging study and preliminary results are presented. The results show that this fully automatic pipeline is suitable for voxel-wise group DTI analysis. PMID:23703686

  10. 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

  11. Tools for creating and manipulating voxel phantoms.

    PubMed

    Kramer, Gary H; Capello, Kevin; Chiang, Albert; Cardenas-Mendez, Erick; Sabourin, Trevor

    2010-03-01

    The National Internal Radiation Assessment Section's Human Monitoring Laboratory (HML) has purchased and developed a number of in-house tools to create and edit voxel phantoms. This paper describes the methodology developed in the HML using those tools to prepare input files for Monte Carlo simulations using voxel phantoms. Three examples are given. The in-house tools described in this paper, and the phantoms that have been created using them, are all publically available upon request from the corresponding author. PMID:20147794

  12. 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

  13. 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.

  14. 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.

  15. 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

  16. Frequency Selectivity of Voxel-by-Voxel Functional Connectivity in Human Auditory Cortex.

    PubMed

    Cha, Kuwook; Zatorre, Robert J; Schönwiesner, Marc

    2016-01-01

    While functional connectivity in the human cortex has been increasingly studied, its relationship to cortical representation of sensory features has not been documented as much. We used functional magnetic resonance imaging to demonstrate that voxel-by-voxel intrinsic functional connectivity (FC) is selective to frequency preference of voxels in the human auditory cortex. Thus, FC was significantly higher for voxels with similar frequency tuning than for voxels with dissimilar tuning functions. Frequency-selective FC, measured via the correlation of residual hemodynamic activity, was not explained by generic FC that is dependent on spatial distance over the cortex. This pattern remained even when FC was computed using residual activity taken from resting epochs. Further analysis showed that voxels in the core fields in the right hemisphere have a higher frequency selectivity in within-area FC than their counterpart in the left hemisphere, or than in the noncore-fields in the same hemisphere. Frequency-selective FC is consistent with previous findings of topographically organized FC in the human visual and motor cortices. The high degree of frequency selectivity in the right core area is in line with findings and theoretical proposals regarding the asymmetry of human auditory cortex for spectral processing. PMID:25183885

  17. Voxel-based morphometry and epilepsy.

    PubMed

    Yasuda, Clarissa Lin; Betting, Luiz Eduardo; Cendes, Fernando

    2010-06-01

    Voxel-based morphometry is an automated technique for MRI analyses, developed to study differences in brain morphology and frequently used to study patients with diverse disorders. In epilepsy, it has been used to investigate areas with reduction or increase of gray and white matter, in different syndromes (i.e., temporal lobe epilepsy, focal cortical dysplasia and generalized epilepsies). In temporal lobe epilepsy, voxel-based morphometry showed gray/white matter atrophy extending beyond the atrophic hippocampus. These widespread abnormalities have been associated with seizure frequency, epilepsy duration, incidence of precipitating factors, cognitive dysfunction and surgical outcome. In generalized epilepsies, gray matter abnormalities were identified mainly in the thalamus and frontal cortex, reinforcing the role of the thalamocortical network in the mechanisms of generalized seizures. PMID:20518612

  18. 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

  19. 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

  20. The contemporary JAEA Japanese voxel phantoms.

    PubMed

    Sato, Kaoru; Takahashi, Fumiaki

    2012-03-01

    Average adult Japanese male (JM-103 phantom) and female (JF-103 phantom) voxel (volume pixel) phantoms were newly constructed by modifying the JM and JF phantoms previously developed at Japan Atomic Energy Agency. The JM-103 and JF-103 have average characteristics with respect to organ masses and body sizes. Their tissue segmentations were based on International Commission on Radiological Protection (ICRP) Publication 103. The anatomical and dosimetric characteristics of JM-103 and JF-103 were compared with those of ICRP adult reference male (AM phantom) and female (AF phantoms) phantoms. This study discusses their anatomical and dosimetric characteristics, and applications to the dose assessment of the atomic bomb survivors. PMID:22003186

  1. Using a prototype voxel for visualizing volumetric data

    NASA Astrophysics Data System (ADS)

    Buckalew, William C.

    1993-07-01

    We present a method for visualizing volumetric data such as NMI or CAT-scan data that makes use of a data structure called the prototype voxel to create images very quickly on common workstation screens. The algorithm speeds up the standard process of casting rays through the volume data by precomputing a great deal of direction and interpolation information, assuming that all voxels are the same size and shape (which is normally the case for medical data sets). As rays are cast, this information, stored in the prototype voxel, is merely looked up when needed rather than being recomputed repeatedly. The prototype voxel must be computed only once for each data configuration; subsequent data sets which use the same size and shape of voxel can use the same prototype voxel information to speed rendering. This algorithm trades memory for speed: it uses 20 to 50 megabytes of memory (already becoming commonly available in modern workstations) for its speed improvements.

  2. 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. PMID:26969297

  3. 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.

  4. 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

  5. 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.

  6. 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

  7. 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

  8. 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. PMID:25756621

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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

  14. Postured voxel-based human models for electromagnetic dosimetry

    NASA Astrophysics Data System (ADS)

    Nagaoka, Tomoaki; Watanabe, Soichi

    2008-12-01

    High-resolution anatomically realistic whole-body voxel models have recently been developed for electromagnetic dosimetry. However, the posture of most models is similar to the standing one, which strongly limits electromagnetic dosimetry when simulating a realistic exposure scenario. In this paper, we present the development of postured models based on anatomically realistic voxel models with standing posture. Voxel models of the Japanese adult male and female were used as the original upright standing models. The Japanese models were composed of 2 mm cubic voxels, each of which was segmented into 51 different tissue types. We developed several different types of posture models using a novel posture transformation method. These posture models were smoothly transformed, while the continuity of the internal tissues and organs was maintained. In this paper, we also present our calculations of the whole-body averaged specific absorption rates (SARs) of sitting male and female models exposed to electromagnetic plane waves at very high (VHF) and ultra high frequency (UHF) bands.

  15. Voxel selection in FMRI data analysis based on sparse representation.

    PubMed

    Li, Yuanqing; Namburi, Praneeth; Yu, Zhuliang; Guan, Cuntai; Feng, Jianfeng; Gu, Zhenghui

    2009-10-01

    Multivariate pattern analysis approaches toward detection of brain regions from fMRI data have been gaining attention recently. In this study, we introduce an iterative sparse-representation-based algorithm for detection of voxels in functional MRI (fMRI) data with task relevant information. In each iteration of the algorithm, a linear programming problem is solved and a sparse weight vector is subsequently obtained. The final weight vector is the mean of those obtained in all iterations. The characteristics of our algorithm are as follows: 1) the weight vector (output) is sparse; 2) the magnitude of each entry of the weight vector represents the significance of its corresponding variable or feature in a classification or regression problem; and 3) due to the convergence of this algorithm, a stable weight vector is obtained. To demonstrate the validity of our algorithm and illustrate its application, we apply the algorithm to the Pittsburgh Brain Activity Interpretation Competition 2007 functional fMRI dataset for selecting the voxels, which are the most relevant to the tasks of the subjects. Based on this dataset, the aforementioned characteristics of our algorithm are analyzed, and a comparison between our method with the univariate general-linear-model-based statistical parametric mapping is performed. Using our method, a combination of voxels are selected based on the principle of effective/sparse representation of a task. Data analysis results in this paper show that this combination of voxels is suitable for decoding tasks and demonstrate the effectiveness of our method. PMID:19567340

  16. Evaluating Voxel Enabled Scalable Intersection of Large Point Clouds

    NASA Astrophysics Data System (ADS)

    Wang, J.; Lindenbergh, R.; Menenti, M.

    2015-08-01

    Laser scanning has become a well established surveying solution for obtaining 3D geo-spatial information on objects and environment. Nowadays scanners acquire up to millions of points per second which makes point cloud huge. Laser scanning is widely applied from airborne, carborne and stable platforms, resulting in point clouds obtained at different attitudes and with different extents. Working with such different large point clouds makes the determination of their overlapping area necessary but often time consuming. In this paper, a scalable point cloud intersection determination method is presented based on voxels. The method takes two overlapping point clouds as input. It consecutively resamples the input point clouds according to a preset voxel cell size. For all non-empty cells the center of gravity of the points in contains is computed. Consecutively for those centers it is checked if they are in a voxel cell of the other point cloud. The same process is repeated after interchanging the role of the two point clouds. The quality of the results is evaluated by the distance to the pints from the other data set. Also computation time and quality of the results are compared for different voxel cell sizes. The results are demonstrated on determining he intersection between an airborne and carborne laser point clouds and show that the proposed method takes 0.10%, 0.15%, 1.26% and 14.35% of computation time compared the the classic method when using cell sizes of of 10, 8, 5 and 3 meters respectively.

  17. 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

  18. Voxel model in BNCT treatment planning: performance analysis and improvements

    NASA Astrophysics Data System (ADS)

    González, Sara J.; Carando, Daniel G.; Santa Cruz, Gustavo A.; Zamenhof, Robert G.

    2005-02-01

    In recent years, many efforts have been made to study the performance of treatment planning systems in deriving an accurate dosimetry of the complex radiation fields involved in boron neutron capture therapy (BNCT). The computational model of the patient's anatomy is one of the main factors involved in this subject. This work presents a detailed analysis of the performance of the 1 cm based voxel reconstruction approach. First, a new and improved material assignment algorithm implemented in NCTPlan treatment planning system for BNCT is described. Based on previous works, the performances of the 1 cm based voxel methods used in the MacNCTPlan and NCTPlan treatment planning systems are compared by standard simulation tests. In addition, the NCTPlan voxel model is benchmarked against in-phantom physical dosimetry of the RA-6 reactor of Argentina. This investigation shows the 1 cm resolution to be accurate enough for all reported tests, even in the extreme cases such as a parallelepiped phantom irradiated through one of its sharp edges. This accuracy can be degraded at very shallow depths in which, to improve the estimates, the anatomy images need to be positioned in a suitable way. Rules for this positioning are presented. The skin is considered one of the organs at risk in all BNCT treatments and, in the particular case of cutaneous melanoma of extremities, limits the delivered dose to the patient. Therefore, the performance of the voxel technique is deeply analysed in these shallow regions. A theoretical analysis is carried out to assess the distortion caused by homogenization and material percentage rounding processes. Then, a new strategy for the treatment of surface voxels is proposed and tested using two different irradiation problems. For a parallelepiped phantom perpendicularly irradiated with a 5 keV neutron source, the large thermal neutron fluence deviation present at shallow depths (from 54% at 0 mm depth to 5% at 4 mm depth) is reduced to 2% on average

  19. Single voxel localization for dynamic hyperpolarized 13C MR spectroscopy

    NASA Astrophysics Data System (ADS)

    Chen, Albert P.; Cunningham, Charles H.

    2015-09-01

    The PRESS technique has been widely used to achieve voxel localization for in vivo1H MRS acquisitions. However, for dynamic hyperpolarized 13C MRS experiments, the transition bands of the refocusing pulses may saturate the pre-polarized substrate spins flowing into the voxel. This limitation may be overcome by designing refocusing pulses that do not perturb the resonance of the hyperpolarized substrate, but selectively refocuses the spins of the metabolic products. In this study, a PRESS pulse sequence incorporating spectral-spatial refocusing pulses that have a stop band ('notch') at the substrate resonance is tested in vivo using hyperpolarized [1-13C]pyruvate. Higher metabolite SNR was observed in experiments using the spectral-spatial refocusing pulses as compared to conventional refocusing pulses.

  20. Single voxel localization for dynamic hyperpolarized (13)C MR spectroscopy.

    PubMed

    Chen, Albert P; Cunningham, Charles H

    2015-09-01

    The PRESS technique has been widely used to achieve voxel localization for in vivo(1)H MRS acquisitions. However, for dynamic hyperpolarized (13)C MRS experiments, the transition bands of the refocusing pulses may saturate the pre-polarized substrate spins flowing into the voxel. This limitation may be overcome by designing refocusing pulses that do not perturb the resonance of the hyperpolarized substrate, but selectively refocuses the spins of the metabolic products. In this study, a PRESS pulse sequence incorporating spectral-spatial refocusing pulses that have a stop band ('notch') at the substrate resonance is tested in vivo using hyperpolarized [1-(13)C]pyruvate. Higher metabolite SNR was observed in experiments using the spectral-spatial refocusing pulses as compared to conventional refocusing pulses. PMID:26232365

  1. 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.

  2. 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

  3. 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.

  4. 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.

  5. 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. PMID:27295304

  6. Generation of voxelized breast phantoms from surgical mastectomy specimens

    PubMed Central

    Michael O’Connor, J.; Das, Mini; Dider, Clay S.; Mahd, Mufeed; Glick, Stephen J.

    2013-01-01

    Purpose: In the research and development of dedicated tomographic breast imaging systems, digital breast object models, also known as digital phantoms, are useful tools. While various digital breast phantoms do exist, the purpose of this study was to develop a realistic high-resolution model suitable for simulating three-dimensional (3D) breast imaging modalities. The primary goal was to design a model capable of producing simulations with realistic breast tissue structure. Methods: The methodology for generating an ensemble of digital breast phantoms was based on imaging surgical mastectomy specimens using a benchtop, cone-beam computed tomography system. This approach allowed low-noise, high-resolution projection views of the mastectomy specimens at each angular position. Reconstructions of these projection sets were processed using correction techniques and diffusion filtering prior to segmentation into breast tissue types in order to generate phantoms. Results: Eight compressed digital phantoms and 20 uncompressed phantoms from which an additional 96 pseudocompressed digital phantoms with voxel dimensions of 0.2 mm3 were generated. Two distinct tissue classification models were used in forming breast phantoms. The binary model classified each tissue voxel as either adipose or fibroglandular. A multivalue scaled model classified each tissue voxel as percentage of adipose tissue (range 1%–99%). Power spectral analysis was performed to compare simulated reconstructions using the breast phantoms to the original breast specimen reconstruction, and fits were observed to be similar. Conclusions: The digital breast phantoms developed herein provide a high-resolution anthropomorphic model of the 3D uncompressed and compressed breast that are suitable for use in evaluating and optimizing tomographic breast imaging modalities. The authors believe that other research groups might find the phantoms useful, and therefore they offer to make them available for wider use

  7. Internal dosimetry estimates using voxelized reference phantoms for thyroid agents

    PubMed Central

    Hoseinian-Azghadi, E.; Rafat-Motavalli, L.; Miri-Hakimabad, H.

    2014-01-01

    This work presents internal dosimetry estimates for diagnostic procedures performed for thyroid disorders by relevant radiopharmaceuticals. The organ doses for 131Iodine, 123Iodine and 99mTc incorporated into the body were calculated for the International Commission on Radiological Protection (ICRP) reference voxel phantoms using the Monte Carlo transport method. A comparison between different thyroid uptakes of iodine in the range of 0–55% was made, and the effect of various techniques for administration of 99mTc on organ doses was studied. To investigate the necessity of calculating organ dose from all source regions, the major source organ and its contribution to total dose were specified for each target organ. Moreover, we compared effective dose in ICRP voxel phantoms with that in stylized phantoms. In our method, we directly calculated the organ dose without using the S values or SAFs, as is commonly done. Hence, a distribution of the absorbed dose to entire tissues was obtained. The chord length distributions (CLDs) were also computed for the selected source–target pairs to make comparison across the genders. The results showed that the S values for radionuclides in the thyroid are not sufficient for calculating the organ doses, especially for 123I and 99mTc. The thyroid and its neighboring organs receive a greater dose as thyroid uptake increases. Our comparisons also revealed an underestimation of organ doses reported for the stylized phantoms compared with the values based on the ICRP voxel phantoms in the uptake range of 5–55%, and an overestimation of absorbed dose by up to 2-fold for Iodine administration using blocking agent and for 99mTc incorporation. PMID:24222311

  8. Monte Carlo based voxel phantoms for in vivo internal dosimetry.

    PubMed

    Ros, J M Gómez; Moraleda, M; López, M A; Navarro, T; Navarro, J F

    2007-01-01

    The purpose of this communication is to describe briefly the computer programs developed to generate the MCNP input file corresponding to any segmented tomographic data and its application to the calibration procedures for in vivo internal dosimetry. The method has been applied to the determination of 241Am in bone by measurement in skull and knee using MCNP voxel models of a real human head and knee based on the tomographic Voxelman and Arms Down phantoms developed by Zubal et al. at Yale University. PMID:17449911

  9. 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

  10. Voxel-based texture mapping for medical data.

    PubMed

    Weng, T L; Lin, S J; Chang, W Y; Sun, Y N

    2002-01-01

    In computerized image and graphic applications, texture mapping is one of the most commonly used methods to improve the realism or to enhance the visual effect of object rendering without too much increase in computational complexity. The conventional method usually has to transfer three-dimensional (3D) object to the polygonal structure, and is computationally expensive. As the medical data are mostly in voxel format, the polygonal structure is not efficient or requires more complicated mechanism in retrieving the internal information of medical data. In this paper, we propose a new texture mapping method, based on flattening a chain-coded 3D surface, to handle the voxel-based data directly. The method flattens the 3D object surface onto a two-dimensional (2D) plane and then uses 2D metamorphosis to generate the correspondences between object surface and texture image. Therefore, polygon transformation is no longer necessary and texture mapping is handled with inexpensive 2D morphing. More importantly, the internal information of medical data can be easily preserved and utilized further. Experimental results have shown the effectiveness and efficiency of the proposed algorithm. PMID:12453508

  11. Visualization using 3D voxelization of full lidar waveforms

    NASA Astrophysics Data System (ADS)

    Park, Joong Yong; Ramnath, Vinod; Feygels, Victor

    2014-11-01

    Airborne bathymetric lidar (Light Detection and Ranging) systems measure photoelectrons on the optical path (range and angle) at the photocathode of a returned laser pulse at high rates, such as every nanosecond. The collected measurement of a single pulse in a time series is called a waveform. Based on the calibration of the lidar system, the return signal is converted into units of received power. This converted value from the lidar waveform data is used to compute an estimate of the reflectance from the returned backscatter, which contains environmental information from along the optical path. This concept led us to develop a novel tool to visualize lidar data in terms of the returned backscatter, and to use this as a data analysis and editing tool. The full lidar waveforms along the optical path, from laser points collected in the region of interest (ROI), are voxelized into a 3D image cube. This allows lidar measurements to be analyzed in three orthogonal directions simultaneously. The laser pulse return (reflection) from the seafloor is visible in the waveform as a pronounced "bump" above the volume backscatter. Floating or submerged objects in the water may also be visible. Similarly, forest canopies and tree branches can be identified in the 3D voxelization. This paper discusses the possibility of using this unique three-orthogonal volume visualizing tool to extract environmental information for carrying out rapid environmental assessments over forests and water.

  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. Automatic detection of coronary artery disease in myocardial perfusion SPECT using image registration and voxel to voxel statistical comparisons.

    PubMed

    Peace, R A; Staff, R T; Gemmell, H G; McKiddie, F I; Metcalfe, M J

    2002-08-01

    The purpose of this study was to compare the performance of automatic detection of coronary artery disease (CAD) with that of expert observers. A male and female normal image template was constructed from normal stress technetium-99m single photon emission computed tomography (SPECT) studies. Mean and standard deviation images for each sex were created by registering normal studies to a standard shape and position. The test group consisted of 104 patients who had been routinely referred for SPECT and angiography. The gold standard for CAD was defined by angiography. The test group studies were registered to the respective templates and the Z-score was calculated for each voxel. Voxels with a Z-score greater than 5 indicated the presence of CAD. The performance of this method and that of three observers were compared by continuous receiver operating characteristic (CROC) analysis. The overall sensitivity and specificity for automatic detection were 73% and 92%, respectively. The area (Az) under the CROC curve (+/-1 SE) for automatic detection of CAD was 0.88+/-0.06. There was no statistically significant difference between the performances of the three observers in terms of Az and that of automatic detection (P> or =0.25, univariate Z-score test). The use of this automated statistical mapping approach shows a performance comparable with experienced observers, but avoids inter-observer and intra-observer variability. PMID:12124485

  15. Creation of a voxel phantom of the ICRP reference crab.

    PubMed

    Caffrey, E A; Higley, K A

    2013-06-01

    The International Commission on Radiological Protection (ICRP) has modeled twelve reference animal and plant (RAP) species using simple geometric shapes in Monte-Carlo (MCNP) based simulations. The focus has now shifted to creating voxel phantoms of each RAP in order to estimate doses to biota with a higher degree of confidence. This paper describes the creation of a voxel model of a Dungeness crab from CT images with shell, gills, gonads, hepatopancreas, and heart identified and segmented. Absorbed fractions were tabulated for each organ as a source and target at twelve photon and nine electron energies: 0.01, 0.015, 0.02, 0.03, 0.05, 0.1, 0.2, 0.5, 1.0, 1.5, 2.0, and 4.0 MeV for photons and 0.1, 0.2, 0.4, 0.5, 0.7, 1.0, 1.5, 2.0 and 4.0 MeV for electrons. AFs whose error exceeded 5% are marked with an underline in the data tables; AFs whose error was higher than 10% were excluded, and are shown in the tabulated data as a dashed line. A representative sample of the data is shown in Figs. 3-8; the entire data set is available as an electronic appendix. The results are consistent with previous small organism studies (Kinase, 2008; Stabin et al., 2006), and suggest that AF values are highly dependent on source organ location and mass. PMID:23410593

  16. 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.

  17. Determining correspondence in 3-D MR brain images using attribute vectors as morphological signatures of voxels.

    PubMed

    Xue, Zhong; Shen, Dinggang; Davatzikos, Christos

    2004-10-01

    Finding point correspondence in anatomical images is a key step in shape analysis and deformable registration. This paper proposes an automatic correspondence detection algorithm for intramodality MR brain images of different subjects using wavelet-based attribute vectors (WAVs) defined on every image voxel. The attribute vector (AV) is extracted from the wavelet subimages and reflects the image structure in a large neighborhood around the respective voxel in a multiscale fashion. It plays the role of a morphological signature for each voxel, and our goal is, therefore, to make it distinctive of the respective voxel. Correspondence is then determined from similarities of AVs. By incorporating the prior knowledge of the spatial relationship among voxels, the ability of the proposed algorithm to find anatomical correspondence is further improved. Experiments with MR images of human brains show that the algorithm performs similarly to experts, even for complex cortical structures. PMID:15493695

  18. 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.

  19. 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

  20. 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

  1. Voxel-Based 3-D Tree Modeling from Lidar Images for Extracting Tree Structual Information

    NASA Astrophysics Data System (ADS)

    Hosoi, F.

    2014-12-01

    Recently, lidar (light detection and ranging) has been used to extracting tree structural information. Portable scanning lidar systems can capture the complex shape of individual trees as a 3-D point-cloud image. 3-D tree models reproduced from the lidar-derived 3-D image can be used to estimate tree structural parameters. We have proposed the voxel-based 3-D modeling for extracting tree structural parameters. One of the tree parameters derived from the voxel modeling is leaf area density (LAD). We refer to the method as the voxel-based canopy profiling (VCP) method. In this method, several measurement points surrounding the canopy and optimally inclined laser beams are adopted for full laser beam illumination of whole canopy up to the internal. From obtained lidar image, the 3-D information is reproduced as the voxel attributes in the 3-D voxel array. Based on the voxel attributes, contact frequency of laser beams on leaves is computed and LAD in each horizontal layer is obtained. This method offered accurate LAD estimation for individual trees and woody canopy trees. For more accurate LAD estimation, the voxel model was constructed by combining airborne and portable ground-based lidar data. The profiles obtained by the two types of lidar complemented each other, thus eliminating blind regions and yielding more accurate LAD profiles than could be obtained by using each type of lidar alone. Based on the estimation results, we proposed an index named laser beam coverage index, Ω, which relates to the lidar's laser beam settings and a laser beam attenuation factor. It was shown that this index can be used for adjusting measurement set-up of lidar systems and also used for explaining the LAD estimation error using different types of lidar systems. Moreover, we proposed a method to estimate woody material volume as another application of the voxel tree modeling. In this method, voxel solid model of a target tree was produced from the lidar image, which is composed of

  2. 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

  3. 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

  4. 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. PMID:19015095

  5. 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.

  6. Voxel-based morphometry in patients with idiopathic generalized epilepsies.

    PubMed

    Betting, Luiz Eduardo; Mory, Susana Barreto; Li, Li Min; Lopes-Cendes, Iscia; Guerreiro, Marilisa M; Guerreiro, Carlos A M; Cendes, Fernando

    2006-08-15

    Idiopathic generalized epilepsies (IGE) are a group of frequent age-related epilepsy syndromes. IGE are clinically characterized by generalized tonic-clonic, myoclonic and absence seizures. According to predominant seizure type and age of onset, IGE are divided in subsyndromes: childhood absence and juvenile absence epilepsy (AE), juvenile myoclonic epilepsy (JME) and generalized tonic-clonic seizures on awakening (GTCS). The limits between these subsyndromes are not well defined, supporting the existence of only one major syndrome. Visual assessment of routine magnetic resonance imaging (MRI) in patients with IGE is normal. MRI voxel-based morphometry (VBM) uses automatically segmented gray and white matter for comparisons, eliminating the investigator bias. We used VBM to study 120 individuals (47 controls, 44 with JME, 24 with AE and 15 with GTCS) to investigate the presence of subtle structural abnormalities in IGE subsyndromes. VBM was performed searching for abnormalities on gray matter concentration (GMC) between patients groups and controls. Compared to controls, JME presented increased GMC in frontobasal region and AE showed increased GMC in the superior mesiofrontal region. The GTCS group did not differ from controls. There were no areas of reduced GMC with the statistical level selected. Region of interest analysis showed increased GMC in the anterior portion of the thalamus in patients with absence seizures. Our results support subtle GMC abnormalities in patients with JME and AE when compared to controls. These findings suggest the existence of different patterns of cortical abnormalities in IGE subsyndromes. PMID:16702001

  7. Voxel Based Morphometry in Optical Coherence Tomography: Validation & Core Findings

    PubMed Central

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

    2016-01-01

    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. PMID:27199503

  8. 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.

  9. 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.

  10. Reconstruction of finer voxel grid transmission images in Tomographic Gamma Scanning

    NASA Astrophysics Data System (ADS)

    Wang, Ke; Li, Zheng; Feng, Wei

    2014-08-01

    Tomographic Gamma Scanning (TGS) is a technique used to assay the nuclide distribution and radioactivity in nuclear waste drums. Limited to few transmission measurements, the drum is divided into large voxels and thus leads to the inhomogeneity of the voxels and negatively affects the results. A new algorithm is presented to reconstruct finer voxel grid transmission images with the same number of measurements. The small voxel size decreases the effect of the inhomogeneity and makes the result more accurate. The algorithm employs total variation minimization and precisely describes the attenuation process. The influences of the different scan modes are discussed with Monte Carlo simulations. Experiments are performed to verify the effectiveness of our method.

  11. Partial-volume Bayesian classification of material mixtures in MR volume data using voxel histograms.

    PubMed

    Laidlaw, D H; Fleischer, K W; Barr, A H

    1998-02-01

    We present a new algorithm for identifying the distribution of different material types in volumetric datasets such as those produced with magnetic resonance imaging (MRI) or computed tomography (CT). Because we allow for mixtures of materials and treat voxels as regions, our technique reduces errors that other classification techniques can create along boundaries between materials and is particularly useful for creating accurate geometric models and renderings from volume data. It also has the potential to make volume measurements more accurately and classifies noisy, low-resolution data well. There are two unusual aspects to our approach. First, we assume that, due to partial-volume effects, or blurring, voxels can contain more than one material, e.g., both muscle and fat; we compute the relative proportion of each material in the voxels. Second, we incorporate information from neighboring voxels into the classification process by reconstructing a continuous function, rho(x), from the samples and then looking at the distribution of values that rho(x) takes on within the region of a voxel. This distribution of values is represented by a histogram taken over the region of the voxel; the mixture of materials that those values measure is identified within the voxel using a probabilistic Bayesian approach that matches the histogram by finding the mixture of materials within each voxel most likely to have created the histogram. The size of regions that we classify is chosen to match the spacing of the samples because the spacing is intrinsically related to the minimum feature size that the reconstructed continuous function can represent. PMID:9617909

  12. Quantifying Colocalization: Thresholding, Void Voxels and the Hcoef

    PubMed Central

    Adler, Jeremy; Parmryd, Ingela

    2014-01-01

    A critical step in the analysis of images is identifying the area of interest e.g. nuclei. When the nuclei are brighter than the remainder of the image an intensity can be chosen to identify the nuclei. Intensity thresholding is complicated by variations in the intensity of individual nuclei and their intensity relative to their surroundings. To compensate thresholds can be based on local rather than global intensities. By testing local thresholding methods we found that the local mean performed poorly while the Phansalkar method and a new method based on identifying the local background were superior. A new colocalization coefficient, the Hcoef, highlights a number of controversial issues. (i) Are molecular interactions measurable (ii) whether to include voxels without fluorophores in calculations, and (iii) the meaning of negative correlations. Negative correlations can arise biologically (a) because the two fluorophores are in different places or (b) when high intensities of one fluorophore coincide with low intensities of a second. The cases are distinct and we argue that it is only relevant to measure correlation using pixels that contain both fluorophores and, when the fluorophores are in different places, to just report the lack of co-occurrence and omit these uninformative negative correlation. The Hcoef could report molecular interactions in a homogenous medium. But biology is not homogenous and distributions also reflect physico-chemical properties, targeted delivery and retention. The Hcoef actually measures a mix of correlation and co-occurrence, which makes its interpretation problematic and in the absence of a convincing demonstration we advise caution, favouring separate measurements of correlation and of co-occurrence. PMID:25375829

  13. An exact general remeshing scheme applied to physically conservative voxelization

    NASA Astrophysics Data System (ADS)

    Powell, Devon; Abel, Tom

    2015-09-01

    We present an exact general remeshing scheme to compute analytic integrals of polynomial functions over the intersections between convex polyhedral cells of old and new meshes. In physics applications this allows one to ensure global mass, momentum, and energy conservation while applying higher-order polynomial interpolation. We elaborate on applications of our algorithm arising in the analysis of cosmological N-body data, computer graphics, and continuum mechanics problems. We focus on the particular case of remeshing tetrahedral cells onto a Cartesian grid such that the volume integral of the polynomial density function given on the input mesh is guaranteed to equal the corresponding integral over the output mesh. We refer to this as "physically conservative voxelization." At the core of our method is an algorithm for intersecting two convex polyhedra by successively clipping one against the faces of the other. This algorithm is an implementation of the ideas presented abstractly by Sugihara [48], who suggests using the planar graph representations of convex polyhedra to ensure topological consistency of the output. This makes our implementation robust to geometric degeneracy in the input. We employ a simplicial decomposition to calculate moment integrals up to quadratic order over the resulting intersection domain. We also address practical issues arising in a software implementation, including numerical stability in geometric calculations, management of cancellation errors, and extension to two dimensions. In a comparison to recent work, we show substantial performance gains. We provide a C implementation intended to be a fast, accurate, and robust tool for geometric calculations on polyhedral mesh elements.

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

    PubMed Central

    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). PMID:23403700

  15. Influence of voxelization on finite difference time domain simulations of head-related transfer functions.

    PubMed

    Prepeliță, Sebastian; Geronazzo, Michele; Avanzini, Federico; Savioja, Lauri

    2016-05-01

    The scattering around the human pinna that is captured by the Head-Related Transfer Functions (HRTFs) is a complex problem that creates uncertainties in both acoustical measurements and simulations. Within the simulation framework of Finite Difference Time Domain (FDTD) with axis-aligned staircase boundaries resulting from a voxelization process, the voxelization-based uncertainty propagating in the HRTF-captured sound field is quantified for one solid and two surface voxelization algorithms. Simulated results utilizing a laser-scanned mesh of Knowles Electronics Manikin for Acoustic Research (KEMAR) show that in the context of complex geometries with local topology comparable to grid spacing such as the human pinna, the voxelization-related uncertainties in simulations emerge at lower frequencies than the generally used accuracy bandwidths. Numerical simulations show that the voxelization process induces both random error and algorithm-dependent bias in the simulated HRTF spectral features. Frequencies fr below which the random error is bounded by various dB thresholds are estimated and predicted. Particular shortcomings of the used voxelization algorithms are identified and the influence of the surface impedance on the induced errors is studied. Simulations are also validated against measurements. PMID:27250145

  16. 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.

  17. 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. PMID:24859803

  18. 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.

  19. 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

  20. 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

  1. 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

  2. A comparison of voxel and surface based cortical thickness estimation methods.

    PubMed

    Clarkson, Matthew J; Cardoso, M Jorge; Ridgway, Gerard R; Modat, Marc; Leung, Kelvin K; Rohrer, Jonathan D; Fox, Nick C; Ourselin, Sébastien

    2011-08-01

    Cortical thickness estimation performed in-vivo via magnetic resonance imaging is an important technique for the diagnosis and understanding of the progression of neurodegenerative diseases. Currently, two different computational paradigms exist, with methods generally classified as either surface or voxel-based. This paper provides a much needed comparison of the surface-based method FreeSurfer and two voxel-based methods using clinical data. We test the effects of computing regional statistics using two different atlases and demonstrate that this makes a significant difference to the cortical thickness results. We assess reproducibility, and show that FreeSurfer has a regional standard deviation of thickness difference on same day scans that is significantly lower than either a Laplacian or Registration based method and discuss the trade off between reproducibility and segmentation accuracy caused by bending energy constraints. We demonstrate that voxel-based methods can detect similar patterns of group-wise differences as well as FreeSurfer in typical applications such as producing group-wise maps of statistically significant thickness change, but that regional statistics can vary between methods. We use a Support Vector Machine to classify patients against controls and did not find statistically significantly different results with voxel based methods compared to FreeSurfer. Finally we assessed longitudinal performance and concluded that currently FreeSurfer provides the most plausible measure of change over time, with further work required for voxel based methods. PMID:21640841

  3. 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.

  4. 3D dose distribution calculation in a voxelized human phantom by means of Monte Carlo method.

    PubMed

    Abella, V; Miró, R; Juste, B; Verdú, G

    2010-01-01

    The aim of this work is to provide the reconstruction of a real human voxelized phantom by means of a MatLab program and the simulation of the irradiation of such phantom with the photon beam generated in a Theratron 780 (MDS Nordion) (60)Co radiotherapy unit, by using the Monte Carlo transport code MCNP (Monte Carlo N-Particle), version 5. The project results in 3D dose mapping calculations inside the voxelized antropomorphic head phantom. The program provides the voxelization by first processing the CT slices; the process follows a two-dimensional pixel and material identification algorithm on each slice and three-dimensional interpolation in order to describe the phantom geometry via small cubic cells, resulting in an MCNP input deck format output. Dose rates are calculated by using the MCNP5 tool FMESH, superimposed mesh tally, which gives the track length estimation of the particle flux in units of particles/cm(2). Furthermore, the particle flux is converted into dose by using the conversion coefficients extracted from the NIST Physical Reference Data. The voxelization using a three-dimensional interpolation technique in combination with the use of the FMESH tool of the MCNP Monte Carlo code offers an optimal simulation which results in 3D dose mapping calculations inside anthropomorphic phantoms. This tool is very useful in radiation treatment assessments, in which voxelized phantoms are widely utilized. PMID:19892556

  5. 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.

  6. 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

  7. Treating voxel geometries in radiation protection dosimetry with a patched version of the Monte Carlo codes MCNP and MCNPX.

    PubMed

    Burn, K W; Daffara, C; Gualdrini, G; Pierantoni, M; Ferrari, P

    2007-01-01

    The question of Monte Carlo simulation of radiation transport in voxel geometries is addressed. Patched versions of the MCNP and MCNPX codes are developed aimed at transporting radiation both in the standard geometry mode and in the voxel geometry treatment. The patched code reads an unformatted FORTRAN file derived from DICOM format data and uses special subroutines to handle voxel-to-voxel radiation transport. The various phases of the development of the methodology are discussed together with the new input options. Examples are given of employment of the code in internal and external dosimetry and comparisons with results from other groups are reported. PMID:17038404

  8. Pixel patterns for voxels in a contact-type three-dimensional imaging system for full-parallax image display

    SciTech Connect

    Son, Jung-Young; Saveljev, Vladmir V.; Javidi, Bahram; Kim, Dae-Sik; Park, Min-Chul

    2006-06-20

    Incomplete voxels, which can be seen only at a part of the viewing zone's cross section in the optical configuration of a full parallax multiview imaging system based on a two-dimensional point light source array, are identified. Their corresponding pixel patterns are found to maximize the space where the voxels can exist in the configuration and to increase the voxel resolution of the displayable three-dimensional images. Furthermore, the pixel patterns for the rhomb-shaped pixel cells are also defined, and some problems related to voxel-based image synthesis are discussed.

  9. The DosS-DosT/DosR Mycobacterial Sensor System.

    PubMed

    Sivaramakrishnan, Santhosh; de Montellano, Paul R Ortiz

    2013-01-01

    DosS/DosR is a two-component regulatory system in which DosS, a heme-containing sensor also known as DevS, under certain conditions undergoes autophosphorylation and then transfers the phosphate to DosR, a DNA-binding protein that controls the entry of Mycobacterium tuberculosis and other mycobacteria into a latent, dormant state. DosT, a second sensor closely related to DosS, is present in M. tuberculosis and participates in the control of the dormancy response mediated by DosR. The binding of phosphorylated DosR to DNA initiates the expression of approximately fifty dormancy-linked genes. DosT is accepted to be a gas sensor that is activated in the ferrous state by the absence of an oxygen ligand or by the binding of NO or CO. DosS functions in a similar fashion as a gas sensor, but contradictory evidence has led to the suggestion that it also functions as a redox state sensor. This review focuses on the structure, biophysical properties, and function of the DosS/DosT heme sensors. PMID:25002970

  10. The DosS-DosT/DosR Mycobacterial Sensor System

    PubMed Central

    Sivaramakrishnan, Santhosh; Ortiz de Montellano, Paul R.

    2013-01-01

    DosS/DosR is a two-component regulatory system in which DosS, a heme-containing sensor also known as DevS, under certain conditions undergoes autophosphorylation and then transfers the phosphate to DosR, a DNA-binding protein that controls the entry of Mycobacterium tuberculosis and other mycobacteria into a latent, dormant state. DosT, a second sensor closely related to DosS, is present in M. tuberculosis and participates in the control of the dormancy response mediated by DosR. The binding of phosphorylated DosR to DNA initiates the expression of approximately fifty dormancy-linked genes. DosT is accepted to be a gas sensor that is activated in the ferrous state by the absence of an oxygen ligand or by the binding of NO or CO. DosS functions in a similar fashion as a gas sensor, but contradictory evidence has led to the suggestion that it also functions as a redox state sensor. This review focuses on the structure, biophysical properties, and function of the DosS/DosT heme sensors. PMID:25002970

  11. 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.

  12. 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.

  13. Fast and robust optical flow for time-lapse microscopy using super-voxels

    PubMed Central

    Amat, Fernando; Myers, Eugene W.; Keller, Philipp J.

    2013-01-01

    Motivation: Optical flow is a key method used for quantitative motion estimation of biological structures in light microscopy. It has also been used as a key module in segmentation and tracking systems and is considered a mature technology in the field of computer vision. However, most of the research focused on 2D natural images, which are small in size and rich in edges and texture information. In contrast, 3D time-lapse recordings of biological specimens comprise up to several terabytes of image data and often exhibit complex object dynamics as well as blurring due to the point-spread-function of the microscope. Thus, new approaches to optical flow are required to improve performance for such data. Results: We solve optical flow in large 3D time-lapse microscopy datasets by defining a Markov random field (MRF) over super-voxels in the foreground and applying motion smoothness constraints between super-voxels instead of voxel-wise. This model is tailored to the specific characteristics of light microscopy datasets: super-voxels help registration in textureless areas, the MRF over super-voxels efficiently propagates motion information between neighboring cells and the background subtraction and super-voxels reduce the dimensionality of the problem by an order of magnitude. We validate our approach on large 3D time-lapse datasets of Drosophila and zebrafish development by analyzing cell motion patterns. We show that our approach is, on average, 10 × faster than commonly used optical flow implementations in the Insight Tool-Kit (ITK) and reduces the average flow end point error by 50% in regions with complex dynamic processes, such as cell divisions. Availability: Source code freely available in the Software section at http://janelia.org/lab/keller-lab. Contact: amatf@janelia.hhmi.org or kellerp@janelia.hhmi.org Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23242263

  14. Evaluation of a voxelized model based on DCE-MRI for tracer transport in tumor.

    PubMed

    Magdoom, K N; Pishko, Gregory L; Kim, Jung Hwan; Sarntinoranont, Malisa

    2012-09-01

    Recent advances in the treatment of cancer involving therapeutic agents have shown promising results. However, treatment efficacy can be limited due to inadequate and uneven uptake in solid tumors, thereby making the prediction of drug transport important for developing effective therapeutic strategies. In this study, a patient-specific computational porous media model (voxelized model) was developed for predicting the interstitial flow field and distribution of a systemically delivered magnetic resonance (MR) visible tracer in a tumor. The benefits of a voxel approach include less labor and less computational time (approximately an order of magnitude reduction compared to the traditional computational fluid dynamics (CFD) approach developed earlier by our group). The model results were compared with that obtained from a previous approach based on unstructured meshes along with MR-measured tracer concentration data within tumors, using statistical analysis and qualitative representations. The statistical analysis indicated the similarity between the structured and unstructured models' results with a low root mean square error (RMS) and a high correlation coefficient. The voxelized model captured features of the flow field and tracer distribution such as high interstitial fluid pressure inside the tumor and the heterogeneous distribution of the tracer. Predictions of tracer distribution by the voxelized approach also resulted in low RMS error when compared with MR-measured data over a 1 h time course. The similarity in the voxelized model results with experiment and the nonvoxelized model predictions were maintained across three different tumors. Overall, the voxelized model serves as a reliable and swift alternative to approaches using unstructured meshes in predicting extracellular transport within tumors. PMID:22938371

  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. High performance cone-beam spiral backprojection with voxel-specific weighting.

    PubMed

    Steckmann, Sven; Knaup, Michael; Kachelriess, Marc

    2009-06-21

    Cone-beam spiral backprojection is computationally highly demanding. At first sight, the backprojection requirements are similar to those of cone-beam backprojection from circular scans such as it is performed in the widely used Feldkamp algorithm. However, there is an additional complication: the illumination of each voxel, i.e. the range of angles the voxel is seen by the x-ray cone, is a complex function of the voxel position. In general, one needs to multiply a voxel-specific weight w(x, y, z, alpha) prior to adding a projection from angle alpha to a voxel at position x, y, z. Often, the weight function has no analytically closed form and must be numerically determined. Storage of the weights is prohibitive since the amount of memory required equals the number of voxels per spiral rotation times the number of projections a voxel receives contributions and therefore is in the order of up to 10(12) floating point values for typical spiral scans. We propose a new algorithm that combines the spiral symmetry with the ability of today's 64 bit operating systems to store large amounts of precomputed weights, even above the 4 GB limit. Our trick is to backproject into slices that are rotated in the same manner as the spiral trajectory rotates. Using the spiral symmetry in this way allows one to exploit data-level paralellism and thereby to achieve a very high level of vectorization. An additional postprocessing step rotates these slices back to normal images. Our new backprojection algorithm achieves up to 17 giga voxel updates per second on our systems that are equipped with four standard Intel X7460 hexa core CPUs (Intel Xeon 7300 platform, 2.66 GHz, Intel Corporation). This equals the reconstruction of 344 images per second assuming that each slice consists of 512 x 512 pixels and receives contributions from 512 projections. Thereby, it is an order of magnitude faster than a highly optimized code that does not make use of the spiral symmetry. In its present version

  17. High performance cone-beam spiral backprojection with voxel-specific weighting

    NASA Astrophysics Data System (ADS)

    Steckmann, Sven; Knaup, Michael; Kachelrieß, Marc

    2009-06-01

    Cone-beam spiral backprojection is computationally highly demanding. At first sight, the backprojection requirements are similar to those of cone-beam backprojection from circular scans such as it is performed in the widely used Feldkamp algorithm. However, there is an additional complication: the illumination of each voxel, i.e. the range of angles the voxel is seen by the x-ray cone, is a complex function of the voxel position. In general, one needs to multiply a voxel-specific weight w(x, y, z, α) prior to adding a projection from angle α to a voxel at position x, y, z. Often, the weight function has no analytically closed form and must be numerically determined. Storage of the weights is prohibitive since the amount of memory required equals the number of voxels per spiral rotation times the number of projections a voxel receives contributions and therefore is in the order of up to 1012 floating point values for typical spiral scans. We propose a new algorithm that combines the spiral symmetry with the ability of today's 64 bit operating systems to store large amounts of precomputed weights, even above the 4 GB limit. Our trick is to backproject into slices that are rotated in the same manner as the spiral trajectory rotates. Using the spiral symmetry in this way allows one to exploit data-level paralellism and thereby to achieve a very high level of vectorization. An additional postprocessing step rotates these slices back to normal images. Our new backprojection algorithm achieves up to 17 giga voxel updates per second on our systems that are equipped with four standard Intel X7460 hexa core CPUs (Intel Xeon 7300 platform, 2.66 GHz, Intel Corporation). This equals the reconstruction of 344 images per second assuming that each slice consists of 512 × 512 pixels and receives contributions from 512 projections. Thereby, it is an order of magnitude faster than a highly optimized code that does not make use of the spiral symmetry. In its present version, the

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

    PubMed

    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

  19. The Relevance Voxel Machine (RVoxM): A Bayesian Method for Image-based Prediction

    PubMed Central

    Sabuncu, Mert R.; Leemput, Koen Van

    2012-01-01

    This paper presents the Relevance Voxel Machine (RVoxM), a Bayesian multivariate pattern analysis (MVPA) algorithm that is specifically designed for making predictions based upon image data. In contrast to generic MVPA algorithms that have often been used for this purpose, the method is designed to utilize a small number of spatially clustered sets of voxels that are particularly suited for clinical interpretation. RVoxM automatically tunes all its free parameters during the training phase, and offers the additional advantage of producing probabilistic prediction outcomes. Experiments on age prediction from structural brain MRI indicate that RVoxM yields biologically meaningful models that provide excellent predictive accuracy. PMID:22003689

  20. 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. PMID:26519793

  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. 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.

  3. 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. PMID:25314558

  4. 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…

  5. Organ dose conversion coefficients for external photon irradiation using the Chinese voxel phantom (CVP).

    PubMed

    Li, Junli; Qiu, Rui; Zhang, Zhan; Liu, Liye; Zeng, Zhi; Bi, Lei; Li, Wenqian

    2009-07-01

    A set of conversion coefficients from kerma free-in-air to the organ absorbed dose are presented for external monoenergetic photon beams from 10 keV to 10 MeV based on a whole-body, Chinese adult male voxel phantom. This computational phantom, called the Chinese voxel phantom (CVP), including totally 23 organs, was developed from magnetic resonance imaging of a young healthy Chinese man at a resolution of 2 x 2 mm. Compared with the ICRP Reference Man, more than half of the organs or tissues in the CVP show mass differences of more than 20. Monte Carlo simulations with MCNP code were carried out to calculate the organ dose conversion coefficients. Irradiation conditions include anterior-posterior, posterior-anterior (PA), right-lateral, left-lateral, rotational and isotropic geometries. Organ dose conversion coefficients from this study are compared with the data from the Asian voxel phantoms Visible Chinese Human and KORMAN. These data sets agree with each other within 10% for photon energy >5 MeV. However, discrepancies of 34-63% were observed for organs of the alimentary tract, such as the oesophagus and stomach, those of the urinary system, such as the bladder wall and thyroid, especially at low photon energy range and PA geometry. These results suggest that the anatomical variation within the Chinese population, as represented by these adult male voxel phantoms, can lead to uncertainties when a standard phantom is used for the entire population. PMID:19457976

  6. 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.

  7. 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

  8. 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. PMID:26216052

  9. 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.

  10. 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.

  11. 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.

  12. Efficient simulation of voxelized phantom in GATE with embedded SimSET multiple photon history generator

    NASA Astrophysics Data System (ADS)

    Lin, Hsin-Hon; Chuang, Keh-Shih; Lin, Yi-Hsing; Ni, Yu-Ching; Wu, Jay; Jan, Meei-Ling

    2014-10-01

    GEANT4 Application for Tomographic Emission (GATE) is a powerful Monte Carlo simulator that combines the advantages of the general-purpose GEANT4 simulation code and the specific software tool implementations dedicated to emission tomography. However, the detailed physical modelling of GEANT4 is highly computationally demanding, especially when tracking particles through voxelized phantoms. To circumvent the relatively slow simulation of voxelized phantoms in GATE, another efficient Monte Carlo code can be used to simulate photon interactions and transport inside a voxelized phantom. The simulation system for emission tomography (SimSET), a dedicated Monte Carlo code for PET/SPECT systems, is well-known for its efficiency in simulation of voxel-based objects. An efficient Monte Carlo workflow integrating GATE and SimSET for simulating pinhole SPECT has been proposed to improve voxelized phantom simulation. Although the workflow achieves a desirable increase in speed, it sacrifices the ability to simulate decaying radioactive sources such as non-pure positron emitters or multiple emission isotopes with complex decay schemes and lacks the modelling of time-dependent processes due to the inherent limitations of the SimSET photon history generator (PHG). Moreover, a large volume of disk storage is needed to store the huge temporal photon history file produced by SimSET that must be transported to GATE. In this work, we developed a multiple photon emission history generator (MPHG) based on SimSET/PHG to support a majority of the medically important positron emitters. We incorporated the new generator codes inside GATE to improve the simulation efficiency of voxelized phantoms in GATE, while eliminating the need for the temporal photon history file. The validation of this new code based on a MicroPET R4 system was conducted for 124I and 18F with mouse-like and rat-like phantoms. Comparison of GATE/MPHG with GATE/GEANT4 indicated there is a slight difference in energy

  13. Efficient simulation of voxelized phantom in GATE with embedded SimSET multiple photon history generator.

    PubMed

    Lin, Hsin-Hon; Chuang, Keh-Shih; Lin, Yi-Hsing; Ni, Yu-Ching; Wu, Jay; Jan, Meei-Ling

    2014-10-21

    GEANT4 Application for Tomographic Emission (GATE) is a powerful Monte Carlo simulator that combines the advantages of the general-purpose GEANT4 simulation code and the specific software tool implementations dedicated to emission tomography. However, the detailed physical modelling of GEANT4 is highly computationally demanding, especially when tracking particles through voxelized phantoms. To circumvent the relatively slow simulation of voxelized phantoms in GATE, another efficient Monte Carlo code can be used to simulate photon interactions and transport inside a voxelized phantom. The simulation system for emission tomography (SimSET), a dedicated Monte Carlo code for PET/SPECT systems, is well-known for its efficiency in simulation of voxel-based objects. An efficient Monte Carlo workflow integrating GATE and SimSET for simulating pinhole SPECT has been proposed to improve voxelized phantom simulation. Although the workflow achieves a desirable increase in speed, it sacrifices the ability to simulate decaying radioactive sources such as non-pure positron emitters or multiple emission isotopes with complex decay schemes and lacks the modelling of time-dependent processes due to the inherent limitations of the SimSET photon history generator (PHG). Moreover, a large volume of disk storage is needed to store the huge temporal photon history file produced by SimSET that must be transported to GATE. In this work, we developed a multiple photon emission history generator (MPHG) based on SimSET/PHG to support a majority of the medically important positron emitters. We incorporated the new generator codes inside GATE to improve the simulation efficiency of voxelized phantoms in GATE, while eliminating the need for the temporal photon history file. The validation of this new code based on a MicroPET R4 system was conducted for (124)I and (18)F with mouse-like and rat-like phantoms. Comparison of GATE/MPHG with GATE/GEANT4 indicated there is a slight difference in energy

  14. Voxel Size and Measures of Individual Resorption Cavities in Three-Dimensional Images of Cancellous Bone

    PubMed Central

    Tkachenko, E.V.; Slyfield, C.R.; Tomlinson, R.E.; Daggett, J.R.; Wilson, D.L.; Hernandez, C.J.

    2009-01-01

    Cavities formed by osteoclasts on the surface of cancellous bone during bone remodeling (resorption cavities) are believed to act as stress risers and impair cancellous bone strength and stiffness. Although resorption cavities are readily detected as eroded surfaces in histology sections, identification of resorption cavities in three-dimensional images of cancellous bone has been rare. Here we use sub-micron resolution images of rat lumbar vertebral cancellous bone obtained through serial milling (n=5) to determine how measures of the number and surface area of resorption cavities are influenced by image resolution. Three-dimensional images of a 1mm cube of cancellous bone were collected at 0.7 X 0.7 X 5.0 μm/voxel using fluorescence based serial milling and uniformly coarsened to four other resolutions ranging from 1.4 X 1.4 X 5.0 to 11.2 X 11.2 X 10 μm/voxel. Cavities were identified in the three-dimensional image as an indentation on the cancellous bone surface and were confirmed as eroded surfaces by viewing two-dimensional cross-sections (mimicking histology techniques). The number of cavities observed in the 0.7 X 0.7 X 5.0 μm/voxel images (22.0 ± 1.43, mean ± SD) was not significantly different from that in the 1.4 X 1.4 X 5.0 μm/voxel images (19.2 ± 2.59) and an average of 79% of the cavities observed at both of these resolutions were coincident. However, at lower resolutions, cavity detection was confounded by low sensitivity (<20%) and high false positive rates (>40%). Our results demonstrate that when image voxel size exceeds 1.4 X 1.4 X 5.0 μm/voxel identification of resorption cavities by bone surface morphology is highly inaccurate. Experimental and computational studies of resorption cavities in three-dimensional images of cancellous bone may therefore require images to be collected at resolutions of 1.4 μm/pixel in-plane or better to ensure consistent identification of resorption cavities. PMID:19482097

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

    NASA Astrophysics Data System (ADS)

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

    2012-06-01

    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 efficiency of navigation algorithms on currently available voxel geometry parameterizations in the Monte Carlo simulation package Geant4: G4VPVParameterisation, G4VNestedParameterisation and G4PhantomParameterisation, the last 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 made 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 runtime ratio for G4PhantomParameterisation with and without boundary skipping for our heterogeneous data was equal to 0.97: 1. The calculated dose distributions agreed with the reference distribution for all but the G4

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

    PubMed

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

    2012-06-01

    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 efficiency of navigation algorithms on currently available voxel geometry parameterizations in the Monte Carlo simulation package Geant4: G4VPVParameterisation, G4VNestedParameterisation and G4PhantomParameterisation, the last 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 made 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 runtime ratio for G4PhantomParameterisation with and without boundary skipping for our heterogeneous data was equal to 0.97: 1. The calculated dose distributions agreed with the reference distribution for all but the G4Phantom

  17. Prospective Motion Correction for Single-Voxel 1H MR Spectroscopy

    PubMed Central

    Keating, Brian; Deng, Weiran; Roddey, J. Cooper; White, Nathan; Dale, Anders; Stenger, V. Andrew; Ernst, Thomas

    2010-01-01

    Head motion during 1H MR spectroscopy (MRS) acquisitions may compromise the quality and reliability of in vivo metabolite measurements. Therefore, a 3-plane image-based motion tracking module was integrated into a single-voxel 1H MRS (PRESS) sequence. A series of 3 orthogonal spiral navigator images were acquired immediately prior to the MRS water suppression module in order to estimate head motion. By applying the appropriate rotations and translations, the MRS voxel position can be updated such that it remains stationary with respect to the brain. Frequency and phase corrections were applied during post-processing to reduce line-width and restore coherent averaging. Spectra acquired during intentional head motion in 11 volunteers demonstrate reduced lipid contamination and increased spectral reproducibility when motion correction is applied. PMID:20806374

  18. A generalization of voxel-wise procedures for high-dimensional statistical inference using ridge regression

    NASA Astrophysics Data System (ADS)

    Sjöstrand, Karl; Cardenas, Valerie A.; Larsen, Rasmus; Studholme, Colin

    2008-03-01

    Whole-brain morphometry denotes a group of methods with the aim of relating clinical and cognitive measurements to regions of the brain. Typically, such methods require the statistical analysis of a data set with many variables (voxels and exogenous variables) paired with few observations (subjects). A common approach to this ill-posed problem is to analyze each spatial variable separately, dividing the analysis into manageable subproblems. A disadvantage of this method is that the correlation structure of the spatial variables is not taken into account. This paper investigates the use of ridge regression to address this issue, allowing for a gradual introduction of correlation information into the model. We make the connections between ridge regression and voxel-wise procedures explicit and discuss relations to other statistical methods. Results are given on an in-vivo data set of deformation based morphometry from a study of cognitive decline in an elderly population.

  19. Effects of CT based Voxel Phantoms on Dose Distribution Calculated with Monte Carlo Method

    NASA Astrophysics Data System (ADS)

    Chen, Chaobin; Huang, Qunying; Wu, Yican

    2005-04-01

    A few CT-based voxel phantoms were produced to investigate the sensitivity of Monte Carlo simulations of x-ray beam and electron beam to the proportions of elements and the mass densities of the materials used to express the patient's anatomical structure. The human body can be well outlined by air, lung, adipose, muscle, soft bone and hard bone to calculate the dose distribution with Monte Carlo method. The effects of the calibration curves established by using various CT scanners are not clinically significant based on our investigation. The deviation from the values of cumulative dose volume histogram derived from CT-based voxel phantoms is less than 1% for the given target.

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

    PubMed Central

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

    2015-01-01

    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. PMID:25451480

  1. 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. PMID:25451480

  2. Specific absorbed fraction for Korean adult voxel phantom from internal photon source.

    PubMed

    Lee, C; Park, S; Lee, J K

    2007-01-01

    Absorbed fraction (AF) and specific absorbed fraction (SAF) are crucial values for the calculation of radionuclide S-values and consequently for internal dose estimates. The formalism of the Medical Internal Radiation Dose (MIRD) committee of the Society of Nuclear Medicine (SNM) has been utilised as a standard in the calculation of individual organ doses for biologically distributed radionuclides and for different types of radiation. Although those quantities are highly sensitive to individual anatomical difference, the SAF dataset calculated by Caucasian-based stylised phantoms have been applied to Korean population until now. This study was intended to calculate the SAFs by using realistic Korean voxel phantom and Monte Carlo transport technique for the first time and compare the results with those of the existing Caucasian-based data and the Korean stylised phantom published recently. The up-to-date realistic Korean voxel phantom, KTMAN-2, which was developed from computed tomography (CT) images of an average Korean adult male, was employed for Monte Carlo calculation using EGSnrc user-code, developed for the purpose of this study. The SAFs for 32 target organs and tissues from the photon source, uniformly deposited in a total of 37 source organs and tissues, were calculated from KTMAN-2. The results were compared with those for an adult phantom of Oak Ridge National Laboratory (ORNL) and Korean adult stylised phantom. Two major reasons of discrepancy were analysed: (1) racial difference between the Korean and the Caucasian and (2) anatomical difference between stylised and voxel phantoms. When the source organ was identical to the target organ, difference in SAF caused by the difference in target-organ mass between the Korean and the Caucasian phantoms was mainly observed. When the source and target organs were not identical, significant difference in SAF was observed which was mainly attributed to the difference in inter-organ distance and organ shape between

  3. 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

  4. 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

  5. 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.

  6. 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. PMID:24411557

  7. 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

  8. Voxel-based cervical spinal cord mapping of diffusion abnormalities in MS-related myelitis

    PubMed Central

    Kou, Nancy; Altmann, Daniel; Wheeler-Kingshott, Claudia A.M.; Thompson, Alan J.; Ciccarelli, Olga

    2014-01-01

    Objective: To apply a novel postprocessing voxel-based analysis for diffusion tensor imaging of the cervical spinal cord in multiple sclerosis (MS) in a prospective cross-sectional study. Methods: Fourteen patients with MS who were within 4 weeks of the onset of cervical myelitis (lesion C1-3) and 11 healthy controls underwent cervical spinal cord diffusion tensor imaging. Cervical spinal cord maps of fractional anisotropy (FA), mean diffusivity, radial diffusivity (RD), and axial diffusivity were registered and compared between patients and controls. Mean FA and RD values from significant thresholded clusters were regressed with clinical scores, after adjusting for cord area and age, to determine associations with physical disability. Results: Cord registrations for subjects were qualitatively assessed (scored out of 5) and those with low scores (1 or 2) were excluded from further analysis. Cord registration was considered good in 11 patients (6 females; mean age = 35.5 years) and 10 controls (6 females; mean age 44 years). Voxel-based comparisons showed patients with MS had lower FA and higher RD at C2-3 levels (left >right mainly in gray matter; p < 0.01, uncorrected). Extracted values of both FA and RD from thresholded clusters were significantly associated with greater disability measured using the Expanded Disability Status Scale and Timed 25-Foot Walk Test in patients with MS. Conclusions: Mapping diffusion abnormalities within the cervical spinal cord using a novel voxel-based approach can localize clinically relevant pathology. PMID:25186861

  9. 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.

  10. 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.

  11. Voxel significance mapping using local image variances in subtraction ictal SPET.

    PubMed

    Brinkmann, B H; O'Brien, T J; Webster, D B; Mullan, B P; Robins, P D; Robb, R A

    2000-06-01

    Subtraction ictal SPET co-registered to MRI (SISCOM) has been shown to aid epileptogenic localization and improve surgical outcome in partial epilepsy patients. This paper reports a method of identifying significant areas of epileptogenic activation in the SISCOM subtraction image, taking into account normal variation between sequential 99Tcm-ethyl cysteinate diethylester SPET scans of single individuals, and attempts to assess the clinical value of statistical mapping in subtraction SPET. Non-linear inter-subject registration is used to combine a group of subtraction images into a common anatomical framework. A map of the pixel intensity standard deviation values in the subtraction images is created, and this map is non-linearly registered to a patient's SISCOM subtraction image. Pixels in the patient subtraction image were then evaluated based upon the statistical characteristics of corresponding pixels in the atlas. SISCOM images created with the voxel variance method were rated higher in quality than the conventional image variance method in 15 patients. No difference in localization rate was observed between the voxel variance mapping and image variance methods. The voxel significance mapping method was shown to improve the quality of clinical SISCOM images. PMID:10894564

  12. An investigation of voxel geometries for MCNP-based radiation dose calculations.

    PubMed

    Zhang, Juying; Bednarz, Bryan; Xu, X George

    2006-11-01

    Voxelized geometry such as those obtained from medical images is increasingly used in Monte Carlo calculations of absorbed doses. One useful application of calculated absorbed dose is the determination of fluence-to-dose conversion factors for different organs. However, confusion still exists about how such a geometry is defined and how the energy deposition is best computed, especially involving a popular code, MCNP5. This study investigated two different types of geometries in the MCNP5 code, cell and lattice definitions. A 10 cm x 10 cm x 10 cm test phantom, which contained an embedded 2 cm x 2 cm x 2 cm target at its center, was considered. A planar source emitting parallel photons was also considered in the study. The results revealed that MCNP5 does not calculate total target volume for multi-voxel geometries. Therefore, tallies which involve total target volume must be divided by the user by the total number of voxels to obtain a correct dose result. Also, using planar source areas greater than the phantom size results in the same fluence-to-dose conversion factor. PMID:17023800

  13. 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. PMID:25594357

  14. Voxel-Wise Meta-Analysis of Gray Matter Changes in Amyotrophic Lateral Sclerosis

    PubMed Central

    Shen, Dongchao; Cui, Liying; Fang, Jia; Cui, Bo; Li, Dawei; Tai, Hongfei

    2016-01-01

    Background: Increasing neuroimaging studies have revealed gray matter (GM) anomalies of several brain regions by voxel-based morphometry (VBM) studies in patients with amyotrophic lateral sclerosis (ALS). A voxel-wise meta-analysis was conducted to integrate the reported studies to determine the consistent GM alterations in ALS based on VBM methods. Methods: Ovid Medline, Pubmed, Emabase, and BrainMap database were searched for relevant studies.Data were extracted by two independent researchers. Voxel-wise meta-analysis was performed using the effect-size signed differential mapping (ES-SDM) software. Results: Twenty-nine VBM studies comprising 638 subjects with ALS and 622 healthy controls (HCs) met inclusion criteria.The global GM volumes of ALS patients were significantly decreased compared with those of HCs. GM reductions in patients were mainly located in the right precentral gyrus, the left Rolandic operculum, the left lenticular nucleus and the right anterior cingulate/paracingulate gyri. The right precentral gyrus and the left inferior frontal gyrus might be potential anatomical biomarkers to evaluate the severity of the disease, and longer disease duration was associated with more GM atrophy in the left frontal aslant tract and the right precentral gyrus in ALS patients. Conclusion: The results support that ALS is a complex degenerative disease involving multisystems besides the motor system.The mechanism of asymmetric atrophy of the motor cortex and the implication of Rolandic operculum involvement in ALS need to be further elucidated in future studies. PMID:27065078

  15. 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.

  16. 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.

  17. 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

  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. CNMAN: a Chinese adult male voxel phantom constructed from color photographs of a visible anatomical data set.

    PubMed

    Zhang, Binquan; Ma, Jizeng; Liu, Liye; Cheng, Jianping

    2007-01-01

    A voxel phantom of Chinese adult male called CNMAN was constructed from color photographs of the first Chinese visible human data set, for radiation protection purpose. This data set was obtained from a 35-y-old Chinese male cadaver by a medical university in China. The man, 170 cm in height and 65 kg in weight, was dead without any pathological changes. The image size for transversal anatomical photographs of the whole body was 3072 x 2048. After the photographs were semi-automatically segmented, the voxel phantom (CNMAN) with a voxel size of 0.16 mm x 0.16 mm x 1 mm, consisting of 29 tissues or organs was constructed. Combined with the MCNP Monte Carlo transport code, preliminary results for radiation protection dosimetry were obtained based on this Chinese voxel phantom. PMID:17526909

  20. Intra-voxel heterogeneity influences the dose prescription for dose-painting with radiotherapy: a modelling study

    NASA Astrophysics Data System (ADS)

    F Petit, Steven; Dekker, André L. A. J.; Seigneuric, Renaud; Murrer, Lars; van Riel, Natal A. W.; Nordsmark, Marianne; Overgaard, Jens; Lambin, Philippe; Wouters, Bradly G.

    2009-04-01

    The purpose of this study was to increase the potential of dose redistribution by incorporating estimates of oxygen heterogeneity within imaging voxels for optimal dose determination. Cellular oxygen tension (pO2) distributions were estimated for imaging-size-based voxels by solving oxygen diffusion-consumption equations around capillaries placed at random locations. The linear-quadratic model was used to determine cell survival in the voxels as a function of pO2 and dose. The dose distribution across the tumour was optimized to yield minimal survival after 30 × 2 Gy fractions by redistributing the dose based on differences in oxygen levels. Eppendorf data of a series of 69 tumours were used as a surrogate of what might be expected from oxygen imaging datasets. Dose optimizations were performed both taking into account cellular heterogeneity in oxygenation within voxels and assuming a homogeneous cellular distribution of oxygen. Our simulations show that dose redistribution based on derived cellular oxygen distributions within voxels result in dose distributions that require less total dose to obtain the same degree of cell kill as dose distributions that were optimized with a model that considered voxels as homogeneous with respect to oxygen. Moderately hypoxic tumours are expected to gain most from dose redistribution. Incorporating cellular-based distributions of radiosensitivity into dose-planning algorithms theoretically improves the potential gains from dose redistribution algorithms.

  1. 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.

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

    NASA Astrophysics Data System (ADS)

    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. Multi-Parametric Representation of Voxel-Based Quantitative Magnetic Resonance Imaging

    PubMed Central

    Engström, Maria; Warntjes, Jan B. M.; Tisell, Anders; Landtblom, Anne-Marie; Lundberg, Peter

    2014-01-01

    The aim of the study was to explore the possibilities of multi-parametric representations of voxel-wise quantitative MRI data to objectively discriminate pathological cerebral tissue in patients with brain disorders. For this purpose, we recruited 19 patients with Multiple Sclerosis (MS) as benchmark samples and 19 age and gender matched healthy subjects as a reference group. The subjects were examined using quantitative Magnetic Resonance Imaging (MRI) measuring the tissue structure parameters: relaxation rates, R and R, and proton density. The resulting parameter images were normalized to a standard template. Tissue structure in MS patients was assessed by voxel-wise comparisons with the reference group and with correlation to a clinical measure, the Expanded Disability Status Scale (EDSS). The results were visualized by conventional geometric representations and also by multi-parametric representations. Data showed that MS patients had lower R and R, and higher proton density in periventricular white matter and in wide-spread areas encompassing central and sub-cortical white matter structures. MS-related tissue abnormality was highlighted in posterior white matter whereas EDSS correlation appeared especially in the frontal cortex. The multi-parameter representation highlighted disease-specific features. In conclusion, the proposed method has the potential to visualize both high-probability focal anomalies and diffuse tissue changes. Results from voxel-based statistical analysis, as exemplified in the present work, may guide radiologists where in the image to inspect for signs of disease. Future clinical studies must validate the usability of the method in clinical practice. PMID:25393722

  6. 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

  7. Imaging Lung Function in Mice Using SPECT/CT and Per-Voxel Analysis

    PubMed Central

    Jobse, Brian N.; Rhem, Rod G.; McCurry, Cory A. J. R.; Wang, Iris Q.; Labiris, N. Renée

    2012-01-01

    Chronic lung disease is a major worldwide health concern but better tools are required to understand the underlying pathologies. Ventilation/perfusion (V/Q) single photon emission computed tomography (SPECT) with per-voxel analysis allows for non-invasive measurement of regional lung function. A clinically adapted V/Q methodology was used in healthy mice to investigate V/Q relationships. Twelve week-old mice were imaged to describe normal lung function while 36 week-old mice were imaged to determine how age affects V/Q. Mice were ventilated with Technegas™ and injected with 99mTc-macroaggregated albumin to trace ventilation and perfusion, respectively. For both processes, SPECT and CT images were acquired, co-registered, and quantitatively analyzed. On a per-voxel basis, ventilation and perfusion were moderately correlated (R = 0.58±0.03) in 12 week old animals and a mean log(V/Q) ratio of −0.07±0.01 and standard deviation of 0.36±0.02 were found, defining the extent of V/Q matching. In contrast, 36 week old animals had significantly increased levels of V/Q mismatching throughout the periphery of the lung. Measures of V/Q were consistent across healthy animals and differences were observed with age demonstrating the capability of this technique in quantifying lung function. Per-voxel analysis and the ability to non-invasively assess lung function will aid in the investigation of chronic lung disease models and drug efficacy studies. PMID:22870297

  8. GPU-accelerated indirect boundary element method for voxel model analyses with fast multipole method

    NASA Astrophysics Data System (ADS)

    Hamada, Shoji

    2011-05-01

    An indirect boundary element method (BEM) that uses the fast multipole method (FMM) was accelerated using graphics processing units (GPUs) to reduce the time required to calculate a three-dimensional electrostatic field. The BEM is designed to handle cubic voxel models and is specialized to consider square voxel walls as boundary surface elements. The FMM handles the interactions among the surface charge elements and directly outputs surface integrals of the fields over each individual element. The CPU code was originally developed for field analysis in human voxel models derived from anatomical images. FMM processes are programmed using the NVIDIA Compute Unified Device Architecture (CUDA) with double-precision floating-point arithmetic on the basis of a shared pseudocode template. The electric field induced by DC-current application between two electrodes is calculated for two models with 499,629 (model 1) and 1,458,813 (model 2) surface elements. The calculation times were measured with a four-GPU configuration (two NVIDIA GTX295 cards) with four CPU cores (an Intel Core i7-975 processor). The times required by a linear system solver are 31 s and 186 s for models 1 and 2, respectively. The speed-up ratios of the FMM range from 5.9 to 8.2 for model 1 and from 5.0 to 5.6 for model 2. The calculation speed for element-interaction in this BEM analysis was comparable to that of particle-interaction using FMM on a GPU.

  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. 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

  11. 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.

  12. 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

  13. 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

  14. 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)

  15. 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

  16. 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.

  17. 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

  18. 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

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

    PubMed Central

    Acosta, Oscar; Drean, Gael; Ospina, Juan David; Simon, Antoine; Haigron, Pascal; Lafond, Caroline; De Crevoisier, Renaud

    2013-01-01

    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 80Gy to the prostate by IMRT. Within the patients presenting bleeding, a significant dose excess (6Gy on average, p<0.01) was found in a region of the anterior rectal wall. This region, close to the prostate (1cm), 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. PMID:23528429

  20. 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

  1. Improved DTI registration allows voxel-based analysis that outperforms tract-based spatial statistics.

    PubMed

    Schwarz, Christopher G; Reid, Robert I; Gunter, Jeffrey L; Senjem, Matthew L; Przybelski, Scott A; Zuk, Samantha M; Whitwell, Jennifer L; Vemuri, Prashanthi; Josephs, Keith A; Kantarci, Kejal; Thompson, Paul M; Petersen, Ronald C; Jack, Clifford R

    2014-07-01

    Tract-Based Spatial Statistics (TBSS) is a popular software pipeline to coregister sets of diffusion tensor Fractional Anisotropy (FA) images for performing voxel-wise comparisons. It is primarily defined by its skeleton projection step intended to reduce effects of local misregistration. A white matter "skeleton" is computed by morphological thinning of the inter-subject mean FA, and then all voxels are projected to the nearest location on this skeleton. Here we investigate several enhancements to the TBSS pipeline based on recent advances in registration for other modalities, principally based on groupwise registration with the ANTS-SyN algorithm. We validate these enhancements using simulation experiments with synthetically-modified images. When used with these enhancements, we discover that TBSS's skeleton projection step actually reduces algorithm accuracy, as the improved registration leaves fewer errors to warrant correction, and the effects of this projection's compromises become stronger than those of its benefits. In our experiments, our proposed pipeline without skeleton projection is more sensitive for detecting true changes and has greater specificity in resisting false positives from misregistration. We also present comparative results of the proposed and traditional methods, both with and without the skeleton projection step, on three real-life datasets: two comparing differing populations of Alzheimer's disease patients to matched controls, and one comparing progressive supranuclear palsy patients to matched controls. The proposed pipeline produces more plausible results according to each disease's pathophysiology. PMID:24650605

  2. 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

  3. Voxel-based mapping of brain hypometabolism in permanent amnesia with PET.

    PubMed

    Aupée, A M; Desgranges, B; Eustache, F; Lalevée, C; de la Sayette, V; Viader, F; Baron, J C

    2001-06-01

    In this study, we used voxel-based mapping methods to compare the resting cerebral metabolic rate of glucose (CMRglc) measured with PET in five patients with permanent amnesia (three with chronic Wernicke-Korsakoff and two with postanoxia syndrome) to that of nine healthy age-matched subjects. We assessed (i) a group pattern of relative hypometabolism; and (ii) the consistency of this group pattern, if any, in individual subjects, according to etiology. The results from the group analysis documented that permanent amnesia is associated with hypometabolism in the thalamus, posterior cingulate cortex, and mesial prefrontal cortex (near the anterior cingulate gyrus), bilaterally, as well as in the left supramarginal and middle temporal gyri. The individual analysis showed that this group pattern was found in essentially each patient, regardless of the cause of amnesia. Thus, permanent amnesia is subtended by dysfunction in structures belonging to Papez/limbic circuits as well as in left-hemisphere areas typically concerned with verbal functions, probably through a mechanism of thalamo-cortical disconnection and possibly involved in retrograde amnesia. The use of a voxel-based method allowed us to map a common network of synaptic dysfunction in a neuropsychological syndrome regardless of etiology. Our results indicate that this should be a powerful method in functional neuropsychology. PMID:11352622

  4. 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.

  5. Quantitative comparison of reconstruction methods for intra-voxel fiber recovery from diffusion MRI.

    PubMed

    Daducci, Alessandro; Canales-Rodríguez, Erick Jorge; Descoteaux, Maxime; Garyfallidis, Eleftherios; Gur, Yaniv; Lin, Ying-Chia; Mani, Merry; Merlet, Sylvain; Paquette, Michael; Ramirez-Manzanares, Alonso; Reisert, Marco; Reis Rodrigues, Paulo; Sepehrband, Farshid; Caruyer, Emmanuel; Choupan, Jeiran; Deriche, Rachid; Jacob, Mathews; Menegaz, Gloria; Prčkovska, Vesna; Rivera, Mariano; Wiaux, Yves; Thiran, Jean-Philippe

    2014-02-01

    Validation is arguably the bottleneck in the diffusion magnetic resonance imaging (MRI) community. This paper evaluates and compares 20 algorithms for recovering the local intra-voxel fiber structure from diffusion MRI data and is based on the results of the "HARDI reconstruction challenge" organized in the context of the "ISBI 2012" conference. Evaluated methods encompass a mixture of classical techniques well known in the literature such as diffusion tensor, Q-Ball and diffusion spectrum imaging, algorithms inspired by the recent theory of compressed sensing and also brand new approaches proposed for the first time at this contest. To quantitatively compare the methods under controlled conditions, two datasets with known ground-truth were synthetically generated and two main criteria were used to evaluate the quality of the reconstructions in every voxel: correct assessment of the number of fiber populations and angular accuracy in their orientation. This comparative study investigates the behavior of every algorithm with varying experimental conditions and highlights strengths and weaknesses of each approach. This information can be useful not only for enhancing current algorithms and develop the next generation of reconstruction methods, but also to assist physicians in the choice of the most adequate technique for their studies. PMID:24132007

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

    NASA Astrophysics Data System (ADS)

    Jjumba, Anthony; Dragićević, Suzana

    2016-05-01

    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.

  7. 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.

  8. 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

  9. An improved MCNP version of the NORMAN voxel phantom for dosimetry studies

    NASA Astrophysics Data System (ADS)

    Ferrari, P.; Gualdrini, G.

    2005-09-01

    In recent years voxel phantoms have been developed on the basis of tomographic data of real individuals allowing new sets of conversion coefficients to be calculated for effective dose. Progress in radiation studies brought ICRP to revise its recommendations and a new report, already circulated in draft form, is expected to change the actual effective dose evaluation method. In the present paper the voxel phantom NORMAN developed at HPA, formerly NRPB, was employed with MCNP Monte Carlo code. A modified version of the phantom, NORMAN-05, was developed to take into account the new set of tissues and weighting factors proposed in the cited ICRP draft. Air kerma to organ equivalent dose and effective dose conversion coefficients for antero-posterior and postero-anterior parallel photon beam irradiations, from 20 keV to 10 MeV, have been calculated and compared with data obtained in other laboratories using different numerical phantoms. Obtained results are in good agreement with published data with some differences for the effective dose calculated employing the proposed new tissue weighting factors set in comparison with previous evaluations based on the ICRP 60 report.

  10. Rhesus macaque brain morphometry: a methodological comparison of voxel-wise approaches.

    PubMed

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

    2010-03-01

    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) [42]) 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

  11. Voxel-based morphometry in eating disorders: correlation of psychopathology with grey matter volume.

    PubMed

    Joos, Andreas; Klöppel, Stefan; Hartmann, Armin; Glauche, Volkmar; Tüscher, Oliver; Perlov, Evgeniy; Saum, Barbara; Freyer, Tobias; Zeeck, Almut; Tebartz van Elst, Ludger

    2010-05-30

    Twenty-nine adult female patients with eating disorders (17 with bulimia nervosa, 12 with restrictive anorexia nervosa) were compared with 18 age-matched female healthy controls, using voxel-based morphometry. Restrictive anorexia nervosa patients showed a decrease of grey matter, particularly affecting the anterior cingulate cortex, frontal operculum, temporoparietal regions and the precuneus. By contrast, patients with bulimia nervosa did not differ from healthy controls. A positive correlation of "drive for thinness" and grey matter volume of the right inferior parietal lobe was found for both eating disorder groups. The strong reduction of grey matter volume in adult patients with restrictive anorexia nervosa is in line with results of adolescent patients. Contrary to other studies, this first voxel-based morphometry report of bulimic patients did not find any structural abnormalities. The inferior parietal cortex is a critical region for sensory integration of body and spatial perception, and the correlation of "drive for thinness" with grey matter volume of this region points to a neural correlate of this core psychopathological feature of eating disorders. PMID:20400273

  12. 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.

  13. An improved MCNP version of the NORMAN voxel phantom for dosimetry studies.

    PubMed

    Ferrari, P; Gualdrini, G

    2005-09-21

    In recent years voxel phantoms have been developed on the basis of tomographic data of real individuals allowing new sets of conversion coefficients to be calculated for effective dose. Progress in radiation studies brought ICRP to revise its recommendations and a new report, already circulated in draft form, is expected to change the actual effective dose evaluation method. In the present paper the voxel phantom NORMAN developed at HPA, formerly NRPB, was employed with MCNP Monte Carlo code. A modified version of the phantom, NORMAN-05, was developed to take into account the new set of tissues and weighting factors proposed in the cited ICRP draft. Air kerma to organ equivalent dose and effective dose conversion coefficients for antero-posterior and postero-anterior parallel photon beam irradiations, from 20 keV to 10 MeV, have been calculated and compared with data obtained in other laboratories using different numerical phantoms. Obtained results are in good agreement with published data with some differences for the effective dose calculated employing the proposed new tissue weighting factors set in comparison with previous evaluations based on the ICRP 60 report. PMID:16148395

  14. 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.

  15. 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

  16. 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.

  17. 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.

  18. Investigating structural brain changes of dehydration using voxel-based morphometry.

    PubMed

    Streitbürger, Daniel-Paolo; Möller, Harald E; Tittgemeyer, Marc; Hund-Georgiadis, Margret; Schroeter, Matthias L; Mueller, Karsten

    2012-01-01

    Dehydration can affect the volume of brain structures, which might imply a confound in volumetric and morphometric studies of normal or diseased brain. Six young, healthy volunteers were repeatedly investigated using three-dimensional T(1)-weighted magnetic resonance imaging during states of normal hydration, hyperhydration, and dehydration to assess volume changes in gray matter (GM), white matter (WM), and cerebrospinal fluid (CSF). The datasets were analyzed using voxel-based morphometry (VBM), a widely used voxel-wise statistical analysis tool, FreeSurfer, a fully automated volumetric segmentation measure, and SIENAr a longitudinal brain-change detection algorithm. A significant decrease of GM and WM volume associated with dehydration was found in various brain regions, most prominently, in temporal and sub-gyral parietal areas, in the left inferior orbito-frontal region, and in the extra-nuclear region. Moreover, we found consistent increases in CSF, that is, an expansion of the ventricular system affecting both lateral ventricles, the third, and the fourth ventricle. Similar degrees of shrinkage in WM volume and increase of the ventricular system have been reported in studies of mild cognitive impairment or Alzheimer's disease during disease progression. Based on these findings, a potential confound in GM and WM or ventricular volume studies due to the subjects' hydration state cannot be excluded and should be appropriately addressed in morphometric studies of the brain. PMID:22952926

  19. 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.

  20. 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

  1. 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

  2. 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

  3. 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

  4. 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.

  5. 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

  6. Voxel-based classification of FDG PET in dementia using inter-scanner normalization.

    PubMed

    Thiele, Frank; Young, Stewart; Buchert, Ralph; Wenzel, Fabian

    2013-08-15

    Statistical mapping of FDG PET brain images has become a common tool in differential diagnosis of patients with dementia. We present a voxel-based classification system of neurodegenerative dementias based on partial least squares (PLS). Such a classifier relies on image databases of normal controls and dementia cases as training data. Variations in PET image characteristics can be expected between databases, for example due to differences in instrumentation, patient preparation, and image reconstruction. This study evaluates (i) the impact of databases from different scanners on classification accuracy and (ii) a method to improve inter-scanner classification. Brain FDG PET databases from three scanners (A, B, C) at two clinical sites were evaluated. Diagnostic categories included normal controls (NC, nA=26, nB=20, nC=24 for each scanner respectively), Alzheimer's disease (AD, nA=44, nB=11, nC=16), and frontotemporal dementia (FTD, nA=13, nB=13, nC=5). Spatially normalized images were classified as NC, AD, or FTD using partial least squares. Supervised learning was employed to determine classifier parameters, whereby available data is sub-divided into training and test sets. Four different database setups were evaluated: (i) "in-scanner": training and test data from the same scanner, (ii) "x-scanner": training and test data from different scanners, (iii) "train other": train on both x-scanners, and (iv) "train all": train on all scanners. In order to moderate the impact of inter-scanner variations on image evaluation, voxel-by-voxel scaling was applied based on "ratio images". Good classification accuracy of on average 94% was achieved for the in-scanner setups. Accuracy deteriorated for setups with mismatched scanners (79-91%). Ratio-image normalization improved all results with mismatched scanners (85-92%). In conclusion, automatic classification of individual FDG PET in differential diagnosis of dementia is feasible. Accuracy can vary with respect to scanner or

  7. The calculation of SAR from limb current in the female voxel phantom, NAOMI.

    PubMed

    Dimbylow, P J

    2006-01-01

    Calculations of localised SAR in the legs and arms have been performed in a female voxel phantom, NAOMI. A finite difference method was used to solve the quasistatic potential equation from 0.1 to 80 MHz for a unit current injected into a limb. The relationship between limb current and SAR has been investigated. The values of localised SAR in the leg as a function of applied plane wave electric field are also predicted from the knowledge of limb currents calculated by the finite-difference time-domain (FDTD) method for whole-body exposure. Comparisons are made with the results of previous work for the normalised male model, NORMAN, and the implications for electromagnetic guidelines are discussed. PMID:16565198

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

    PubMed

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

    2016-03-01

    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. Volumetric and Voxel-Based Morphometry Findings in Autism Subjects With and Without Macrocephaly

    PubMed Central

    Bigler, Erin D.; Abildskov, Tracy J.; Petrie, Jo Ann; Johnson, Michael; Lange, Nicholas; Chipman, Jonathan; Lu, Jeffrey; McMahon, William; Lainhart, Janet E.

    2015-01-01

    This study sought to replicate Herbert et al. (2003a), which found increased overall white matter (WM) volume in subjects with autism, even after controlling for head size differences. To avoid the possibility that greater WM volume in autism is merely an epiphenomena of macrocephaly over-representation associated with the disorder, the current study included control subjects with benign macrocephaly. The control group also included subjects with a reading disability to insure cognitive heterogeneity. WM volume in autism was significantly larger, even when controlling for brain volume, rate of macrocephaly, and other demographic variables. Autism and controls differed little on whole-brain WM voxel-based morphometry (VBM) analyses suggesting that the overall increase in WM volume was non-localized. Autism subjects exhibited a differential pattern of IQ relationships with brain volumetry findings from controls. Current theories of brain overgrowth and their importance in the development of autism are discussed in the context of these findings. PMID:20446133

  10. 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.

  11. 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

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

    PubMed Central

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

    2015-01-01

    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. PMID:26151911

  13. 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

  14. 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

  15. Monte Carlo analysis of voxel resolution of off-axially distributed image sensing system

    NASA Astrophysics Data System (ADS)

    Zhang, Miao; Piao, Yongri; Cho, Myungjin

    2016-03-01

    In this paper, we present a generalization framework to analyze the effect of voxel resolution on Monte Carlo simulation for off-axially distributed image sensing (ODIS) system under fixed resource constraints. Our framework can evaluate the performance of ODIS systems based on various sensing parameters such as the slanted angle between the optical axis and the moving direction, the number of cameras, the pixel size, the distance between the optical axis and the point source plane and so on. We carry out Monte Carlo simulations based on this framework to evaluate ODIS system performance as a function of sensing parameters. To the best of our knowledge, this is the first report on quantitative analysis of ODIS systems under fixed resource constraints.

  16. Application of digital image processing for the generation of voxels phantoms for Monte Carlo simulation.

    PubMed

    Boia, L S; Menezes, A F; Cardoso, M A C; da Rosa, L A R; Batista, D V S; Cardoso, S C; Silva, A X; Facure, A

    2012-01-01

    This paper presents the application of a computational methodology for optimizing the conversion of medical tomographic images in voxel anthropomorphic models for simulation of radiation transport using the MCNP code. A computational system was developed for digital image processing that compresses the information from the DICOM medical image before it is converted to the Scan2MCNP software input file for optimization of the image data. In order to validate the computational methodology, a radiosurgery treatment simulation was performed using the Alderson Rando phantom and the acquisition of DICOM images was performed. The simulation results were compared with data obtained with the BrainLab planning system. The comparison showed good agreement for three orthogonal treatment beams of (60)Co gamma radiation. The percentage differences were 3.07%, 0.77% and 6.15% for axial, coronal and sagital projections, respectively. PMID:21945017

  17. Comparison between voxelized, volumized and analytical phantoms applied to radiotherapy simulation with Monte Carlo.

    PubMed

    Abella, V; Miro, R; Juste, B; Verdu, G

    2009-01-01

    The purpose of this paper is to provide a comparison between the different methods utilized for building up anthropomorphic phantoms in Radiotherapy Treatment Plans. A simplified model of the Snyder Head Phantom was used in order to construct an analytical, voxelized and volumized phantom, throughout a segmentation program and different algorithms programmed in Matlab code. The irradiation of the resulting phantoms was simulated with the MCNP5 (Monte Carlo N-Particle) transport code, version 5, and the calculations presented in particle flux maps inside the phantoms by utilizing the FMESH tool, superimposed mesh tally. The different variables involved in the simulation were analyzed, like particle flux, MCNP standard deviation and real simulation CPU time cost. In the end the volumized model resulted to have the largest computer time cost and bigger discrepancies in the particle flux distribution. PMID:19964509

  18. The relationship between trait positive empathy and brain structure: a voxel-based morphometry study.

    PubMed

    Yue, Tong; Pan, Weigang; Huang, Xiting

    2016-04-13

    Although studies relating to positive empathy have received increased attention in recent years, no studies have been carried out to explore the neural basis of positive empathy. Using a voxel-based morphometry analysis, this study investigates the relationship between trait positive empathy (as measured by the Positive Empathy Scale) and its association with brain structure in 86 healthy college students. The results indicate that an individual's ability to show positive empathy is positively correlated with the volume of gray matter in the right insula, left anterior cingulate cortex, dorsolateral prefrontal cortex, and medial prefrontal cortex. It may be suggested that the differences between the abilities of emotion processing and regulating play important roles in shaping an individual's positive empathy traits from the perspective of brain morphometry. PMID:26963166

  19. 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.

  20. 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.

  1. Whole-body voxel phantoms of paediatric patients--UF Series B.

    PubMed

    Lee, Choonik; Lee, Choonsik; Williams, Jonathan L; Bolch, Wesley E

    2006-09-21

    Following the previous development of the head and torso voxel phantoms of paediatric patients for use in medical radiation protection (UF Series A), a set of whole-body voxel phantoms of paediatric patients (9-month male, 4-year female, 8-year female, 11-year male and 14-year male) has been developed through the attachment of arms and legs from segmented CT images of a healthy Korean adult (UF Series B). Even though partial-body phantoms (head-torso) may be used in a variety of medical dose reconstruction studies where the extremities are out-of-field or receive only very low levels of scatter radiation, whole-body phantoms play important roles in general radiation protection and in nuclear medicine dosimetry. Inclusion of the arms and legs is critical for dosimetry studies of paediatric patients due to the presence of active bone marrow within the extremities of children. While the UF Series A phantoms preserved the body dimensions and organ masses as seen in the original patients who were scanned, comprehensive adjustments were made for the Series B phantoms to better match International Commission on Radiological Protection (ICRP) age-interpolated reference body masses, body heights, sitting heights and internal organ masses. The CT images of arms and legs of a Korean adult were digitally rescaled and attached to each phantom of the UF series. After completion, the resolutions of the phantoms for the 9-month, 4-year, 8-year, 11-year and 14-year were set at 0.86 mm x 0.86 mm x 3.0 mm, 0.90 mm x 0.90 mm x 5.0 mm, 1.16 mm x 1.16 mm x 6.0 mm, 0.94 mm x 0.94 mm x 6.00 mm and 1.18 mm x 1.18 mm x 6.72 mm, respectively. PMID:16953048

  2. 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.

  3. Whole-body voxel phantoms of paediatric patients—UF Series B

    NASA Astrophysics Data System (ADS)

    Lee, Choonik; Lee, Choonsik; Williams, Jonathan L.; Bolch, Wesley E.

    2006-09-01

    Following the previous development of the head and torso voxel phantoms of paediatric patients for use in medical radiation protection (UF Series A), a set of whole-body voxel phantoms of paediatric patients (9-month male, 4-year female, 8-year female, 11-year male and 14-year male) has been developed through the attachment of arms and legs from segmented CT images of a healthy Korean adult (UF Series B). Even though partial-body phantoms (head-torso) may be used in a variety of medical dose reconstruction studies where the extremities are out-of-field or receive only very low levels of scatter radiation, whole-body phantoms play important roles in general radiation protection and in nuclear medicine dosimetry. Inclusion of the arms and legs is critical for dosimetry studies of paediatric patients due to the presence of active bone marrow within the extremities of children. While the UF Series A phantoms preserved the body dimensions and organ masses as seen in the original patients who were scanned, comprehensive adjustments were made for the Series B phantoms to better match International Commission on Radiological Protection (ICRP) age-interpolated reference body masses, body heights, sitting heights and internal organ masses. The CT images of arms and legs of a Korean adult were digitally rescaled and attached to each phantom of the UF series. After completion, the resolutions of the phantoms for the 9-month, 4-year, 8-year, 11-year and 14-year were set at 0.86 mm × 0.86 mm × 3.0 mm, 0.90 mm × 0.90 mm × 5.0 mm, 1.16 mm × 1.16 mm × 6.0 mm, 0.94 mm × 0.94 mm × 6.00 mm and 1.18 mm × 1.18 mm × 6.72 mm, respectively.

  4. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

    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.

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

    PubMed

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

    2013-04-21

    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. PMID:23528429

  7. 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

  8. 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.

  9. 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

  10. Voxel Based Analysis of T2 Hyperintensities in White Matter During Treatment for Childhood Leukemia

    PubMed Central

    Reddick, Wilburn E.; Glass, John O.; Johnson, David P.; Laningham, Fred H.; Pui, Ching-Hon

    2009-01-01

    Background and Purpose White matter (WM) hyperintensities on T2-weighted MRI are the most common imaging manifestation of neurotoxic effects of therapy for central nervous system prophylaxis in childhood acute lymphoblastic leukemia (ALL). This project uses voxel-based analyses of T2-weighted imaging of patients during treatment to identify which WM regions are preferentially damaged. Material and Methods Two sets of conventional T2-weighted axial images were acquired on a 1.5T MRI from 197 consecutive patients (85 female / 112 male; aged 1.0-18.9 years) enrolled on an institutional ALL treatment protocol. Images were acquired after completion of induction therapy and after the final of the four courses of intravenous high-dose methotrexate in consolidation therapy (3.9±0.8 months apart). Voxel-wise statistical testing of the incremental change between normalized longitudinal T2 images was performed with radiologist reading (normal or abnormal) and treatment risk-arm as covariates. Results Two highly significant bilateral clusters of T2 signal intensity change were identified in both one-group and two-group analyses. The regions were symmetrical in size, shape, and average signal intensity. Increased T2-weighted signal intensity from these regions both within and between examinations were nonlinear functions of age at examination and the difference between the examinations was greater for older subjects which received more intense therapy. Conclusion These analyses identified specific WM tracts involving predominantly the anterior, superior, and posterior corona radiata and superior longitudinal fasciculus, which were at increased risk of developing T2-weighted hyperintensities during therapy for childhood ALL. These vulnerable regions may be the etiology of subsequent cognitive difficulties consistently observed in survivors. PMID:19643920

  11. A voxel-based mouse for internal dose calculations using Monte Carlo simulations (MCNP)

    NASA Astrophysics Data System (ADS)

    Bitar, A.; Lisbona, A.; Thedrez, P.; Sai Maurel, C.; LeForestier, D.; Barbet, J.; Bardies, M.

    2007-02-01

    Murine models are useful for targeted radiotherapy pre-clinical experiments. These models can help to assess the potential interest of new radiopharmaceuticals. In this study, we developed a voxel-based mouse for dosimetric estimates. A female nude mouse (30 g) was frozen and cut into slices. High-resolution digital photographs were taken directly on the frozen block after each section. Images were segmented manually. Monoenergetic photon or electron sources were simulated using the MCNP4c2 Monte Carlo code for each source organ, in order to give tables of S-factors (in Gy Bq-1 s-1) for all target organs. Results obtained from monoenergetic particles were then used to generate S-factors for several radionuclides of potential interest in targeted radiotherapy. Thirteen source and 25 target regions were considered in this study. For each source region, 16 photon and 16 electron energies were simulated. Absorbed fractions, specific absorbed fractions and S-factors were calculated for 16 radionuclides of interest for targeted radiotherapy. The results obtained generally agree well with data published previously. For electron energies ranging from 0.1 to 2.5 MeV, the self-absorbed fraction varies from 0.98 to 0.376 for the liver, and from 0.89 to 0.04 for the thyroid. Electrons cannot be considered as 'non-penetrating' radiation for energies above 0.5 MeV for mouse organs. This observation can be generalized to radionuclides: for example, the beta self-absorbed fraction for the thyroid was 0.616 for I-131; absorbed fractions for Y-90 for left kidney-to-left kidney and for left kidney-to-spleen were 0.486 and 0.058, respectively. Our voxel-based mouse allowed us to generate a dosimetric database for use in preclinical targeted radiotherapy experiments.

  12. Attention enhances multi-voxel representation of novel objects in frontal, parietal and visual cortices.

    PubMed

    Woolgar, Alexandra; Williams, Mark A; Rich, Anina N

    2015-04-01

    Selective attention is fundamental for human activity, but the details of its neural implementation remain elusive. One influential theory, the adaptive coding hypothesis (Duncan, 2001, An adaptive coding model of neural function in prefrontal cortex, Nature Reviews Neuroscience 2:820-829), proposes that single neurons in certain frontal and parietal regions dynamically adjust their responses to selectively encode relevant information. This selective representation may in turn support selective processing in more specialized brain regions such as the visual cortices. Here, we use multi-voxel decoding of functional magnetic resonance images to demonstrate selective representation of attended--and not distractor--objects in frontal, parietal, and visual cortices. In addition, we highlight a critical role for task demands in determining which brain regions exhibit selective coding. Strikingly, representation of attended objects in frontoparietal cortex was highest under conditions of high perceptual demand, when stimuli were hard to perceive and coding in early visual cortex was weak. Coding in early visual cortex varied as a function of attention and perceptual demand, while coding in higher visual areas was sensitive to the allocation of attention but robust to changes in perceptual difficulty. Consistent with high-profile reports, peripherally presented objects could also be decoded from activity at the occipital pole, a region which corresponds to the fovea. Our results emphasize the flexibility of frontoparietal and visual systems. They support the hypothesis that attention enhances the multi-voxel representation of information in the brain, and suggest that the engagement of this attentional mechanism depends critically on current task demands. PMID:25583612

  13. The application of muscle wrapping to voxel-based finite element models of skeletal structures.

    PubMed

    Liu, Jia; Shi, Junfen; Fitton, Laura C; Phillips, Roger; O'Higgins, Paul; Fagan, Michael J

    2012-01-01

    Finite elements analysis (FEA) is now used routinely to interpret skeletal form in terms of function in both medical and biological applications. To produce accurate predictions from FEA models, it is essential that the loading due to muscle action is applied in a physiologically reasonable manner. However, it is common for muscle forces to be represented as simple force vectors applied at a few nodes on the model's surface. It is certainly rare for any wrapping of the muscles to be considered, and yet wrapping not only alters the directions of muscle forces but also applies an additional compressive load from the muscle belly directly to the underlying bone surface. This paper presents a method of applying muscle wrapping to high-resolution voxel-based finite element (FE) models. Such voxel-based models have a number of advantages over standard (geometry-based) FE models, but the increased resolution with which the load can be distributed over a model's surface is particularly advantageous, reflecting more closely how muscle fibre attachments are distributed. In this paper, the development, application and validation of a muscle wrapping method is illustrated using a simple cylinder. The algorithm: (1) calculates the shortest path over the surface of a bone given the points of origin and ultimate attachment of the muscle fibres; (2) fits a Non-Uniform Rational B-Spline (NURBS) curve from the shortest path and calculates its tangent, normal vectors and curvatures so that normal and tangential components of the muscle force can be calculated and applied along the fibre; and (3) automatically distributes the loads between adjacent fibres to cover the bone surface with a fully distributed muscle force, as is observed in vivo. Finally, we present a practical application of this approach to the wrapping of the temporalis muscle around the cranium of a macaque skull. PMID:21308392

  14. 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

  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. Diffuse Decreased Gray Matter in Patients with Idiopathic Craniocervical Dystonia: A Voxel-Based Morphometry Study

    PubMed Central

    Piccinin, Camila C.; Piovesana, Luiza G.; Santos, Maria C. A.; Guimarães, Rachel P.; De Campos, Brunno M.; Rezende, Thiago J. R.; Campos, Lidiane S.; Torres, Fabio R.; Amato-Filho, Augusto C.; França, Marcondes C.; Lopes-Cendes, Iscia; Cendes, Fernando; D’Abreu, Anelyssa

    2015-01-01

    Background: Recent studies have addressed the role of structures other than the basal ganglia in the pathophysiology of craniocervical dystonia (CCD). Neuroimaging studies have attempted to identify structural abnormalities in CCD but a clear pattern of alteration has not been established. We performed whole-brain evaluation using voxel-based morphometry (VBM) to identify patterns of gray matter (GM) changes in CCD. Methods: We compared 27 patients with CCD matched in age and gender to 54 healthy controls. VBM was used to compare GM volumes. We created a two-sample t-test corrected for subjects’ age, and we tested with a level of significance of p < 0.001 and false discovery rate (FDR) correction (p < 0.05). Results: Voxel-based morphometry demonstrated significant reductions of GM using p < 0.001 in the cerebellar vermis IV/V, bilaterally in the superior frontal gyrus, precuneus, anterior cingulate and paracingulate, insular cortex, lingual gyrus, and calcarine fissure; in the left hemisphere in the supplementary motor area, inferior frontal gyrus, inferior parietal gyrus, temporal pole, supramarginal gyrus, rolandic operculum, hippocampus, middle occipital gyrus, cerebellar lobules IV/V, superior, and middle temporal gyri; in the right hemisphere, the middle cingulate and precentral gyrus. Our study did not report any significant result using the FDR correction. We also detected correlations between GM volume and age, disease duration, duration of botulinum toxin treatment, and the Marsden–Fahn dystonia scale scores. Conclusion: We detected large clusters of GM changes chiefly in structures primarily involved in sensorimotor integration, motor planning, visuospatial function, and emotional processing. PMID:25620953

  17. 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

  18. 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

  19. 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…

  20. 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…

  1. Application of voxel phantoms in whole-body counting for the validation of calibration phantoms and the assessment of uncertainties.

    PubMed

    de Carlan, L; Roch, P; Blanchardon, E; Franck, D

    2007-01-01

    This article is dedicated to the application of voxel phantoms in whole-body counting calibration. The first study was performed to validate this approach using IGOR, a physical phantom dedicated to fission and activation product (FAP) measurement, and a graphical user interface, developed at the IRSN internal dose assessment laboratory, called OEDIPE (French acronym for the tool for personalised internal dose assessment) associated with the Monte Carlo code MCNP. The method was validated by comparing the results of real measurements and simulations using voxel phantoms obtained from CT scan images of IGOR. To take this application further, two studies were carried out and are presented in this article. First, a comparison was made between the IGOR voxel based phantom (IGOVOX) and a voxel human body (Zubal Phantom) to confirm whether IGOR could be considered as a realistic representation of a human. Second, the errors made when considering sources homogeneously distributed in the body were assessed against real contamination by taking into account the biokinetic behaviour of the radioactive material for two modes of exposure: the ingestion of 137Cs in soluble form and the inhalation of insoluble 60Co several days after acute incorporation. PMID:17018545

  2. 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)…

  3. Standardized method to quantify the variation in voxel value distribution in patient-simulated CBCT data sets

    PubMed Central

    Gotfredsen, E; Wenzel, A

    2015-01-01

    Objectives: To suggest a standardized method to assess the variation in voxel value distribution in patient-simulated CBCT data sets and the effect of time between exposures (TBE). Additionally, a measurement of reproducibility, Aarhus measurement of reproducibility (AMORe), is introduced, which could be used for quality assurance purposes. Methods: Six CBCT units were tested [Cranex® 3D/CRAN (Soredex Oy, Tuusula, Finland); Scanora® 3D/SCAN (Soredex Oy); NewTom™ 5G/NEW5 (QR srl, Verona, Italy); i-CAT/ICAT (Imaging Sciences International, Hatfield, PA); 3D Accuitomo FPD80/ACCU (Morita, Kyoto, Japan); and NewTom VG/NEWV (QR srl)]. Two sets of volumetric data of a wax-imbedded dry human skull (containing a titanium implant) were acquired by each CBCT unit at two sessions on separate days. Each session consisted 21 exposures: 1 “initial” followed by a 30-min interval (initial data set), 10 acquired with 30-min TBE (data sets 1–10) and 10 acquired with 15-min TBE (data sets 11–20). CBCT data were exported as digital imaging and communications in medicine files and converted to text files containing x, y and z positions and grey shade for each voxel. Subtractions were performed voxel-by-voxel in two set-ups: (1) between two consecutive data sets and (2) between any subsequent data set and data set 1. The mean grey shade variation for each voxel was calculated for each unit/session. Results: The largest mean grey shade variation was found in the subtraction set-up 2 (27–447 shades of grey, depending on the unit). Considering subtraction set-up 1, the highest variation was seen for NEW5, between data sets 1 and the initial. Conclusions: Discrepancies in voxel value distribution were found by comparing the initial examination of the day with the subsequent examinations. TBE had no predictable effect on the variation of CBCT-derived voxel values. AMORe ranged between 0 and 64. PMID:25354021

  4. 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

  5. Penalized likelihood phenotyping: unifying voxelwise analyses and multi-voxel pattern analyses in neuroimaging: penalized likelihood phenotyping.

    PubMed

    Adluru, Nagesh; Hanlon, Bret M; Lutz, Antoine; Lainhart, Janet E; Alexander, Andrew L; Davidson, Richard J

    2013-04-01

    Neuroimage phenotyping for psychiatric and neurological disorders is performed using voxelwise analyses also known as voxel based analyses or morphometry (VBM). A typical voxelwise analysis treats measurements at each voxel (e.g., fractional anisotropy, gray matter probability) as outcome measures to study the effects of possible explanatory variables (e.g., age, group) in a linear regression setting. Furthermore, each voxel is treated independently until the stage of correction for multiple comparisons. Recently, multi-voxel pattern analyses (MVPA), such as classification, have arisen as an alternative to VBM. The main advantage of MVPA over VBM is that the former employ multivariate methods which can account for interactions among voxels in identifying significant patterns. They also provide ways for computer-aided diagnosis and prognosis at individual subject level. However, compared to VBM, the results of MVPA are often more difficult to interpret and prone to arbitrary conclusions. In this paper, first we use penalized likelihood modeling to provide a unified framework for understanding both VBM and MVPA. We then utilize statistical learning theory to provide practical methods for interpreting the results of MVPA beyond commonly used performance metrics, such as leave-one-out-cross validation accuracy and area under the receiver operating characteristic (ROC) curve. Additionally, we demonstrate that there are challenges in MVPA when trying to obtain image phenotyping information in the form of statistical parametric maps (SPMs), which are commonly obtained from VBM, and provide a bootstrap strategy as a potential solution for generating SPMs using MVPA. This technique also allows us to maximize the use of available training data. We illustrate the empirical performance of the proposed framework using two different neuroimaging studies that pose different levels of challenge for classification using MVPA. PMID:23397550

  6. Construction of anthropomorphic hybrid, dual-lattice voxel models for optimizing image quality and dose in radiography

    NASA Astrophysics Data System (ADS)

    Petoussi-Henss, Nina; Becker, Janine; Greiter, Matthias; Schlattl, Helmut; Zankl, Maria; Hoeschen, Christoph

    2014-03-01

    In radiography there is generally a conflict between the best image quality and the lowest possible patient dose. A proven method of dosimetry is the simulation of radiation transport in virtual human models (i.e. phantoms). However, while the resolution of these voxel models is adequate for most dosimetric purposes, they cannot provide the required organ fine structures necessary for the assessment of the imaging quality. The aim of this work is to develop hybrid/dual-lattice voxel models (called also phantoms) as well as simulation methods by which patient dose and image quality for typical radiographic procedures can be determined. The results will provide a basis to investigate by means of simulations the relationships between patient dose and image quality for various imaging parameters and develop methods for their optimization. A hybrid model, based on NURBS (Non Linear Uniform Rational B-Spline) and PM (Polygon Mesh) surfaces, was constructed from an existing voxel model of a female patient. The organs of the hybrid model can be then scaled and deformed in a non-uniform way i.e. organ by organ; they can be, thus, adapted to patient characteristics without losing their anatomical realism. Furthermore, the left lobe of the lung was substituted by a high resolution lung voxel model, resulting in a dual-lattice geometry model. "Dual lattice" means in this context the combination of voxel models with different resolution. Monte Carlo simulations of radiographic imaging were performed with the code EGS4nrc, modified such as to perform dual lattice transport. Results are presented for a thorax examination.

  7. 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

  8. Voxel-wise information theoretic EEG-fMRI feature integration.

    PubMed

    Ostwald, Dirk; Porcaro, Camillo; Bagshaw, Andrew P

    2011-04-01

    We have recently proposed the evaluation of a set of information theoretic quantities (ITQs) for the integration of simultaneously acquired EEG-fMRI data (Ostwald, D., Porcaro, C., Bagshaw, A.P., 2010. An information theoretic approach to EEG-fMRI integration of visually evoked responses. Neuroimage. 49, 498-516). In our previous experimental evaluation of the information theoretic framework, we defined the data subsets from which to calculate the ITQs using a priori constraints. In the case of EEG, this meant that data were extracted from a single electrode, while for fMRI the analysed data came from voxels contained within a sphere surrounding the most responsive voxel of visual cortex. While this approach was a natural starting point for the evaluation of the framework in the application to combined EEG-fMRI data sets, a more principled approach to data selection is desirable. Here, we propose to combine standard fMRI data pre-processing and low-resolution electromagnetic tomography (LORETA) for the evaluation of ITQs across the entire three-dimensional brain space. We apply the proposed method to a simultaneous EEG-fMRI data set acquired during checkerboard stimulation and assess the topographical informativeness of EEG (time and frequency domain) and fMRI features with respect to the stimulus and each other. The resulting information theoretic effect size maps are supplemented with a statistical evaluation based on Gaussian null model simulations using a false-discovery rate procedure. Given the contamination of EEG recordings by artefacts induced by the MR scanning environment we further assessed the influence of different advanced EEG pre-processing methods (independent component analysis and functional source separation) on the information topography. The results of this analysis provide evidence for the topographically focussed informativeness of both EEG and fMRI features with respect to the stimulus, but for the current feature selection do not detect

  9. Kilovoltage beam Monte Carlo dose calculations in submillimeter voxels for small animal radiotherapy

    PubMed Central

    Bazalova, Magdalena; Zhou, Hu; Keall, Paul J.; Graves, Edward E.

    2009-01-01

    Purpose: Small animal conformal radiotherapy (RT) is essential for preclinical cancer research studies and therefore various microRT systems have been recently designed. The aim of this paper is to efficiently calculate the dose delivered using our microRT system based on a microCT scanner with the Monte Carlo (MC) method and to compare the MC calculations to film measurements. Methods: Doses from 2–30 mm diameter 120 kVp photon beams deposited in a solid water phantom with 0.2×0.2×0.2 mm3 voxels are calculated using the latest versions of the EGSnrc codes BEAMNRC and DOSXYZNRC. Two dose calculation approaches are studied: a two-step approach using phase-space files and direct dose calculation with BEAMNRC simulation sources. Due to the small beam size and submillimeter voxel size resulting in long calculation times, variance reduction techniques are studied. The optimum bremsstrahlung splitting number (NBRSPL in BEAMNRC) and the optimum DOSXYZNRC photon splitting (Nsplit) number are examined for both calculation approaches and various beam sizes. The dose calculation efficiencies and the required number of histories to achieve 1% statistical uncertainty—with no particle recycling—are evaluated for 2–30 mm beams. As a final step, film dose measurements are compared to MC calculated dose distributions. Results: The optimum NBRSPL is approximately 1×106 for both dose calculation approaches. For the dose calculations with phase-space files, Nsplit varies only slightly for 2–30 mm beams and is established to be 300. Nsplit for the DOSXYZNRC calculation with the BEAMNRC source ranges from 300 for the 30 mm beam to 4000 for the 2 mm beam. The calculation time significantly increases for small beam sizes when the BEAMNRC simulation source is used compared to the simulations with phase-space files. For the 2 and 30 mm beams, the dose calculations with phase-space files are more efficient than the dose calculations with BEAMNRC sources by factors of 54 and 1

  10. Voxel modeling of rabbits for use in radiological dose rate calculations.

    PubMed

    Caffrey, E A; Johansen, M P; Higley, K A

    2016-01-01

    Radiation dose to biota is generally calculated using Monte Carlo simulations of whole body ellipsoids with homogeneously distributed radioactivity throughout. More complex anatomical phantoms, termed voxel phantoms, have been developed to test the validity of these simplistic geometric models. In most voxel models created to date, human tissue composition and density values have been used in lieu of biologically accurate values for non-human biota. This has raised questions regarding variable tissue composition and density effects on the fraction of radioactive emission energy absorbed within tissues (e.g. the absorbed fraction - AF), along with implications for age-dependent dose rates as organisms mature. The results of this study on rabbits indicates that the variation in composition between two mammalian tissue types (e.g. human vs rabbit bones) made little difference in self-AF (SAF) values (within 5% over most energy ranges). However, variable tissue density (e.g. bone vs liver) can significantly impact SAF values. An examination of differences across life-stages revealed increasing SAF with testis and ovary size of over an order of magnitude for photons and several factors for electrons, indicating the potential for increasing dose rates to these sensitive organs as animals mature. AFs for electron energies of 0.1, 0.2, 0.4, 0.5, 0.7, 1.0, 1.5, 2.0, and 4.0 MeV and photon energies of 0.01, 0.015, 0.02, 0.03, 0.05, 0.1, 0.2, 0.5, 1.0, 1.5, 2.0, and 4.0 MeV are provided for eleven rabbit tissues. The data presented in this study can be used to calculate accurate organ dose rates for rabbits and other small rodents; to aide in extending dose results among different mammal species; and to validate the use of ellipsoidal models for regulatory purposes. PMID:25971772

  11. 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.

  12. Differences among Monte Carlo codes in the calculations of voxel S values for radionuclide targeted therapy and analysis of their impact on absorbed dose evaluations

    SciTech Connect

    Pacilio, M.; Lanconelli, N.; Lo Meo, S.; Betti, M.; Montani, L.; Torres Aroche, L. A.; Coca Perez, M. A.

    2009-05-15

    Several updated Monte Carlo (MC) codes are available to perform calculations of voxel S values for radionuclide targeted therapy. The aim of this work is to analyze the differences in the calculations obtained by different MC codes and their impact on absorbed dose evaluations performed by voxel dosimetry. Voxel S values for monoenergetic sources (electrons and photons) and different radionuclides ({sup 90}Y, {sup 131}I, and {sup 188}Re) were calculated. Simulations were performed in soft tissue. Three general-purpose MC codes were employed for simulating radiation transport: MCNP4C, EGSnrc, and GEANT4. The data published by the MIRD Committee in Pamphlet No. 17, obtained with the EGS4 MC code, were also included in the comparisons. The impact of the differences (in terms of voxel S values) among the MC codes was also studied by convolution calculations of the absorbed dose in a volume of interest. For uniform activity distribution of a given radionuclide, dose calculations were performed on spherical and elliptical volumes, varying the mass from 1 to 500 g. For simulations with monochromatic sources, differences for self-irradiation voxel S values were mostly confined within 10% for both photons and electrons, but with electron energy less than 500 keV, the voxel S values referred to the first neighbor voxels showed large differences (up to 130%, with respect to EGSnrc) among the updated MC codes. For radionuclide simulations, noticeable differences arose in voxel S values, especially in the bremsstrahlung tails, or when a high contribution from electrons with energy of less than 500 keV is involved. In particular, for {sup 90}Y the updated codes showed a remarkable divergence in the bremsstrahlung region (up to about 90% in terms of voxel S values) with respect to the EGS4 code. Further, variations were observed up to about 30%, for small source-target voxel distances, when low-energy electrons cover an important part of the emission spectrum of the radionuclide

  13. Parallel solutions for voxel-based simulations of reaction-diffusion systems.

    PubMed

    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

  14. 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.

  15. Influence of regional cerebral blood volume on voxel-based morphometry.

    PubMed

    Zheng, Lei; Cleppien, Dirk; Gass, Natalia; Falfan-Melgoza, Claudia; Vollmayr, Barbara; Hesser, Jürgen; Weber-Fahr, Wolfgang; Sartorius, Alexander

    2016-06-01

    The investigation of structural brain alterations is one focus in research of brain diseases like depression. Voxel-based morphometry (VBM) based on high-resolution 3D MRI images is a widely used non-invasive tool for such investigations. However, the result of VBM might be sensitive to local physiological parameters such as regional cerebral blood volume (rCBV) changes. In order to investigate whether rCBV changes may contribute to variation in VBM, we performed analyses in a study with the congenital learned helplessness (cLH) model for long-term findings. The 3D structural and rCBV data were acquired with T2 -weighted rapid acquisition with relaxation enhancement (RARE) pulse sequences. The group effects were determined by standard statistical parametric mapping (SPM) and biological parametric mapping (BPM) and examined further using atlas-based regions. In our genetic animal model of depression, we found co-occurrence of differences in gray matter volume and rCBV, while there was no evidence of significant interaction between both. However, the multimodal analysis showed similar gray matter differences compared with the standard VBM approach. Our data corroborate the idea that two group VBM differences might not be influenced by rCBV differences in genetically different strains. Copyright © 2016 John Wiley & Sons, Ltd. PMID:27074152

  16. 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. PMID:24397344

  17. Gray matter correlates of creative potential: a latent variable voxel-based morphometry study.

    PubMed

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

    2015-05-01

    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

  18. Focal retrograde amnesia: voxel-based morphometry findings in a case without MRI lesions.

    PubMed

    Sehm, Bernhard; Frisch, Stefan; Thöne-Otto, Angelika; Horstmann, Annette; Villringer, Arno; Obrig, Hellmuth

    2011-01-01

    Focal retrograde amnesia (FRA) is a rare neurocognitive disorder presenting with an isolated loss of retrograde memory. In the absence of detectable brain lesions, a differentiation of FRA from psychogenic causes is difficult. Here we report a case study of persisting FRA after an epileptic seizure. A thorough neuropsychological assessment confirmed severe retrograde memory deficits while anterograde memory abilities were completely normal. Neurological and psychiatric examination were unremarkable and high-resolution MRI showed no neuroradiologically apparent lesion. However, voxel-based morphometry (VBM)-comparing the MRI to an education-, age-and sex-matched control group (n = 20) disclosed distinct gray matter decreases in left temporopolar cortex and a region between right posterior parahippocampal and lingual cortex. Although the results of VBM-based comparisons between a single case and a healthy control group are generally susceptible to differences unrelated to the specific symptoms of the case, we believe that our data suggest a causal role of the cortical areas detected since the retrograde memory deficit is the preeminent neuropsychological difference between patient and controls. This was paralleled by grey matter differences in central nodes of the retrograde memory network. We therefore suggest that these subtle alterations represent structural correlates of the focal retrograde amnesia in our patient. Beyond the implications for the diagnosis and etiology of FRA, our results advocate the use of VBM in conditions that do not show abnormalities in clinical radiological assessment, but show distinct neuropsychological deficits. PMID:22028902

  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. 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

  1. 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

  2. Meditation effects within the hippocampal complex revealed by voxel-based morphometry and cytoarchitectonic probabilistic mapping.

    PubMed

    Luders, Eileen; Kurth, Florian; Toga, Arthur W; Narr, Katherine L; Gaser, Christian

    2013-01-01

    Scientific studies addressing anatomical variations in meditators' brains have emerged rapidly over the last few years, where significant links are most frequently reported with respect to gray matter (GM). To advance prior work, this study examined GM characteristics in a large sample of 100 subjects (50 meditators, 50 controls), where meditators have been practicing close to 20 years, on average. A standard, whole-brain voxel-based morphometry approach was applied and revealed significant meditation effects in the vicinity of the hippocampus, showing more GM in meditators than in controls as well as positive correlations with the number of years practiced. However, the hippocampal complex is regionally segregated by architecture, connectivity, and functional relevance. Thus, to establish differential effects within the hippocampal formation (cornu ammonis, fascia dentata, entorhinal cortex, subiculum) as well as the hippocampal-amygdaloid transition area, we utilized refined cytoarchitectonic probabilistic maps of (peri-) hippocampal subsections. Significant meditation effects were observed within the subiculum specifically. Since the subiculum is known to play a key role in stress regulation and meditation is an established form of stress reduction, these GM findings may reflect neuronal preservation in long-term meditators-perhaps due to an attenuated release of stress hormones and decreased neurotoxicity. PMID:23847572

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  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