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Sample records for 3d brain mri

  1. 3-D brain MRI tissue classification on FPGAs.

    PubMed

    Koo, Jahyun J; Evans, Alan C; Gross, Warren J

    2009-12-01

    Many automatic algorithms have been proposed for analyzing magnetic resonance imaging (MRI) data sets. With the increasingly large data sets being used in brain mapping, there has been a significant rise in the need for accelerating these algorithms. Partial volume estimation (PVE), a brain tissue classification algorithm for MRI, was implemented on a field-programmable gate array (FPGA)-based high performance reconfigurable computer using the Mitrion-C high-level language (HLL). This work develops on prior work in which we conducted initial studies on accelerating the prior information estimation algorithm. In this paper, we extend the work to include probability density estimation and present new results and additional analysis. We used several simulated and real human brain MR images to evaluate the accuracy and performance improvement of the proposed algorithm. The FPGA-based probability density estimation and prior information estimation implementation achieved an average speedup over an Itanium 2 CPU of 2.5 x and 9.4 x , respectively. The overall performance improvement of the FPGA-based PVE algorithm was 5.1 x with four FPGAs.

  2. Custom Fit 3D-Printed Brain Holders for Comparison of Histology with MRI in Marmosets

    PubMed Central

    Guy, Joseph R.; Sati, Pascal; Leibovitch, Emily; Jacobson, Steven; Silva, Afonso C.; Reich, Daniel S.

    2015-01-01

    Background MRI has the advantage of sampling large areas of tissue and locating areas of interest in 3D space in both living and ex vivo systems, whereas histology has the ability to examine thin slices of ex vivo tissue with high detail and specificity. Although both are valuable tools, it is currently difficult to make high-precision comparisons between MRI and histology due to large differences inherent to the techniques. A method combining the advantages would be an asset to understanding the pathological correlates of MRI. New Method 3D-printed brain holders were used to maintain marmoset brains in the same orientation during acquisition of ex vivo MRI and pathologic cutting of the tissue. Results The results of maintaining this same orientation show that sub-millimeter, discrete neuropathological features in marmoset brain consistently share size, shape, and location between histology and ex vivo MRI, which facilitates comparison with serial imaging acquired in vivo. Comparison with Existing Methods Existing methods use computational approaches sensitive to data input in order to warp histologic images to match large-scale features on MRI, but the new method requires no warping of images, due to a preregistration accomplished in the technique, and is insensitive to data formatting and artifacts in both MRI and histology. Conclusions The simple method of using 3D-printed brain holders to match brain orientation during pathologic sectioning and MRI acquisition enables rapid and precise comparison of small features seen on MRI to their underlying histology. PMID:26365332

  3. Toward the automatic quantification of in utero brain development in 3D structural MRI: A review.

    PubMed

    Benkarim, Oualid M; Sanroma, Gerard; Zimmer, Veronika A; Muñoz-Moreno, Emma; Hahner, Nadine; Eixarch, Elisenda; Camara, Oscar; González Ballester, Miguel Angel; Piella, Gemma

    2017-02-14

    Investigating the human brain in utero is important for researchers and clinicians seeking to understand early neurodevelopmental processes. With the advent of fast magnetic resonance imaging (MRI) techniques and the development of motion correction algorithms to obtain high-quality 3D images of the fetal brain, it is now possible to gain more insight into the ongoing maturational processes in the brain. In this article, we present a review of the major building blocks of the pipeline toward performing quantitative analysis of in vivo MRI of the developing brain and its potential applications in clinical settings. The review focuses on T1- and T2-weighted modalities, and covers state of the art methodologies involved in each step of the pipeline, in particular, 3D volume reconstruction, spatio-temporal modeling of the developing brain, segmentation, quantification techniques, and clinical applications. Hum Brain Mapp, 2017. © 2017 Wiley Periodicals, Inc.

  4. Correlation of preoperative MRI and intraoperative 3D ultrasound to measure brain tissue shift

    NASA Astrophysics Data System (ADS)

    Gobbi, David G.; Lee, Belinda K. H.; Peters, Terence M.

    2001-05-01

    B-Mode ultrasound is often used during neurosurgery to provide intra-operative images of the brain though a craniotomy, but the use of 3D ultrasound during surgery is still in its infancy. We have developed a system that provides real-time freehand 3D ultrasound reconstruction at a reduced resolution. The reconstruction proceeds incrementally and the 3D image is overlayed, via a computer, on a pre-operative 3D MRI scan. This provides the operator with the necessary feedback to maintain a constant freehand sweep-rate, and also ensures that the sweep covers the desired anatomical volume. All of the ultrasound video frames are buffered, and a full-resolution, compounded reconstruction proceeds once the manual sweep is complete. We have also developed tools for manual tagging of homologous landmarks in the 3D MRI and 3D ultrasound volumes that use a piecewise cubic approximation of thin-plate spline interpolation to achieve interactive nonlinear registration and warping of the MRI volume to the ultrasound volume: Each time a homologous point-pair is identified by the use, the image of the warped MRI is updated on the computer screen after less than 0.5 s.

  5. Fractality in the neuron axonal topography of the human brain based on 3-D diffusion MRI

    NASA Astrophysics Data System (ADS)

    Katsaloulis, P.; Ghosh, A.; Philippe, A. C.; Provata, A.; Deriche, R.

    2012-05-01

    In this work the fractal architecture of the neuron axonal topography of the human brain is evaluated, as derived from 3-D diffusion MRI (dMRI) acquisitions. This is a 3D extension of work performed previously in 2D regions of interest (ROIs), where the fractal dimension of the neuron axonal topography was computed from dMRI data. A group study with 18 subjects is here conducted and the fractal dimensions D f of the entire 3-D volume of the brains is estimated via the box counting, the correlation dimension and the fractal mass dimension methods. The neuron axon data is obtained using tractography algorithms on diffusion tensor imaging of the brain. We find that all three calculations of D f give consistent results across subjects, namely, they demonstrate fractal characteristics in the short and medium length scales: different fractal exponents prevail at different length scales, an indication of multifractality. We surmise that this complexity stems as a collective property emerging when many local brain units, performing different functional tasks and having different local topologies, are recorded together.

  6. Utilizing 3D Printing Technology to Merge MRI with Histology: A Protocol for Brain Sectioning

    PubMed Central

    Luciano, Nicholas J; Sati, Pascal; Nair, Govind; Guy, Joseph R; Ha, Seung-Kwon; Absinta, Martina; Chiang, Wen-Yang; Leibovitch, Emily C; Jacobson, Steven; Silva, Afonso C; Reich, Daniel S.

    2016-01-01

    Magnetic resonance imaging (MRI) allows for the delineation between normal and abnormal tissue on a macroscopic scale, sampling an entire tissue volume three-dimensionally. While MRI is an extremely sensitive tool for detecting tissue abnormalities, association of signal changes with an underlying pathological process is usually not straightforward. In the central nervous system, for example, inflammation, demyelination, axonal damage, gliosis, and neuronal death may all induce similar findings on MRI. As such, interpretation of MRI scans depends on the context, and radiological-histopathological correlation is therefore of the utmost importance. Unfortunately, traditional pathological sectioning of brain tissue is often imprecise and inconsistent, thus complicating the comparison between histology sections and MRI. This article presents novel methodology for accurately sectioning primate brain tissues and thus allowing precise matching between histology and MRI. The detailed protocol described in this article will assist investigators in applying this method, which relies on the creation of 3D printed brain slicers. Slightly modified, it can be easily implemented for brains of other species, including humans. PMID:28060281

  7. Utilizing 3D Printing Technology to Merge MRI with Histology: A Protocol for Brain Sectioning.

    PubMed

    Luciano, Nicholas J; Sati, Pascal; Nair, Govind; Guy, Joseph R; Ha, Seung-Kwon; Absinta, Martina; Chiang, Wen-Yang; Leibovitch, Emily C; Jacobson, Steven; Silva, Afonso C; Reich, Daniel S

    2016-12-06

    Magnetic resonance imaging (MRI) allows for the delineation between normal and abnormal tissue on a macroscopic scale, sampling an entire tissue volume three-dimensionally. While MRI is an extremely sensitive tool for detecting tissue abnormalities, association of signal changes with an underlying pathological process is usually not straightforward. In the central nervous system, for example, inflammation, demyelination, axonal damage, gliosis, and neuronal death may all induce similar findings on MRI. As such, interpretation of MRI scans depends on the context, and radiological-histopathological correlation is therefore of the utmost importance. Unfortunately, traditional pathological sectioning of brain tissue is often imprecise and inconsistent, thus complicating the comparison between histology sections and MRI. This article presents novel methodology for accurately sectioning primate brain tissues and thus allowing precise matching between histology and MRI. The detailed protocol described in this article will assist investigators in applying this method, which relies on the creation of 3D printed brain slicers. Slightly modified, it can be easily implemented for brains of other species, including humans.

  8. Deformable templates guided discriminative models for robust 3D brain MRI segmentation.

    PubMed

    Liu, Cheng-Yi; Iglesias, Juan Eugenio; Tu, Zhuowen

    2013-10-01

    Automatically segmenting anatomical structures from 3D brain MRI images is an important task in neuroimaging. One major challenge is to design and learn effective image models accounting for the large variability in anatomy and data acquisition protocols. A deformable template is a type of generative model that attempts to explicitly match an input image with a template (atlas), and thus, they are robust against global intensity changes. On the other hand, discriminative models combine local image features to capture complex image patterns. In this paper, we propose a robust brain image segmentation algorithm that fuses together deformable templates and informative features. It takes advantage of the adaptation capability of the generative model and the classification power of the discriminative models. The proposed algorithm achieves both robustness and efficiency, and can be used to segment brain MRI images with large anatomical variations. We perform an extensive experimental study on four datasets of T1-weighted brain MRI data from different sources (1,082 MRI scans in total) and observe consistent improvement over the state-of-the-art systems.

  9. 3D geometric split-merge segmentation of brain MRI datasets.

    PubMed

    Marras, Ioannis; Nikolaidis, Nikolaos; Pitas, Ioannis

    2014-05-01

    In this paper, a novel method for MRI volume segmentation based on region adaptive splitting and merging is proposed. The method, called Adaptive Geometric Split Merge (AGSM) segmentation, aims at finding complex geometrical shapes that consist of homogeneous geometrical 3D regions. In each volume splitting step, several splitting strategies are examined and the most appropriate is activated. A way to find the maximal homogeneity axis of the volume is also introduced. Along this axis, the volume splitting technique divides the entire volume in a number of large homogeneous 3D regions, while at the same time, it defines more clearly small homogeneous regions within the volume in such a way that they have greater probabilities of survival at the subsequent merging step. Region merging criteria are proposed to this end. The presented segmentation method has been applied to brain MRI medical datasets to provide segmentation results when each voxel is composed of one tissue type (hard segmentation). The volume splitting procedure does not require training data, while it demonstrates improved segmentation performance in noisy brain MRI datasets, when compared to the state of the art methods.

  10. Growth trajectories of the human fetal brain tissues estimated from 3D reconstructed in utero MRI

    PubMed Central

    Scott, Julia A.; Habas, Piotr A.; Kim, Kio; Rajagopalan, Vidya; Hamzelou, Kia S.; Corbett-Detig, James M.; Barkovich, A. James; Glenn, Orit A.; Studholme, Colin

    2012-01-01

    In the latter half of gestation (20 to 40 gestational weeks), human brain growth accelerates in conjunction with cortical folding and the deceleration of ventricular zone progenitor cell proliferation. These processes are reflected in changes in the volume of respective fetal tissue zones. Thus far, growth trajectories of the fetal tissue zones have been extracted primarily from 2D measurements on histological sections and magnetic resonance imaging (MRI). In this study, the volumes of major fetal zones—cortical plate (CP), subplate and intermediate zone (SP+IZ), germinal matrix (GMAT), deep gray nuclei (DG), and ventricles (VENT)—are calculated from automatic segmentation of motion-corrected, 3D reconstructed MRI. We analyzed 48 T2-weighted MRI scans from 39 normally developing fetuses in utero between 20.57 and 31.14 gestational weeks (GW). The supratentorial volume (STV) increased linearly at a rate of 15.22% per week. The SP+IZ (14.75% per week) and DG (15.56% per week) volumes increased at similar rates. The CP increased at a greater relative rate (18.00% per week), while the VENT (9.18% per week) changed more slowly. Therefore, CP increased as a fraction of STV and the VENT fraction declined. The total GMAT volume slightly increased then decreased after 25 GW. We did not detect volumetric sexual dimorphisms or total hemispheric volume asymmetries, which may emerge later in gestation. Further application of the automated fetal brain segmentation to later gestational ages will bridge the gap between volumetric studies of premature brain development and normal brain development in utero. PMID:21530634

  11. Growth trajectories of the human fetal brain tissues estimated from 3D reconstructed in utero MRI.

    PubMed

    Scott, Julia A; Habas, Piotr A; Kim, Kio; Rajagopalan, Vidya; Hamzelou, Kia S; Corbett-Detig, James M; Barkovich, A James; Glenn, Orit A; Studholme, Colin

    2011-08-01

    In the latter half of gestation (20-40 gestational weeks), human brain growth accelerates in conjunction with cortical folding and the deceleration of ventricular zone progenitor cell proliferation. These processes are reflected in changes in the volume of respective fetal tissue zones. Thus far, growth trajectories of the fetal tissue zones have been extracted primarily from 2D measurements on histological sections and magnetic resonance imaging (MRI). In this study, the volumes of major fetal zones-cortical plate (CP), subplate and intermediate zone (SP+IZ), germinal matrix (GMAT), deep gray nuclei (DG), and ventricles (VENT)--are calculated from automatic segmentation of motion-corrected, 3D reconstructed MRI. We analyzed 48 T2-weighted MRI scans from 39 normally developing fetuses in utero between 20.57 and 31.14 gestational weeks (GW). The supratentorial volume (STV) increased linearly at a rate of 15.22% per week. The SP+IZ (14.75% per week) and DG (15.56% per week) volumes increased at similar rates. The CP increased at a greater relative rate (18.00% per week), while the VENT (9.18% per week) changed more slowly. Therefore, CP increased as a fraction of STV and the VENT fraction declined. The total GMAT volume slightly increased then decreased after 25 GW. We did not detect volumetric sexual dimorphisms or total hemispheric volume asymmetries, which may emerge later in gestation. Further application of the automated fetal brain segmentation to later gestational ages will bridge the gap between volumetric studies of premature brain development and normal brain development in utero.

  12. Correlation of pre-operative MRI and intra-operative 3D ultrasound to measure brain tissue shift

    NASA Astrophysics Data System (ADS)

    Gobbi, David G.; Comeau, Roch M.; Lee, Belinda K. H.; Peters, Terence M.

    2000-04-01

    The usefulness of stereotactic neurosurgery performed via a craniotomy is limited because the craniotomy leads to a brain tissue shift of 10 mm on average. We have recently completed an examination of 2D intra-operative ultrasound as a means of visualization and measurement of brain shift. A commercial 3D tracking system was used for real-time registration of the ultrasound video to pre-operative MR images, and annotation of the images was used to measure the shift. More than 15 surgical cases have been performed thus far with the 2D system. We are now undertaking phantom studies with tracked 3D ultrasound, and have developed sophisticated tools for real- time overlay of ultrasound and MRI volumes. These tools include a virtual-reality view of the ultrasound probe with live ultrasound video superimposed over a 3D -rendered MRI of the brain, as well as 3D ultrasound/MRI transparency overlay views. Algorithms to automatically extract landmarks from MRI and 3D ultrasound images are under development. We aim to use these landmarks to automatically generate nonlinear warp transformations to correct the pre-operative MRI as well as surgical target coordinates for brain shift. Portions of the C++ code developed for this project have been contributed to the open-source Visualization Toolkit (VTK).

  13. Fast Bayesian whole-brain fMRI analysis with spatial 3D priors.

    PubMed

    Sidén, Per; Eklund, Anders; Bolin, David; Villani, Mattias

    2017-02-01

    Spatial whole-brain Bayesian modeling of task-related functional magnetic resonance imaging (fMRI) is a great computational challenge. Most of the currently proposed methods therefore do inference in subregions of the brain separately or do approximate inference without comparison to the true posterior distribution. A popular such method, which is now the standard method for Bayesian single subject analysis in the SPM software, is introduced in Penny et al. (2005b). The method processes the data slice-by-slice and uses an approximate variational Bayes (VB) estimation algorithm that enforces posterior independence between activity coefficients in different voxels. We introduce a fast and practical Markov chain Monte Carlo (MCMC) scheme for exact inference in the same model, both slice-wise and for the whole brain using a 3D prior on activity coefficients. The algorithm exploits sparsity and uses modern techniques for efficient sampling from high-dimensional Gaussian distributions, leading to speed-ups without which MCMC would not be a practical option. Using MCMC, we are for the first time able to evaluate the approximate VB posterior against the exact MCMC posterior, and show that VB can lead to spurious activation. In addition, we develop an improved VB method that drops the assumption of independent voxels a posteriori. This algorithm is shown to be much faster than both MCMC and the original VB for large datasets, with negligible error compared to the MCMC posterior.

  14. Interactive algorithms for the segmentation and quantitation of 3-D MRI brain scans.

    PubMed

    Freeborough, P A; Fox, N C; Kitney, R I

    1997-05-01

    Interactive algorithms are an attractive approach to the accurate segmentation of 3D brain scans as they potentially improve the reliability of fully automated segmentation while avoiding the labour intensiveness and inaccuracies of manual segmentation. We present a 3D image analysis package (MIDAS) with a novel architecture enabling highly interactive segmentation algorithms to be implemented as add on modules. Interactive methods based on intensity thresholding, region growing and the constrained application of morphological operators are also presented. The methods involve the application of constraints and freedoms on the algorithms coupled with real time visualisation of the effect. This methodology has been applied to the segmentation, visualisation and measurement of the whole brain and a small irregular neuroanatomical structure, the hippocampus. We demonstrate reproducible and anatomically accurate segmentations of these structures. The efficacy of one method in measuring volume loss (atrophy) of the hippocampus in Alzheimer's disease is shown and is compared to conventional methods.

  15. Sparse Bayesian framework applied to 3D super-resolution reconstruction in fetal brain MRI

    NASA Astrophysics Data System (ADS)

    Becerra, Laura C.; Velasco Toledo, Nelson; Romero Castro, Eduardo

    2015-01-01

    Fetal Magnetic Resonance (FMR) is an imaging technique that is becoming increasingly important as allows assessing brain development and thus make an early diagnostic of congenital abnormalities, spatial resolution is limited by the short acquisition time and the unpredictable fetus movements, in consequence the resulting images are characterized by non-parallel projection planes composed by anisotropic voxels. The sparse Bayesian representation is a flexible strategy which is able to model complex relationships. The Super-resolution is approached as a regression problem, the main advantage is the capability to learn data relations from observations. Quantitative performance evaluation was carried out using synthetic images, the proposed method demonstrates a better reconstruction quality compared with standard interpolation approach. The presented method is a promising approach to improve the information quality related with the 3-D fetal brain structure. It is important because allows assessing brain development and thus make an early diagnostic of congenital abnormalities.

  16. Segmentation of Brain MRI Using SOM-FCM-Based Method and 3D Statistical Descriptors

    PubMed Central

    Ortiz, Andrés; Palacio, Antonio A.; Górriz, Juan M.; Ramírez, Javier; Salas-González, Diego

    2013-01-01

    Current medical imaging systems provide excellent spatial resolution, high tissue contrast, and up to 65535 intensity levels. Thus, image processing techniques which aim to exploit the information contained in the images are necessary for using these images in computer-aided diagnosis (CAD) systems. Image segmentation may be defined as the process of parcelling the image to delimit different neuroanatomical tissues present on the brain. In this paper we propose a segmentation technique using 3D statistical features extracted from the volume image. In addition, the presented method is based on unsupervised vector quantization and fuzzy clustering techniques and does not use any a priori information. The resulting fuzzy segmentation method addresses the problem of partial volume effect (PVE) and has been assessed using real brain images from the Internet Brain Image Repository (IBSR). PMID:23762192

  17. Computation of a high-resolution MRI 3D stereotaxic atlas of the sheep brain.

    PubMed

    Ella, Arsène; Delgadillo, José A; Chemineau, Philippe; Keller, Matthieu

    2017-02-15

    The sheep model was first used in the fields of animal reproduction and veterinary sciences and then was utilized in fundamental and preclinical studies. For more than a decade, magnetic resonance (MR) studies performed on this model have been increasingly reported, especially in the field of neuroscience. To contribute to MR translational neuroscience research, a brain template and an atlas are necessary. We have recently generated the first complete T1-weighted (T1W) and T2W MR population average images (or templates) of in vivo sheep brains. In this study, we 1) defined a 3D stereotaxic coordinate system for previously established in vivo population average templates; 2) used deformation fields obtained during optimized nonlinear registrations to compute nonlinear tissues or prior probability maps (nlTPMs) of cerebrospinal fluid (CSF), gray matter (GM), and white matter (WM) tissues; 3) delineated 25 external and 28 internal sheep brain structures by segmenting both templates and nlTPMs; and 4) annotated and labeled these structures using an existing histological atlas. We built a quality high-resolution 3D atlas of average in vivo sheep brains linked to a reference stereotaxic space. The atlas and nlTPMs, associated with previously computed T1W and T2W in vivo sheep brain templates and nlTPMs, provide a complete set of imaging space that are able to be imported into other imaging software programs and could be used as standardized tools for neuroimaging studies or other neuroscience methods, such as image registration, image segmentation, identification of brain structures, implementation of recording devices, or neuronavigation. J. Comp. Neurol. 525:676-692, 2017. © 2016 Wiley Periodicals, Inc.

  18. Segmentation and quantitative evaluation of brain MRI data with a multiphase 3D implicit deformable model

    NASA Astrophysics Data System (ADS)

    Angelini, Elsa D.; Song, Ting; Mensh, Brett D.; Laine, Andrew

    2004-05-01

    Segmentation of three-dimensional anatomical brain images into tissue classes has applications in both clinical and research settings. This paper presents the implementation and quantitative evaluation of a four-phase three-dimensional active contour implemented with a level set framework for automated segmentation of brain MRIs. The segmentation algorithm performs an optimal partitioning of three-dimensional data based on homogeneity measures that naturally evolves to the extraction of different tissue types in the brain. Random seed initialization was used to speed up numerical computation and avoid the need for a priori information. This random initialization ensures robustness of the method to variation of user expertise, biased a priori information and errors in input information that could be influenced by variations in image quality. Experimentation on three MRI brain data sets showed that an optimal partitioning successfully labeled regions that accurately identified white matter, gray matter and cerebrospinal fluid in the ventricles. Quantitative evaluation of the segmentation was performed with comparison to manually labeled data and computed false positive and false negative assignments of voxels for the three organs. We report high accuracy for the two comparison cases. These results demonstrate the efficiency and flexibility of this segmentation framework to perform the challenging task of automatically extracting brain tissue volume contours.

  19. A Novel Multiparametric Approach to 3D Quantitative MRI of the Brain.

    PubMed

    Palma, Giuseppe; Tedeschi, Enrico; Borrelli, Pasquale; Cocozza, Sirio; Russo, Carmela; Liu, Saifeng; Ye, Yongquan; Comerci, Marco; Alfano, Bruno; Salvatore, Marco; Haacke, E Mark; Mancini, Marcello

    2015-01-01

    Magnetic Resonance properties of tissues can be quantified in several respects: relaxation processes, density of imaged nuclei, magnetism of environmental molecules, etc. In this paper, we propose a new comprehensive approach to obtain 3D high resolution quantitative maps of arbitrary body districts, mainly focusing on the brain. The theory presented makes it possible to map longitudinal (R1), pure transverse (R2) and free induction decay ([Formula: see text]) rates, along with proton density (PD) and magnetic susceptibility (χ), from a set of fast acquisition sequences in steady-state that are highly insensitive to flow phenomena. A novel denoising scheme is described and applied to the acquired datasets to enhance the signal to noise ratio of the derived maps and an information theory approach compensates for biases from radio frequency (RF) inhomogeneities, if no direct measure of the RF field is available. Finally, the results obtained on sample brain scans of healthy controls and multiple sclerosis patients are presented and discussed.

  20. Global brain atrophy and corticospinal tract alterations in ALS, as investigated by voxel-based morphometry of 3-D MRI.

    PubMed

    Kassubek, Jan; Unrath, Alexander; Huppertz, Hans-Jürgen; Lulé, Dorothée; Ethofer, Thomas; Sperfeld, Anne-Dorte; Ludolph, Albert C

    2005-12-01

    In ALS, advanced magnetic resonance imaging (MRI) techniques are increasingly used to investigate the underlying pathology. In this study, the technique of voxel-based morphometry (VBM) was applied to 3-D MRI data in ALS patients to localize regional grey and white matter changes. Twenty-two ALS patients (mean age 58+/-9 years) with clinically definite ALS by revised El Escorial criteria were studied. None of the patients had any signs of associated frontotemporal dementia. High-resolution 3-D MRI data sets of the whole brain, collected on a 1.5 T scanner, were analysed by statistical parametric mapping (SPM) and VBM in comparison to an age-matched normal data base consisting of 22 healthy volunteers (mean age 59+/-11 years), for grey matter and white matter segments separately. Global brain atrophy was assessed by calculation of brain parenchymal fractions (BPF). In ALS patients, BPF were significantly reduced compared to controls (p = 0.0003), indicating global brain atrophy. Regional decreases of grey matter density were found in the ALS patients at corrected p<0.01 in the right-hemispheric primary motor cortex (area of the highest Z-score) and in the left medial frontal gyrus. Furthermore, regional white matter alterations were observed along the corticospinal tracts bilaterally and in multiple smaller areas including corpus callosum, cerebellum, frontal and occipital subcortical regions. Besides considerable global atrophy in ALS, the topography of ALS-associated cerebral morphological changes could be mapped using VBM, in particular white matter signal changes along the bilateral corticospinal tracts, but also in extra-motor areas. VBM might be a potential tool to visualize disease progression in future longitudinal studies.

  1. Volumetric and surface-based 3D MRI analyses of fetal isolated mild ventriculomegaly: brain morphometry in ventriculomegaly.

    PubMed

    Scott, Julia A; Habas, Piotr A; Rajagopalan, Vidya; Kim, Kio; Barkovich, A James; Glenn, Orit A; Studholme, Colin

    2013-05-01

    Diagnosis of fetal isolated mild ventriculomegaly (IMVM) is the most common brain abnormality on prenatal ultrasound. We have set to identify potential alterations in brain development specific to IMVM in tissue volume and cortical and ventricular local surface curvature derived from in utero magnetic resonance imaging (MRI). Multislice 2D T2-weighted MRI were acquired from 32 fetuses (16 IMVM, 16 controls) between 22 and 25.5 gestational weeks. The images were motion-corrected and reconstructed into 3D volumes for volumetric and curvature analyses. The brain images were automatically segmented into cortical plate, cerebral mantle, deep gray nuclei, and ventricles. Volumes were compared between IMVM and control subjects. Surfaces were extracted from the segmentations for local mean surface curvature measurement on the inner cortical plate and the ventricles. Linear models were estimated for age-related and ventricular volume-associated changes in local curvature in both the inner cortical plate and ventricles. While ventricular volume was enlarged in IMVM, all other tissue volumes were not different from the control group. Ventricles increased in curvature with age along the atrium and anterior body. Increasing ventricular volume was associated with reduced curvature over most of the ventricular surface. The cortical plate changed in curvature with age at multiple sites of primary sulcal formation. Reduced cortical folding was detected near the parieto-occipital sulcus in IMVM subjects. While tissue volume appears to be preserved in brains with IMVM, cortical folding may be affected in regions where ventricles are dilated.

  2. Evaluation of sub-voxel registration accuracy between MRI and 3D MR spectroscopy of the brain

    NASA Astrophysics Data System (ADS)

    Rousseau, Francois; Maudsley, Andrew; Ebel, Andreas; Darkazanli, Ammar; Weber, Patrice; Sivasankaran, Krishnakumar; Yu, Yingjian; Studholme, Colin

    2005-04-01

    The implementation of Magnetic Resonance Spectroscopic Imaging (MRSI) for diagnostic imaging benefits from close integration of the lower-spatial resolution MRSI information with information from high-resolution structural MRI. Since patients can commonly move between acquisitions, it is necessary to account for possible mis-registration between the datasets arising from differences in patient positioning. In this paper we evaluate the use of 4 common multi-modality registration criteria to recover alignment between high resolution structural MRI and 3D MRSI data of the brain with sub-voxel accuracy. We explore the use of alternative MRSI water reference images to provide different types of structural information for the alignment process. The alignment accuracy was evaluated using both synthetically created MRSI and MRI data and a set of carefully collected subject image data with known ground truth spatial transformation between image volumes. The final accuracy and precision of estimates were assessed using multiple random starts of the registration algorithm. Sub voxel accuracy was found by all four similarity criteria with normalized mutual information providing the lowest target registration error for the 7 subject images. This effort supports the ongoing development of a database of brain metabolite distributions in normal subjects, which will be used in the evaluation of metabolic changes in neurological diseases.

  3. A discriminative model-constrained EM approach to 3D MRI brain tissue classification and intensity non-uniformity correction

    NASA Astrophysics Data System (ADS)

    Wels, Michael; Zheng, Yefeng; Huber, Martin; Hornegger, Joachim; Comaniciu, Dorin

    2011-06-01

    We describe a fully automated method for tissue classification, which is the segmentation into cerebral gray matter (GM), cerebral white matter (WM), and cerebral spinal fluid (CSF), and intensity non-uniformity (INU) correction in brain magnetic resonance imaging (MRI) volumes. It combines supervised MRI modality-specific discriminative modeling and unsupervised statistical expectation maximization (EM) segmentation into an integrated Bayesian framework. While both the parametric observation models and the non-parametrically modeled INUs are estimated via EM during segmentation itself, a Markov random field (MRF) prior model regularizes segmentation and parameter estimation. Firstly, the regularization takes into account knowledge about spatial and appearance-related homogeneity of segments in terms of pairwise clique potentials of adjacent voxels. Secondly and more importantly, patient-specific knowledge about the global spatial distribution of brain tissue is incorporated into the segmentation process via unary clique potentials. They are based on a strong discriminative model provided by a probabilistic boosting tree (PBT) for classifying image voxels. It relies on the surrounding context and alignment-based features derived from a probabilistic anatomical atlas. The context considered is encoded by 3D Haar-like features of reduced INU sensitivity. Alignment is carried out fully automatically by means of an affine registration algorithm minimizing cross-correlation. Both types of features do not immediately use the observed intensities provided by the MRI modality but instead rely on specifically transformed features, which are less sensitive to MRI artifacts. Detailed quantitative evaluations on standard phantom scans and standard real-world data show the accuracy and robustness of the proposed method. They also demonstrate relative superiority in comparison to other state-of-the-art approaches to this kind of computational task: our method achieves average

  4. CT and MRI Assessment and Characterization Using Segmentation and 3D Modeling Techniques: Applications to Muscle, Bone and Brain.

    PubMed

    Gargiulo, Paolo; Helgason, Thordur; Ramon, Ceon; Jr, Halldór Jónsson; Carraro, Ugo

    2014-03-31

    This paper reviews the novel use of CT and MRI data and image processing tools to segment and reconstruct tissue images in 3D to determine characteristics of muscle, bone and brain. This to study and simulate the structural changes occurring in healthy and pathological conditions as well as in response to clinical treatments. Here we report the application of this methodology to evaluate and quantify: 1. progression of atrophy in human muscle subsequent to permanent lower motor neuron (LMN) denervation, 2. muscle recovery as induced by functional electrical stimulation (FES), 3. bone quality in patients undergoing total hip replacement and 4. to model the electrical activity of the brain. Study 1: CT data and segmentation techniques were used to quantify changes in muscle density and composition by associating the Hounsfield unit values of muscle, adipose and fibrous connective tissue with different colors. This method was employed to monitor patients who have permanent muscle LMN denervation in the lower extremities under two different conditions: permanent LMN denervated not electrically stimulated and stimulated. Study 2: CT data and segmentation techniques were employed, however, in this work we assessed bone and muscle conditions in the pre-operative CT scans of patients scheduled to undergo total hip replacement. In this work, the overall anatomical structure, the bone mineral density (BMD) and compactness of quadriceps muscles and proximal femoral was computed to provide a more complete view for surgeons when deciding which implant technology to use. Further, a Finite element analysis provided a map of the strains around the proximal femur socket when solicited by typical stresses caused by an implant press fitting. Study 3 describes a method to model the electrical behavior of human brain using segmented MR images. The aim of the work is to use these models to predict the electrical activity of the human brain under normal and pathological conditions by

  5. Predicting Alzheimer's disease by classifying 3D-Brain MRI images using SVM and other well-defined classifiers

    NASA Astrophysics Data System (ADS)

    Matoug, S.; Abdel-Dayem, A.; Passi, K.; Gross, W.; Alqarni, M.

    2012-02-01

    Alzheimer's disease (AD) is the most common form of dementia affecting seniors age 65 and over. When AD is suspected, the diagnosis is usually confirmed with behavioural assessments and cognitive tests, often followed by a brain scan. Advanced medical imaging and pattern recognition techniques are good tools to create a learning database in the first step and to predict the class label of incoming data in order to assess the development of the disease, i.e., the conversion from prodromal stages (mild cognitive impairment) to Alzheimer's disease, which is the most critical brain disease for the senior population. Advanced medical imaging such as the volumetric MRI can detect changes in the size of brain regions due to the loss of the brain tissues. Measuring regions that atrophy during the progress of Alzheimer's disease can help neurologists in detecting and staging the disease. In the present investigation, we present a pseudo-automatic scheme that reads volumetric MRI, extracts the middle slices of the brain region, performs segmentation in order to detect the region of brain's ventricle, generates a feature vector that characterizes this region, creates an SQL database that contains the generated data, and finally classifies the images based on the extracted features. For our results, we have used the MRI data sets from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database.

  6. Intersection Based Motion Correction of Multi-Slice MRI for 3D in utero Fetal Brain Image Formation

    PubMed Central

    Kim, Kio; Habas, Piotr A.; Rousseau, Francois; Glenn, Orit A.; Barkovich, Anthony J.; Studholme, Colin

    2012-01-01

    In recent years post-processing of fast multi-slice MR imaging to correct fetal motion has provided the first true 3D MR images of the developing human brain in utero. Early approaches have used reconstruction based algorithms, employing a two step iterative process, where slices from the acquired data are re-aligned to an approximate 3D reconstruction of the fetal brain, which is then refined further using the improved slice alignment. This two step slice-to-volume process, although powerful, is computationally expensive in needing a 3D reconstruction, and is limited in its ability to recover sub-voxel alignment. Here, we describe an alternative approach which we term slice intersection motion correction (SIMC), that seeks to directly co-align multiple slice stacks by considering the matching structure along all intersecting slice pairs in all orthogonally planned slices that are acquired in clinical imaging studies. A collective update scheme for all slices is then derived, to simultaneously drive slices into a consistent match along their lines of intersection. We then describe a 3D reconstruction algorithm that, using the final motion corrected slice locations, suppresses through-plane partial volume effects to provide a single high isotropic resolution 3D image. The method is tested on simulated data with known motions and is applied to retrospectively reconstruct 3D images from a range of clinically acquired imaging studies. The quantitative evaluation of the registration accuracy for the simulated data sets demonstrated a significant improvement over previous approaches. An initial application of the technique to studying clinical pathology is included, where the proposed method recovered up to 15 mm of translation and 30 degrees of rotation for individual slices, and produced full 3D reconstructions containing clinically useful additional information not visible in the original 2D slices. PMID:19744911

  7. [Pathophysiological diagnosis of facial paralysis using 3-D MRI].

    PubMed

    Ishihara, T; Hirata, K; Yuki, N; Sato, T

    2001-04-01

    Bilateral facial paralysis(facial diplesia) is often observed in Guillain-Barré syndrome(GBS) and Fisher's syndrome (FS). We tried to observe injured facial nerves using three-dimensional(3-D) MRI in facial diplesia due to GBS and its variants and examined function of blood nerve barrier and clinical use of 3-D MRI for detecting injured facial nerves. In the four patients with GBS and its variants(GBS three cases, FS one case), while routine brain MRI did not show any abnormal findings, contrast-enhanced 3-D MRI revealed Gd-enhancement of the facial nerves. On the other hand, only one case showed visualization using contrast-enhanced 3-D MRI in twelve cases of Bell's palsy. Therefore, it may be presumed that the reason why the significantly higher rate of visualization in facial paralysis in GBS and its variants than in Bell's palsy is attributable to a difference in the mechanism of injury or the extreme seriousness of the disease. In conclusion, the observation of facial nerve using 3-D MRI was very useful to know the condition of the facial diplesia in GBS and its variants.

  8. Sodium 3D COncentration MApping (COMA 3D) using 23Na and proton MRI

    NASA Astrophysics Data System (ADS)

    Truong, Milton L.; Harrington, Michael G.; Schepkin, Victor D.; Chekmenev, Eduard Y.

    2014-10-01

    Functional changes of sodium 3D MRI signals were converted into millimolar concentration changes using an open-source fully automated MATLAB toolbox. These concentration changes are visualized via 3D sodium concentration maps, and they are overlaid over conventional 3D proton images to provide high-resolution co-registration for easy correlation of functional changes to anatomical regions. Nearly 5000/h concentration maps were generated on a personal computer (ca. 2012) using 21.1 T 3D sodium MRI brain images of live rats with spatial resolution of 0.8 × 0.8 × 0.8 mm3 and imaging matrices of 60 × 60 × 60. The produced concentration maps allowed for non-invasive quantitative measurement of in vivo sodium concentration in the normal rat brain as a functional response to migraine-like conditions. The presented work can also be applied to sodium-associated changes in migraine, cancer, and other metabolic abnormalities that can be sensed by molecular imaging. The MATLAB toolbox allows for automated image analysis of the 3D images acquired on the Bruker platform and can be extended to other imaging platforms. The resulting images are presented in a form of series of 2D slices in all three dimensions in native MATLAB and PDF formats. The following is provided: (a) MATLAB source code for image processing, (b) the detailed processing procedures, (c) description of the code and all sub-routines, (d) example data sets of initial and processed data. The toolbox can be downloaded at: http://www.vuiis.vanderbilt.edu/~truongm/COMA3D/.

  9. Sodium 3D COncentration MApping (COMA 3D) Using 23Na and Proton MRI

    PubMed Central

    Truong, Milton L.; Harrington, Michael G.; Schepkin, Victor D.; Chekmenev, Eduard Y.

    2014-01-01

    Functional changes of sodium 3D MRI signals were converted into millimolar concentration changes using an open-source fully automated MATLAB toolbox. These concentration changes are visualized via 3D sodium concentration maps, and they are overlaid over conventional 3D proton images to provide high-resolution co-registration for easy correlation of functional changes to anatomical regions. Nearly 5000/hour concentration maps were generated on a personal computer (ca. 2012) using 21.1 T 3D sodium MRI brain images of live rats with spatial resolution of 0.8×0.8×0.8 mm3 and imaging matrices of 60×60×60. The produced concentration maps allowed for non-invasive quantitative measurement of in vivo sodium concentration in the normal rat brain as a functional response to migraine-like conditions. The presented work can also be applied to sodium-associated changes in migraine, cancer, and other metabolic abnormalities that can be sensed by molecular imaging. The MATLAB toolbox allows for automated image analysis of the 3D images acquired on the Bruker platform and can be extended to other imaging platforms. The resulting images are presented in a form of series of 2D slices in all three dimensions in native MATLAB and PDF formats. The following is provided: (a) MATLAB source code for image processing, (b) the detailed processing procedures, (c) description of the code and all sub-routines, (d) example data sets of initial and processed data. The toolbox can be downloaded at: http://www.vuiis.vanderbilt.edu/~truongm/COMA3D/ PMID:25261742

  10. Development and Assessment of a New 3D Neuroanatomy Teaching Tool for MRI Training

    ERIC Educational Resources Information Center

    Drapkin, Zachary A.; Lindgren, Kristen A.; Lopez, Michael J.; Stabio, Maureen E.

    2015-01-01

    A computerized three-dimensional (3D) neuroanatomy teaching tool was developed for training medical students to identify subcortical structures on a magnetic resonance imaging (MRI) series of the human brain. This program allows the user to transition rapidly between two-dimensional (2D) MRI slices, 3D object composites, and a combined model in…

  11. Streamlined, Inexpensive 3D Printing of the Brain and Skull

    PubMed Central

    Cash, Sydney S.

    2015-01-01

    Neuroimaging technologies such as Magnetic Resonance Imaging (MRI) and Computed Tomography (CT) collect three-dimensional data (3D) that is typically viewed on two-dimensional (2D) screens. Actual 3D models, however, allow interaction with real objects such as implantable electrode grids, potentially improving patient specific neurosurgical planning and personalized clinical education. Desktop 3D printers can now produce relatively inexpensive, good quality prints. We describe our process for reliably generating life-sized 3D brain prints from MRIs and 3D skull prints from CTs. We have integrated a standardized, primarily open-source process for 3D printing brains and skulls. We describe how to convert clinical neuroimaging Digital Imaging and Communications in Medicine (DICOM) images to stereolithography (STL) files, a common 3D object file format that can be sent to 3D printing services. We additionally share how to convert these STL files to machine instruction gcode files, for reliable in-house printing on desktop, open-source 3D printers. We have successfully printed over 19 patient brain hemispheres from 7 patients on two different open-source desktop 3D printers. Each brain hemisphere costs approximately $3–4 in consumable plastic filament as described, and the total process takes 14–17 hours, almost all of which is unsupervised (preprocessing = 4–6 hr; printing = 9–11 hr, post-processing = <30 min). Printing a matching portion of a skull costs $1–5 in consumable plastic filament and takes less than 14 hr, in total. We have developed a streamlined, cost-effective process for 3D printing brain and skull models. We surveyed healthcare providers and patients who confirmed that rapid-prototype patient specific 3D models may help interdisciplinary surgical planning and patient education. The methods we describe can be applied for other clinical, research, and educational purposes. PMID:26295459

  12. Streamlined, Inexpensive 3D Printing of the Brain and Skull.

    PubMed

    Naftulin, Jason S; Kimchi, Eyal Y; Cash, Sydney S

    2015-01-01

    Neuroimaging technologies such as Magnetic Resonance Imaging (MRI) and Computed Tomography (CT) collect three-dimensional data (3D) that is typically viewed on two-dimensional (2D) screens. Actual 3D models, however, allow interaction with real objects such as implantable electrode grids, potentially improving patient specific neurosurgical planning and personalized clinical education. Desktop 3D printers can now produce relatively inexpensive, good quality prints. We describe our process for reliably generating life-sized 3D brain prints from MRIs and 3D skull prints from CTs. We have integrated a standardized, primarily open-source process for 3D printing brains and skulls. We describe how to convert clinical neuroimaging Digital Imaging and Communications in Medicine (DICOM) images to stereolithography (STL) files, a common 3D object file format that can be sent to 3D printing services. We additionally share how to convert these STL files to machine instruction gcode files, for reliable in-house printing on desktop, open-source 3D printers. We have successfully printed over 19 patient brain hemispheres from 7 patients on two different open-source desktop 3D printers. Each brain hemisphere costs approximately $3-4 in consumable plastic filament as described, and the total process takes 14-17 hours, almost all of which is unsupervised (preprocessing = 4-6 hr; printing = 9-11 hr, post-processing = <30 min). Printing a matching portion of a skull costs $1-5 in consumable plastic filament and takes less than 14 hr, in total. We have developed a streamlined, cost-effective process for 3D printing brain and skull models. We surveyed healthcare providers and patients who confirmed that rapid-prototype patient specific 3D models may help interdisciplinary surgical planning and patient education. The methods we describe can be applied for other clinical, research, and educational purposes.

  13. Development and assessment of a new 3D neuroanatomy teaching tool for MRI training.

    PubMed

    Drapkin, Zachary A; Lindgren, Kristen A; Lopez, Michael J; Stabio, Maureen E

    2015-01-01

    A computerized three-dimensional (3D) neuroanatomy teaching tool was developed for training medical students to identify subcortical structures on a magnetic resonance imaging (MRI) series of the human brain. This program allows the user to transition rapidly between two-dimensional (2D) MRI slices, 3D object composites, and a combined model in which 3D objects are overlaid onto the 2D MRI slices, all while rotating the brain in any direction and advancing through coronal, sagittal, or axial planes. The efficacy of this tool was assessed by comparing scores from an MRI identification quiz and survey in two groups of first-year medical students. The first group was taught using this new 3D teaching tool, and the second group was taught the same content for the same amount of time but with traditional methods, including 2D images of brain MRI slices and 3D models from widely used textbooks and online sources. Students from the experimental group performed marginally better than the control group on overall test score (P = 0.07) and significantly better on test scores extracted from questions involving C-shaped internal brain structures (P < 0.01). Experimental participants also expressed higher confidence in their abilities to visualize the 3D structure of the brain (P = 0.02) after using this tool. Furthermore, when surveyed, 100% of the students in the experimental group recommended this tool for future students. These results suggest that this neuroanatomy teaching tool is an effective way to train medical students to read an MRI of the brain and is particularly effective for teaching C-shaped internal brain structures.

  14. Cetacean brain evolution: Dwarf sperm whale (Kogia sima) and common dolphin (Delphinus delphis) - An investigation with high-resolution 3D MRI.

    PubMed

    Oelschläger, H H A; Ridgway, S H; Knauth, M

    2010-01-01

    This study compares a whole brain of the dwarf sperm whale (Kogia sima) with that of a common dolphin (Delphinus delphis) using high-resolution magnetic resonance imaging (MRI). The Kogia brain was scanned with a Siemens Trio Magnetic Resonance scanner in the three main planes. As in the common dolphin and other marine odontocetes, the brain of the dwarf sperm whale is large, with the telencephalic hemispheres remarkably dominating the brain stem. The neocortex is voluminous and the cortical grey matter thin but expansive and densely convoluted. The corpus callosum is thin and the anterior commissure hard to detect whereas the posterior commissure is well-developed. There is consistency as to the lack of telencephalic structures (olfactory bulb and peduncle, olfactory ventricular recess) and neither an occipital lobe of the telencephalic hemisphere nor the posterior horn of the lateral ventricle are present. A pineal organ could not be detected in Kogia. Both species show a tiny hippocampus and thin fornix and the mammillary body is very small whereas other structures of the limbic system are well-developed. The brain stem is thick and underlies a large cerebellum, both of which, however, are smaller in Kogia. The vestibular system is markedly reduced with the exception of the lateral (Deiters') nucleus. The visual system, although well-developed in both species, is exceeded by the impressive absolute and relative size of the auditory system. The brainstem and cerebellum comprise a series of structures (elliptic nucleus, medial accessory inferior olive, paraflocculus and posterior interpositus nucleus) showing characteristic odontocete dimensions and size correlations. All these structures seem to serve the auditory system with respect to echolocation, communication, and navigation.

  15. Framework for 2D-3D image fusion of infrared thermography with preoperative MRI.

    PubMed

    Hoffmann, Nico; Weidner, Florian; Urban, Peter; Meyer, Tobias; Schnabel, Christian; Radev, Yordan; Schackert, Gabriele; Petersohn, Uwe; Koch, Edmund; Gumhold, Stefan; Steiner, Gerald; Kirsch, Matthias

    2017-01-23

    Multimodal medical image fusion combines information of one or more images in order to improve the diagnostic value. While previous applications mainly focus on merging images from computed tomography, magnetic resonance imaging (MRI), ultrasonic and single-photon emission computed tomography, we propose a novel approach for the registration and fusion of preoperative 3D MRI with intraoperative 2D infrared thermography. Image-guided neurosurgeries are based on neuronavigation systems, which further allow us track the position and orientation of arbitrary cameras. Hereby, we are able to relate the 2D coordinate system of the infrared camera with the 3D MRI coordinate system. The registered image data are now combined by calibration-based image fusion in order to map our intraoperative 2D thermographic images onto the respective brain surface recovered from preoperative MRI. In extensive accuracy measurements, we found that the proposed framework achieves a mean accuracy of 2.46 mm.

  16. Comparison of 3D Orientation Distribution Functions Measured with Confocal Microscopy and Diffusion MRI

    PubMed Central

    Schilling, Kurt; Janve, Vaibhav; Gao, Yurui; Stepniewska, Iwona; Landman, Bennett A; Anderson, Adam W

    2016-01-01

    The ability of diffusion MRI (dMRI) fiber tractography to non-invasively map three-dimensional (3D) anatomical networks in the human brain has made it a valuable tool in both clinical and research settings. However, there are many assumptions inherent to any tractography algorithm that can limit the accuracy of the reconstructed fiber tracts. Among them is the assumption that the diffusion-weighted images accurately reflect the underlying fiber orientation distribution (FOD) in the MRI voxel. Consequently, validating dMRI’s ability to assess the underlying fiber orientation in each voxel is critical for its use as a biomedical tool. Here, using post-mortem histology and confocal microscopy, we present a method to perform histological validation of orientation functions in 3D, which has previously been limited to two-dimensional analysis of tissue sections. We demonstrate the ability to extract the 3D FOD from confocal z-stacks, and quantify the agreement between the MRI estimates of orientation information obtained using constrained spherical deconvolution (CSD) and the true geometry of the fibers. We find an orientation error of approximately 6° in voxels containing nearly parallel fibers, and 10-11° in crossing fiber regions, and note that CSD was unable to resolve fibers crossing at angles below 60° in our dataset. This is the first time the 3D white matter orientation distribution is calculated from histology and compared to dMRI. Thus, this technique serves as a gold standard for dMRI validation studies - providing the ability to determine the extent to which the dMRI signal is consistent with the histological FOD, and to establish how well different dMRI models can predict the ground truth FOD. PMID:26804781

  17. [Detection of oculomotor nerve compression by 3D-FIESTA MRI in a patient with pituitary apoplexy and diabetes mellitus].

    PubMed

    Yamauchi, Takahiro; Kitai, Ryuhei; Neishi, Hiroyuki; Tsunetoshi, Kenzo; Matsuda, Ken; Arishima, Hidetaka; Kodera, Toshiaki; Arai, Yoshikazu; Takeuchi, Hiroaki; Kikuta, Ken-ichiro

    2014-02-01

    We report the usefulness of 3D-FIESTA magnetic resonance imaging(MRI)for the detection of oculomotor nerve palsy in a case of pituitary apoplexy. A 69-year-old man with diabetes mellitus presented with complete left-side blepharoptosis. Computed tomography of the brain showed an intrasellar mass with hemorrhage. MRI demonstrated a pituitary adenoma with a cyst toward the left cavernous sinus, which was diagnosed as pituitary apoplexy. 3D-FIESTA revealed that the left oculomotor nerve was compressed by the cyst. He underwent trans-sphenoid tumor resection at 5 days after his hospitalization. Post-operative 3D-FIESTA MRI revealed decrease in compression of the left oculomotor nerve by the cyst. His left oculomotor palsy recovered completely within a few months. Oculomotor nerve palsy can occur due to various diseases, and 3D-FIESTA MRI is useful for detection of oculomotor nerve compression, especially in the field of parasellar lesions.

  18. Dynamic deformable models for 3D MRI heart segmentation

    NASA Astrophysics Data System (ADS)

    Zhukov, Leonid; Bao, Zhaosheng; Gusikov, Igor; Wood, John; Breen, David E.

    2002-05-01

    Automated or semiautomated segmentation of medical images decreases interstudy variation, observer bias, and postprocessing time as well as providing clincally-relevant quantitative data. In this paper we present a new dynamic deformable modeling approach to 3D segmentation. It utilizes recently developed dynamic remeshing techniques and curvature estimation methods to produce high-quality meshes. The approach has been implemented in an interactive environment that allows a user to specify an initial model and identify key features in the data. These features act as hard constraints that the model must not pass through as it deforms. We have employed the method to perform semi-automatic segmentation of heart structures from cine MRI data.

  19. 3D mapping of somatotopic reorganization with small animal functional MRI

    PubMed Central

    Yu, Xin; Wang, Shumin; Chen, Der-Yow; Dodd, Stephen; Goloshevsky, Artem; Koretsky, Alan P.

    2009-01-01

    There are few in vivo noninvasive methods to study neuroplasticity in animal brains. Functional MRI (fMRI) has been developed for animal brain mapping, but few fMRI studies have analyzed functional alteration due to plasticity in animal models. One major limitation is that fMRI maps are characterized by statistical parametric mapping making the apparent boundary dependent on the statistical threshold used. Here, we developed a method to characterize the location of center-of-mass in fMRI maps that is shown not to be sensitive to statistical threshold. Utilizing centers-of-mass as anchor points to fit the spatial distribution of the BOLD response enabled quantitative group analysis of altered boundaries of functional somatosensory maps. This approach was used to study cortical reorganization in the rat primary somatosensory cortex (S1) after sensory deprivation to the barrel cortex by follicle ablation (F.A.). FMRI demonstrated an enlarged nose S1 representation in the 3D somatotopic functional maps. This result clearly demonstrates that fMRI enables the spatial mapping of functional changes that can characterize multiple regions of S1 cortex and still be sensitive to changes due to plasticity. PMID:19770051

  20. 3D structure tensor analysis of light microscopy data for validating diffusion MRI

    PubMed Central

    Khan, Ahmad Raza; Cornea, Anda; Leigland, Lindsey A.; Kohama, Steven G.; Jespersen, Sune Nørhøj; Kroenke, Christopher D.

    2015-01-01

    Diffusion magnetic resonance imaging (d-MRI) is a powerful non-invasive and non-destructive technique for characterizing brain tissue on the microscopic scale. However, the lack of validation of d-MRI by independent experimental means poses an obstacle to accurate interpretation of data acquired using this method. Recently, structure tensor analysis has been applied to light microscopy images, and this technique holds promise to be a powerful validation strategy for d-MRI. Advantages of this approach include its similarity to d-MRI in terms of averaging the effects of a large number of cellular structures, and its simplicity, which enables it to be implemented in a high-throughput manner. However, a drawback of previous implementations of this technique arises from it being restricted to 2D. As a result, structure tensor analyses have been limited to tissue sectioned in a direction orthogonal to the direction of interest. Here we describe the analytical framework for extending structure tensor analysis to 3D, and utilize the results to analyze serial image “stacks” acquired with confocal microscopy of rhesus macaque hippocampal tissue. Implementation of 3D structure tensor procedures requires removal of sources of anisotropy introduced in tissue preparation and confocal imaging. This is accomplished with image processing steps to mitigate the effects of anisotropic tissue shrinkage, and the effects of anisotropy in the point spread function (PSF). In order to address the latter confound, we describe procedures for measuring the dependence of PSF anisotropy on distance from the microscope objective within tissue. Prior to microscopy, ex vivo d-MRI measurements performed on the hippocampal tissue revealed three regions of tissue with mutually orthogonal directions of least restricted diffusion that correspond to CA1, alveus and inferior longitudinal fasciculus. We demonstrate the ability of 3D structure tensor analysis to identify structure tensor orientations

  1. 3D printing from MRI Data: Harnessing strengths and minimizing weaknesses.

    PubMed

    Ripley, Beth; Levin, Dmitry; Kelil, Tatiana; Hermsen, Joshua L; Kim, Sooah; Maki, Jeffrey H; Wilson, Gregory J

    2017-03-01

    3D printing facilitates the creation of accurate physical models of patient-specific anatomy from medical imaging datasets. While the majority of models to date are created from computed tomography (CT) data, there is increasing interest in creating models from other datasets, such as ultrasound and magnetic resonance imaging (MRI). MRI, in particular, holds great potential for 3D printing, given its excellent tissue characterization and lack of ionizing radiation. There are, however, challenges to 3D printing from MRI data as well. Here we review the basics of 3D printing, explore the current strengths and weaknesses of printing from MRI data as they pertain to model accuracy, and discuss considerations in the design of MRI sequences for 3D printing. Finally, we explore the future of 3D printing and MRI, including creative applications and new materials.

  2. 3D-EAUS and MRI in the Activity of Anal Fistulas in Crohn's Disease.

    PubMed

    Alabiso, Maria Eleonora; Iasiello, Francesca; Pellino, Gianluca; Iacomino, Aniello; Roberto, Luca; Pinto, Antonio; Riegler, Gabriele; Selvaggi, Francesco; Reginelli, Alfonso

    2016-01-01

    Aim. This study aspires to assess the role of 3D-Endoanal Ultrasound (3D-EAUS) and Magnetic Resonance Imaging (MRI) in preoperative evaluation of the primary tract and internal opening of perianal fistulas, of secondary extensions and abscess. Methods. During 2014, 51 Crohn's disease patients suspected for perianal fistula were enrolled. All patients underwent physical examination with both the methods and subsequent surgery. Results. In the evaluation of CD perianal fistulas, there are no significant differences between 3D-EAUS and MRI in the identification of abscess and secondary extension. Considering the location, 3D-EAUS was more accurate than MRI in the detection of intersphincteric fistulas (p value = 10(-6)); conversely, MRI was more accurate than 3D-EAUS in the detection of suprasphincteric fistulas (p value = 0.0327) and extrasphincteric fistulas (p  value = 4 ⊕ 10(-6)); there was no significant difference between MRI and 3D-EAUS in the detection of transsphincteric fistulas. Conclusions. Both 3D-EAUS and MRI have a crucial role in the evaluation and detection of CD perianal fistulas. 3D-EAUS was preferable to MRI in the detection of intersphincteric fistulas; conversely, in the evaluation of suprasphincteric and extrasphincteric fistulas the MRI was preferable to 3D-EAUS.

  3. Hybrid atlas-based and image-based approach for segmenting 3D brain MRIs

    NASA Astrophysics Data System (ADS)

    Bueno, Gloria; Musse, Olivier; Heitz, Fabrice; Armspach, Jean-Paul

    2001-07-01

    This work is a contribution to the problem of localizing key cerebral structures in 3D MRIs and its quantitative evaluation. In pursuing it, the cooperation between an image-based segmentation method and a hierarchical deformable registration approach has been considered. The segmentation relies on two main processes: homotopy modification and contour decision. The first one is achieved by a marker extraction stage where homogeneous 3D regions of an image, I(s), from the data set are identified. These regions, M(I), are obtained combining information from deformable atlas, achieved by the warping of eight previous labeled maps on I(s). Then, the goal of the decision stage is to precisely locate the contours of the 3D regions set by the markers. This contour decision is performed by a 3D extension of the watershed transform. The anatomical structures taken into consideration and embedded into the atlas are brain, ventricles, corpus callosum, cerebellum, right and left hippocampus, medulla and midbrain. The hybrid method operates fully automatically and in 3D, successfully providing segmented brain structures. The quality of the segmentation has been studied in terms of the detected volume ratio by using kappa statistic and ROC analysis. Results of the method are shown and validated on a 3D MRI phantom. This study forms part of an on-going long term research aiming at the creation of a 3D probabilistic multi-purpose anatomical brain atlas.

  4. Brain tumor locating in 3D MR volume using symmetry

    NASA Astrophysics Data System (ADS)

    Dvorak, Pavel; Bartusek, Karel

    2014-03-01

    This work deals with the automatic determination of a brain tumor location in 3D magnetic resonance volumes. The aim of this work is not the precise segmentation of the tumor and its parts but only the detection of its location. This work is the first step in the tumor segmentation process, an important topic in neuro-image processing. The algorithm expects 3D magnetic resonance volumes of brain containing a tumor. The detection is based on locating the area that breaks the left-right symmetry of the brain. This is done by multi-resolution comparing of corresponding regions in left and right hemisphere. The output of the computation is the probabilistic map of the tumor location. The created algorithm was tested on 80 volumes from publicly available BRATS databases containing 3D brain volumes afflicted by a brain tumor. These pathological structures had various sizes and shapes and were located in various parts of the brain. The locating performance of the algorithm was 85% for T1-weighted volumes, 91% for T1-weighted contrast enhanced volumes, 96% for FLAIR and T2-wieghted volumes and 95% for their combinations.

  5. 3D quantitative analysis of brain SPECT images

    NASA Astrophysics Data System (ADS)

    Loncaric, Sven; Ceskovic, Ivan; Petrovic, Ratimir; Loncaric, Srecko

    2001-07-01

    The main purpose of this work is to develop a computer-based technique for quantitative analysis of 3-D brain images obtained by single photon emission computed tomography (SPECT). In particular, the volume and location of ischemic lesion and penumbra is important for early diagnosis and treatment of infracted regions of the brain. SPECT imaging is typically used as diagnostic tool to assess the size and location of the ischemic lesion. The segmentation method presented in this paper utilizes a 3-D deformable model in order to determine size and location of the regions of interest. The evolution of the model is computed using a level-set implementation of the algorithm. In addition to 3-D deformable model the method utilizes edge detection and region growing for realization of a pre-processing. Initial experimental results have shown that the method is useful for SPECT image analysis.

  6. EEG-MRI co-registration and sensor labeling using a 3D laser scanner.

    PubMed

    Koessler, L; Cecchin, T; Caspary, O; Benhadid, A; Vespignani, H; Maillard, L

    2011-03-01

    This paper deals with the co-registration of an MRI scan with EEG sensors. We set out to evaluate the effectiveness of a 3D handheld laser scanner, a device that is not widely used for co-registration, applying a semi-automatic procedure that also labels EEG sensors. The scanner acquired the sensors' positions and the face shape, and the scalp mesh was obtained from the MRI scan. A pre-alignment step, using the position of three fiducial landmarks, provided an initial value for co-registration, and the sensors were automatically labeled. Co-registration was then performed using an iterative closest point algorithm applied to the face shape. The procedure was conducted on five subjects with two scans of EEG sensors and one MRI scan each. The mean time for the digitization of the 64 sensors and three landmarks was 53 s. The average scanning time for the face shape was 2 min 6 s for an average number of 5,263 points. The mean residual error of the sensors co-registration was 2.11 mm. These results suggest that the laser scanner associated with an efficient co-registration and sensor labeling algorithm is sufficiently accurate, fast and user-friendly for longitudinal and retrospective brain sources imaging studies.

  7. Application of whole-brain CBV-weighted fMRI to a cognitive stimulation paradigm: robust activation detection in a stroop task experiment using 3D GRASE VASO.

    PubMed

    Poser, Benedikt A; Norris, David G

    2011-06-01

    Brain activation studies generally utilize blood oxygenation level dependent (BOLD) contrast, most commonly measured using the gradient-echo echo-planar imaging (EPI) technique. BOLD contrast arises from regional changes in cerebral blood flow (CBF), cerebral blood volume (CBV), and the local metabolic rate of oxygen consumption. An alternative to BOLD is the detection of activation through direct measurement of these parameters. A noninvasive approach to measure activation-related CBV changes is the vascular space occupancy (VASO) method, which exploits blood as an endogenous contrast agent by selectively nulling the magnetization of the water spins in the blood. Using a recently developed multislice variant of VASO that enables single-shot whole-brain coverage by virtue of a three-dimensional GRASE readout, we here present the first application of VASO to an fMRI study with a whole-brain cognitive task. Within acceptable measurement times (∼12 minutes), brain activation during a Stroop color-word matching task could be detected reliably both on the group (N = 12) and single subject level, as evident from a qualitative comparison with separately acquired BOLD data and literature reports.

  8. SU-E-J-231: Comparison of 3D Angiogram and MRI in Delineating the AVM Target for Frameless Stereotactic Radiosurgery

    SciTech Connect

    Avkshtol, V; Tanny, S; Reddy, K; Chen, C; Parsai, E

    2014-06-01

    Purpose: Stereotactic radiation therapy (SRT) provides an excellent alternative to embolization and surgical excision for the management of appropriately selected cerebral arteriovenous malformations (AVMs). The currently accepted standard for delineating AVMs is planar digital subtraction angiography (DSA). DSA can be used to acquire a 3D data set that preserves osseous structures (3D-DA) at the time of the angiography for SRT planning. Magnetic resonance imaging (MRI) provides an alternative noninvasive method of visualizing the AVM nidus with comparable spatial resolution. We utilized 3D-DA and T1 post-contrast MRI data to evaluate the differences in SRT target volumes. Methods: Four patients underwent 3D-DA and high-resolution MRI. 3D T1 post-contrast images were obtained in all three reconstruction planes. A planning CT was fused with MRI and 3D-DA data sets. The AVMs were contoured utilizing one of the image sets at a time. Target volume, centroid, and maximum and minimum dimensions were analyzed for each patient. Results: Targets delineated using post-contrast MRI demonstrated a larger mean volume. AVMs >2 cc were found to have a larger difference between MRI and 3D-DA volumes. Larger AVMs also demonstrated a smaller relative uncertainty in contour centroid position (1 mm). AVM targets <2 cc had smaller absolute differences in volume, but larger differences in contour centroid position (2.5 mm). MRI targets demonstrated a more irregular shape compared to 3D-DA targets. Conclusions: Our preliminary data supports the use of MRI alone to delineate AVM targets >2 cc. The greater centroid stability for AVMs >2 cc ensures accurate target localization during image fusion. The larger MRI target volumes did not result in prohibitively greater volumes of normal brain tissue receiving the prescription dose. The larger centroid instability for AVMs <2 cc precludes the use of MRI alone for target delineation. We recommend incorporating a 3D-DA for these patients.

  9. Guided Interventions for Prostate Cancer Using 3D-Transurethral Ultrasound and MRI Fusion

    DTIC Science & Technology

    2015-10-01

    prostate may be visualized at once; improving image registration and reducing motion errors. 3D TUUS imaging has been demonstrated in a phantom setting... registration error 10-21 UCLA Milestone(s) Achieved: Validation of MR-TUUS image registration error with MRI and compared to 3D TRUS 21...TRUS ultrasound images of prostate phantom with 20 deg urethra bend, (left) 2D prostate image, (right) 3D volume of prostate phantom. 6 image

  10. A 3D digital map of rat brain.

    PubMed

    Toga, A W; Santori, E M; Hazani, R; Ambach, K

    1995-01-01

    A three dimensional (3D) computerized map of rat brain anatomy created with digital imaging techniques is described. Six male Sprague-Dawley rats, weighing 270-320 g, were used in the generation of this atlas. Their heads were frozen, and closely spaced cryosectional images were digitally captured. Each serial data set was organized into a digital volume, reoriented into a flat skull position, and brought into register with each other. A volume representative of the group following registration was chosen based on its anatomic correspondence with the other specimens as measured by image correlation coefficients and landmark matching. Mean positions of lambda, bregma, and the interaural plane of the group within the common coordinate system were used to transform the representative volume into a 3D map of rat neuroanatomy. images reconstructed from this 3D map are available to the public via Internet with an anonymous file transfer protocol (FTP) and World Wide Web. A complete description of the digital map is provided in a comprehensive set of sagittal planes (up to 0.031 mm spacing) containing stereotaxic reference grids. Sets of coronal and horizontal planes, resampled at the same increment, also are included. Specific anatomic features are identified in a second collection of images. Stylized anatomic boundaries and structural labels were incorporated into selected orthogonal planes. Electronic sharing and interactive use are benefits afforded by a digital format, but the foremost advantage of this 3D map is its whole brain integrated representation of rat in situ neuroanatomy.

  11. 3D mapping of neuronal migration in the embryonic mouse brain with magnetic resonance microimaging.

    PubMed

    Deans, Abby E; Wadghiri, Youssef Zaim; Aristizábal, Orlando; Turnbull, Daniel H

    2015-07-01

    A prominent feature of the developing mammalian brain is the widespread migration of neural progenitor (NP) cells during embryogenesis. A striking example is provided by NP cells born in the ventral forebrain of mid-gestation stage mice, which subsequently migrate long distances to their final positions in the cortex and olfactory bulb. Previous studies have used two-dimensional histological methods, making it difficult to analyze three-dimensional (3D) migration patterns. Unlike histology, magnetic resonance microimaging (micro-MRI) is a non-destructive, quantitative and inherently 3D imaging method for analyzing mouse embryos. To allow mapping of migrating NP cells with micro-MRI, cells were labeled in situ in the medial (MGE) and lateral (LGE) ganglionic eminences, using targeted in utero ultrasound-guided injection of micron-sized particles of iron-oxide (MPIO). Ex vivo micro-MRI and histology were then performed 5-6days after injection, demonstrating that the MPIO had magnetically labeled the migrating NP populations, which enabled 3D visualization and automated segmentation of the labeled cells. This approach was used to analyze the distinct patterns of migration from the MGE and LGE, and to construct rostral-caudal migration maps from each progenitor region. Furthermore, abnormal migratory phenotypes were observed in Nkx2.1(-/-) embryos, most notably a significant increase in cortical neurons derived from the Nkx2.1(-/-) LGE. Taken together, these results demonstrate that MPIO labeling and micro-MRI provide an efficient and powerful approach for analyzing 3D cell migration patterns in the normal and mutant mouse embryonic brain.

  12. 3D variational brain tumor segmentation on a clustered feature set

    NASA Astrophysics Data System (ADS)

    Popuri, Karteek; Cobzas, Dana; Jagersand, Martin; Shah, Sirish L.; Murtha, Albert

    2009-02-01

    Tumor segmentation from MRI data is a particularly challenging and time consuming task. Tumors have a large diversity in shape and appearance with intensities overlapping the normal brain tissues. In addition, an expanding tumor can also deflect and deform nearby tissue. Our work addresses these last two difficult problems. We use the available MRI modalities (T1, T1c, T2) and their texture characteristics to construct a multi-dimensional feature set. Further, we extract clusters which provide a compact representation of the essential information in these features. The main idea in this paper is to incorporate these clustered features into the 3D variational segmentation framework. In contrast to the previous variational approaches, we propose a segmentation method that evolves the contour in a supervised fashion. The segmentation boundary is driven by the learned inside and outside region voxel probabilities in the cluster space. We incorporate prior knowledge about the normal brain tissue appearance, during the estimation of these region statistics. In particular, we use a Dirichlet prior that discourages the clusters in the ventricles to be in the tumor and hence better disambiguate the tumor from brain tissue. We show the performance of our method on real MRI scans. The experimental dataset includes MRI scans, from patients with difficult instances, with tumors that are inhomogeneous in appearance, small in size and in proximity to the major structures in the brain. Our method shows good results on these test cases.

  13. The influence of familiarity on brain activation during haptic exploration of 3-D facemasks.

    PubMed

    James, Thomas W; Servos, Philip; Kilgour, Andrea R; Huh, Eunji; Lederman, Susan

    2006-04-24

    Little is known about the neural substrates that underlie difficult haptic discrimination of 3-D within-class object stimuli. Recent work [A.R. Kilgour, R. Kitada, P. Servos, T.W. James, S.J. Lederman, Haptic face identification activates ventral occipital and temporal areas: an fMRI study, Brain Cogn. (in press)] suggests that the left fusiform gyrus may contribute to the identification of facemasks that are haptically explored in the absence of vision. Here, we extend this line of research to investigate the influence of familiarity. Subjects were trained extensively to individuate a set of facemasks in the absence of vision using only haptic exploration. Brain activation was then measured using fMRI while subjects performed a haptic face recognition task on familiar and unfamiliar facemasks. A group analysis contrasting familiar and unfamiliar facemasks found that the left fusiform gyrus produced greater activation with familiar facemasks.

  14. Automatic procedure for realistic 3D finite element modelling of human brain for bioelectromagnetic computations

    NASA Astrophysics Data System (ADS)

    Aristovich, K. Y.; Khan, S. H.

    2010-07-01

    Realistic computer modelling of biological objects requires building of very accurate and realistic computer models based on geometric and material data, type, and accuracy of numerical analyses. This paper presents some of the automatic tools and algorithms that were used to build accurate and realistic 3D finite element (FE) model of whole-brain. These models were used to solve the forward problem in magnetic field tomography (MFT) based on Magnetoencephalography (MEG). The forward problem involves modelling and computation of magnetic fields produced by human brain during cognitive processing. The geometric parameters of the model were obtained from accurate Magnetic Resonance Imaging (MRI) data and the material properties - from those obtained from Diffusion Tensor MRI (DTMRI). The 3D FE models of the brain built using this approach has been shown to be very accurate in terms of both geometric and material properties. The model is stored on the computer in Computer-Aided Parametrical Design (CAD) format. This allows the model to be used in a wide a range of methods of analysis, such as finite element method (FEM), Boundary Element Method (BEM), Monte-Carlo Simulations, etc. The generic model building approach presented here could be used for accurate and realistic modelling of human brain and many other biological objects.

  15. Fast 3D Chemical Exchange Saturation Transfer (CEST) Imaging of the Human Brain

    PubMed Central

    Zhu, He; Jones, Craig K.; van Zijl, Peter C. M.; Barker, Peter B.; Zhou, Jinyuan

    2010-01-01

    Chemical exchange saturation transfer (CEST) MRI can detect low-concentration compounds with exchangeable protons through saturation transfer to water. CEST imaging is generally slow, as it requires acquisition of saturation images at multiple frequencies. In addition, multi-slice imaging is complicated by saturation effects differing from slice to slice because of relaxation losses. In this study, a fast three-dimensional (3D) CEST imaging sequence is presented that allows whole-brain coverage for a frequency-dependent saturation spectrum (z-spectrum, 26 frequencies) in less than 10 min. The approach employs a 3D gradient- and spin-echo (GRASE) readout using a prototype 32-channel phased-array coil, combined with two-dimensional SENSE accelerations. Results from a homogenous protein-containing phantom at 3T show that the sequence produced a uniform contrast across all slices. To show translational feasibility, scans were also performed on five healthy human subjects. Results for CEST images at 3.5ppm downfield of the water resonance, so-called amide proton transfer (APT) images, show that lipid signals are sufficiently suppressed and artifacts caused by B0 inhomogeneity can be removed in post-processing. The scan time and image quality of these in vivo results show that 3D CEST MRI using GRASE acquisition is feasible for whole-brain CEST studies at 3T in a clinical time frame. PMID:20632402

  16. Spatio-temporal registration in multiplane MRI acquisitions for 3D colon motiliy analysis

    NASA Astrophysics Data System (ADS)

    Kutter, Oliver; Kirchhoff, Sonja; Berkovich, Marina; Reiser, Maximilian; Navab, Nassir

    2008-03-01

    In this paper we present a novel method for analyzing and visualizing dynamic peristaltic motion of the colon in 3D from two series of differently oriented 2D MRI images. To this end, we have defined an MRI examination protocol, and introduced methods for spatio-temporal alignment of the two MRI image series into a common reference. This represents the main contribution of this paper, which enables the 3D analysis of peristaltic motion. The objective is to provide a detailed insight into this complex motion, aiding in the diagnosis and characterization of colon motion disorders. We have applied the proposed spatio-temporal method on Cine MRI data sets of healthy volunteers. The results have been inspected and validated by an expert radiologist. Segmentation and cylindrical approximation of the colon results in a 4D visualization of the peristaltic motion.

  17. 3D MRI-based tumor delineation of ocular melanoma and its comparison with conventional techniques

    SciTech Connect

    Daftari, Inder k; Aghaian, Elsa; O'Brien, Joan M.; Dillon, William; Phillips, Theodore L.

    2005-11-15

    The aim of this study is to (1) compare the delineation of the tumor volume for ocular melanoma on high-resolution three-dimensional (3D) T2-weighted fast spin echo magnetic resonance imaging (MRI) images with conventional techniques of A- and B-scan ultrasound, transcleral illumination, and placement of tantalum markers around tumor base and (2) to evaluate whether the surgically placed marker ring tumor delineation can be replaced by 3D MRI based tumor delineation. High-resolution 3D T2-weighted fast spin echo (3D FSE) MRI scans were obtained for 60 consecutive ocular melanoma patients using a 1.5 T MRI (GE Medical Systems, Milwaukee, WI), in a standard head coil. These patients were subsequently treated with proton beam therapy at the UC Davis Cyclotron, Davis, CA. The tumor was delineated by placement of tantalum rings (radio-opaque markers) around the tumor periphery as defined by pupillary transillumination during surgery. A point light source, placed against the sclera, was also used to confirm ring agreement with indirect ophthalmoscopy. When necessary, intraoperative ultrasound was also performed. The patients were planned using EYEPLAN software and the tumor volumes were obtained. For analysis, the tumors were divided into four categories based on tumor height and basal diameter. In order to assess the impact of high-resolution 3D T2 FSE MRI, the tumor volumes were outlined on the MRI scans by two independent observers and the tumor volumes calculated for each patient. Six (10%) of 60 patients had tumors, which were not visible on 3D MRI images. These six patients had tumors with tumor heights {<=}3 mm. A small intraobserver variation with a mean of (-0.22{+-}4)% was seen in tumor volumes delineated by 3D T2 FSE MR images. The ratio of tumor volumes measured on MRI to EYEPLAN for the largest to the smallest tumor volumes varied between 0.993 and 1.02 for 54 patients. The tumor volumes measured directly on 3D T2 FSE MRI ranged from 4.03 to 0.075 cm{sup 3

  18. 3D MRI-based tumor delineation of ocular melanoma and its comparison with conventional techniques.

    PubMed

    Daftari, Inder k; Aghaian, Elsa; O'Brien, Joan M; Dillon, William; Phillips, Theodore L

    2005-11-01

    The aim of this study is to (1) compare the delineation of the tumor volume for ocular melanoma on high-resolution three-dimensional (3D) T2-weighted fast spin echo magnetic resonance imaging (MRI) images with conventional techniques of A- and B-scan ultrasound, transcleral illumination, and placement of tantalum markers around tumor base and (2) to evaluate whether the surgically placed marker ring tumor delineation can be replaced by 3D MRI based tumor delineation. High-resolution 3D T2-weighted fast spin echo (3D FSE) MRI scans were obtained for 60 consecutive ocular melanoma patients using a 1.5 T MRI (GE Medical Systems, Milwaukee, WI), in a standard head coil. These patients were subsequently treated with proton beam therapy at the UC Davis Cyclotron, Davis, CA. The tumor was delineated by placement of tantalum rings (radio-opaque markers) around the tumor periphery as defined by pupillary transillumination during surgery. A point light source, placed against the sclera, was also used to confirm ring agreement with indirect ophthalmoscopy. When necessary, intraoperative ultrasound was also performed. The patients were planned using EYEPLAN software and the tumor volumes were obtained. For analysis, the tumors were divided into four categories based on tumor height and basal diameter. In order to assess the impact of high-resolution 3D T2 FSE MRI, the tumor volumes were outlined on the MRI scans by two independent observers and the tumor volumes calculated for each patient. Six (10%) of 60 patients had tumors, which were not visible on 3D MRI images. These six patients had tumors with tumor heights < or = 3 mm. A small intraobserver variation with a mean of (-0.22 +/- 4)% was seen in tumor volumes delineated by 3D T2 FSE MR images. The ratio of tumor volumes measured on MRI to EYEPLAN for the largest to the smallest tumor volumes varied between 0.993 and 1.02 for 54 patients. The tumor volumes measured directly on 3D T2 FSE MRI ranged from 4.03 to 0.075 cm3

  19. Parameterization of 3D brain structures for statistical shape analysis

    NASA Astrophysics Data System (ADS)

    Zhu, Litao; Jiang, Tianzi

    2004-05-01

    Statistical Shape Analysis (SSA) is a powerful tool for noninvasive studies of pathophysiology and diagnosis of brain diseases. It also provides a shape constraint for the segmentation of brain structures. There are two key problems in SSA: the representation of shapes and their alignments. The widely used parameterized representations are obtained by preserving angles or areas and the alignments of shapes are achieved by rotating parameter net. However, representations preserving angles or areas do not really guarantee the anatomical correspondence of brain structures. In this paper, we incorporate shape-based landmarks into parameterization of banana-like 3D brain structures to address this problem. Firstly, we get the triangulated surface of the object and extract two landmarks from the mesh, i.e. the ends of the banana-like object. Then the surface is parameterized by creating a continuous and bijective mapping from the surface to a spherical surface based on a heat conduction model. The correspondence of shapes is achieved by mapping the two landmarks to the north and south poles of the sphere and using an extracted origin orientation to select the dateline during parameterization. We apply our approach to the parameterization of lateral ventricle and a multi-resolution shape representation is obtained by using the Discrete Fourier Transform.

  20. 3D pattern of brain atrophy in HIV/AIDS visualized using tensor-based morphometry

    PubMed Central

    Chiang, Ming-Chang; Dutton, Rebecca A.; Hayashi, Kiralee M.; Lopez, Oscar L.; Aizenstein, Howard J.; Toga, Arthur W.; Becker, James T.; Thompson, Paul M.

    2011-01-01

    35% of HIV-infected patients have cognitive impairment, but the profile of HIV-induced brain damage is still not well understood. Here we used tensor-based morphometry (TBM) to visualize brain deficits and clinical/anatomical correlations in HIV/AIDS. To perform TBM, we developed a new MRI-based analysis technique that uses fluid image warping, and a new α-entropy-based information-theoretic measure of image correspondence, called the Jensen–Rényi divergence (JRD). Methods 3D T1-weighted brain MRIs of 26 AIDS patients (CDC stage C and/or 3 without HIV-associated dementia; 47.2 ± 9.8 years; 25M/1F; CD4+ T-cell count: 299.5 ± 175.7/µl; log10 plasma viral load: 2.57 ± 1.28 RNA copies/ml) and 14 HIV-seronegative controls (37.6 ± 12.2 years; 8M/6F) were fluidly registered by applying forces throughout each deforming image to maximize the JRD between it and a target image (from a control subject). The 3D fluid registration was regularized using the linearized Cauchy–Navier operator. Fine-scale volumetric differences between diagnostic groups were mapped. Regions were identified where brain atrophy correlated with clinical measures. Results Severe atrophy (~15–20% deficit) was detected bilaterally in the primary and association sensorimotor areas. Atrophy of these regions, particularly in the white matter, correlated with cognitive impairment (P=0.033) and CD4+ T-lymphocyte depletion (P=0.005). Conclusion TBM facilitates 3D visualization of AIDS neuropathology in living patients scanned with MRI. Severe atrophy in frontoparietal and striatal areas may underlie early cognitive dysfunction in AIDS patients, and may signal the imminent onset of AIDS dementia complex. PMID:17035049

  1. Magnetic Resonance Imaging (MRI): Brain (For Parents)

    MedlinePlus

    ... to 2-Year-Old Magnetic Resonance Imaging (MRI): Brain KidsHealth > For Parents > Magnetic Resonance Imaging (MRI): Brain ... child may be given headphones to listen to music or earplugs to block the noise, and will ...

  2. Individualised 3D printed vaginal template for MRI guided brachytherapy in locally advanced cervical cancer.

    PubMed

    Lindegaard, Jacob Christian; Madsen, Mikkel Lænsø; Traberg, Anders; Meisner, Bjarne; Nielsen, Søren Kynde; Tanderup, Kari; Spejlborg, Harald; Fokdal, Lars Ulrik; Nørrevang, Ole

    2016-01-01

    Intracavitary-interstitial applicators for MRI guided brachytherapy are becoming increasingly important in locally advanced cervical cancer. The 3D printing technology enables a versatile method for obtaining a high degree of individualisation of the implant. Our clinical workflow is presented and exemplified by a stage IVA cervical cancer with superior dose distribution.

  3. Registration of 3D ultrasound computer tomography and MRI for evaluation of tissue correspondences

    NASA Astrophysics Data System (ADS)

    Hopp, T.; Dapp, R.; Zapf, M.; Kretzek, E.; Gemmeke, H.; Ruiter, N. V.

    2015-03-01

    3D Ultrasound Computer Tomography (USCT) is a new imaging method for breast cancer diagnosis. In the current state of development it is essential to correlate USCT with a known imaging modality like MRI to evaluate how different tissue types are depicted. Due to different imaging conditions, e.g. with the breast subject to buoyancy in USCT, a direct correlation is demanding. We present a 3D image registration method to reduce positioning differences and allow direct side-by-side comparison of USCT and MRI volumes. It is based on a two-step approach including a buoyancy simulation with a biomechanical model and free form deformations using cubic B-Splines for a surface refinement. Simulation parameters are optimized patient-specifically in a simulated annealing scheme. The method was evaluated with in-vivo datasets resulting in an average registration error below 5mm. Correlating tissue structures can thereby be located in the same or nearby slices in both modalities and three-dimensional non-linear deformations due to the buoyancy are reduced. Image fusion of MRI volumes and USCT sound speed volumes was performed for intuitive display. By applying the registration to data of our first in-vivo study with the KIT 3D USCT, we could correlate several tissue structures in MRI and USCT images and learn how connective tissue, carcinomas and breast implants observed in the MRI are depicted in the USCT imaging modes.

  4. Realistic microwave breast models through T1-weighted 3-D MRI data.

    PubMed

    Tunçay, Ahmet Hakan; Akduman, Ibrahim

    2015-02-01

    In this paper we present an effective method for developing realistic numerical three-dimensional (3-D) microwave breast models of different shape, size, and tissue density. These models are especially convenient for microwave breast cancer imaging applications and numerical analysis of human breast-microwave interactions. As in the recent studies on this area, anatomical information of the breast tissue is collected from T1-weighted 3-D MRI data of different patients' in prone position. The method presented in this paper offers significant improvements including efficient noise reduction and tissue segmentation, nonlinear mapping of electromagnetic properties, realistically asymmetric phantom shape, and a realistic classification of breast phantoms. Our method contains a five-step approach where each MRI voxel is classified and mapped to the appropriate dielectric properties. In the first step, the MRI data are denoised by estimating and removing the bias field from each slice, after which the voxels are segmented into two main tissues as fibro-glandular and adipose. Using the distribution of the voxel intensities in MRI histogram, two nonlinear mapping functions are generated for dielectric permittivity and conductivity profiles, which allow each MRI voxel to map to its proper dielectric properties. Obtained dielectric profiles are then converted into 3-D numerical breast phantoms using several image processing techniques, including morphologic operations, filtering. Resultant phantoms are classified according to their adipose content, which is a critical parameter that affects penetration depth during microwave breast imaging.

  5. MRI Slice Segmentation and 3D Modelling of Temporomandibular Joint Measured by Microscopic Coil

    NASA Astrophysics Data System (ADS)

    Smirg, O.; Liberda, O.; Smekal, Z.; Sprlakova-Pukova, A.

    2012-01-01

    The paper focuses on the segmentation of magnetic resonance imaging (MRI) slices and 3D modelling of the temporomandibular joint disc in order to help physicians diagnose patients with dysfunction of the temporomandibular joint (TMJ). The TMJ is one of the most complex joints in the human body. The most common joint dysfunction is due to the disc. The disc is a soft tissue, which in principle cannot be diagnosed by the CT method. Therefore, a 3D model is made from the MRI slices, which can image soft tissues. For the segmentation of the disc in individual slices a new method is developed based on spatial distribution and anatomical TMJ structure with automatic thresholding. The thresholding is controlled by a genetic algorithm. The 3D model is realized using the marching cube method.

  6. Robust automatic rodent brain extraction using 3-D pulse-coupled neural networks (PCNN).

    PubMed

    Chou, Nigel; Wu, Jiarong; Bai Bingren, Jordan; Qiu, Anqi; Chuang, Kai-Hsiang

    2011-09-01

    Brain extraction is an important preprocessing step for further processing (e.g., registration and morphometric analysis) of brain MRI data. Due to the operator-dependent and time-consuming nature of manual extraction, automated or semi-automated methods are essential for large-scale studies. Automatic methods are widely available for human brain imaging, but they are not optimized for rodent brains and hence may not perform well. To date, little work has been done on rodent brain extraction. We present an extended pulse-coupled neural network algorithm that operates in 3-D on the entire image volume. We evaluated its performance under varying SNR and resolution and tested this method against the brain-surface extractor (BSE) and a level-set algorithm proposed for mouse brain. The results show that this method outperforms existing methods and is robust under low SNR and with partial volume effects at lower resolutions. Together with the advantage of minimal user intervention, this method will facilitate automatic processing of large-scale rodent brain studies.

  7. Fast 3D fluid registration of brain magnetic resonance images

    NASA Astrophysics Data System (ADS)

    Leporé, Natasha; Chou, Yi-Yu; Lopez, Oscar L.; Aizenstein, Howard J.; Becker, James T.; Toga, Arthur W.; Thompson, Paul M.

    2008-03-01

    Fluid registration is widely used in medical imaging to track anatomical changes, to correct image distortions, and to integrate multi-modality data. Fluid mappings guarantee that the template image deforms smoothly into the target, without tearing or folding, even when large deformations are required for accurate matching. Here we implemented an intensity-based fluid registration algorithm, accelerated by using a filter designed by Bro-Nielsen and Gramkow. We validated the algorithm on 2D and 3D geometric phantoms using the mean square difference between the final registered image and target as a measure of the accuracy of the registration. In tests on phantom images with different levels of overlap, varying amounts of Gaussian noise, and different intensity gradients, the fluid method outperformed a more commonly used elastic registration method, both in terms of accuracy and in avoiding topological errors during deformation. We also studied the effect of varying the viscosity coefficients in the viscous fluid equation, to optimize registration accuracy. Finally, we applied the fluid registration algorithm to a dataset of 2D binary corpus callosum images and 3D volumetric brain MRIs from 14 healthy individuals to assess its accuracy and robustness.

  8. Unsupervised fuzzy segmentation of 3D magnetic resonance brain images

    NASA Astrophysics Data System (ADS)

    Velthuizen, Robert P.; Hall, Lawrence O.; Clarke, Laurence P.; Bensaid, Amine M.; Arrington, J. A.; Silbiger, Martin L.

    1993-07-01

    Unsupervised fuzzy methods are proposed for segmentation of 3D Magnetic Resonance images of the brain. Fuzzy c-means (FCM) has shown promising results for segmentation of single slices. FCM has been investigated for volume segmentations, both by combining results of single slices and by segmenting the full volume. Different strategies and initializations have been tried. In particular, two approaches have been used: (1) a method by which, iteratively, the furthest sample is split off to form a new cluster center, and (2) the traditional FCM in which the membership grade matrix is initialized in some way. Results have been compared with volume segmentations by k-means and with two supervised methods, k-nearest neighbors and region growing. Results of individual segmentations are presented as well as comparisons on the application of the different methods to a number of tumor patient data sets.

  9. A Web platform for the interactive visualization and analysis of the 3D fractal dimension of MRI data.

    PubMed

    Jiménez, J; López, A M; Cruz, J; Esteban, F J; Navas, J; Villoslada, P; Ruiz de Miras, J

    2014-10-01

    This study presents a Web platform (http://3dfd.ujaen.es) for computing and analyzing the 3D fractal dimension (3DFD) from volumetric data in an efficient, visual and interactive way. The Web platform is specially designed for working with magnetic resonance images (MRIs) of the brain. The program estimates the 3DFD by calculating the 3D box-counting of the entire volume of the brain, and also of its 3D skeleton. All of this is done in a graphical, fast and optimized way by using novel technologies like CUDA and WebGL. The usefulness of the Web platform presented is demonstrated by its application in a case study where an analysis and characterization of groups of 3D MR images is performed for three neurodegenerative diseases: Multiple Sclerosis, Intrauterine Growth Restriction and Alzheimer's disease. To the best of our knowledge, this is the first Web platform that allows the users to calculate, visualize, analyze and compare the 3DFD from MRI images in the cloud.

  10. Computerized Liver Volumetry on MRI by Using 3D Geodesic Active Contour Segmentation

    PubMed Central

    Huynh, Hieu Trung; Karademir, Ibrahim; Oto, Aytekin; Suzuki, Kenji

    2014-01-01

    OBJECTIVE Our purpose was to develop an accurate automated 3D liver segmentation scheme for measuring liver volumes on MRI. SUBJECTS AND METHODS Our scheme for MRI liver volumetry consisted of three main stages. First, the preprocessing stage was applied to T1-weighted MRI of the liver in the portal venous phase to reduce noise and produce the boundary-enhanced image. This boundary-enhanced image was used as a speed function for a 3D fast-marching algorithm to generate an initial surface that roughly approximated the shape of the liver. A 3D geodesic-active-contour segmentation algorithm refined the initial surface to precisely determine the liver boundaries. The liver volumes determined by our scheme were compared with those manually traced by a radiologist, used as the reference standard. RESULTS The two volumetric methods reached excellent agreement (intraclass correlation coefficient, 0.98) without statistical significance (p = 0.42). The average (± SD) accuracy was 99.4% ± 0.14%, and the average Dice overlap coefficient was 93.6% ± 1.7%. The mean processing time for our automated scheme was 1.03 ± 0.13 minutes, whereas that for manual volumetry was 24.0 ± 4.4 minutes (p < 0.001). CONCLUSION The MRI liver volumetry based on our automated scheme agreed excellently with reference-standard volumetry, and it required substantially less completion time. PMID:24370139

  11. MRI depiction and 3D visualization of three anterior cruciate ligament bundles.

    PubMed

    Otsubo, H; Akatsuka, Y; Takashima, H; Suzuki, T; Suzuki, D; Kamiya, T; Ikeda, Y; Matsumura, T; Yamashita, T; Shino, K

    2017-03-01

    The anterior cruciate ligament (ACL) is divided into three fiber bundles (AM-M: anteromedial-medial, AM-L: anteromedial-lateral, PL: posterolateral). We attempted to depict the three bundles of the human ACL on MRI images and to obtain 3-dimensional visualization of them. Twenty-four knees of healthy volunteers (14 males, 10 females) were scanned by 3T-MRI using the fat suppression 3D coherent oscillatory state acquisition for the manipulation of imaging contrast (FS 3D-COSMIC). The scanned images were reconstructed after the isotropic voxel data, which allows the images to be reconstructed in any plane, was acquired. We conducted statistical examination on the identification rate of the three ACL bundles by 2D planes. Segmentation and 3D visualization of the fiber bundles using volume rendering were performed. The triple-bundle ACL was best depicted in the oblique axial plane. While the AM-M and AM-L bundles were clearly depicted in all cases, the PL bundle was not clearly visualized in two knees (8%). Therefore, the three ACL bundles were depicted in 22 knees (92%). The results of 3D visualization of the fiber arrangement agreed well with macroscopic findings of previous anatomical studies. 3T-MRI and the isotropic voxel data from FS 3D-COSMIC made it possible to demonstrate the identifiable depiction of three ACL bundles in nearly all cases. 3D visualization of the bundles could be a useful tool to understand the ACL fiber arrangement. Clin. Anat. 30:276-283, 2017. 2016 The Authors. Clinical Anatomy published by Wiley Periodicals, Inc. on behalf of American Association of Clinical Anatomists.

  12. Improved 3D wavelet-based de-noising of fMRI data

    NASA Astrophysics Data System (ADS)

    Khullar, Siddharth; Michael, Andrew M.; Correa, Nicolle; Adali, Tulay; Baum, Stefi A.; Calhoun, Vince D.

    2011-03-01

    Functional MRI (fMRI) data analysis deals with the problem of detecting very weak signals in very noisy data. Smoothing with a Gaussian kernel is often used to decrease noise at the cost of losing spatial specificity. We present a novel wavelet-based 3-D technique to remove noise in fMRI data while preserving the spatial features in the component maps obtained through group independent component analysis (ICA). Each volume is decomposed into eight volumetric sub-bands using a separable 3-D stationary wavelet transform. Each of the detail sub-bands are then treated through the main denoising module. This module facilitates computation of shrinkage factors through a hierarchical framework. It utilizes information iteratively from the sub-band at next higher level to estimate denoised coefficients at the current level. These de-noised sub-bands are then reconstructed back to the spatial domain using an inverse wavelet transform. Finally, the denoised group fMRI data is analyzed using ICA where the data is decomposed in to clusters of functionally correlated voxels (spatial maps) as indicators of task-related neural activity. The proposed method enables the preservation of shape of the actual activation regions associated with the BOLD activity. In addition it is able to achieve high specificity as compared to the conventionally used FWHM (full width half maximum) Gaussian kernels for smoothing fMRI data.

  13. Segmentation and length measurement of the abdominal blood vessels in 3-D MRI images.

    PubMed

    Babin, Danilo; Vansteenkiste, Ewout; Pizurica, Aleksandra; Philips, Wilfried

    2009-01-01

    In diagnosing diseases and planning surgeries the structure and length of blood vessels is of great importance. In this research we develop a novel method for the segmentation of 2-D and 3-D images with an application to blood vessel length measurements in 3-D abdominal MRI images. Our approach is robust to noise and does not require contrast-enhanced images for segmentation. We use an effective algorithm for skeletonization, graph construction and shortest path estimation to measure the length of blood vessels of interest.

  14. MRI Technologies in Recent Human Brain Mapping

    NASA Astrophysics Data System (ADS)

    Sasaki, Yuka

    The recent magnetic resonance imaging (MRI) technology and techniques used in human brain mapping are remarkable. They are getting, faster, stronger and better. The advanced MRI technologies and techniques include, but not to limited to, the magnetic resonance imaging at higher magnetic field strengths, diffusion tensor imaging, multimodal neuroimaging, and monkey functional MRI. In this article, these advanced MRI techniques are briefly overviewed.

  15. High-Performance 3D Compressive Sensing MRI Reconstruction Using Many-Core Architectures

    PubMed Central

    Kim, Daehyun; Trzasko, Joshua; Smelyanskiy, Mikhail; Haider, Clifton; Dubey, Pradeep; Manduca, Armando

    2011-01-01

    Compressive sensing (CS) describes how sparse signals can be accurately reconstructed from many fewer samples than required by the Nyquist criterion. Since MRI scan duration is proportional to the number of acquired samples, CS has been gaining significant attention in MRI. However, the computationally intensive nature of CS reconstructions has precluded their use in routine clinical practice. In this work, we investigate how different throughput-oriented architectures can benefit one CS algorithm and what levels of acceleration are feasible on different modern platforms. We demonstrate that a CUDA-based code running on an NVIDIA Tesla C2050 GPU can reconstruct a 256 × 160 × 80 volume from an 8-channel acquisition in 19 seconds, which is in itself a significant improvement over the state of the art. We then show that Intel's Knights Ferry can perform the same 3D MRI reconstruction in only 12 seconds, bringing CS methods even closer to clinical viability. PMID:21922017

  16. MRI-Derived 3-D-Printed Breast Phantom for Microwave Breast Imaging Validation

    PubMed Central

    Burfeindt, Matthew J.; Colgan, Timothy J.; Mays, R. Owen; Shea, Jacob D.; Behdad, Nader; Van Veen, Barry D.; Hagness, Susan C.

    2014-01-01

    We propose a 3-D-printed breast phantom for use in preclinical experimental microwave imaging studies. The phantom is derived from an MRI of a human subject; thus, it is anthropomorphic, and its interior is very similar to an actual distribution of fibroglandular tissues. Adipose tissue in the breast is represented by the solid plastic (printed) regions of the phantom, while fibroglandular tissue is represented by liquid-filled voids in the plastic. The liquid is chosen to provide a biologically relevant dielectric contrast with the printed plastic. Such a phantom enables validation of microwave imaging techniques. We describe the procedure for generating the 3-D-printed breast phantom and present the measured dielectric properties of the 3-D-printed plastic over the frequency range 0.5–3.5 GHz. We also provide an example of a suitable liquid for filling the fibroglandular voids in the plastic. PMID:25132808

  17. MRI-Derived 3-D-Printed Breast Phantom for Microwave Breast Imaging Validation.

    PubMed

    Burfeindt, Matthew J; Colgan, Timothy J; Mays, R Owen; Shea, Jacob D; Behdad, Nader; Van Veen, Barry D; Hagness, Susan C

    2012-01-01

    We propose a 3-D-printed breast phantom for use in preclinical experimental microwave imaging studies. The phantom is derived from an MRI of a human subject; thus, it is anthropomorphic, and its interior is very similar to an actual distribution of fibroglandular tissues. Adipose tissue in the breast is represented by the solid plastic (printed) regions of the phantom, while fibroglandular tissue is represented by liquid-filled voids in the plastic. The liquid is chosen to provide a biologically relevant dielectric contrast with the printed plastic. Such a phantom enables validation of microwave imaging techniques. We describe the procedure for generating the 3-D-printed breast phantom and present the measured dielectric properties of the 3-D-printed plastic over the frequency range 0.5-3.5 GHz. We also provide an example of a suitable liquid for filling the fibroglandular voids in the plastic.

  18. Real-time 3D imaging of microstructure growth in battery cells using indirect MRI

    PubMed Central

    Ilott, Andrew J.; Mohammadi, Mohaddese; Chang, Hee Jung; Grey, Clare P.; Jerschow, Alexej

    2016-01-01

    Lithium metal is a promising anode material for Li-ion batteries due to its high theoretical specific capacity and low potential. The growth of dendrites is a major barrier to the development of high capacity, rechargeable Li batteries with lithium metal anodes, and hence, significant efforts have been undertaken to develop new electrolytes and separator materials that can prevent this process or promote smooth deposits at the anode. Central to these goals, and to the task of understanding the conditions that initiate and propagate dendrite growth, is the development of analytical and nondestructive techniques that can be applied in situ to functioning batteries. MRI has recently been demonstrated to provide noninvasive imaging methodology that can detect and localize microstructure buildup. However, until now, monitoring dendrite growth by MRI has been limited to observing the relatively insensitive metal nucleus directly, thus restricting the temporal and spatial resolution and requiring special hardware and acquisition modes. Here, we present an alternative approach to detect a broad class of metallic dendrite growth via the dendrites’ indirect effects on the surrounding electrolyte, allowing for the application of fast 3D 1H MRI experiments with high resolution. We use these experiments to reconstruct 3D images of growing Li dendrites from MRI, revealing details about the growth rate and fractal behavior. Radiofrequency and static magnetic field calculations are used alongside the images to quantify the amount of the growing structures. PMID:27621444

  19. Visualization and mapping of neurosurgical functional brain data onto a 3-D MR-based model of the brain surface.

    PubMed

    Modayur, B R; Prothero, J; Rosse, C; Jakobovits, R; Brinkley, J F

    1996-01-01

    The Human Brain Project was initiated with the goal of developing methods for managing and sharing information about the brain. As a prototype Human Brain Project application we are developing a system for organizing, visualizing, integrating and sharing information about human language function. The goal of the brain mapping component of our work, described in this article, is to generate the 3D location and extent of cortical language sites with respect to a uniform, 3D patient coordinate system. The language sites of individual patients can then be combined with or related to other patient data in terms of a Talairach, surface-based, or other deformable coordinate systems. Language site mapping is done by visually comparing an intraoperative photograph with the rendered image (from MRI data). The techniques outlined in this article have been utilized to map cortical language sites of six patients. Preliminary results point to the adequacy of our volume visualizations for language mapping. The strength of the visualization scheme lies in the combination of interactive segmentation with volume and surface visualization. We are now in the process of acquiring more patient data to further validate the usefulness of our method.

  20. Diagnostic Value of 3D Fast Low-Angle Shot Dynamic MRI of Breast Papillomas

    PubMed Central

    Kim, Eun-Kyung; Kim, Jeong-Ah; Kwak, Jin Young; Jeong, Joon

    2009-01-01

    Purpose To evaluate the value of breast MRI in analysis of papillomas of the breast. Materials and Methods From 1996 to 2004, 94 patients underwent surgery due to papillomas of the breast. Among them, 21 patients underwent 3D fast low angle shot (FLASH) dynamic breast MRI. Eight masses were palpable and 11 of 21 patients had nipple discharge. Two radiologists indifferently analyzed the location, size of the lesions and shape, margin of the masses, multiplicity and ductal relation. The MRI findings were categorized according to breast imaging reporting and data system (BI-RADS) lexicon. The amount and pattern of enhancement and associated findings were also evaluated according to BI-RADS. We then compared the MRI findings with galactography, mammography and breast ultrasonography (US) and examined histopathologic correlation. Results On breast MRI, the lesion size was 0.4-1.59 cm, and 18 patients showed subareolar location. On 4.25 cm (mean 1.54) dynamic enhanced images, imaging findings showed mass (n = 10), intracystic mass (n = 3), focus (n = 5), ductal enhancement (n = 2), and segmental enhancement (n = 1). In cases of the masses, the shapes of the masses were round (n = 4), lobulated (n = 3), and irregular (n = 6), and margins were circumscribed (n = 6), microlobulated (n = 5), and indistinct (n = 2). The enhancement patterns were homogeneous enhancement (n = 7), heterogeneous (n = 3) or rim enhancement (n = 3). Conclusion The contrast enhanced dynamic breast MRI was highly sensitive for diagnosis of breast papillomas. MRI could play a key role in the pre-operative work-up for multiple papillomas and papillomatosis. PMID:20046427

  1. Brain tumor segmentation in 3D MRIs using an improved Markov random field model

    NASA Astrophysics Data System (ADS)

    Yousefi, Sahar; Azmi, Reza; Zahedi, Morteza

    2011-10-01

    Markov Random Field (MRF) models have been recently suggested for MRI brain segmentation by a large number of researchers. By employing Markovianity, which represents the local property, MRF models are able to solve a global optimization problem locally. But they still have a heavy computation burden, especially when they use stochastic relaxation schemes such as Simulated Annealing (SA). In this paper, a new 3D-MRF model is put forward to raise the speed of the convergence. Although, search procedure of SA is fairly localized and prevents from exploring the same diversity of solutions, it suffers from several limitations. In comparison, Genetic Algorithm (GA) has a good capability of global researching but it is weak in hill climbing. Our proposed algorithm combines SA and an improved GA (IGA) to optimize the solution which speeds up the computation time. What is more, this proposed algorithm outperforms the traditional 2D-MRF in quality of the solution.

  2. MRI assessment of internal acoustic canal variations using 3D-FIESTA sequences.

    PubMed

    Erdogan, Nezahat; Altay, Canan; Akay, Emrah; Karakas, Levent; Uluc, Engin; Mete, Berna; Oygen, Aysegul; Oyar, Orhan; Gelal, Fazıl; Songu, Murat; Katilmis, Huseyin; Calli, Cağlar

    2013-02-01

    Magnetic resonance imaging (MRI) of the internal acoustic canal is the standard diagnostic tool for a wide range of indications in patients. This study aims to investigate the vascular variations and compression of the cranial nerves (CNs) VII and VIII at the cerebellopontine angle in patients with neuro-otologic symptoms using 3D-fast imaging employing steady-state acquisition (FIESTA) MR imaging. One hundred and eighty-seven patients (374 temporal bones) were examined on a 1.5-T MRI. In addition to conventional MR sequences, a 3D-FIESTA MR imaging was acquired. Magnetic resonance images thus obtained were evaluated with special regard to the presence of vascular contact to the CNs VII and VIII, as well as the presence of the vascular variations of the anterior inferior cerebellar artery (AICA) causing the compression of CNs. The Chi-squared test was used for statistical analysis. No statistically significant differences were found between the presence and absence of the AICA loop and/or vascular contact for the clinical symptoms of patients (P > 0.05). The cisternal and canalicular segments of CNs VII and VIII and adjacent vascular variations are well identified using 3D-FIESTA, especially by determining the relationship of the AICA variations between CNs.

  3. Wavelet-based fMRI analysis: 3-D denoising, signal separation, and validation metrics.

    PubMed

    Khullar, Siddharth; Michael, Andrew; Correa, Nicolle; Adali, Tulay; Baum, Stefi A; Calhoun, Vince D

    2011-02-14

    We present a novel integrated wavelet-domain based framework (w-ICA) for 3-D denoising functional magnetic resonance imaging (fMRI) data followed by source separation analysis using independent component analysis (ICA) in the wavelet domain. We propose the idea of a 3-D wavelet-based multi-directional denoising scheme where each volume in a 4-D fMRI data set is sub-sampled using the axial, sagittal and coronal geometries to obtain three different slice-by-slice representations of the same data. The filtered intensity value of an arbitrary voxel is computed as an expected value of the denoised wavelet coefficients corresponding to the three viewing geometries for each sub-band. This results in a robust set of denoised wavelet coefficients for each voxel. Given the de-correlated nature of these denoised wavelet coefficients, it is possible to obtain more accurate source estimates using ICA in the wavelet domain. The contributions of this work can be realized as two modules: First, in the analysis module we combine a new 3-D wavelet denoising approach with signal separation properties of ICA in the wavelet domain. This step helps obtain an activation component that corresponds closely to the true underlying signal, which is maximally independent with respect to other components. Second, we propose and describe two novel shape metrics for post-ICA comparisons between activation regions obtained through different frameworks. We verified our method using simulated as well as real fMRI data and compared our results against the conventional scheme (Gaussian smoothing+spatial ICA: s-ICA). The results show significant improvements based on two important features: (1) preservation of shape of the activation region (shape metrics) and (2) receiver operating characteristic curves. It was observed that the proposed framework was able to preserve the actual activation shape in a consistent manner even for very high noise levels in addition to significant reduction in false

  4. MRI 3D CISS– A Novel Imaging Modality in Diagnosing Trigeminal Neuralgia – A Review

    PubMed Central

    Besta, Radhika; Shankar, Y. Uday; Kumar, Ashwini; Prakash, S. Bhanu

    2016-01-01

    Trigeminal Neuralgia (TN) is considered as one of the most painful neurologic disorders affecting oro-facial region. TN is often diagnosed clinically based on the patients complete history of pain (severity, duration, episodes etc), relief of pain on test dose of Carbamazepine, regional block of long acting anaesthetic. However, Magnetic Resonance Imaging (MRI) plays an important and confirmatory role in showing Neuro Vascular Conflict (NVC) which is the commonest causative factor for TN. This article reviews the effectiveness of three-dimensional constructive interference in steady-state (3D-CISS) MRI in diagnosing the exact location, degree of neurovascular conflict responsible for classical as well as atypical TN and possible pre-treatment evaluation and treatment outcome. PMID:27135019

  5. On-line 3D motion estimation using low resolution MRI

    NASA Astrophysics Data System (ADS)

    Glitzner, M.; de Senneville, B. Denis; Lagendijk, J. J. W.; Raaymakers, B. W.; Crijns, S. P. M.

    2015-08-01

    Image processing such as deformable image registration finds its way into radiotherapy as a means to track non-rigid anatomy. With the advent of magnetic resonance imaging (MRI) guided radiotherapy, intrafraction anatomy snapshots become technically feasible. MRI provides the needed tissue signal for high-fidelity image registration. However, acquisitions, especially in 3D, take a considerable amount of time. Pushing towards real-time adaptive radiotherapy, MRI needs to be accelerated without degrading the quality of information. In this paper, we investigate the impact of image resolution on the quality of motion estimations. Potentially, spatially undersampled images yield comparable motion estimations. At the same time, their acquisition times would reduce greatly due to the sparser sampling. In order to substantiate this hypothesis, exemplary 4D datasets of the abdomen were downsampled gradually. Subsequently, spatiotemporal deformations are extracted consistently using the same motion estimation for each downsampled dataset. Errors between the original and the respectively downsampled version of the dataset are then evaluated. Compared to ground-truth, results show high similarity of deformations estimated from downsampled image data. Using a dataset with {{≤ft(2.5 \\text{mm}\\right)}3} voxel size, deformation fields could be recovered well up to a downsampling factor of 2, i.e. {{≤ft(5 \\text{mm}\\right)}3} . In a therapy guidance scenario MRI, imaging speed could accordingly increase approximately fourfold, with acceptable loss of estimated motion quality.

  6. Plaque characterization in ex vivo MRI evaluated by dense 3D correspondence with histology

    NASA Astrophysics Data System (ADS)

    van Engelen, Arna; de Bruijne, Marleen; Klein, Stefan; Verhagen, Hence; Groen, Harald; Wentzel, Jolanda; van der Lugt, Aad; Niessen, Wiro

    2011-03-01

    Automatic quantification of carotid artery plaque composition is important in the development of methods that distinguish vulnerable from stable plaques. MRI has shown to be capable of imaging different components noninvasively. We present a new plaque classification method which uses 3D registration of histology data with ex vivo MRI data, using non-rigid registration, both for training and evaluation. This is more objective than previously presented methods, as it eliminates selection bias that is introduced when 2D MRI slices are manually matched to histological slices before evaluation. Histological slices of human atherosclerotic plaques were manually segmented into necrotic core, fibrous tissue and calcification. Classification of these three components was voxelwise evaluated. As features the intensity, gradient magnitude and Laplacian in four MRI sequences after different degrees of Gaussian smoothing, and the distances to the lumen and the outer vessel wall, were used. Performance of linear and quadratic discriminant classifiers for different combinations of features was evaluated. Best accuracy (72.5 +/- 7.7%) was reached with the linear classifier when all features were used. Although this was only a minor improvement to the accuracy of a classifier that only included the intensities and distance features (71.6 +/- 7.9%), the difference was statistically significant (paired t-test, p<0.05). Good sensitivity and specificity for calcification was reached (83% and 95% respectively), however, differentiation between fibrous (sensitivity 85%, specificity 60%) and necrotic tissue (sensitivity 49%, specificity 89%) was more difficult.

  7. Motion corrected LV quantification based on 3D modelling for improved functional assessment in cardiac MRI

    NASA Astrophysics Data System (ADS)

    Liew, Y. M.; McLaughlin, R. A.; Chan, B. T.; Aziz, Y. F. Abdul; Chee, K. H.; Ung, N. M.; Tan, L. K.; Lai, K. W.; Ng, S.; Lim, E.

    2015-04-01

    Cine MRI is a clinical reference standard for the quantitative assessment of cardiac function, but reproducibility is confounded by motion artefacts. We explore the feasibility of a motion corrected 3D left ventricle (LV) quantification method, incorporating multislice image registration into the 3D model reconstruction, to improve reproducibility of 3D LV functional quantification. Multi-breath-hold short-axis and radial long-axis images were acquired from 10 patients and 10 healthy subjects. The proposed framework reduced misalignment between slices to subpixel accuracy (2.88 to 1.21 mm), and improved interstudy reproducibility for 5 important clinical functional measures, i.e. end-diastolic volume, end-systolic volume, ejection fraction, myocardial mass and 3D-sphericity index, as reflected in a reduction in the sample size required to detect statistically significant cardiac changes: a reduction of 21-66%. Our investigation on the optimum registration parameters, including both cardiac time frames and number of long-axis (LA) slices, suggested that a single time frame is adequate for motion correction whereas integrating more LA slices can improve registration and model reconstruction accuracy for improved functional quantification especially on datasets with severe motion artefacts.

  8. A novel Hessian based algorithm for rat kidney glomerulus detection in 3D MRI

    NASA Astrophysics Data System (ADS)

    Zhang, Min; Wu, Teresa; Bennett, Kevin M.

    2015-03-01

    The glomeruli of the kidney perform the key role of blood filtration and the number of glomeruli in a kidney is correlated with susceptibility to chronic kidney disease and chronic cardiovascular disease. This motivates the development of new technology using magnetic resonance imaging (MRI) to measure the number of glomeruli and nephrons in vivo. However, there is currently a lack of computationally efficient techniques to perform fast, reliable and accurate counts of glomeruli in MR images due to the issues inherent in MRI, such as acquisition noise, partial volume effects (the mixture of several tissue signals in a voxel) and bias field (spatial intensity inhomogeneity). Such challenges are particularly severe because the glomeruli are very small, (in our case, a MRI image is ~16 million voxels, each glomerulus is in the size of 8~20 voxels), and the number of glomeruli is very large. To address this, we have developed an efficient Hessian based Difference of Gaussians (HDoG) detector to identify the glomeruli on 3D rat MR images. The image is first smoothed via DoG followed by the Hessian process to pre-segment and delineate the boundary of the glomerulus candidates. This then provides a basis to extract regional features used in an unsupervised clustering algorithm, completing segmentation by removing the false identifications occurred in the pre-segmentation. The experimental results show that Hessian based DoG has the potential to automatically detect glomeruli,from MRI in 3D, enabling new measurements of renal microstructure and pathology in preclinical and clinical studies.

  9. Audiovisual biofeedback improves image quality and reduces scan time for respiratory-gated 3D MRI

    NASA Astrophysics Data System (ADS)

    Lee, D.; Greer, P. B.; Arm, J.; Keall, P.; Kim, T.

    2014-03-01

    The purpose of this study was to test the hypothesis that audiovisual (AV) biofeedback can improve image quality and reduce scan time for respiratory-gated 3D thoracic MRI. For five healthy human subjects respiratory motion guidance in MR scans was provided using an AV biofeedback system, utilizing real-time respiratory motion signals. To investigate the improvement of respiratory-gated 3D MR images between free breathing (FB) and AV biofeedback (AV), each subject underwent two imaging sessions. Respiratory-related motion artifacts and imaging time were qualitatively evaluated in addition to the reproducibility of external (abdominal) motion. In the results, 3D MR images in AV biofeedback showed more anatomic information such as a clear distinction of diaphragm, lung lobes and sharper organ boundaries. The scan time was reduced from 401±215 s in FB to 334±94 s in AV (p-value 0.36). The root mean square variation of the displacement and period of the abdominal motion was reduced from 0.4±0.22 cm and 2.8±2.5 s in FB to 0.1±0.15 cm and 0.9±1.3 s in AV (p-value of displacement <0.01 and p-value of period 0.12). This study demonstrated that audiovisual biofeedback improves image quality and reduces scan time for respiratory-gated 3D MRI. These results suggest that AV biofeedback has the potential to be a useful motion management tool in medical imaging and radiation therapy procedures.

  10. Whole-brain 3D mapping of human neural transplant innervation

    PubMed Central

    Doerr, Jonas; Schwarz, Martin Karl; Wiedermann, Dirk; Leinhaas, Anke; Jakobs, Alina; Schloen, Florian; Schwarz, Inna; Diedenhofen, Michael; Braun, Nils Christian; Koch, Philipp; Peterson, Daniel A.; Kubitscheck, Ulrich; Hoehn, Mathias; Brüstle, Oliver

    2017-01-01

    While transplantation represents a key tool for assessing in vivo functionality of neural stem cells and their suitability for neural repair, little is known about the integration of grafted neurons into the host brain circuitry. Rabies virus-based retrograde tracing has developed into a powerful approach for visualizing synaptically connected neurons. Here, we combine this technique with light sheet fluorescence microscopy (LSFM) to visualize transplanted cells and connected host neurons in whole-mouse brain preparations. Combined with co-registration of high-precision three-dimensional magnetic resonance imaging (3D MRI) reference data sets, this approach enables precise anatomical allocation of the host input neurons. Our data show that the same neural donor cell population grafted into different brain regions receives highly orthotopic input. These findings indicate that transplant connectivity is largely dictated by the circuitry of the target region and depict rabies-based transsynaptic tracing and LSFM as efficient tools for comprehensive assessment of host–donor cell innervation. PMID:28102196

  11. Whole-brain 3D mapping of human neural transplant innervation.

    PubMed

    Doerr, Jonas; Schwarz, Martin Karl; Wiedermann, Dirk; Leinhaas, Anke; Jakobs, Alina; Schloen, Florian; Schwarz, Inna; Diedenhofen, Michael; Braun, Nils Christian; Koch, Philipp; Peterson, Daniel A; Kubitscheck, Ulrich; Hoehn, Mathias; Brüstle, Oliver

    2017-01-19

    While transplantation represents a key tool for assessing in vivo functionality of neural stem cells and their suitability for neural repair, little is known about the integration of grafted neurons into the host brain circuitry. Rabies virus-based retrograde tracing has developed into a powerful approach for visualizing synaptically connected neurons. Here, we combine this technique with light sheet fluorescence microscopy (LSFM) to visualize transplanted cells and connected host neurons in whole-mouse brain preparations. Combined with co-registration of high-precision three-dimensional magnetic resonance imaging (3D MRI) reference data sets, this approach enables precise anatomical allocation of the host input neurons. Our data show that the same neural donor cell population grafted into different brain regions receives highly orthotopic input. These findings indicate that transplant connectivity is largely dictated by the circuitry of the target region and depict rabies-based transsynaptic tracing and LSFM as efficient tools for comprehensive assessment of host-donor cell innervation.

  12. Semi-automatic segmentation for 3D motion analysis of the tongue with dynamic MRI.

    PubMed

    Lee, Junghoon; Woo, Jonghye; Xing, Fangxu; Murano, Emi Z; Stone, Maureen; Prince, Jerry L

    2014-12-01

    Dynamic MRI has been widely used to track the motion of the tongue and measure its internal deformation during speech and swallowing. Accurate segmentation of the tongue is a prerequisite step to define the target boundary and constrain the tracking to tissue points within the tongue. Segmentation of 2D slices or 3D volumes is challenging because of the large number of slices and time frames involved in the segmentation, as well as the incorporation of numerous local deformations that occur throughout the tongue during motion. In this paper, we propose a semi-automatic approach to segment 3D dynamic MRI of the tongue. The algorithm steps include seeding a few slices at one time frame, propagating seeds to the same slices at different time frames using deformable registration, and random walker segmentation based on these seed positions. This method was validated on the tongue of five normal subjects carrying out the same speech task with multi-slice 2D dynamic cine-MR images obtained at three orthogonal orientations and 26 time frames. The resulting semi-automatic segmentations of a total of 130 volumes showed an average dice similarity coefficient (DSC) score of 0.92 with less segmented volume variability between time frames than in manual segmentations.

  13. Quantification of Diaphragm Mechanics in Pompe Disease Using Dynamic 3D MRI

    PubMed Central

    Mogalle, Katja; Perez-Rovira, Adria; Ciet, Pierluigi; Wens, Stephan C. A.; van Doorn, Pieter A.; Tiddens, Harm A. W. M.; van der Ploeg, Ans T.; de Bruijne, Marleen

    2016-01-01

    Background Diaphragm weakness is the main reason for respiratory dysfunction in patients with Pompe disease, a progressive metabolic myopathy affecting respiratory and limb-girdle muscles. Since respiratory failure is the major cause of death among adult patients, early identification of respiratory muscle involvement is necessary to initiate treatment in time and possibly prevent irreversible damage. In this paper we investigate the suitability of dynamic MR imaging in combination with state-of-the-art image analysis methods to assess respiratory muscle weakness. Methods The proposed methodology relies on image registration and lung surface extraction to quantify lung kinematics during breathing. This allows for the extraction of geometry and motion features of the lung that characterize the independent contribution of the diaphragm and the thoracic muscles to the respiratory cycle. Results Results in 16 3D+t MRI scans (10 Pompe patients and 6 controls) of a slow expiratory maneuver show that kinematic analysis from dynamic 3D images reveals important additional information about diaphragm mechanics and respiratory muscle involvement when compared to conventional pulmonary function tests. Pompe patients with severely reduced pulmonary function showed severe diaphragm weakness presented by minimal motion of the diaphragm. In patients with moderately reduced pulmonary function, cranial displacement of posterior diaphragm parts was reduced and the diaphragm dome was oriented more horizontally at full inspiration compared to healthy controls. Conclusion Dynamic 3D MRI provides data for analyzing the contribution of both diaphragm and thoracic muscles independently. The proposed image analysis method has the potential to detect less severe diaphragm weakness and could thus be used to determine the optimal start of treatment in adult patients with Pompe disease in prospect of increased treatment response. PMID:27391236

  14. 3D cardiac motion reconstruction from CT data and tagged MRI.

    PubMed

    Wang, Xiaoxu; Mihalef, Viorel; Qian, Zhen; Voros, Szilard; Metaxas, Dimitris

    2012-01-01

    In this paper we present a novel method for left ventricle (LV) endocardium motion reconstruction using high resolution CT data and tagged MRI. High resolution CT data provide anatomic details on the LV endocardial surface, such as the papillary muscle and trabeculae carneae. Tagged MRI provides better time resolution. The combination of these two imaging techniques can give us better understanding on left ventricle motion. The high resolution CT images are segmented with mean shift method and generate the LV endocardium mesh. The meshless deformable model built with high resolution endocardium surface from CT data fit to the tagged MRI of the same phase. 3D deformation of the myocardium is computed with the Lagrangian dynamics and local Laplacian deformation. The segmented inner surface of left ventricle is compared with the heart inner surface picture and show high agreement. The papillary muscles are attached to the inner surface with roots. The free wall of the left ventricle inner surface is covered with trabeculae carneae. The deformation of the heart wall and the papillary muscle in the first half of the cardiac cycle is presented. The motion reconstruction results are very close to the live heart video.

  15. TU-F-BRF-06: 3D Pancreas MRI Segmentation Using Dictionary Learning and Manifold Clustering

    SciTech Connect

    Gou, S; Rapacchi, S; Hu, P; Sheng, K

    2014-06-15

    Purpose: The recent advent of MRI guided radiotherapy machines has lent an exciting platform for soft tissue target localization during treatment. However, tools to efficiently utilize MRI images for such purpose have not been developed. Specifically, to efficiently quantify the organ motion, we develop an automated segmentation method using dictionary learning and manifold clustering (DLMC). Methods: Fast 3D HASTE and VIBE MR images of 2 healthy volunteers and 3 patients were acquired. A bounding box was defined to include pancreas and surrounding normal organs including the liver, duodenum and stomach. The first slice of the MRI was used for dictionary learning based on mean-shift clustering and K-SVD sparse representation. Subsequent images were iteratively reconstructed until the error is less than a preset threshold. The preliminarily segmentation was subject to the constraints of manifold clustering. The segmentation results were compared with the mean shift merging (MSM), level set (LS) and manual segmentation methods. Results: DLMC resulted in consistently higher accuracy and robustness than comparing methods. Using manual contours as the ground truth, the mean Dices indices for all subjects are 0.54, 0.56 and 0.67 for MSM, LS and DLMC, respectively based on the HASTE image. The mean Dices indices are 0.70, 0.77 and 0.79 for the three methods based on VIBE images. DLMC is clearly more robust on the patients with the diseased pancreas while LS and MSM tend to over-segment the pancreas. DLMC also achieved higher sensitivity (0.80) and specificity (0.99) combining both imaging techniques. LS achieved equivalent sensitivity on VIBE images but was more computationally inefficient. Conclusion: We showed that pancreas and surrounding normal organs can be reliably segmented based on fast MRI using DLMC. This method will facilitate both planning volume definition and imaging guidance during treatment.

  16. Nanofabricated Neural Probes for Dense 3-D Recordings of Brain Activity

    PubMed Central

    2016-01-01

    Computations in brain circuits involve the coordinated activation of large populations of neurons distributed across brain areas. However, monitoring neuronal activity in the brain of intact animals with high temporal and spatial resolution has remained a technological challenge. Here we address this challenge by developing dense, three-dimensional (3-D) electrode arrays for electrophysiology. The 3-D arrays constitute the front-end of a modular and configurable system architecture that enables monitoring neuronal activity with unprecedented scale and resolution. PMID:27766885

  17. Atlas-guided segmentation of vervet monkey brain MRI.

    PubMed

    Fedorov, Andriy; Li, Xiaoxing; Pohl, Kilian M; Bouix, Sylvain; Styner, Martin; Addicott, Merideth; Wyatt, Chris; Daunais, James B; Wells, William M; Kikinis, Ron

    2011-01-01

    The vervet monkey is an important nonhuman primate model that allows the study of isolated environmental factors in a controlled environment. Analysis of monkey MRI often suffers from lower quality images compared with human MRI because clinical equipment is typically used to image the smaller monkey brain and higher spatial resolution is required. This, together with the anatomical differences of the monkey brains, complicates the use of neuroimage analysis pipelines tuned for human MRI analysis. In this paper we developed an open source image analysis framework based on the tools available within the 3D Slicer software to support a biological study that investigates the effect of chronic ethanol exposure on brain morphometry in a longitudinally followed population of male vervets. We first developed a computerized atlas of vervet monkey brain MRI, which was used to encode the typical appearance of the individual brain structures in MRI and their spatial distribution. The atlas was then used as a spatial prior during automatic segmentation to process two longitudinal scans per subject. Our evaluation confirms the consistency and reliability of the automatic segmentation. The comparison of atlas construction strategies reveals that the use of a population-specific atlas leads to improved accuracy of the segmentation for subcortical brain structures. The contribution of this work is twofold. First, we describe an image processing workflow specifically tuned towards the analysis of vervet MRI that consists solely of the open source software tools. Second, we develop a digital atlas of vervet monkey brain MRIs to enable similar studies that rely on the vervet model.

  18. Atlas-Guided Segmentation of Vervet Monkey Brain MRI

    PubMed Central

    Fedorov, Andriy; Li, Xiaoxing; Pohl, Kilian M; Bouix, Sylvain; Styner, Martin; Addicott, Merideth; Wyatt, Chris; Daunais, James B; Wells, William M; Kikinis, Ron

    2011-01-01

    The vervet monkey is an important nonhuman primate model that allows the study of isolated environmental factors in a controlled environment. Analysis of monkey MRI often suffers from lower quality images compared with human MRI because clinical equipment is typically used to image the smaller monkey brain and higher spatial resolution is required. This, together with the anatomical differences of the monkey brains, complicates the use of neuroimage analysis pipelines tuned for human MRI analysis. In this paper we developed an open source image analysis framework based on the tools available within the 3D Slicer software to support a biological study that investigates the effect of chronic ethanol exposure on brain morphometry in a longitudinally followed population of male vervets. We first developed a computerized atlas of vervet monkey brain MRI, which was used to encode the typical appearance of the individual brain structures in MRI and their spatial distribution. The atlas was then used as a spatial prior during automatic segmentation to process two longitudinal scans per subject. Our evaluation confirms the consistency and reliability of the automatic segmentation. The comparison of atlas construction strategies reveals that the use of a population-specific atlas leads to improved accuracy of the segmentation for subcortical brain structures. The contribution of this work is twofold. First, we describe an image processing workflow specifically tuned towards the analysis of vervet MRI that consists solely of the open source software tools. Second, we develop a digital atlas of vervet monkey brain MRIs to enable similar studies that rely on the vervet model. PMID:22253661

  19. 3D perfused brain phantom for interstitial ultrasound thermal therapy and imaging: design, construction and characterization

    NASA Astrophysics Data System (ADS)

    Martínez, José M.; Jarosz, Boguslaw J.

    2015-03-01

    Thermal therapy has emerged as an independent modality of treating some tumors. In many clinics the hyperthermia, one of the thermal therapy modalities, has been used adjuvant to radio- or chemotherapy to substantially improve the clinical treatment outcomes. In this work, a methodology for building a realistic brain phantom for interstitial ultrasound low dose-rate thermal therapy of the brain is proposed. A 3D brain phantom made of the tissue mimicking material (TMM) had the acoustic and thermal properties in the 20-32 °C range, which is similar to that of a brain at 37 °C. The phantom had 10-11% by mass of bovine gelatin powder dissolved in ethylene glycol. The TMM sonicated at 1 MHz, 1.6 MHz and 2.5 MHz yielded the amplitude attenuation coefficients of 62  ±  1 dB m-1, 115  ±  4 dB m-1 and 175  ±  9 dB m-1, respectively. The density and acoustic speed determination at room temperature (~24 °C) gave 1040  ±  40 kg m-3 and 1545  ±  44 m s-1, respectively. The average thermal conductivity was 0.532 W m-1 K-1. The T1 and T2 values of the TMM were 207  ±  4 and 36.2  ±  0.4 ms, respectively. We envisage the use of our phantom for treatment planning and for quality assurance in MRI based temperature determination. Our phantom preparation methodology may be readily extended to other thermal therapy technologies.

  20. 3D perfused brain phantom for interstitial ultrasound thermal therapy and imaging: design, construction and characterization.

    PubMed

    Martínez, José M; Jarosz, Boguslaw J

    2015-03-07

    Thermal therapy has emerged as an independent modality of treating some tumors. In many clinics the hyperthermia, one of the thermal therapy modalities, has been used adjuvant to radio- or chemotherapy to substantially improve the clinical treatment outcomes. In this work, a methodology for building a realistic brain phantom for interstitial ultrasound low dose-rate thermal therapy of the brain is proposed. A 3D brain phantom made of the tissue mimicking material (TMM) had the acoustic and thermal properties in the 20-32 °C range, which is similar to that of a brain at 37 °C. The phantom had 10-11% by mass of bovine gelatin powder dissolved in ethylene glycol. The TMM sonicated at 1 MHz, 1.6 MHz and 2.5 MHz yielded the amplitude attenuation coefficients of 62  ±  1 dB m(-1), 115  ±  4 dB m(-1) and 175  ±  9 dB m(-1), respectively. The density and acoustic speed determination at room temperature (~24 °C) gave 1040  ±  40 kg m(-3) and 1545  ±  44 m s(-1), respectively. The average thermal conductivity was 0.532 W m(-1) K(-1). The T1 and T2 values of the TMM were 207  ±  4 and 36.2  ±  0.4 ms, respectively. We envisage the use of our phantom for treatment planning and for quality assurance in MRI based temperature determination. Our phantom preparation methodology may be readily extended to other thermal therapy technologies.

  1. MRI-based aortic blood flow model in 3D ballistocardiography.

    PubMed

    Lejeune, L; Prisk, G K; Nonclercq, A; Migeotte, P-F

    2015-01-01

    Ballistocardiography (BCG) is a non-invasive technique which measures the acceleration of a body induced by cardiovascular activity, namely the force exerted by the beating heart. A one dimensional aortic flow model based on the transmission lines theory is developped and applied to the simulation of three dimensional BCG. A four-element Windkessel model is used to generate the pressure-wave. Using transverse MRI slices of a human subject, a reconstruction of the aorta allows the extraction of parameters used to relate the local change in mass of the 1D flow model to 3D acceleration BCG. Simulated BCG curves are then compared qualitatively with the ensemble average curves of the same subject recorded in sustained microgravity. Confirming previous studies, the main features of the y-axis are well simulated. The simulated z-axis, never attempted before, shows important similarities. The simulated x-axis is less faithful and suggests the presence of reflections.

  2. Brain morphology imaging by 3D microscopy and fluorescent Nissl staining.

    PubMed

    Lazutkin, A A; Komissarova, N V; Toptunov, D M; Anokhin, K V

    2013-07-01

    Modern optical methods (multiphoton and light-sheet fluorescent microscopy) allow 3D imaging of large specimens of the brain with cell resolution. It is therefore essential to refer the resultant 3D pictures of expression of transgene, protein, and other markers in the brain to the corresponding structures in the atlas. This implies counterstaining of specimens with morphological dyes. However, there are no methods for contrasting large samples of the brain without their preliminary slicing. We have developed a method for fluorescent Nissl staining of whole brain samples. 3D reconstructions of specimens of the hippocampus, olfactory bulbs, and cortex were created. The method can be used for morphological control and evaluation of the effects of various factors on the brain using 3D microscopy technique.

  3. Thermal analysis of the surrounding anatomy during 3-D MRI-guided transurethral ultrasound prostate therapy

    NASA Astrophysics Data System (ADS)

    Burtnyk, Mathieu; Chopra, Rajiv; Bronskill, Michael

    2010-03-01

    Previous numerical simulations have shown that MRI-guided transurethral ultrasound therapy can generate highly accurate volumes of thermal coagulation conforming to 3-D human prostate geometries. The goal of this work is to simulate, quantify and evaluate the thermal impact of these treatments on the rectum, pelvic bone, neurovascular bundles (NVB) and urinary sphincters. This study used twenty 3-D anatomical models of prostate cancer patients and detailed bio-acoustic simulations incorporating an active feedback algorithm which controlled a rotating, planar ultrasound transducer (17-4×3 mm elements, 4.7/9.7 MHz, 10 Wac/cm2). Heating of the adjacent surrounding anatomy was evaluated using thermal tolerances reported in the literature. Heating of the rectum poses the most important safety concern and is influenced largely by the water temperature flowing through an endorectal cooling device; temperatures of 7-37° C are required to limit potential damage to less than 10 mm3 on the outer 1 mm layer of rectum. Significant heating of the pelvic bone was predicted in 30% of the patient models with an ultrasound frequency of 4.7 MHz; setting the frequency to 9.7 MHz when the bone is less than 10 mm away from the prostate reduced heating in all cases below the threshold for irreversible damage. Heating of the NVB was significant in 75% of the patient models in the absence of treatment planning; this proportion was reduced to 5% by using treatment margins of up to 4 mm. To avoid damaging the urinary sphincters, margins from the transducer of 2-4 mm should be used, depending on the transurethral cooling temperature. Simulations show that MRI-guided transurethral therapy can treat the entire prostate accurately. Strategies have been developed which, along with careful treatment planning, can be used to avoid causing thermal injury to the rectum, pelvic bone, NVB and urinary sphincters.

  4. Brain development in preterm infants assessed using advanced MRI techniques.

    PubMed

    Tusor, Nora; Arichi, Tomoki; Counsell, Serena J; Edwards, A David

    2014-03-01

    Infants who are born preterm have a high incidence of neurocognitive and neurobehavioral abnormalities, which may be associated with impaired brain development. Advanced magnetic resonance imaging (MRI) approaches, such as diffusion MRI (d-MRI) and functional MRI (fMRI), provide objective and reproducible measures of brain development. Indices derived from d-MRI can be used to provide quantitative measures of preterm brain injury. Although fMRI of the neonatal brain is currently a research tool, future studies combining d-MRI and fMRI have the potential to assess the structural and functional properties of the developing brain and its response to injury.

  5. A new strategy for respiration compensation, applied toward 3D free-breathing cardiac MRI.

    PubMed

    Madore, Bruno; Farnebäck, Gunnar; Westin, Carl-Fredrik; Durán-Mendicuti, Alejandra

    2006-07-01

    In thorax and abdomen imaging, image quality may be affected by breathing motion. Cardiac MR images are typically obtained while the patient holds his or her breath, to avoid respiration-related artifacts. Although useful, breath-holding imposes constraints on scan duration, which in turn limits the achievable resolution and SNR. Longer scan times would be required to improve image quality, and effective strategies are needed to compensate for respiratory motion. A novel approach at respiratory compensation, targeted toward 3D free-breathing cardiac MRI, is presented here. The method aims at suppressing the negative effects of respiratory-induced cardiac motion while capturing the heart's beating motion. The method is designed so that the acquired data can be reconstructed in two different ways: First, a time series of images is reconstructed to quantify and correct for respiratory motion. Then, the corrected data are reconstructed a final time into a cardiac-phase series of images to capture the heart's beating motion. The method was implemented, and initial results are presented. A cardiac-phase series of 3D images, covering the entire heart, was obtained for two free-breathing volunteers. The present method may prove especially useful in situations where breath-holding is not an option, for example, for very sick, mentally impaired or infant patients.

  6. 3D Deep Learning for Multi-modal Imaging-Guided Survival Time Prediction of Brain Tumor Patients

    PubMed Central

    Nie, Dong; Zhang, Han; Adeli, Ehsan; Liu, Luyan

    2016-01-01

    High-grade glioma is the most aggressive and severe brain tumor that leads to death of almost 50% patients in 1–2 years. Thus, accurate prognosis for glioma patients would provide essential guidelines for their treatment planning. Conventional survival prediction generally utilizes clinical information and limited handcrafted features from magnetic resonance images (MRI), which is often time consuming, laborious and subjective. In this paper, we propose using deep learning frameworks to automatically extract features from multi-modal preoperative brain images (i.e., T1 MRI, fMRI and DTI) of high-grade glioma patients. Specifically, we adopt 3D convolutional neural networks (CNNs) and also propose a new network architecture for using multi-channel data and learning supervised features. Along with the pivotal clinical features, we finally train a support vector machine to predict if the patient has a long or short overall survival (OS) time. Experimental results demonstrate that our methods can achieve an accuracy as high as 89.9% We also find that the learned features from fMRI and DTI play more important roles in accurately predicting the OS time, which provides valuable insights into functional neuro-oncological applications. PMID:28149967

  7. 3D Deep Learning for Multi-modal Imaging-Guided Survival Time Prediction of Brain Tumor Patients.

    PubMed

    Nie, Dong; Zhang, Han; Adeli, Ehsan; Liu, Luyan; Shen, Dinggang

    2016-10-01

    High-grade glioma is the most aggressive and severe brain tumor that leads to death of almost 50% patients in 1-2 years. Thus, accurate prognosis for glioma patients would provide essential guidelines for their treatment planning. Conventional survival prediction generally utilizes clinical information and limited handcrafted features from magnetic resonance images (MRI), which is often time consuming, laborious and subjective. In this paper, we propose using deep learning frameworks to automatically extract features from multi-modal preoperative brain images (i.e., T1 MRI, fMRI and DTI) of high-grade glioma patients. Specifically, we adopt 3D convolutional neural networks (CNNs) and also propose a new network architecture for using multi-channel data and learning supervised features. Along with the pivotal clinical features, we finally train a support vector machine to predict if the patient has a long or short overall survival (OS) time. Experimental results demonstrate that our methods can achieve an accuracy as high as 89.9% We also find that the learned features from fMRI and DTI play more important roles in accurately predicting the OS time, which provides valuable insights into functional neuro-oncological applications.

  8. Registration of 2D x-ray images to 3D MRI by generating pseudo-CT data

    NASA Astrophysics Data System (ADS)

    van der Bom, M. J.; Pluim, J. P. W.; Gounis, M. J.; van de Kraats, E. B.; Sprinkhuizen, S. M.; Timmer, J.; Homan, R.; Bartels, L. W.

    2011-02-01

    Spatial and soft tissue information provided by magnetic resonance imaging can be very valuable during image-guided procedures, where usually only real-time two-dimensional (2D) x-ray images are available. Registration of 2D x-ray images to three-dimensional (3D) magnetic resonance imaging (MRI) data, acquired prior to the procedure, can provide optimal information to guide the procedure. However, registering x-ray images to MRI data is not a trivial task because of their fundamental difference in tissue contrast. This paper presents a technique that generates pseudo-computed tomography (CT) data from multi-spectral MRI acquisitions which is sufficiently similar to real CT data to enable registration of x-ray to MRI with comparable accuracy as registration of x-ray to CT. The method is based on a k-nearest-neighbors (kNN)-regression strategy which labels voxels of MRI data with CT Hounsfield Units. The regression method uses multi-spectral MRI intensities and intensity gradients as features to discriminate between various tissue types. The efficacy of using pseudo-CT data for registration of x-ray to MRI was tested on ex vivo animal data. 2D-3D registration experiments using CT and pseudo-CT data of multiple subjects were performed with a commonly used 2D-3D registration algorithm. On average, the median target registration error for registration of two x-ray images to MRI data was approximately 1 mm larger than for x-ray to CT registration. The authors have shown that pseudo-CT data generated from multi-spectral MRI facilitate registration of MRI to x-ray images. From the experiments it could be concluded that the accuracy achieved was comparable to that of registering x-ray images to CT data.

  9. In vivo MEMRI characterization of brain metastases using a 3D Look-Locker T1-mapping sequence

    PubMed Central

    Castets, Charles R.; Koonjoo, Néha; Hertanu, Andreea; Voisin, Pierre; Franconi, Jean-Michel; Miraux, Sylvain; Ribot, Emeline J.

    2016-01-01

    Although MEMRI (Manganese Enhanced MRI) informations were obtained on primary tumors in small animals, MEMRI data on metastases are lacking. Thus, our goal was to determine if 3D Look-Locker T1 mapping was an efficient method to evaluate Mn ions transport in brain metastases in vivo. The high spatial resolution in 3D (156 × 156 × 218 μm) of the sequence enabled to detect metastases of 0.3 mm3. In parallel, the T1 quantitation enabled to distinguish three populations of MDA-MB-231 derived brain metastases after MnCl2 intravenous injection: one with a healthy blood-tumor barrier that did not internalize Mn2+ ions, and two others, which T1 shortened drastically by 54.2% or 24%. Subsequent scans of the mice, enabled by the fast acquisition (23 min), demonstrated that these T1 reached back their pre-injection values in 24 h. Contrarily to metastases, the T1 of U87-MG glioma remained 26.2% shorter for one week. In vitro results supported the involvement of the Transient Receptor Potential channels and the Calcium-Sensing Receptor in the uptake and efflux of Mn2+ ions, respectively. This study highlights the ability of the 3D Look-Locker T1 mapping sequence to study heterogeneities (i) amongst brain metastases and (ii) between metastases and glioma regarding Mn transport. PMID:27995976

  10. Midsagittal plane extraction from brain images based on 3D SIFT

    NASA Astrophysics Data System (ADS)

    Wu, Huisi; Wang, Defeng; Shi, Lin; Wen, Zhenkun; Ming, Zhong

    2014-03-01

    Midsagittal plane (MSP) extraction from 3D brain images is considered as a promising technique for human brain symmetry analysis. In this paper, we present a fast and robust MSP extraction method based on 3D scale-invariant feature transform (SIFT). Unlike the existing brain MSP extraction methods, which mainly rely on the gray similarity, 3D edge registration or parameterized surface matching to determine the fissure plane, our proposed method is based on distinctive 3D SIFT features, in which the fissure plane is determined by parallel 3D SIFT matching and iterative least-median of squares plane regression. By considering the relative scales, orientations and flipped descriptors between two 3D SIFT features, we propose a novel metric to measure the symmetry magnitude for 3D SIFT features. By clustering and indexing the extracted SIFT features using a k-dimensional tree (KD-tree) implemented on graphics processing units, we can match multiple pairs of 3D SIFT features in parallel and solve the optimal MSP on-the-fly. The proposed method is evaluated by synthetic and in vivo datasets, of normal and pathological cases, and validated by comparisons with the state-of-the-art methods. Experimental results demonstrated that our method has achieved a real-time performance with better accuracy yielding an average yaw angle error below 0.91° and an average roll angle error no more than 0.89°.

  11. Low-Amplitude Craniofacial EMG Power Spectral Density and 3D Muscle Reconstruction from MRI

    PubMed Central

    Wiedemann, Lukas; Chaberova, Jana; Edmunds, Kyle; Einarsdóttir, Guðrún; Ramon, Ceon

    2015-01-01

    Improving EEG signal interpretation, specificity, and sensitivity is a primary focus of many current investigations, and the successful application of EEG signal processing methods requires a detailed knowledge of both the topography and frequency spectra of low-amplitude, high-frequency craniofacial EMG. This information remains limited in clinical research, and as such, there is no known reliable technique for the removal of these artifacts from EEG data. The results presented herein outline a preliminary investigation of craniofacial EMG high-frequency spectra and 3D MRI segmentation that offers insight into the development of an anatomically-realistic model for characterizing these effects. The data presented highlights the potential for confounding signal contribution from around 60 to 200 Hz, when observed in frequency space, from both low and high-amplitude EMG signals. This range directly overlaps that of both low γ (30-50 Hz) and high γ (50-80 Hz) waves, as defined traditionally in standatrd EEG measurements, and mainly with waves presented in dense-array EEG recordings. Likewise, average EMG amplitude comparisons from each condition highlights the similarities in signal contribution of low-activity muscular movements and resting, control conditions. In addition to the FFT analysis performed, 3D segmentation and reconstruction of the craniofacial muscles whose EMG signals were measured was successful. This recapitulation of the relevant EMG morphology is a crucial first step in developing an anatomical model for the isolation and removal of confounding low-amplitude craniofacial EMG signals from EEG data. Such a model may be eventually applied in a clinical setting to ultimately help to extend the use of EEG in various clinical roles. PMID:26913150

  12. Automatic 3D segmentation of spinal cord MRI using propagated deformable models

    NASA Astrophysics Data System (ADS)

    De Leener, B.; Cohen-Adad, J.; Kadoury, S.

    2014-03-01

    Spinal cord diseases or injuries can cause dysfunction of the sensory and locomotor systems. Segmentation of the spinal cord provides measures of atrophy and allows group analysis of multi-parametric MRI via inter-subject registration to a template. All these measures were shown to improve diagnostic and surgical intervention. We developed a framework to automatically segment the spinal cord on T2-weighted MR images, based on the propagation of a deformable model. The algorithm is divided into three parts: first, an initialization step detects the spinal cord position and orientation by using the elliptical Hough transform on multiple adjacent axial slices to produce an initial tubular mesh. Second, a low-resolution deformable model is iteratively propagated along the spinal cord. To deal with highly variable contrast levels between the spinal cord and the cerebrospinal fluid, the deformation is coupled with a contrast adaptation at each iteration. Third, a refinement process and a global deformation are applied on the low-resolution mesh to provide an accurate segmentation of the spinal cord. Our method was evaluated against a semi-automatic edge-based snake method implemented in ITK-SNAP (with heavy manual adjustment) by computing the 3D Dice coefficient, mean and maximum distance errors. Accuracy and robustness were assessed from 8 healthy subjects. Each subject had two volumes: one at the cervical and one at the thoracolumbar region. Results show a precision of 0.30 +/- 0.05 mm (mean absolute distance error) in the cervical region and 0.27 +/- 0.06 mm in the thoracolumbar region. The 3D Dice coefficient was of 0.93 for both regions.

  13. Isotropic 3D Black Blood MRI of Abdominal Aortic Aneurysm Wall and Intraluminal Thrombus

    PubMed Central

    Zhu, Chengcheng; Haraldsson, Henrik; Faraji, Farshid; Owens, Christopher; Gasper, Warren; Ahn, Sinyeob; Liu, Jing; Laub, Gerhard; Hope, Michael D.; Saloner, David

    2015-01-01

    Introduction The aortic wall and intraluminal thrombus (ILT) have been increasingly studied as potential markers of progressive disease with abdominal aortic aneurysms (AAAs). Our goal was to develop a high resolution, 3D black blood MR technique for AAA wall and ILT imaging within a clinically acceptable scan time. Methods Twenty two patients with AAAs (maximal diameter 4.3±1.0cm), along with five healthy volunteers, were imaged at 3T with a 3D T1-weighted fast-spin-echo sequence using variable flip angle trains (SPACE) with a preparation pulse (DANTE) for suppressing blood signal. Volunteers and ten patients were also scanned with SPACE alone for comparison purposes. The signal to noise ratio (SNR) and the aortic wall/ILT to lumen contrast to noise ratio (CNR) were measured. Qualitative image scores (1–4 scale) assessing the inner lumen and outer wall boundaries of AAA were performed by two blinded reviewers. In patients with ILT, the ratio of ILT signal intensity (ILTSI) over psoas muscle SI (MuscleSI) was calculated, and the signal heterogeneity of ILT was quantified as standard deviation (SD) over the mean. Results All subjects were imaged successfully with an average scan time of 7.8±0.7 minutes. The DANTE preparation pulse for blood suppression substantially reduced flow artifacts in SPACE with lower lumen SNR (8.8 vs. 21.4, p<0.001) and improved the wall/ILT to lumen CNR (9.9 vs. 6.3, p<0.001) in patients. Qualitative assessment showed improved visualization of lumen boundaries (73% higher scores on average, p=0.01) and comparable visualization of outer wall boundary (p>0.05). ILT was present in ten patients, with relatively high signal and a wide SD (average ILTSI/MuscleSI 1.42±0.48 (range 0.75–2.11) ) and with SD/mean of 27.7%±6.6% (range 19.6% – 39.4%). Conclusion High resolution, 3D black blood MRI of AAAs can be achieved in a clinical accepted scan time with reduction of flow artifacts using the DANTE preparation pulse. Signal characteristics

  14. Practical MRI atlas of neonatal brain development

    SciTech Connect

    Barkovich, A.J.; Truwit, C.L.

    1990-01-01

    This book is an anatomical reference for cranial magnetic resonance imaging (MRI) studies in neonates and infants. It contains 122 clear, sharp MRI scans and drawings showing changes in the normal appearance of the brain and skull during development. Sections of the atlas depict the major processes of maturation: brain myelination, development of the corpus callosum, development of the cranial bone marrow, and iron deposition in the brain. High-quality scans illustrate how these changes appear on magnetic resonance images during various stages of development.

  15. 3D source localization of interictal spikes in epilepsy patients with MRI lesions

    NASA Astrophysics Data System (ADS)

    Ding, Lei; Worrell, Gregory A.; Lagerlund, Terrence D.; He, Bin

    2006-08-01

    The present study aims to accurately localize epileptogenic regions which are responsible for epileptic activities in epilepsy patients by means of a new subspace source localization approach, i.e. first principle vectors (FINE), using scalp EEG recordings. Computer simulations were first performed to assess source localization accuracy of FINE in the clinical electrode set-up. The source localization results from FINE were compared with the results from a classic subspace source localization approach, i.e. MUSIC, and their differences were tested statistically using the paired t-test. Other factors influencing the source localization accuracy were assessed statistically by ANOVA. The interictal epileptiform spike data from three adult epilepsy patients with medically intractable partial epilepsy and well-defined symptomatic MRI lesions were then studied using both FINE and MUSIC. The comparison between the electrical sources estimated by the subspace source localization approaches and MRI lesions was made through the coregistration between the EEG recordings and MRI scans. The accuracy of estimations made by FINE and MUSIC was also evaluated and compared by R2 statistic, which was used to indicate the goodness-of-fit of the estimated sources to the scalp EEG recordings. The three-concentric-spheres head volume conductor model was built for each patient with three spheres of different radii which takes the individual head size and skull thickness into consideration. The results from computer simulations indicate that the improvement of source spatial resolvability and localization accuracy of FINE as compared with MUSIC is significant when simulated sources are closely spaced, deep, or signal-to-noise ratio is low in a clinical electrode set-up. The interictal electrical generators estimated by FINE and MUSIC are in concordance with the patients' structural abnormality, i.e. MRI lesions, in all three patients. The higher R2 values achieved by FINE than MUSIC

  16. Evaluation of 3D cognitive fatigue using heart-brain synchronization.

    PubMed

    Park, Sangin; Won, Myoung Ju; Lee, Eui Chul; Mun, Sungchul; Park, Min-Chul; Whang, Mincheol

    2015-08-01

    The purpose of this study was to identify an evaluation method for 3D cognitive fatigue based on a heart-brain synchronization phenomenon known as the heartbeat evoked potential (HEP). Thirty undergraduate students (15 females) watched a video in both 2D and 3D for an hour. Because visual fatigue is related to cognitive load, the HEP was used as an indicator of communication between the heart and the brain and therefore of cognitive function; responses were compared after 2D and 3D viewing. At the standard EEG sites F3 and F4, the alpha activity of the first and second HEP components was significantly increased after 3D video viewing relative to 2D. This increase likely indicates that sensory input from 3D video requires heavy computation by the brain, stimulating heart activity. The conclusion is that the first and second HEP components are significant parameters that can quantitatively evaluate 3D visual fatigue. Further work is needed to uncover the cause of 3D visual fatigue.

  17. Wearable 3-D Photoacoustic Tomography for Functional Brain Imaging in Behaving Rats

    PubMed Central

    Tang, Jianbo; Coleman, Jason E.; Dai, Xianjin; Jiang, Huabei

    2016-01-01

    Understanding the relationship between brain function and behavior remains a major challenge in neuroscience. Photoacoustic tomography (PAT) is an emerging technique that allows for noninvasive in vivo brain imaging at micrometer-millisecond spatiotemporal resolution. In this article, a novel, miniaturized 3D wearable PAT (3D-wPAT) technique is described for brain imaging in behaving rats. 3D-wPAT has three layers of fully functional acoustic transducer arrays. Phantom imaging experiments revealed that the in-plane X-Y spatial resolutions were ~200 μm for each acoustic detection layer. The functional imaging capacity of 3D-wPAT was demonstrated by mapping the cerebral oxygen saturation via multi-wavelength irradiation in behaving hyperoxic rats. In addition, we demonstrated that 3D-wPAT could be used for monitoring sensory stimulus-evoked responses in behaving rats by measuring hemodynamic responses in the primary visual cortex during visual stimulation. Together, these results show the potential of 3D-wPAT for brain study in behaving rodents. PMID:27146026

  18. Wearable 3-D Photoacoustic Tomography for Functional Brain Imaging in Behaving Rats.

    PubMed

    Tang, Jianbo; Coleman, Jason E; Dai, Xianjin; Jiang, Huabei

    2016-05-05

    Understanding the relationship between brain function and behavior remains a major challenge in neuroscience. Photoacoustic tomography (PAT) is an emerging technique that allows for noninvasive in vivo brain imaging at micrometer-millisecond spatiotemporal resolution. In this article, a novel, miniaturized 3D wearable PAT (3D-wPAT) technique is described for brain imaging in behaving rats. 3D-wPAT has three layers of fully functional acoustic transducer arrays. Phantom imaging experiments revealed that the in-plane X-Y spatial resolutions were ~200 μm for each acoustic detection layer. The functional imaging capacity of 3D-wPAT was demonstrated by mapping the cerebral oxygen saturation via multi-wavelength irradiation in behaving hyperoxic rats. In addition, we demonstrated that 3D-wPAT could be used for monitoring sensory stimulus-evoked responses in behaving rats by measuring hemodynamic responses in the primary visual cortex during visual stimulation. Together, these results show the potential of 3D-wPAT for brain study in behaving rodents.

  19. Perceptual integration for qualitatively different 3-D cues in the human brain.

    PubMed

    Dövencioğlu, Dicle; Ban, Hiroshi; Schofield, Andrew J; Welchman, Andrew E

    2013-09-01

    The visual system's flexibility in estimating depth is remarkable: We readily perceive 3-D structure under diverse conditions from the seemingly random dots of a "magic eye" stereogram to the aesthetically beautiful, but obviously flat, canvasses of the Old Masters. Yet, 3-D perception is often enhanced when different cues specify the same depth. This perceptual process is understood as Bayesian inference that improves sensory estimates. Despite considerable behavioral support for this theory, insights into the cortical circuits involved are limited. Moreover, extant work tested quantitatively similar cues, reducing some of the challenges associated with integrating computationally and qualitatively different signals. Here we address this challenge by measuring fMRI responses to depth structures defined by shading, binocular disparity, and their combination. We quantified information about depth configurations (convex "bumps" vs. concave "dimples") in different visual cortical areas using pattern classification analysis. We found that fMRI responses in dorsal visual area V3B/KO were more discriminable when disparity and shading concurrently signaled depth, in line with the predictions of cue integration. Importantly, by relating fMRI and psychophysical tests of integration, we observed a close association between depth judgments and activity in this area. Finally, using a cross-cue transfer test, we found that fMRI responses evoked by one cue afford classification of responses evoked by the other. This reveals a generalized depth representation in dorsal visual cortex that combines qualitatively different information in line with 3-D perception.

  20. Seeing biological actions in 3D: An fMRI study

    PubMed Central

    Jastorff, Jan; Abdollahi, Rouhollah O.; Fasano, Fabrizio

    2015-01-01

    Abstract Precise kinematics or body configuration cannot be recovered from visual input without disparity information. Yet, no imaging study has investigated the role of disparity on action observation. Here, we investigated the interaction between disparity and the main cues of biological motion, kinematics and configuration, in two fMRI experiments. Stimuli were presented as point‐light figures, depicting complex action sequences lasting 21 s. We hypothesized that interactions could occur at any of the three levels of the action observation network, comprising occipitotemporal, parietal and premotor cortex, with premotor cortex being the most likely location. The main effects of kinematics and configuration confirmed that the biological motion sequences activated all three levels of the action observation network, validating our approach. The interaction between configuration and disparity activated only premotor cortex, whereas interactions between kinematics and disparity occurred at all levels of the action observation network but were strongest at the premotor level. Control experiments demonstrated that these interactions could not be accounted for by low level motion in depth, task effects, spatial attention, or eye movements, including vergence. These results underscore the role of premotor cortex in action observation, and in imitating others or responding to their actions. Hum Brain Mapp 37:203–219, 2016. © 2015 The Authors Human Brain Mapping Published by Wiley Periodicals, Inc. PMID:26510637

  1. Use of brain MRI after deep brain stimulation hardware implantation.

    PubMed

    Nazzaro, Jules M; Lyons, Kelly E; Wetzel, Louis H; Pahwa, Rajesh

    2010-03-01

    The objective of this study was to examine the experience with and safety of brain 1.5 Tesla (T) magnetic resonance imaging (MRI) in deep brain stimulation (DBS) patients. This was a retrospective review of brain MRI scanning performed on DBS patients at the University of Kansas Medical Center between January 1995 and December 2007. A total of 249 DBS patients underwent 445 brain 1.5 T MRI scan sessions encompassing 1,092 individual scans using a transmit-receive head coil, representing the cumulative scanning of 1,649 DBS leads. Patients with complete implanted DBS systems as well as those with externalized leads underwent brain imaging. For the majority of scans, specific absorption rates localized to the head (SAR(H)) were estimated and in all cases SAR(H) were higher than that specified in the present product labeling. There were no clinical or hardware related adverse events secondary to brain MRI scanning. Our data should not be extrapolated to encourage MRI scanning beyond the present labeling. Rather, our data may contribute to further defining safe MRI scanning parameters that might ultimately be adopted in future product labeling as more centers report in detail their experiences.

  2. 3D Texture Analysis Reveals Imperceptible MRI Textural Alterations in the Thalamus and Putamen in Progressive Myoclonic Epilepsy Type 1, EPM1

    PubMed Central

    Suoranta, Sanna; Holli-Helenius, Kirsi; Koskenkorva, Päivi; Niskanen, Eini; Könönen, Mervi; Äikiä, Marja; Eskola, Hannu; Kälviäinen, Reetta; Vanninen, Ritva

    2013-01-01

    Progressive myoclonic epilepsy type 1 (EPM1) is an autosomal recessively inherited neurodegenerative disorder characterized by young onset age, myoclonus and tonic-clonic epileptic seizures. At the time of diagnosis, the visual assessment of the brain MRI is usually normal, with no major changes found later. Therefore, we utilized texture analysis (TA) to characterize and classify the underlying properties of the affected brain tissue by means of 3D texture features. Sixteen genetically verified patients with EPM1 and 16 healthy controls were included in the study. TA was performed upon 3D volumes of interest that were placed bilaterally in the thalamus, amygdala, hippocampus, caudate nucleus and putamen. Compared to the healthy controls, EPM1 patients had significant textural differences especially in the thalamus and right putamen. The most significantly differing texture features included parameters that measure the complexity and heterogeneity of the tissue, such as the co-occurrence matrix-based entropy and angular second moment, and also the run-length matrix-based parameters of gray-level non-uniformity, short run emphasis and long run emphasis. This study demonstrates the usability of 3D TA for extracting additional information from MR images. Textural alterations which suggest complex, coarse and heterogeneous appearance were found bilaterally in the thalamus, supporting the previous literature on thalamic pathology in EPM1. The observed putamenal involvement is a novel finding. Our results encourage further studies on the clinical applications, feasibility, reproducibility and reliability of 3D TA. PMID:23922849

  3. Trans3D: a free tool for dynamical visualization of EEG activity transmission in the brain.

    PubMed

    Blinowski, Grzegorz; Kamiński, Maciej; Wawer, Dariusz

    2014-08-01

    The problem of functional connectivity in the brain is in the focus of attention nowadays, since it is crucial for understanding information processing in the brain. A large repertoire of measures of connectivity have been devised, some of them being capable of estimating time-varying directed connectivity. Hence, there is a need for a dedicated software tool for visualizing the propagation of electrical activity in the brain. To this aim, the Trans3D application was developed. It is an open access tool based on widely available libraries and supporting both Windows XP/Vista/7(™), Linux and Mac environments. Trans3D can create animations of activity propagation between electrodes/sensors, which can be placed by the user on the scalp/cortex of a 3D model of the head. Various interactive graphic functions for manipulating and visualizing components of the 3D model and input data are available. An application of the Trans3D tool has helped to elucidate the dynamics of the phenomena of information processing in motor and cognitive tasks, which otherwise would have been very difficult to observe. Trans3D is available at: http://www.eeg.pl/.

  4. Segmentation of human brain using structural MRI.

    PubMed

    Helms, Gunther

    2016-04-01

    Segmentation of human brain using structural MRI is a key step of processing in imaging neuroscience. The methods have undergone a rapid development in the past two decades and are now widely available. This non-technical review aims at providing an overview and basic understanding of the most common software. Starting with the basis of structural MRI contrast in brain and imaging protocols, the concepts of voxel-based and surface-based segmentation are discussed. Special emphasis is given to the typical contrast features and morphological constraints of cortical and sub-cortical grey matter. In addition to the use for voxel-based morphometry, basic applications in quantitative MRI, cortical thickness estimations, and atrophy measurements as well as assignment of cortical regions and deep brain nuclei are briefly discussed. Finally, some fields for clinical applications are given.

  5. Sub-millimeter T2 weighted fMRI at 7 T: comparison of 3D-GRASE and 2D SE-EPI.

    PubMed

    Kemper, Valentin G; De Martino, Federico; Vu, An T; Poser, Benedikt A; Feinberg, David A; Goebel, Rainer; Yacoub, Essa

    2015-01-01

    Functional magnetic resonance imaging (fMRI) allows studying human brain function non-invasively up to the spatial resolution of cortical columns and layers. Most fMRI acquisitions rely on the blood oxygenation level dependent (BOLD) contrast employing T(*) 2 weighted 2D multi-slice echo-planar imaging (EPI). At ultra-high magnetic field (i.e., 7 T and above), it has been shown experimentally and by simulation, that T2 weighted acquisitions yield a signal that is spatially more specific to the site of neuronal activity at the cost of functional sensitivity. This study compared two T2 weighted imaging sequences, inner-volume 3D Gradient-and-Spin-Echo (3D-GRASE) and 2D Spin-Echo EPI (SE-EPI), with evaluation of their imaging point-spread function (PSF), functional specificity, and functional sensitivity at sub-millimeter resolution. Simulations and measurements of the imaging PSF revealed that the strongest anisotropic blurring in 3D-GRASE (along the second phase-encoding direction) was about 60% higher than the strongest anisotropic blurring in 2D SE-EPI (along the phase-encoding direction). In a visual paradigm, the BOLD sensitivity of 3D-GRASE was found to be superior due to its higher temporal signal-to-noise ratio (tSNR). High resolution cortical depth profiles suggested that the contrast mechanisms are similar between the two sequences, however, 2D SE-EPI had a higher surface bias owing to the higher T(*) 2 contribution of the longer in-plane EPI echo-train for full field of view compared to the reduced field of view of zoomed 3D-GRASE.

  6. 3D printing of layered brain-like structures using peptide modified gellan gum substrates.

    PubMed

    Lozano, Rodrigo; Stevens, Leo; Thompson, Brianna C; Gilmore, Kerry J; Gorkin, Robert; Stewart, Elise M; in het Panhuis, Marc; Romero-Ortega, Mario; Wallace, Gordon G

    2015-10-01

    The brain is an enormously complex organ structured into various regions of layered tissue. Researchers have attempted to study the brain by modeling the architecture using two dimensional (2D) in vitro cell culturing methods. While those platforms attempt to mimic the in vivo environment, they do not truly resemble the three dimensional (3D) microstructure of neuronal tissues. Development of an accurate in vitro model of the brain remains a significant obstacle to our understanding of the functioning of the brain at the tissue or organ level. To address these obstacles, we demonstrate a new method to bioprint 3D brain-like structures consisting of discrete layers of primary neural cells encapsulated in hydrogels. Brain-like structures were constructed using a bio-ink consisting of a novel peptide-modified biopolymer, gellan gum-RGD (RGD-GG), combined with primary cortical neurons. The ink was optimized for a modified reactive printing process and developed for use in traditional cell culturing facilities without the need for extensive bioprinting equipment. Furthermore the peptide modification of the gellan gum hydrogel was found to have a profound positive effect on primary cell proliferation and network formation. The neural cell viability combined with the support of neural network formation demonstrated the cell supportive nature of the matrix. The facile ability to form discrete cell-containing layers validates the application of this novel printing technique to form complex, layered and viable 3D cell structures. These brain-like structures offer the opportunity to reproduce more accurate 3D in vitro microstructures with applications ranging from cell behavior studies to improving our understanding of brain injuries and neurodegenerative diseases.

  7. Towards real-time MRI-guided 3D localization of deforming targets for non-invasive cardiac radiosurgery.

    PubMed

    Ipsen, S; Blanck, O; Lowther, N J; Liney, G P; Rai, R; Bode, F; Dunst, J; Schweikard, A; Keall, P J

    2016-11-21

    Radiosurgery to the pulmonary vein antrum in the left atrium (LA) has recently been proposed for non-invasive treatment of atrial fibrillation (AF). Precise real-time target localization during treatment is necessary due to complex respiratory and cardiac motion and high radiation doses. To determine the 3D position of the LA for motion compensation during radiosurgery, a tracking method based on orthogonal real-time MRI planes was developed for AF treatments with an MRI-guided radiotherapy system. Four healthy volunteers underwent cardiac MRI of the LA. Contractile motion was quantified on 3D LA models derived from 4D scans with 10 phases acquired in end-exhalation. Three localization strategies were developed and tested retrospectively on 2D real-time scans (sagittal, temporal resolution 100 ms, free breathing). The best-performing method was then used to measure 3D target positions in 2D-2D orthogonal planes (sagittal-coronal, temporal resolution 200-252 ms, free breathing) in 20 configurations of a digital phantom and in the volunteer data. The 3D target localization accuracy was quantified in the phantom and qualitatively assessed in the real data. Mean cardiac contraction was  ⩽  3.9 mm between maximum dilation and contraction but anisotropic. A template matching approach with two distinct template phases and ECG-based selection yielded the highest 2D accuracy of 1.2 mm. 3D target localization showed a mean error of 3.2 mm in the customized digital phantoms. Our algorithms were successfully applied to the 2D-2D volunteer data in which we measured a mean 3D LA motion extent of 16.5 mm (SI), 5.8 mm (AP) and 3.1 mm (LR). Real-time target localization on orthogonal MRI planes was successfully implemented for highly deformable targets treated in cardiac radiosurgery. The developed method measures target shifts caused by respiration and cardiac contraction. If the detected motion can be compensated accordingly, an MRI-guided radiotherapy

  8. Towards real-time MRI-guided 3D localization of deforming targets for non-invasive cardiac radiosurgery

    NASA Astrophysics Data System (ADS)

    Ipsen, S.; Blanck, O.; Lowther, N. J.; Liney, G. P.; Rai, R.; Bode, F.; Dunst, J.; Schweikard, A.; Keall, P. J.

    2016-11-01

    Radiosurgery to the pulmonary vein antrum in the left atrium (LA) has recently been proposed for non-invasive treatment of atrial fibrillation (AF). Precise real-time target localization during treatment is necessary due to complex respiratory and cardiac motion and high radiation doses. To determine the 3D position of the LA for motion compensation during radiosurgery, a tracking method based on orthogonal real-time MRI planes was developed for AF treatments with an MRI-guided radiotherapy system. Four healthy volunteers underwent cardiac MRI of the LA. Contractile motion was quantified on 3D LA models derived from 4D scans with 10 phases acquired in end-exhalation. Three localization strategies were developed and tested retrospectively on 2D real-time scans (sagittal, temporal resolution 100 ms, free breathing). The best-performing method was then used to measure 3D target positions in 2D-2D orthogonal planes (sagittal-coronal, temporal resolution 200-252 ms, free breathing) in 20 configurations of a digital phantom and in the volunteer data. The 3D target localization accuracy was quantified in the phantom and qualitatively assessed in the real data. Mean cardiac contraction was  ⩽  3.9 mm between maximum dilation and contraction but anisotropic. A template matching approach with two distinct template phases and ECG-based selection yielded the highest 2D accuracy of 1.2 mm. 3D target localization showed a mean error of 3.2 mm in the customized digital phantoms. Our algorithms were successfully applied to the 2D-2D volunteer data in which we measured a mean 3D LA motion extent of 16.5 mm (SI), 5.8 mm (AP) and 3.1 mm (LR). Real-time target localization on orthogonal MRI planes was successfully implemented for highly deformable targets treated in cardiac radiosurgery. The developed method measures target shifts caused by respiration and cardiac contraction. If the detected motion can be compensated accordingly, an MRI-guided radiotherapy

  9. Computer-aided diagnosis of breast DCE-MRI using pharmacokinetic model and 3-D morphology analysis.

    PubMed

    Wang, Teh-Chen; Huang, Yan-Hao; Huang, Chiun-Sheng; Chen, Jeon-Hor; Huang, Guei-Yu; Chang, Yeun-Chung; Chang, Ruey-Feng

    2014-04-01

    Three-dimensional (3-D) dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) consists of a large number of images in different enhancement phases which are used to identify and characterize breast lesions. The purpose of this study was to develop a computer-assisted algorithm for tumor segmentation and characterization using both kinetic information and morphological features of 3-D breast DCE-MRI. An integrated color map created by intersecting kinetic and area under the curve (AUC) color maps was used to detect potential breast lesions, followed by the application of a region growing algorithm to segment the tumor. Modified fuzzy c-means clustering was used to identify the most representative kinetic curve of the whole segmented tumor, which was then characterized by using conventional curve analysis or pharmacokinetic model. The 3-D morphological features including shape features (compactness, margin, and ellipsoid fitting) and texture features (based on the grey level co-occurrence matrix) of the segmented tumor were obtained to characterize the lesion. One hundred and thirty-two biopsy-proven lesions (63 benign and 69 malignant) were used to evaluate the performance of the proposed computer-aided system for breast MRI. Five combined features including rate constant (kep), volume of plasma (vp), energy (G1), entropy (G2), and compactness (C1), had the best performance with an accuracy of 91.67% (121/132), sensitivity of 91.30% (63/69), specificity of 92.06% (58/63), and Az value of 0.9427. Combining the kinetic and morphological features of 3-D breast MRI is a potentially useful and robust algorithm when attempting to differentiate benign and malignant lesions.

  10. Mapping Fetal Brain Development in utero Using MRI: The Big Bang of Brain Mapping

    PubMed Central

    Studholme, Colin

    2012-01-01

    The development of tools to construct and investigate probabilistic maps of the adult human brain from MRI have led to advances in both basic neuroscience and clinical diagnosis. These tools are increasingly being applied to brain development in adolescence, childhood and even neonatal and premature neonatal imaging. Looking even earlier in development, parallel developments in clinical fetal Magnetic Resonance Imaging (MRI) have led to its growing use as a tool in challenging medical conditions. This has motivated new engineering developments that combine optimal fast MRI scans with techniques derived from computer vision that allow full 3D imaging of the moving fetal brain in utero without sedation. These promise to provide a new and unprecedented window into early human brain growth. This article will review the developments that have led us to this point, and examine the current state of the art in the fields of fast fetal imaging, motion correction and the tools to analyze dynamically changing fetal brain structure. New methods to deal with developmental tissue segmentation and the construction of spatio-temporal atlases will be examined, together with techniques to map fetal brain growth patterns. PMID:21568716

  11. Computer-aided segmentation and 3D analysis of in vivo MRI examinations of the human vocal tract during phonation

    NASA Astrophysics Data System (ADS)

    Wismüller, Axel; Behrends, Johannes; Hoole, Phil; Leinsinger, Gerda L.; Meyer-Baese, Anke; Reiser, Maximilian F.

    2008-03-01

    We developed, tested, and evaluated a 3D segmentation and analysis system for in vivo MRI examinations of the human vocal tract during phonation. For this purpose, six professionally trained speakers, age 22-34y, were examined using a standardized MRI protocol (1.5 T, T1w FLASH, ST 4mm, 23 slices, acq. time 21s). The volunteers performed a prolonged (>=21s) emission of sounds of the German phonemic inventory. Simultaneous audio tape recording was obtained to control correct utterance. Scans were made in axial, coronal, and sagittal planes each. Computer-aided quantitative 3D evaluation included (i) automated registration of the phoneme-specific data acquired in different slice orientations, (ii) semi-automated segmentation of oropharyngeal structures, (iii) computation of a curvilinear vocal tract midline in 3D by nonlinear PCA, (iv) computation of cross-sectional areas of the vocal tract perpendicular to this midline. For the vowels /a/,/e/,/i/,/o/,/ø/,/u/,/y/, the extracted area functions were used to synthesize phoneme sounds based on an articulatory-acoustic model. For quantitative analysis, recorded and synthesized phonemes were compared, where area functions extracted from 2D midsagittal slices were used as a reference. All vowels could be identified correctly based on the synthesized phoneme sounds. The comparison between synthesized and recorded vowel phonemes revealed that the quality of phoneme sound synthesis was improved for phonemes /a/ and /y/, if 3D instead of 2D data were used, as measured by the average relative frequency shift between recorded and synthesized vowel formants (p<0.05, one-sided Wilcoxon rank sum test). In summary, the combination of fast MRI followed by subsequent 3D segmentation and analysis is a novel approach to examine human phonation in vivo. It unveils functional anatomical findings that may be essential for realistic modelling of the human vocal tract during speech production.

  12. Histograms of Oriented 3D Gradients for Fully Automated Fetal Brain Localization and Robust Motion Correction in 3 T Magnetic Resonance Images

    PubMed Central

    Macnaught, Gillian; Denison, Fiona C.; Reynolds, Rebecca M.; Semple, Scott I.; Boardman, James P.

    2017-01-01

    Fetal brain magnetic resonance imaging (MRI) is a rapidly emerging diagnostic imaging tool. However, automated fetal brain localization is one of the biggest obstacles in expediting and fully automating large-scale fetal MRI processing. We propose a method for automatic localization of fetal brain in 3 T MRI when the images are acquired as a stack of 2D slices that are misaligned due to fetal motion. First, the Histogram of Oriented Gradients (HOG) feature descriptor is extended from 2D to 3D images. Then, a sliding window is used to assign a score to all possible windows in an image, depending on the likelihood of it containing a brain, and the window with the highest score is selected. In our evaluation experiments using a leave-one-out cross-validation strategy, we achieved 96% of complete brain localization using a database of 104 MRI scans at gestational ages between 34 and 38 weeks. We carried out comparisons against template matching and random forest based regression methods and the proposed method showed superior performance. We also showed the application of the proposed method in the optimization of fetal motion correction and how it is essential for the reconstruction process. The method is robust and does not rely on any prior knowledge of fetal brain development. PMID:28251155

  13. 3D brain MR angiography displayed by a multi-autostereoscopic screen

    NASA Astrophysics Data System (ADS)

    Magalhães, Daniel S. F.; Ribeiro, Fádua H.; Lima, Fabrício O.; Serra, Rolando L.; Moreno, Alfredo B.; Li, Li M.

    2012-02-01

    The magnetic resonance angiography (MRA) can be used to examine blood vessels in key areas of the body, including the brain. In the MRA, a powerful magnetic field, radio waves and a computer produce the detailed images. Physicians use the procedure in brain images mainly to detect atherosclerosis disease in the carotid artery of the neck, which may limit blood flow to the brain and cause a stroke and identify a small aneurysm or arteriovenous malformation inside the brain. Multi-autostereoscopic displays provide multiple views of the same scene, rather than just two, as in autostereoscopic systems. Each view is visible from a different range of positions in front of the display. This allows the viewer to move left-right in front of the display and see the correct view from any position. The use of 3D imaging in the medical field has proven to be a benefit to doctors when diagnosing patients. For different medical domains a stereoscopic display could be advantageous in terms of a better spatial understanding of anatomical structures, better perception of ambiguous anatomical structures, better performance of tasks that require high level of dexterity, increased learning performance, and improved communication with patients or between doctors. In this work we describe a multi-autostereoscopic system and how to produce 3D MRA images to be displayed with it. We show results of brain MR angiography images discussing, how a 3D visualization can help physicians to a better diagnosis.

  14. Estimation of Pulmonary Motion in Healthy Subjects and Patients with Intrathoracic Tumors Using 3D-Dynamic MRI: Initial Results

    PubMed Central

    Schoebinger, Max; Herth, Felix; Tuengerthal, Siegfried; Meinzer, Heinz-Peter; Kauczor, Hans-Ulrich

    2009-01-01

    Objective To estimate a new technique for quantifying regional lung motion using 3D-MRI in healthy volunteers and to apply the technique in patients with intra- or extrapulmonary tumors. Materials and Methods Intraparenchymal lung motion during a whole breathing cycle was quantified in 30 healthy volunteers using 3D-dynamic MRI (FLASH [fast low angle shot] 3D, TRICKS [time-resolved interpolated contrast kinetics]). Qualitative and quantitative vector color maps and cumulative histograms were performed using an introduced semiautomatic algorithm. An analysis of lung motion was performed and correlated with an established 2D-MRI technique for verification. As a proof of concept, the technique was applied in five patients with non-small cell lung cancer (NSCLC) and 5 patients with malignant pleural mesothelioma (MPM). Results The correlation between intraparenchymal lung motion of the basal lung parts and the 2D-MRI technique was significant (r = 0.89, p < 0.05). Also, the vector color maps quantitatively illustrated regional lung motion in all healthy volunteers. No differences were observed between both hemithoraces, which was verified by cumulative histograms. The patients with NSCLC showed a local lack of lung motion in the area of the tumor. In the patients with MPM, there was global diminished motion of the tumor bearing hemithorax, which improved siginificantly after chemotherapy (CHT) (assessed by the 2D- and 3D-techniques) (p < 0.01). Using global spirometry, an improvement could also be shown (vital capacity 2.9 ± 0.5 versus 3.4 L ± 0.6, FEV1 0.9 ± 0.2 versus 1.4 ± 0.2 L) after CHT, but this improvement was not significant. Conclusion A 3D-dynamic MRI is able to quantify intraparenchymal lung motion. Local and global parenchymal pathologies can be precisely located and might be a new tool used to quantify even slight changes in lung motion (e.g. in therapy monitoring, follow-up studies or even benign lung diseases). PMID:19885311

  15. A graph theoretic approach for computing 3D+time biventricular cardiac strain from tagged MRI data.

    PubMed

    Li, Ming; Gupta, Himanshu; Lloyd, Steven G; Dell'Italia, Louis J; Denney, Thomas S

    2017-01-01

    Tagged magnetic resonance imaging (tMRI) is a well-established method for evaluating regional mechanical function of the heart. Many techniques have been developed to compute 2D or 3D cardiac deformation and strain from tMRI images. In this paper, we present a new method for measuring 3D plus time biventricular myocardial strain from tMRI data. The method is composed of two parts. First, we use a Gabor filter bank to extract tag points along tag lines. Second, each tag point is classified to one of a set of indexed reference tag lines using a point classification with graph cuts (PCGC) algorithm and a motion compensation technique. 3D biventricular deformation and strain is computed at each image time frame from the classified tag points using a previously published finite difference method. The strain computation is fully automatic after myocardial contours are defined near end-diastole and end-systole. An in-vivo dataset composed of 30 human imaging studies with a range of pathologies was used for validation. Strains computed with the PCGC method with no manual corrections were compared to strains computed from both manually placed tag points and a manually-corrected unwrapped phase method. A typical cardiac imaging study with 10 short-axis slices and 6 long-axis slices required 30 min for contouring followed by 44 min of automated processing. The results demonstrate that the proposed method can reconstruct accurate 3D plus time cardiac strain maps with minimal user intervention.

  16. Robust extrapolation scheme for fast estimation of 3D ising field partition functions: application to within-subject fMRI data analysis.

    PubMed

    Risser, Laurent; Vincent, Thomas; Ciuciu, Philippe; Idier, Jérôme

    2009-01-01

    In this paper, we present a fast numerical scheme to estimate Partition Functions (PF) of 3D Ising fields. Our strategy is applied to the context of the joint detection-estimation of brain activity from functional Magnetic Resonance Imaging (fMRI) data, where the goal is to automatically recover activated regions and estimate region-dependent hemodynamic filters. For any region, a specific binary Markov random field may embody spatial correlation over the hidden states of the voxels by modeling whether they are activated or not. To make this spatial regularization fully adaptive, our approach is first based upon a classical path-sampling method to approximate a small subset of reference PFs corresponding to prespecified regions. Then, the proposed extrapolation method allows us to approximate the PFs associated with the Ising fields defined over the remaining brain regions. In comparison with preexisting approaches, our method is robust to topological inhomogeneities in the definition of the reference regions. As a result, it strongly alleviates the computational burden and makes spatially adaptive regularization of whole brain fMRI datasets feasible.

  17. Implementation of a fully 3D system model for brain SPECT with fan- beam-collimator OSEM reconstruction with 3D total variation regularization

    NASA Astrophysics Data System (ADS)

    Ye, Hongwei; Krol, Andrzej; Lipson, Edward D.; Lu, Yao; Xu, Yuesheng; Lee, Wei; Feiglin, David H.

    2007-03-01

    In order to improve tomographically reconstructed image quality, we have implemented a fully 3D reconstruction, using an ordered subsets expectation maximization (OSEM) algorithm for fan-beam collimator (FBC) SPECT, along with a volumetric system model-fan-volume system model (FVSM), a modified attenuation compensation, a 3D depth- and angle-dependent resolution and sensitivity correction, and a 3D total variation (TV) regularization. SPECT data were acquired in a 128x64 matrix, in 120 views with a circular orbit. The numerical Zubal brain phantom was used to simulate a FBC HMPAO Tc-99m brain SPECT scan, and a low noise and scatter-free projection dataset was obtained using the SimSET Monte Carlo package. A SPECT scan for a mini-Defrise phantom and brain HMPAO SPECT scans for five patients were acquired with a triple-head gamma camera (Triad 88) equipped with a low-energy high-resolution (LEHR) FBC. The reconstructed images, obtained using clinical filtered back projection (FBP), OSEM with a line-length system model (LLSM) and 3D TV regularization, and OSEM with FVSM and 3D TV regularization were quantitatively studied. Overall improvement in the image quality has been observed, including better axial and transaxial resolution, better integral uniformity, higher contrast-to-noise ration between the gray matter and the white matter, and better accuracy and lower bias in OSEM-FVSM, compared with OSEM-LLSM and clinical FBP.

  18. Interactive 3D visualization of structural changes in the brain of a person with corticobasal syndrome.

    PubMed

    Hänel, Claudia; Pieperhoff, Peter; Hentschel, Bernd; Amunts, Katrin; Kuhlen, Torsten

    2014-01-01

    The visualization of the progression of brain tissue loss in neurodegenerative diseases like corticobasal syndrome (CBS) can provide not only information about the localization and distribution of the volume loss, but also helps to understand the course and the causes of this neurodegenerative disorder. The visualization of such medical imaging data is often based on 2D sections, because they show both internal and external structures in one image. Spatial information, however, is lost. 3D visualization of imaging data is capable to solve this problem, but it faces the difficulty that more internally located structures may be occluded by structures near the surface. Here, we present an application with two designs for the 3D visualization of the human brain to address these challenges. In the first design, brain anatomy is displayed semi-transparently; it is supplemented by an anatomical section and cortical areas for spatial orientation, and the volumetric data of volume loss. The second design is guided by the principle of importance-driven volume rendering: A direct line-of-sight to the relevant structures in the deeper parts of the brain is provided by cutting out a frustum-like piece of brain tissue. The application was developed to run in both, standard desktop environments and in immersive virtual reality environments with stereoscopic viewing for improving the depth perception. We conclude, that the presented application facilitates the perception of the extent of brain degeneration with respect to its localization and affected regions.

  19. Comparative brain morphology of Neotropical parrots (Aves, Psittaciformes) inferred from virtual 3D endocasts.

    PubMed

    Carril, Julieta; Tambussi, Claudia Patricia; Degrange, Federico Javier; Benitez Saldivar, María Juliana; Picasso, Mariana Beatriz Julieta

    2016-08-01

    Psittaciformes are a very diverse group of non-passerine birds, with advanced cognitive abilities and highly developed locomotor and feeding behaviours. Using computed tomography and three-dimensional (3D) visualization software, the endocasts of 14 extant Neotropical parrots were reconstructed, with the aim of analysing, comparing and exploring the morphology of the brain within the clade. A 3D geomorphometric analysis was performed, and the encephalization quotient (EQ) was calculated. Brain morphology character states were traced onto a Psittaciformes tree in order to facilitate interpretation of morphological traits in a phylogenetic context. Our results indicate that: (i) there are two conspicuously distinct brain morphologies, one considered walnut type (quadrangular and wider than long) and the other rounded (narrower and rostrally tapered); (ii) Psittaciformes possess a noticeable notch between hemisphaeria that divides the bulbus olfactorius; (iii) the plesiomorphic and most frequently observed characteristics of Neotropical parrots are a rostrally tapered telencephalon in dorsal view, distinctly enlarged dorsal expansion of the eminentia sagittalis and conspicuous fissura mediana; (iv) there is a positive correlation between body mass and brain volume; (v) psittacids are characterized by high EQ values that suggest high brain volumes in relation to their body masses; and (vi) the endocranial morphology of the Psittaciformes as a whole is distinctive relative to other birds. This new knowledge of brain morphology offers much potential for further insight in paleoneurological, phylogenetic and evolutionary studies.

  20. Motion correction in MRI of the brain

    PubMed Central

    Godenschweger, F; Kägebein, U; Stucht, D; Yarach, U; Sciarra, A; Yakupov, R; Lüsebrink, F; Schulze, P; Speck, O

    2016-01-01

    Subject motion in MRI is a relevant problem in the daily clinical routine as well as in scientific studies. Since the beginning of clinical use of MRI, many research groups have developed methods to suppress or correct motion artefacts. This review focuses on rigid body motion correction of head and brain MRI and its application in diagnosis and research. It explains the sources and types of motion and related artefacts, classifies and describes existing techniques for motion detection, compensation and correction and lists established and experimental approaches. Retrospective motion correction modifies the MR image data during the reconstruction, while prospective motion correction performs an adaptive update of the data acquisition. Differences, benefits and drawbacks of different motion correction methods are discussed. PMID:26864183

  1. Motion correction in MRI of the brain

    NASA Astrophysics Data System (ADS)

    Godenschweger, F.; Kägebein, U.; Stucht, D.; Yarach, U.; Sciarra, A.; Yakupov, R.; Lüsebrink, F.; Schulze, P.; Speck, O.

    2016-03-01

    Subject motion in MRI is a relevant problem in the daily clinical routine as well as in scientific studies. Since the beginning of clinical use of MRI, many research groups have developed methods to suppress or correct motion artefacts. This review focuses on rigid body motion correction of head and brain MRI and its application in diagnosis and research. It explains the sources and types of motion and related artefacts, classifies and describes existing techniques for motion detection, compensation and correction and lists established and experimental approaches. Retrospective motion correction modifies the MR image data during the reconstruction, while prospective motion correction performs an adaptive update of the data acquisition. Differences, benefits and drawbacks of different motion correction methods are discussed.

  2. Reconstruction of a 3D stereotactic brain atlas and its contour-to-contour elastic deformation

    NASA Astrophysics Data System (ADS)

    Kimura, Masahiko; Otsuki, Taisuke

    1993-06-01

    We describe a refined method for estimating the 3-D geometry of cerebral structures of a patient's brain from magnetic resonance (MR) images by adapting a 3-D atlas to the images. The 3-D atlas represents the figures of anatomical subdivisions of deep cerebral structures as series of contours reconstructed from a stereotactic printed atlas. The method correlates corresponding points and curve segments that are recognizable in both the atlas and the image, by elastically deforming the atlas two-dimensionally, while maintaining the point-to-point and contour-to-contour correspondence, until equilibrium is reached. We have used the method experimentally for a patient with Parkinson's disease, and successfully estimated the substructures of the thalamus to be treated.

  3. 3D texture-based classification applied on brain white matter lesions on MR images

    NASA Astrophysics Data System (ADS)

    Leite, Mariana; Gobbi, David; Salluzi, Marina; Frayne, Richard; Lotufo, Roberto; Rittner, Letícia

    2016-03-01

    Lesions in the brain white matter are among the most frequently observed incidental findings on MR images. This paper presents a 3D texture-based classification to distinguish normal appearing white matter from white matter containing lesions, and compares it with the 2D approach. Texture analysis were based on 55 texture attributes extracted from gray-level histogram, gray-level co-occurrence matrix, run-length matrix and gradient. The results show that the 3D approach achieves an accuracy rate of 99.28%, against 97.41% of the 2D approach by using a support vector machine classifier. Furthermore, the most discriminating texture attributes on both 2D and 3D cases were obtained from the image histogram and co-occurrence matrix.

  4. Imaging of prostate cancer: a platform for 3D co-registration of in-vivo MRI ex-vivo MRI and pathology

    NASA Astrophysics Data System (ADS)

    Orczyk, Clément; Mikheev, Artem; Rosenkrantz, Andrew; Melamed, Jonathan; Taneja, Samir S.; Rusinek, Henry

    2012-02-01

    Objectives: Multi-parametric MRI is emerging as a promising method for prostate cancer diagnosis. prognosis and treatment planning. However, the localization of in-vivo detected lesions and pathologic sites of cancer remains a significant challenge. To overcome this limitation we have developed and tested a system for co-registration of in-vivo MRI, ex-vivo MRI and histology. Materials and Methods: Three men diagnosed with localized prostate cancer (ages 54-72, PSA levels 5.1-7.7 ng/ml) were prospectively enrolled in this study. All patients underwent 3T multi-parametric MRI that included T2W, DCEMRI, and DWI prior to robotic-assisted prostatectomy. Ex-vivo multi-parametric MRI was performed on fresh prostate specimen. Excised prostates were then sliced at regular intervals and photographed both before and after fixation. Slices were perpendicular to the main axis of the posterior capsule, i.e., along the direction of the rectal wall. Guided by the location of the urethra, 2D digital images were assembled into 3D models. Cancer foci, extra-capsular extensions and zonal margins were delineated by the pathologist and included in 3D histology data. A locally-developed software was applied to register in-vivo, ex-vivo and histology using an over-determined set of anatomical landmarks placed in anterior fibro-muscular stroma, central. transition and peripheral zones. The mean root square distance across corresponding control points was used to assess co-registration error. Results: Two specimens were pT3a and one pT2b (negative margin) at pathology. The software successfully fused invivo MRI. ex-vivo MRI fresh specimen and histology using appropriate (rigid and affine) transformation models with mean square error of 1.59 mm. Coregistration accuracy was confirmed by multi-modality viewing using operator-guided variable transparency. Conclusion: The method enables successful co-registration of pre-operative MRI, ex-vivo MRI and pathology and it provides initial evidence

  5. MRI atlas of the brain

    SciTech Connect

    Bradley, W.G. ); Bydder, G. )

    1990-01-01

    Since most radiologists will start from a basic of familiarity with pathophysiology of disease and a knowledge of cross-sectional imaging (at least in the transaxial plane), they are in a good position to recognize and diagnose many of the abnormalities we can currently see with CT. The appearance of these lesions on MRI is the basis for the majority of the images in this book. Chapters on Tumors, Infarcts and Ischemia, Demyelination and Infection. Hydrocephalus, and Pediatrics feature multiple images displaying the MR appearance of many common lesions with minimal associated text. Instead of focusing on pathophysiology, attention is directed to the variable appearance of these disease states using various MR imaging techniques. Although the MR contrast agent, Gadolinium-DTPA, has similar behavior (physiologically) to meglumine diatrizoate in CT, the MR techniques which result in optimal visualization of enhancing lesions are nonintuitive and are discussed. Similarly, the appearance of flowing blood and CSF and hemorrhage does not follow easily from a pre-existing CT base, therefore additional text has been devoted to these subjects.

  6. Lossy to lossless object-based coding of 3-D MRI data.

    PubMed

    Menegaz, Gloria; Thiran, Jean-Philippe

    2002-01-01

    We propose a fully three-dimensional (3-D) object-based coding system exploiting the diagnostic relevance of the different regions of the volumetric data for rate allocation. The data are first decorrelated via a 3-D discrete wavelet transform. The implementation via the lifting steps scheme allows to map integer-to-integer values, enabling lossless coding, and facilitates the definition of the object-based inverse transform. The coding process assigns disjoint segments of the bitstream to the different objects, which can be independently accessed and reconstructed at any up-to-lossless quality. Two fully 3-D coding strategies are considered: embedded zerotree coding (EZW-3D) and multidimensional layered zero coding (MLZC), both generalized for region of interest (ROI)-based processing. In order to avoid artifacts along region boundaries, some extra coefficients must be encoded for each object. This gives rise to an overheading of the bitstream with respect to the case where the volume is encoded as a whole. The amount of such extra information depends on both the filter length and the decomposition depth. The system is characterized on a set of head magnetic resonance images. Results show that MLZC and EZW-3D have competitive performances. In particular, the best MLZC mode outperforms the others state-of-the-art techniques on one of the datasets for which results are available in the literature.

  7. Brain MRI findings in Wernicke encephalopathy.

    PubMed

    Wicklund, Meredith R; Knopman, David S

    2013-08-01

    A 71-year-old woman with myelofibrosis on chemotherapy experienced an acute illness with nausea, vomiting, and diarrhea. Two weeks later, she developed an acute confusional state characterized by disorientation and fluctuating alertness with normal speech and language. Her neurologic examination demonstrated an upper motor neuron pattern of right hemiparesis. She reported double vision though ophthalmoparesis was not appreciated. Her gait was normal. While hospitalized, she developed generalized tonic-clonic seizures. Brain MRI revealed a small area of restricted diffusion of the left precentral gyrus (figure). She was diagnosed with a stroke with secondary seizures; however, as the confusional state resolved, she developed profound retrograde and anterograde amnesia. Review of the brain MRI showed high T2 signal in the medial thalamus and contrast enhancement of the mamillary bodies; a diagnosis of Wernicke-Korsakoff syndrome was entertained and she was started on thiamine replacement. The encephalopathy and hemiparesis resolved though she remains severely amnestic.

  8. MRI as a tool to study brain structure from mouse models for mental retardation

    NASA Astrophysics Data System (ADS)

    Verhoye, Marleen; Sijbers, Jan; Kooy, R. F.; Reyniers, E.; Fransen, E.; Oostra, B. A.; Willems, Peter; Van der Linden, Anne-Marie

    1998-07-01

    Nowadays, transgenic mice are a common tool to study brain abnormalities in neurological disorders. These studies usually rely on neuropathological examinations, which have a number of drawbacks, including the risk of artefacts introduced by fixation and dehydration procedures. Here we present 3D Fast Spin Echo Magnetic Resonance Imaging (MRI) in combination with 2D and 3D segmentation techniques as a powerful tool to study brain anatomy. We set up MRI of the brain in mouse models for the fragile X syndrome (FMR1 knockout) and Corpus callosum hypoplasia, mental Retardation, Adducted thumbs, Spastic paraplegia and Hydrocephalus (CRASH) syndrome (L1CAM knockout). Our major goal was to determine qualitative and quantitative differences in specific brain structures. MRI of the brain of fragile X and CRASH patients has revealed alterations in the size of specific brain structures, including the cerebellar vermis and the ventricular system. In the present MRI study of the brain from fragile X knockout mice, we have measured the size of the brain, cerebellum and 4th ventricle, which were reported as abnormal in human fragile X patients, but found no evidence for altered brain regions in the mouse model. In CRASH syndrome, the most specific brain abnormalities are vermis hypoplasia and abnormalities of the ventricular system with some degree of hydrocephalus. With the MRI study of L1CAM knockout mice we found vermis hypoplasia, abnormalities of the ventricular system including dilatation of the lateral and the 4th ventricles. These subtle abnormalities were not detected upon standard neuropathological examination. Here we proved that this sensitive MRI technique allows to measure small differences which can not always be detected by means of pathology.

  9. Analysis and 3D visualization of structures of animal brains obtained from histological sections

    NASA Astrophysics Data System (ADS)

    Forero-Vargas, Manuel G.; Fuentes, Veronica; Lopez, D.; Moscoso, A.; Merchan, Miguel A.

    2002-11-01

    This paper presents a new application for the analysis of histological sections and their 3D visualization. The process is performed in few steps. First, a manual process is necessary to determine the regions of interest, including image digitalization, drawing of borders and alignment between all images. Then, a reconstruction process is made. After sampling the contour, the structure of interest is displayed. The application is experimentally validated and some results on histological sections of a rodent's brain (hamster and rat) are shown.

  10. 3D high spectral and spatial resolution imaging of ex vivo mouse brain

    SciTech Connect

    Foxley, Sean Karczmar, Gregory S.; Domowicz, Miriam; Schwartz, Nancy

    2015-03-15

    Purpose: Widely used MRI methods show brain morphology both in vivo and ex vivo at very high resolution. Many of these methods (e.g., T{sub 2}{sup *}-weighted imaging, phase-sensitive imaging, or susceptibility-weighted imaging) are sensitive to local magnetic susceptibility gradients produced by subtle variations in tissue composition. However, the spectral resolution of commonly used methods is limited to maintain reasonable run-time combined with very high spatial resolution. Here, the authors report on data acquisition at increased spectral resolution, with 3-dimensional high spectral and spatial resolution MRI, in order to analyze subtle variations in water proton resonance frequency and lineshape that reflect local anatomy. The resulting information compliments previous studies based on T{sub 2}{sup *} and resonance frequency. Methods: The proton free induction decay was sampled at high resolution and Fourier transformed to produce a high-resolution water spectrum for each image voxel in a 3D volume. Data were acquired using a multigradient echo pulse sequence (i.e., echo-planar spectroscopic imaging) with a spatial resolution of 50 × 50 × 70 μm{sup 3} and spectral resolution of 3.5 Hz. Data were analyzed in the spectral domain, and images were produced from the various Fourier components of the water resonance. This allowed precise measurement of local variations in water resonance frequency and lineshape, at the expense of significantly increased run time (16–24 h). Results: High contrast T{sub 2}{sup *}-weighted images were produced from the peak of the water resonance (peak height image), revealing a high degree of anatomical detail, specifically in the hippocampus and cerebellum. In images produced from Fourier components of the water resonance at −7.0 Hz from the peak, the contrast between deep white matter tracts and the surrounding tissue is the reverse of the contrast in water peak height images. This indicates the presence of a shoulder in

  11. 3D Brain Segmentation Using Dual-Front Active Contours with Optional User Interaction

    PubMed Central

    Yezzi, Anthony; Cohen, Laurent D.

    2006-01-01

    Important attributes of 3D brain cortex segmentation algorithms include robustness, accuracy, computational efficiency, and facilitation of user interaction, yet few algorithms incorporate all of these traits. Manual segmentation is highly accurate but tedious and laborious. Most automatic techniques, while less demanding on the user, are much less accurate. It would be useful to employ a fast automatic segmentation procedure to do most of the work but still allow an expert user to interactively guide the segmentation to ensure an accurate final result. We propose a novel 3D brain cortex segmentation procedure utilizing dual-front active contours which minimize image-based energies in a manner that yields flexibly global minimizers based on active regions. Region-based information and boundary-based information may be combined flexibly in the evolution potentials for accurate segmentation results. The resulting scheme is not only more robust but much faster and allows the user to guide the final segmentation through simple mouse clicks which add extra seed points. Due to the flexibly global nature of the dual-front evolution model, single mouse clicks yield corrections to the segmentation that extend far beyond their initial locations, thus minimizing the user effort. Results on 15 simulated and 20 real 3D brain images demonstrate the robustness, accuracy, and speed of our scheme compared with other methods. PMID:23165037

  12. Theoretical Analysis of the Accuracy and Safety of MRI-Guided Transurethral 3-D Conformal Ultrasound Prostate Therapy

    NASA Astrophysics Data System (ADS)

    Burtnyk, Mathieu; Chopra, Rajiv; Bronskill, Michael

    2009-04-01

    MRI-guided transurethral ultrasound therapy is a promising new approach for the treatment of localized prostate cancer. Several studies have demonstrated the feasibility of producing large regions of thermal coagulation adequate for prostate therapy; however, the quantitative assessment of shaping these regions to complex 3-D human prostate geometries has not been fully explored. This study used numerical simulations and twenty manually-segmented pelvic anatomical models derived from high-quality MR images of prostate cancer patients to evaluate the treatment accuracy and safety of 3-D conformal MRI-guided transurethral ultrasound therapy. The simulations incorporated a rotating multi-element planar dual-frequency ultrasound transducer (seventeen 4×3 mm elements) operating at 4.7/9.7 MHz and 10 W/cm2 maximum acoustic power. Results using a novel feedback control algorithm which modulated the ultrasound frequency, power and device rate of rotation showed that regions of thermal coagulation could be shaped to predefined prostate volumes within 1.0 mm across the vast majority of these glands. Treatment times were typically 30 min and remained below 60 min for large 60 cc prostates. With a rectal cooling temperature of 15° C, the rectal wall did not exceed 30EM43 in half of the twenty patient models with only a few 1 mm3 voxels above this threshold in the other cases. At 4.7 MHz, heating of the pelvic bone can become significant when it is located less than 10 mm from the prostate. Numerical simulations show that MRI-guided transurethral ultrasound therapy can thermally coagulate whole prostate glands accurately and safely in 3-D.

  13. Manifold learning for shape guided segmentation of cardiac boundaries: application to 3D+t cardiac MRI.

    PubMed

    Eslami, Abouzar; Yigitsoy, Mehmet; Navab, Nassir

    2011-01-01

    In this paper we propose a new method for shape guided segmentation of cardiac boundaries based on manifold learning of the shapes represented by the phase field approximation of the Mumford-Shah functional. A novel distance is defined to measure the similarity of shapes without requiring deformable registration. Cardiac motion is compensated and phases are mapped into one reference phase, that is the end of diastole, to avoid time warping and synchronization at all cardiac phases. Non-linear embedding of these 3D shapes extracts the manifold of the inter-subject variation of the heart shape to be used for guiding the segmentation for a new subject. For validation the method is applied to a comprehensive dataset of 3D+t cardiac Cine MRI from normal subjects and patients.

  14. Rule-based fuzzy vector median filters for 3D phase contrast MRI segmentation

    NASA Astrophysics Data System (ADS)

    Sundareswaran, Kartik S.; Frakes, David H.; Yoganathan, Ajit P.

    2008-02-01

    Recent technological advances have contributed to the advent of phase contrast magnetic resonance imaging (PCMRI) as standard practice in clinical environments. In particular, decreased scan times have made using the modality more feasible. PCMRI is now a common tool for flow quantification, and for more complex vector field analyses that target the early detection of problematic flow conditions. Segmentation is one component of this type of application that can impact the accuracy of the final product dramatically. Vascular segmentation, in general, is a long-standing problem that has received significant attention. Segmentation in the context of PCMRI data, however, has been explored less and can benefit from object-based image processing techniques that incorporate fluids specific information. Here we present a fuzzy rule-based adaptive vector median filtering (FAVMF) algorithm that in combination with active contour modeling facilitates high-quality PCMRI segmentation while mitigating the effects of noise. The FAVMF technique was tested on 111 synthetically generated PC MRI slices and on 15 patients with congenital heart disease. The results were compared to other multi-dimensional filters namely the adaptive vector median filter, the adaptive vector directional filter, and the scalar low pass filter commonly used in PC MRI applications. FAVMF significantly outperformed the standard filtering methods (p < 0.0001). Two conclusions can be drawn from these results: a) Filtering should be performed after vessel segmentation of PC MRI; b) Vector based filtering methods should be used instead of scalar techniques.

  15. 3D phase unwrapping using global expected phase as a reference: application to MRI global shimming.

    PubMed

    Liu, Wentao; Tang, Xin; Ma, Yajun; Gao, Jia-Hong

    2013-07-01

    MRI phase data often suffers from phase wrapping (i.e., phase may be discontinuous by 2π jumps). Numerous MRI phase unwrapping strategies were developed in the past using a criterion based on phase information of local or neighboring voxels. In this study, an alternative and novel three dimensional phase unwrapping strategy is introduced. This method considers the global character of the phase distribution and utilizes continuous trigonometric functions to construct an expected phase map as an unwrapping reference, which is then used to guide the phase correction of every individual voxel. The original phase is estimated by analyzing the derivative of the wrapped phase image. Simulations of various phase wrapped situations were performed and this new method was also used for an in vivo application (i.e., MRI automatic global shimming). Both simulated and experimental results demonstrate that our proposed method is more reliable and robust than traditional algorithms at obtaining correct phase maps, especially in regions of low-signal and air cavities, such as the abdomen and pelvis.

  16. Bias Field Inconsistency Correction of Motion-Scattered Multislice MRI for Improved 3D Image Reconstruction

    PubMed Central

    Kim, Kio; Habas, Piotr A.; Rajagopalan, Vidya; Scott, Julia A.; Corbett-Detig, James M.; Rousseau, Francois; Barkovich, A. James; Glenn, Orit A.; Studholme, Colin

    2012-01-01

    A common solution to clinical MR imaging in the presence of large anatomical motion is to use fast multi-slice 2D studies to reduce slice acquisition time and provide clinically usable slice data. Recently, techniques have been developed which retrospectively correct large scale 3D motion between individual slices allowing the formation of a geometrically correct 3D volume from the multiple slice stacks. One challenge, however, in the final reconstruction process is the possibility of varying intensity bias in the slice data, typically due to the motion of the anatomy relative to imaging coils. As a result, slices which cover the same region of anatomy at different times may exhibit different sensitivity. This bias field inconsistency can induce artifacts in the final 3D reconstruction that can impact both clinical interpretation of key tissue boundaries and the automated analysis of the data. Here we describe a framework to estimate and correct the bias field inconsistency in each slice collectively across all motion corrupted image slices. Experiments using synthetic and clinical data show that the proposed method reduces intensity variability in tissues and improves the distinction between key tissue types. PMID:21511561

  17. Bias field inconsistency correction of motion-scattered multislice MRI for improved 3D image reconstruction.

    PubMed

    Kim, Kio; Habas, Piotr A; Rajagopalan, Vidya; Scott, Julia A; Corbett-Detig, James M; Rousseau, Francois; Barkovich, A James; Glenn, Orit A; Studholme, Colin

    2011-09-01

    A common solution to clinical MR imaging in the presence of large anatomical motion is to use fast multislice 2D studies to reduce slice acquisition time and provide clinically usable slice data. Recently, techniques have been developed which retrospectively correct large scale 3D motion between individual slices allowing the formation of a geometrically correct 3D volume from the multiple slice stacks. One challenge, however, in the final reconstruction process is the possibility of varying intensity bias in the slice data, typically due to the motion of the anatomy relative to imaging coils. As a result, slices which cover the same region of anatomy at different times may exhibit different sensitivity. This bias field inconsistency can induce artifacts in the final 3D reconstruction that can impact both clinical interpretation of key tissue boundaries and the automated analysis of the data. Here we describe a framework to estimate and correct the bias field inconsistency in each slice collectively across all motion corrupted image slices. Experiments using synthetic and clinical data show that the proposed method reduces intensity variability in tissues and improves the distinction between key tissue types.

  18. D-BRAIN: Anatomically Accurate Simulated Diffusion MRI Brain Data.

    PubMed

    Perrone, Daniele; Jeurissen, Ben; Aelterman, Jan; Roine, Timo; Sijbers, Jan; Pizurica, Aleksandra; Leemans, Alexander; Philips, Wilfried

    2016-01-01

    Diffusion Weighted (DW) MRI allows for the non-invasive study of water diffusion inside living tissues. As such, it is useful for the investigation of human brain white matter (WM) connectivity in vivo through fiber tractography (FT) algorithms. Many DW-MRI tailored restoration techniques and FT algorithms have been developed. However, it is not clear how accurately these methods reproduce the WM bundle characteristics in real-world conditions, such as in the presence of noise, partial volume effect, and a limited spatial and angular resolution. The difficulty lies in the lack of a realistic brain phantom on the one hand, and a sufficiently accurate way of modeling the acquisition-related degradation on the other. This paper proposes a software phantom that approximates a human brain to a high degree of realism and that can incorporate complex brain-like structural features. We refer to it as a Diffusion BRAIN (D-BRAIN) phantom. Also, we propose an accurate model of a (DW) MRI acquisition protocol to allow for validation of methods in realistic conditions with data imperfections. The phantom model simulates anatomical and diffusion properties for multiple brain tissue components, and can serve as a ground-truth to evaluate FT algorithms, among others. The simulation of the acquisition process allows one to include noise, partial volume effects, and limited spatial and angular resolution in the images. In this way, the effect of image artifacts on, for instance, fiber tractography can be investigated with great detail. The proposed framework enables reliable and quantitative evaluation of DW-MR image processing and FT algorithms at the level of large-scale WM structures. The effect of noise levels and other data characteristics on cortico-cortical connectivity and tractography-based grey matter parcellation can be investigated as well.

  19. Rapid brain MRI acquisition techniques at ultra-high fields

    PubMed Central

    Setsompop, Kawin; Feinberg, David A.; Polimeni, Jonathan R.

    2017-01-01

    Ultra-high-field MRI provides large increases in signal-to-noise ratio as well as enhancement of several contrast mechanisms in both structural and functional imaging. Combined, these gains result in a substantial boost in contrast-to-noise ratio that can be exploited for higher spatial resolution imaging to extract finer-scale information about the brain. With increased spatial resolution, however, is a concurrent increased image encoding burden that can cause unacceptably long scan times for structural imaging and slow temporal sampling of the hemodynamic response in functional MRI—particularly when whole-brain imaging is desired. To address this issue, new directions of imaging technology development—such as the move from conventional 2D slice-by-slice imaging to more efficient Simultaneous MultiSlice (SMS) or MultiBand imaging (which can be viewed as “pseudo-3D” encoding) as well as full 3D imaging—have provided dramatic improvements in acquisition speed. Such imaging paradigms provide higher SNR efficiency as well as improved encoding efficiency. Moreover, SMS and 3D imaging can make better use of coil sensitivity information in multi-channel receiver arrays used for parallel imaging acquisitions through controlled aliasing in multiple spatial directions. This has enabled unprecedented acceleration factors of an order of magnitude or higher in these imaging acquisition schemes, with low image artifact levels and high SNR. Here we review the latest developments of SMS and 3D imaging methods and related technologies at ultra-high field for rapid high-resolution functional and structural imaging of the brain. PMID:26835884

  20. In vitro MRI of brain development.

    PubMed

    Rados, Marko; Judas, Milos; Kostović, Ivica

    2006-02-01

    In this review, we demonstrate the developmental appearance, structural features, and reorganization of transient cerebral zones and structures in the human fetal brain using a correlative histological and MRI analysis. The analysis of postmortem aldehyde-fixed specimens (age range: 10 postovulatory weeks to term) revealed that, at 10 postovulatory weeks, the cerebral wall already has a trilaminar appearance and consists of: (1) a ventricular zone of high cell-packing density; (2) an intermediate zone; (3) the cortical plate (in a stage of primary consolidation) with high MRI signal intensity. The anlage of the hippocampus is present as a prominent bulging in the thin limbic telencephalon. The early fetal telencephalon impar also contains the first commissural fibers and fornix bundles in the septal area. The ganglionic eminence is clearly visible as an expanded continuation of the proliferative ventricular zone. The basal ganglia showed an initial aggregation of cells. The most massive fiber system is in the hemispheric stalk, which is in continuity with thalamocortical fibers. During the mid-fetal period (15-22 postovulatory weeks), the typical fetal lamination pattern develops and the cerebral wall consists of the following zones: (a) a marginal zone (visible on MRI exclusively in the hippocampus); (b) the cortical plate with high cell-packing density and high MRI signal intensity; (c) the subplate zone, which is the most prominent zone rich in extracellular matrix and with a very low MRI signal intensity; (d) the intermediate zone (fetal "white matter"); (e) the subventricular zone; (f) the periventricular fiber-rich zone; (g) the ventricular zone. The ganglionic eminence is still a very prominent structure with an intense proliferative activity. During the next period (22-26 postovulatory weeks), there is the developmental peak of transient MRI features, caused by the high content of hydrophyllic extracellular matrix in the subplate zone and the accumulation

  1. Coculture system with an organotypic brain slice and 3D spheroid of carcinoma cells.

    PubMed

    Chuang, Han-Ning; Lohaus, Raphaela; Hanisch, Uwe-Karsten; Binder, Claudia; Dehghani, Faramarz; Pukrop, Tobias

    2013-10-09

    Patients with cerebral metastasis of carcinomas have a poor prognosis. However, the process at the metastatic site has barely been investigated, in particular the role of the resident (stromal) cells. Studies in primary carcinomas demonstrate the influence of the microenvironment on metastasis, even on prognosis(1,2). Especially the tumor associated macrophages (TAM) support migration, invasion and proliferation(3). Interestingly, the major target sites of metastasis possess tissue-specific macrophages, such as Kupffer cells in the liver or microglia in the CNS. Moreover, the metastatic sites also possess other tissue-specific cells, like astrocytes. Recently, astrocytes were demonstrated to foster proliferation and persistence of cancer cells(4,5). Therefore, functions of these tissue-specific cell types seem to be very important in the process of brain metastasis(6,7). Despite these observations, however, up to now there is no suitable in vivo/in vitro model available to directly visualize glial reactions during cerebral metastasis formation, in particular by bright field microscopy. Recent in vivo live imaging of carcinoma cells demonstrated their cerebral colonization behavior(8). However, this method is very laborious, costly and technically complex. In addition, these kinds of animal experiments are restricted to small series and come with a substantial stress for the animals (by implantation of the glass plate, injection of tumor cells, repetitive anaesthesia and long-term fixation). Furthermore, in vivo imaging is thus far limited to the visualization of the carcinoma cells, whereas interactions with resident cells have not yet been illustrated. Finally, investigations of human carcinoma cells within immunocompetent animals are impossible(8). For these reasons, we established a coculture system consisting of an organotypic mouse brain slice and epithelial cells embedded in matrigel (3D cell sphere). The 3D carcinoma cell spheres were placed directly next to

  2. Individual 3D region-of-interest atlas of the human brain: automatic training point extraction for neural-network-based classification of brain tissue types

    NASA Astrophysics Data System (ADS)

    Wagenknecht, Gudrun; Kaiser, Hans-Juergen; Obladen, Thorsten; Sabri, Osama; Buell, Udalrich

    2000-04-01

    Individual region-of-interest atlas extraction consists of two main parts: T1-weighted MRI grayscale images are classified into brain tissues types (gray matter (GM), white matter (WM), cerebrospinal fluid (CSF), scalp/bone (SB), background (BG)), followed by class image analysis to define automatically meaningful ROIs (e.g., cerebellum, cerebral lobes, etc.). The purpose of this algorithm is the automatic detection of training points for neural network-based classification of brain tissue types. One transaxial slice of the patient data set is analyzed. Background separation is done by simple region growing. A random generator extracts spatially uniformly distributed training points of class BG from that region. For WM training point extraction (TPE), the homogeneity operator is the most important. The most homogeneous voxels define the region for WM TPE. They are extracted by analyzing the cumulative histogram of the homogeneity operator response. Assuming a Gaussian gray value distribution in WM, a random number is used as a probabilistic threshold for TPE. Similarly, non-white matter and non-background regions are analyzed for GM and CSF training points. For SB TPE, the distance from the BG region is an additional feature. Simulated and real 3D MRI images are analyzed and error rates for TPE and classification calculated.

  3. Structured light 3D tracking system for measuring motions in PET brain imaging

    NASA Astrophysics Data System (ADS)

    Olesen, Oline V.; Jørgensen, Morten R.; Paulsen, Rasmus R.; Højgaard, Liselotte; Roed, Bjarne; Larsen, Rasmus

    2010-02-01

    Patient motion during scanning deteriorates image quality, especially for high resolution PET scanners. A new proposal for a 3D head tracking system for motion correction in high resolution PET brain imaging is set up and demonstrated. A prototype tracking system based on structured light with a DLP projector and a CCD camera is set up on a model of the High Resolution Research Tomograph (HRRT). Methods to reconstruct 3D point clouds of simple surfaces based on phase-shifting interferometry (PSI) are demonstrated. The projector and camera are calibrated using a simple stereo vision procedure where the projector is treated as a camera. Additionally, the surface reconstructions are corrected for the non-linear projector output prior to image capture. The results are convincing and a first step toward a fully automated tracking system for measuring head motions in PET imaging.

  4. 3D-Dixon MRI based volumetry of peri- and epicardial fat.

    PubMed

    Homsi, Rami; Meier-Schroers, Michael; Gieseke, Jürgen; Dabir, Darius; Luetkens, Julian A; Kuetting, Daniel L; Naehle, Claas P; Marx, Christian; Schild, Hans H; Thomas, Daniel K; Sprinkart, Alois M

    2016-02-01

    There is growing evidence that pericardial and epicardial fat volume (PFV, EFV) are associated with cardiovascular risk. We evaluated a novel method for accurate measurement of PFV and EFV using a 3D-Dixon based cardiac magnetic resonance (CMR) approach. An electrocardiography triggered and respiratory navigator gated 3D-gradient echo pulse sequence was used for cardiac Dixon imaging. Based on this sequence, voxels predominantly containing fat were identified and added up for volumetry. After accuracy assessment in phantoms, consisting of muscle tissue and seven different fat samples (50-200 ml), the sequence was acquired in 34 healthy volunteers (22 male, BMI range 14-42 kg/m(2), age range 21-79 years) at 1.5 T. Analysis was performed independently by two readers who draw two 3D-regions of interest, one for EFV and one for PFV. Additionally, EFV and PFV were compared between overweighted and non-overweighted subjects. The phantom study showed an excellent agreement of measured and true fat volumes (maximum difference = 6 %, linear correlation coefficient R = 1.00). PFV over all volunteers was 158.0 ± 126.4 ml and EFV was 77.0 ± 55.3 ml. PFV and EFV were highly correlated (R = 0.96). Inter-reader agreement was good with a mean difference of 0.2 ± 5.6 and 4.5 ± 4.2 ml for PFV/EFV, (R > 0.99, each). EFV and PFV differed significantly between subjects with BMI > 25 kg/m(2) and BMI < 25 kg/m(2), n = 17 each (PFV 219.0 ± 151.8 vs. 96.9 ± 44.7 ml and EFV 102.3 ± 66.3 vs. 51.7 ± 23.6 ml, p < 0.001, each). The proposed 3D-Dixon based method allows accurate measurement of cardiac fat volumes. It provides a valuable tool for cardiovascular risk stratification by CMR.

  5. Generation and transplantation of reprogrammed human neurons in the brain using 3D microtopographic scaffolds

    PubMed Central

    Carlson, Aaron L.; Bennett, Neal K.; Francis, Nicola L.; Halikere, Apoorva; Clarke, Stephen; Moore, Jennifer C.; Hart, Ronald P.; Paradiso, Kenneth; Wernig, Marius; Kohn, Joachim; Pang, Zhiping P.; Moghe, Prabhas V.

    2016-01-01

    Cell replacement therapy with human pluripotent stem cell-derived neurons has the potential to ameliorate neurodegenerative dysfunction and central nervous system injuries, but reprogrammed neurons are dissociated and spatially disorganized during transplantation, rendering poor cell survival, functionality and engraftment in vivo. Here, we present the design of three-dimensional (3D) microtopographic scaffolds, using tunable electrospun microfibrous polymeric substrates that promote in situ stem cell neuronal reprogramming, neural network establishment and support neuronal engraftment into the brain. Scaffold-supported, reprogrammed neuronal networks were successfully grafted into organotypic hippocampal brain slices, showing an ∼3.5-fold improvement in neurite outgrowth and increased action potential firing relative to injected isolated cells. Transplantation of scaffold-supported neuronal networks into mouse brain striatum improved survival ∼38-fold at the injection site relative to injected isolated cells, and allowed delivery of multiple neuronal subtypes. Thus, 3D microscale biomaterials represent a promising platform for the transplantation of therapeutic human neurons with broad neuro-regenerative relevance. PMID:26983594

  6. Image segmentation and registration for the analysis of joint motion from 3D MRI

    NASA Astrophysics Data System (ADS)

    Hu, Yangqiu; Haynor, David R.; Fassbind, Michael; Rohr, Eric; Ledoux, William

    2006-03-01

    We report an image segmentation and registration method for studying joint morphology and kinematics from in vivo MRI scans and its application to the analysis of ankle joint motion. Using an MR-compatible loading device, a foot was scanned in a single neutral and seven dynamic positions including maximal flexion, rotation and inversion/eversion. A segmentation method combining graph cuts and level sets was developed which allows a user to interactively delineate 14 bones in the neutral position volume in less than 30 minutes total, including less than 10 minutes of user interaction. In the subsequent registration step, a separate rigid body transformation for each bone is obtained by registering the neutral position dataset to each of the dynamic ones, which produces an accurate description of the motion between them. We have processed six datasets, including 3 normal and 3 pathological feet. For validation our results were compared with those obtained from 3DViewnix, a semi-automatic segmentation program, and achieved good agreement in volume overlap ratios (mean: 91.57%, standard deviation: 3.58%) for all bones. Our tool requires only 1/50 and 1/150 of the user interaction time required by 3DViewnix and NIH Image Plus, respectively, an improvement that has the potential to make joint motion analysis from MRI practical in research and clinical applications.

  7. Automated scoring of regional lung perfusion in children from contrast enhanced 3D MRI

    NASA Astrophysics Data System (ADS)

    Heimann, Tobias; Eichinger, Monika; Bauman, Grzegorz; Bischoff, Arved; Puderbach, Michael; Meinzer, Hans-Peter

    2012-03-01

    MRI perfusion images give information about regional lung function and can be used to detect pulmonary pathologies in cystic fibrosis (CF) children. However, manual assessment of the percentage of pathologic tissue in defined lung subvolumes features large inter- and intra-observer variation, making it difficult to determine disease progression consistently. We present an automated method to calculate a regional score for this purpose. First, lungs are located based on thresholding and morphological operations. Second, statistical shape models of left and right children's lungs are initialized at the determined locations and used to precisely segment morphological images. Segmentation results are transferred to perfusion maps and employed as masks to calculate perfusion statistics. An automated threshold to determine pathologic tissue is calculated and used to determine accurate regional scores. We evaluated the method on 10 MRI images and achieved an average surface distance of less than 1.5 mm compared to manual reference segmentations. Pathologic tissue was detected correctly in 9 cases. The approach seems suitable for detecting early signs of CF and monitoring response to therapy.

  8. Posterior Compartment Anatomy as seen in MRI and 3-D Reconstruction from Asymptomatic Nulliparas

    PubMed Central

    HSU, Yvonne; LEWICKY-GAUPP, Christina; De LANCEY, John O.L.

    2010-01-01

    Objective To identify characteristic anatomical features of the posterior compartment using MR cross-sectional anatomy and 3-D modeling. Study Design Supine, static proton-density MR images of 20 nulliparas were analyzed. MR images were used to create models in a selected exemplar. Results The compartment’s upper, mid, and lower segments are best seen in the axial plane. It is bounded inferiorly by the perineal body, ventrally by the posterior vaginal wall and dorsally by the levator ani muscles and coccyx. In the upper portion, the compartment is bordered laterally by the uterosacral ligaments while in the mid portion, there is more direct contact with the lateral levator ani muscles. In the lower portion, the contact becomes obliterated as the vagina and levator ani muscles become fused to one another and to the perineal body. Conclusion The posterior compartment has characteristic anatomic features in MR cross-sectional anatomy that can be further elucidated and integrated with 3-D anatomy. PMID:18241813

  9. High resolution 3D MRI of mouse mammary glands with intra-ductal injection of contrast media.

    PubMed

    Markiewicz, Erica; Fan, Xiaobing; Mustafi, Devkumar; Zamora, Marta; Roman, Brian B; Jansen, Sanaz A; Macleod, Kay; Conzen, Suzanne D; Karczmar, Gregory S

    2015-01-01

    The purpose of this study was to use high resolution three-dimensional (3D) magnetic resonance imaging (MRI) to study mouse mammary gland ductal architecture based on intra-ductal injection of contrast agents. Female FVB/N mice age 12-20 weeks (n=12), were used in this study. A 34G, 45° tip Hamilton needle with a 25μL Hamilton syringe was inserted into the tip of the nipple. Approximately 20-25μL of a Gadodiamide/Trypan blue/saline solution was injected slowly over one minute into the nipple and duct. To prevent washout of contrast media from ducts due to perfusion, and maximize the conspicuity of ducts on MRI, mice were sacrificed one minute after injection. High resolution 3D T1-weighted images were acquired on a 9.4T Bruker scanner after sacrifice to eliminate motion artifacts and reduce contrast media leakage from ducts. Trypan blue staining was well distributed throughout the ductal tree. MRI showed the mammary gland ductal structure clearly. In spoiled gradient echo T1-weighted images, the signal-to-noise ratio of regions identified as enhancing mammary ducts following contrast injection was significantly higher than that of muscle (p<0.02) and significantly higher than that of contralateral mammary ducts that were not injected with contrast media (p<0.0001). The methods described here could be adapted for injection of specialized contrast agents to measure metabolism or target receptors in normal ducts and ducts with in situ cancers.

  10. Rapid Isotropic 3D-Sodium MRI of the Knee Joint In-vivo at 7T

    PubMed Central

    Wang, Ligong; Wu, Yan; Chang, Gregory; Oesingmann, Niels; Schweitzer, Mark E.; Jerschow, Alexej; Regatte, Ravinder R.

    2009-01-01

    Purpose To demonstrate the feasibility of acquiring high resolution, isotropic 3D-sodium MR images of the whole knee joint in vivo at ultra high field strength (7.0T) via a 3D-radial acquisition with ultra short echo times and clinically acceptable acquisition times. Materials and Methods Five healthy controls (4 males, 1 female; mean ± standard deviation (SD) age 28.7 ± 4.8 years) and five patients with osteoarthritis (OA) (3 males, 2 females; mean ± SD age 52.4 ± 5.6 years) underwent 23Na–MRI on a 7T, multi-nuclei equipped whole body scanner. A quadrature 23Na knee coil and a 3D-gradient echo (GRE) imaging sequence with a radial acquisition were utilized. Cartilage sodium concentration was measured and compared between the healthy controls and OA patients. Results The average signal-to-noise ratio (SNR) for different spatial resolutions (1.2 mm – 4 mm) varied from ∼14 – 120, respectively. The mean sodium concentration of healthy subjects ranged from ∼240 ± 28 mM/L – 280 ± 22 mM/L. However, in OA patients the sodium concentrations were reduced, significantly by ∼30 – 60%, depending upon the degree of cartilage degeneration. Conclusion The preliminary results suggest that sodium imaging at 7T may be a feasible potential alternative for physiologic OA imaging and clinical diagnosis. PMID:19711406

  11. Brain Morphometry using MRI in Schizophrenia Patients

    NASA Astrophysics Data System (ADS)

    Abanshina, I.; Pirogov, Yu.; Kupriyanov, D.; Orlova, V.

    2010-01-01

    Schizophrenia has been the focus of intense neuroimaging research. Although its fundamental pathobiology remains elusive, neuroimaging studies provide evidence of abnormalities of cerebral structure and function in patients with schizophrenia. We used morphometry as a quantitative method for estimation of volume of brain structures. Seventy eight right-handed subjects aged 18-45 years were exposed to MRI-examination. Patients were divided into 3 groups: patients with schizophrenia, their relatives and healthy controls. The volumes of interested structures (caudate nucleus, putamen, ventricles, frontal and temporal lobe) were measured using T2-weighted MR-images. Correlations between structural differences and functional deficit were evaluated.

  12. 3-D Cytoarchitectonic parcellation of human orbitofrontal cortex. Correlation with postmortem MRI

    PubMed Central

    Uylings, Harry B.M.; Sanz-Arigita, Ernesto J.; de Vos, Koos; Pool, Chris W.; Evers, Paul; Rajkowska, Grazyna

    2010-01-01

    The orbitofrontal cortex (OFC) is located on the basal surface of the frontal lobe and is distinguished by its unique anatomical and functional features. Clinical and postmortem studies suggest the involvement of the orbitofrontal cortex in psychiatric disorders. However, the exact parcellation of this cortical region is still a matter of debate. Therefore, the goal of this study is to provide a detailed description of the extent of borders of individual orbitofrontal cortical areas using cytoarchitectonic criteria in a large sample of human brains, which could be applied by independent neuroanatomists. To make this microscopic parcellation useful to neuroimaging studies, magnetic resonance images of postmortem brains in the coronal plane were collected prior to the preparation of coronal histological sections from the same brains. A complete series of coronal sections from 6 normal human brains and partial sections from the frontal cortex of 21 normal human brains were stained with general histological and immunohistochemical methods specific for different cell-types, These sections were examined microscopically by two independent neuroanatomists (HBMU and GR) to achieve reproducible delineations. After the borders were determined, the tissue sections were superimposed on corresponding MR images. Based on our cytoarchitectonical criteria, Brodmann's areas 47 and 11 were included in the human orbitofrontal cortex. Area 47 was further subdivided into three medial (located on the medial, anterior and posterior orbital gyri) and two lateral (located on the lateral orbital gyrus) subareas. In addition, we observed an anterior-posterior gradient in the cytoarchitecture of areas 11 and 47. The transverse orbital sulcus corresponds roughly to the transition between the subregions of the anterior and posterior OFC. Finally, the present delineation is contrasted with an overview of the different published nomenclatures for the OFC parcellation. PMID:20538437

  13. Real-Time Estimation of 3-D Needle Shape and Deflection for MRI-Guided Interventions

    PubMed Central

    Park, Yong-Lae; Elayaperumal, Santhi; Daniel, Bruce; Ryu, Seok Chang; Shin, Mihye; Savall, Joan; Black, Richard J.; Moslehi, Behzad; Cutkosky, Mark R.

    2015-01-01

    We describe a MRI-compatible biopsy needle instrumented with optical fiber Bragg gratings for measuring bending deflections of the needle as it is inserted into tissues. During procedures, such as diagnostic biopsies and localized treatments, it is useful to track any tool deviation from the planned trajectory to minimize positioning errors and procedural complications. The goal is to display tool deflections in real time, with greater bandwidth and accuracy than when viewing the tool in MR images. A standard 18 ga × 15 cm inner needle is prepared using a fixture, and 350-μm-deep grooves are created along its length. Optical fibers are embedded in the grooves. Two sets of sensors, located at different points along the needle, provide an estimate of the bent profile, as well as temperature compensation. Tests of the needle in a water bath showed that it produced no adverse imaging artifacts when used with the MR scanner. PMID:26405428

  14. 3D Segmentation with an application of level set-method using MRI volumes for image guided surgery.

    PubMed

    Bosnjak, A; Montilla, G; Villegas, R; Jara, I

    2007-01-01

    This paper proposes an innovation in the application for image guided surgery using a comparative study of three different method of segmentation. This segmentation method is faster than the manual segmentation of images, with the advantage that it allows to use the same patient as anatomical reference, which has more precision than a generic atlas. This new methodology for 3D information extraction is based on a processing chain structured of the following modules: 1) 3D Filtering: the purpose is to preserve the contours of the structures and to smooth the homogeneous areas; several filters were tested and finally an anisotropic diffusion filter was used. 2) 3D Segmentation. This module compares three different methods: Region growing Algorithm, Cubic spline hand assisted, and Level Set Method. It then proposes a Level Set-based on the front propagation method that allows the making of the reconstruction of the internal walls of the anatomical structures of the brain. 3) 3D visualization. The new contribution of this work consists on the visualization of the segmented model and its use in the pre-surgery planning.

  15. Fast 3D visualization of endogenous brain signals with high-sensitivity laser scanning photothermal microscopy

    PubMed Central

    Miyazaki, Jun; Iida, Tadatsune; Tanaka, Shinji; Hayashi-Takagi, Akiko; Kasai, Haruo; Okabe, Shigeo; Kobayashi, Takayoshi

    2016-01-01

    A fast, high-sensitivity photothermal microscope was developed by implementing a spatially segmented balanced detection scheme into a laser scanning microscope. We confirmed a 4.9 times improvement in signal-to-noise ratio in the spatially segmented balanced detection compared with that of conventional detection. The system demonstrated simultaneous bi-modal photothermal and confocal fluorescence imaging of transgenic mouse brain tissue with a pixel dwell time of 20 μs. The fluorescence image visualized neurons expressing yellow fluorescence proteins, while the photothermal signal detected endogenous chromophores in the mouse brain, allowing 3D visualization of the distribution of various features such as blood cells and fine structures probably due to lipids. This imaging modality was constructed using compact and cost-effective laser diodes, and will thus be widely useful in the life and medical sciences. PMID:27231615

  16. Mechanics of the ankle and subtalar joints revealed through a 3D quasi-static stress MRI technique.

    PubMed

    Siegler, S; Udupa, J K; Ringleb, S I; Imhauser, C W; Hirsch, B E; Odhner, D; Saha, P K; Okereke, E; Roach, N

    2005-03-01

    A technique to study the three-dimensional (3D) mechanical characteristics of the ankle and of the subtalar joints in vivo and in vitro is described. The technique uses an MR scanner compatible 3D positioning and loading linkage to load the hindfoot with precise loads while the foot is being scanned. 3D image processing algorithms are used to derive from the acquired MR images bone morphology, hindfoot architecture, and joint kinematics. The technique was employed to study these properties both in vitro and in vivo. The ankle and subtler joint motion and the changes in architecture produced in response to an inversion load and an anterior drawer load were evaluated. The technique was shown to provide reliable measures of bone morphology. The left-to-right variations in bone morphology were less than 5%. The left-to-right variations in unloaded hindfoot architecture parameters were less than 10%, and these properties were only slightly affected by inversion and anterior drawer loads. Inversion and anterior drawer loads produced motion both at the ankle and at the subtalar joint. In addition, high degree of coupling, primarily of internal rotation with inversion, was observed both at the ankle and at the subtalar joint. The in vitro motion produced in response to inversion and anterior drawer load was greater than the in vivo motion. Finally, external motion, measured directly across the ankle complex, produced in response to load was much greater than the bone movements measured through the 3D stress MRI technique indicating the significant effect of soft tissue and skin interference.

  17. Novel brain MRI abnormalities in Gitelman syndrome

    PubMed Central

    Norbash, Alexander; Vattoth, Surjith

    2015-01-01

    Gitelman syndrome is an autosomal recessive renal tubular disorder characterized by hypokalemic metabolic alkalosis, hypomagnesemia and hypocalciuria. The syndrome is caused by a defective thiazide-sensitive sodium chloride co-transporter in the distal convoluted tubules of the kidneys. Gitelman syndrome could be confused with Bartter syndrome; the main differentiating feature is the presence of low urinary calcium excretion in the former. Descriptions of neuroradiological imaging findings associated with Gitelman syndrome are very scarce in the literature and include basal ganglia calcification, idiopathic intracranial hypertension and sclerochoroidal calcification. Cauda equina syndrome-like presentation has been reported, but without any corresponding imaging findings on lumbar spine MRI. We report a 13-year-old male with Gitelman syndrome who presented with altered mental status following a fall and scalp laceration and unremarkable brain CT, followed during hospitalization by somnolence and seizures. Metabolically the patient demonstrated hypokalemia and hypomagnesemia. MRI demonstrated features of encephalopathy including predominantly right-sided cerebral hemispheric signal abnormality and cytotoxic edema, with bilateral symmetric involvement of the thalami, midbrain tegmentum and tectum and cerebellar dentate nuclei. MRI after five months obtained during a later episode of encephalopathy showed resolution of the signal abnormalities with setting in of brain atrophy and also areas of newly developed cytotoxic edema in the left thalamus, bilateral dorsal midbrain and right greater than left dentate nuclei. The described abnormalities, either recurrent or in isolation, have not previously been published in patients with Gitelman syndrome. We believe that the findings are due to alteration of respiratory chain function secondary to the metabolic derangement and hence have a similar imaging appearance as encephalopathy related to mitochondrial cytopathy or

  18. Patient-specific respiratory models using dynamic 3D MRI: preliminary volunteer results.

    PubMed

    Miquel, M E; Blackall, J M; Uribe, S; Hawkes, D J; Schaeffter, T

    2013-03-01

    Organ and tumour motion has a significant impact on the planning and delivery of radiotherapy treatment. At present imaging modality such as four-dimensional computer tomography (4DCT) cannot be used to measure the variability of motion between different respiratory cycles. To create reliable motion models, one needs to acquire volumetric data sets of the lungs with sufficient sampling of the breathing cycle. In this paper we investigate the use of highly parallel MRI to acquire such data. A 32 channel coil in conjunction with a balanced SSFP sequence and a SENSE factor of 6 were used to acquire volumetric data sets in five healthy volunteers. The acquisition was repeated for seven series of different breathing patterns. The data acquired was of sufficient spatial resolution (5 × 5 × 5 mm(3)) and image quality to carry out automated non-rigid registration. The acquisition rate (c.a. 2 volumes per second) allowed for a meaningful sampling of the different respiratory curves that were automatically obtained from the skin surface motion. This acquisition technique should provide images of high enough quality to create statistical respiratory models.

  19. Constrained reverse diffusion for thick slice interpolation of 3D volumetric MRI images.

    PubMed

    Neubert, Aleš; Salvado, Olivier; Acosta, Oscar; Bourgeat, Pierrick; Fripp, Jurgen

    2012-03-01

    Due to physical limitations inherent in magnetic resonance imaging scanners, three dimensional volumetric scans are often acquired with anisotropic voxel resolution. We investigate several interpolation approaches to reduce the anisotropy and present a novel approach - constrained reverse diffusion for thick slice interpolation. This technique was compared to common methods: linear and cubic B-Spline interpolation and a technique based on non-rigid registration of neighboring slices. The methods were evaluated on artificial MR phantoms and real MR scans of human brain. The constrained reverse diffusion approach delivered promising results and provides an alternative for thick slice interpolation, especially for higher anisotropy factors.

  20. Adaptive Image Enhancement for Tracing 3D Morphologies of Neurons and Brain Vasculatures.

    PubMed

    Zhou, Zhi; Sorensen, Staci; Zeng, Hongkui; Hawrylycz, Michael; Peng, Hanchuan

    2015-04-01

    It is important to digitally reconstruct the 3D morphology of neurons and brain vasculatures. A number of previous methods have been proposed to automate the reconstruction process. However, in many cases, noise and low signal contrast with respect to the image background still hamper our ability to use automation methods directly. Here, we propose an adaptive image enhancement method specifically designed to improve the signal-to-noise ratio of several types of individual neurons and brain vasculature images. Our method is based on detecting the salient features of fibrous structures, e.g. the axon and dendrites combined with adaptive estimation of the optimal context windows where such saliency would be detected. We tested this method for a range of brain image datasets and imaging modalities, including bright-field, confocal and multiphoton fluorescent images of neurons, and magnetic resonance angiograms. Applying our adaptive enhancement to these datasets led to improved accuracy and speed in automated tracing of complicated morphology of neurons and vasculatures.

  1. A brain-computer interface method combined with eye tracking for 3D interaction.

    PubMed

    Lee, Eui Chul; Woo, Jin Cheol; Kim, Jong Hwa; Whang, Mincheol; Park, Kang Ryoung

    2010-07-15

    With the recent increase in the number of three-dimensional (3D) applications, the need for interfaces to these applications has increased. Although the eye tracking method has been widely used as an interaction interface for hand-disabled persons, this approach cannot be used for depth directional navigation. To solve this problem, we propose a new brain computer interface (BCI) method in which the BCI and eye tracking are combined to analyze depth navigation, including selection and two-dimensional (2D) gaze direction, respectively. The proposed method is novel in the following five ways compared to previous works. First, a device to measure both the gaze direction and an electroencephalogram (EEG) pattern is proposed with the sensors needed to measure the EEG attached to a head-mounted eye tracking device. Second, the reliability of the BCI interface is verified by demonstrating that there is no difference between the real and the imaginary movements for the same work in terms of the EEG power spectrum. Third, depth control for the 3D interaction interface is implemented by an imaginary arm reaching movement. Fourth, a selection method is implemented by an imaginary hand grabbing movement. Finally, for the independent operation of gazing and the BCI, a mode selection method is proposed that measures a user's concentration by analyzing the pupil accommodation speed, which is not affected by the operation of gazing and the BCI. According to experimental results, we confirmed the feasibility of the proposed 3D interaction method using eye tracking and a BCI.

  2. TBIdoc: 3D content-based CT image retrieval system for traumatic brain injury

    NASA Astrophysics Data System (ADS)

    Li, Shimiao; Gong, Tianxia; Wang, Jie; Liu, Ruizhe; Tan, Chew Lim; Leong, Tze Yun; Pang, Boon Chuan; Lim, C. C. Tchoyoson; Lee, Cheng Kiang; Tian, Qi; Zhang, Zhuo

    2010-03-01

    Traumatic brain injury (TBI) is a major cause of death and disability. Computed Tomography (CT) scan is widely used in the diagnosis of TBI. Nowadays, large amount of TBI CT data is stacked in the hospital radiology department. Such data and the associated patient information contain valuable information for clinical diagnosis and outcome prediction. However, current hospital database system does not provide an efficient and intuitive tool for doctors to search out cases relevant to the current study case. In this paper, we present the TBIdoc system: a content-based image retrieval (CBIR) system which works on the TBI CT images. In this web-based system, user can query by uploading CT image slices from one study, retrieval result is a list of TBI cases ranked according to their 3D visual similarity to the query case. Specifically, cases of TBI CT images often present diffuse or focal lesions. In TBIdoc system, these pathological image features are represented as bin-based binary feature vectors. We use the Jaccard-Needham measure as the similarity measurement. Based on these, we propose a 3D similarity measure for computing the similarity score between two series of CT slices. nDCG is used to evaluate the system performance, which shows the system produces satisfactory retrieval results. The system is expected to improve the current hospital data management in TBI and to give better support for the clinical decision-making process. It may also contribute to the computer-aided education in TBI.

  3. Using 3-D shape models to guide segmentation of MR brain images.

    PubMed Central

    Hinshaw, K. P.; Brinkley, J. F.

    1997-01-01

    Accurate segmentation of medical images poses one of the major challenges in computer vision. Approaches that rely solely on intensity information frequently fail because similar intensity values appear in multiple structures. This paper presents a method for using shape knowledge to guide the segmentation process, applying it to the task of finding the surface of the brain. A 3-D model that includes local shape constraints is fitted to an MR volume dataset. The resulting low-resolution surface is used to mask out regions far from the cortical surface, enabling an isosurface extraction algorithm to isolate a more detailed surface boundary. The surfaces generated by this technique are comparable to those achieved by other methods, without requiring user adjustment of a large number of ad hoc parameters. Images Figure 1 Figure 2 Figure 3 Figure 4 PMID:9357670

  4. Initialisation of 3D level set for hippocampus segmentation from volumetric brain MR images

    NASA Astrophysics Data System (ADS)

    Hajiesmaeili, Maryam; Dehmeshki, Jamshid; Bagheri Nakhjavanlo, Bashir; Ellis, Tim

    2014-04-01

    Shrinkage of the hippocampus is a primary biomarker for Alzheimer's disease and can be measured through accurate segmentation of brain MR images. The paper will describe the problem of initialisation of a 3D level set algorithm for hippocampus segmentation that must cope with the some challenging characteristics, such as small size, wide range of intensities, narrow width, and shape variation. In addition, MR images require bias correction, to account for additional inhomogeneity associated with the scanner technology. Due to these inhomogeneities, using a single initialisation seed region inside the hippocampus is prone to failure. Alternative initialisation strategies are explored, such as using multiple initialisations in different sections (such as the head, body and tail) of the hippocampus. The Dice metric is used to validate our segmentation results with respect to ground truth for a dataset of 25 MR images. Experimental results indicate significant improvement in segmentation performance using the multiple initialisations techniques, yielding more accurate segmentation results for the hippocampus.

  5. 3D Reconstructed Cyto-, Muscarinic M2 Receptor, and Fiber Architecture of the Rat Brain Registered to the Waxholm Space Atlas

    PubMed Central

    Schubert, Nicole; Axer, Markus; Schober, Martin; Huynh, Anh-Minh; Huysegoms, Marcel; Palomero-Gallagher, Nicola; Bjaalie, Jan G.; Leergaard, Trygve B.; Kirlangic, Mehmet E.; Amunts, Katrin; Zilles, Karl

    2016-01-01

    High-resolution multiscale and multimodal 3D models of the brain are essential tools to understand its complex structural and functional organization. Neuroimaging techniques addressing different aspects of brain organization should be integrated in a reference space to enable topographically correct alignment and subsequent analysis of the various datasets and their modalities. The Waxholm Space (http://software.incf.org/software/waxholm-space) is a publicly available 3D coordinate-based standard reference space for the mapping and registration of neuroanatomical data in rodent brains. This paper provides a newly developed pipeline combining imaging and reconstruction steps with a novel registration strategy to integrate new neuroimaging modalities into the Waxholm Space atlas. As a proof of principle, we incorporated large scale high-resolution cyto-, muscarinic M2 receptor, and fiber architectonic images of rat brains into the 3D digital MRI based atlas of the Sprague Dawley rat in Waxholm Space. We describe the whole workflow, from image acquisition to reconstruction and registration of these three modalities into the Waxholm Space rat atlas. The registration of the brain sections into the atlas is performed by using both linear and non-linear transformations. The validity of the procedure is qualitatively demonstrated by visual inspection, and a quantitative evaluation is performed by measurement of the concordance between representative atlas-delineated regions and the same regions based on receptor or fiber architectonic data. This novel approach enables for the first time the generation of 3D reconstructed volumes of nerve fibers and fiber tracts, or of muscarinic M2 receptor density distributions, in an entire rat brain. Additionally, our pipeline facilitates the inclusion of further neuroimaging datasets, e.g., 3D reconstructed volumes of histochemical stainings or of the regional distributions of multiple other receptor types, into the Waxholm Space

  6. 3D Reconstructed Cyto-, Muscarinic M2 Receptor, and Fiber Architecture of the Rat Brain Registered to the Waxholm Space Atlas.

    PubMed

    Schubert, Nicole; Axer, Markus; Schober, Martin; Huynh, Anh-Minh; Huysegoms, Marcel; Palomero-Gallagher, Nicola; Bjaalie, Jan G; Leergaard, Trygve B; Kirlangic, Mehmet E; Amunts, Katrin; Zilles, Karl

    2016-01-01

    High-resolution multiscale and multimodal 3D models of the brain are essential tools to understand its complex structural and functional organization. Neuroimaging techniques addressing different aspects of brain organization should be integrated in a reference space to enable topographically correct alignment and subsequent analysis of the various datasets and their modalities. The Waxholm Space (http://software.incf.org/software/waxholm-space) is a publicly available 3D coordinate-based standard reference space for the mapping and registration of neuroanatomical data in rodent brains. This paper provides a newly developed pipeline combining imaging and reconstruction steps with a novel registration strategy to integrate new neuroimaging modalities into the Waxholm Space atlas. As a proof of principle, we incorporated large scale high-resolution cyto-, muscarinic M2 receptor, and fiber architectonic images of rat brains into the 3D digital MRI based atlas of the Sprague Dawley rat in Waxholm Space. We describe the whole workflow, from image acquisition to reconstruction and registration of these three modalities into the Waxholm Space rat atlas. The registration of the brain sections into the atlas is performed by using both linear and non-linear transformations. The validity of the procedure is qualitatively demonstrated by visual inspection, and a quantitative evaluation is performed by measurement of the concordance between representative atlas-delineated regions and the same regions based on receptor or fiber architectonic data. This novel approach enables for the first time the generation of 3D reconstructed volumes of nerve fibers and fiber tracts, or of muscarinic M2 receptor density distributions, in an entire rat brain. Additionally, our pipeline facilitates the inclusion of further neuroimaging datasets, e.g., 3D reconstructed volumes of histochemical stainings or of the regional distributions of multiple other receptor types, into the Waxholm Space

  7. Evaluation and validation methods for intersubject nonrigid 3D image registration of the human brain

    NASA Astrophysics Data System (ADS)

    Guo, Ting; Starreveld, Yves P.; Peters, Terry M.

    2005-04-01

    This work presents methodologies for assessing the accuracy of non-rigid intersubject registration algorithms from both qualitative and quantitative perspectives. The first method was based on a set of 43 anatomical landmarks. MRI brain images of 12 subjects were non-rigidly registered to the standard MRI dataset. The "gold-standard" coordinates of the 43 landmarks in the target were estimated by averaging their coordinates after 6 tagging sessions. The Euclidean distance between each landmark of a subject after warping to the reference space and the homologous "gold-standard" landmark on the reference image was considered as the registration error. Another method based on visual inspection software displaying the spatial change of colour-coded spheres, before and after warping, was also developed to evaluate the performance of the non-rigid warping algorithms within the homogeneous regions in the deep-brain. Our methods were exemplified by assessing and comparing the accuracy of two intersubject non-rigid registration approaches, AtamaiWarp and ANIMAL algorithms. From the first method, the average registration error was 1.04mm +/- 0.65mm for AtamaiWarp, and 1.59mm +/- 1.47mm for ANIMAL. With maximum registration errors of 2.78mm and 3.90mm respectively, AtamaiWarp and ANIMAL located 58% and 35% landmarks respectively with registration errors less than 1mm. A paired t-test showed that the differences in registration error between AtamaiWarp and ANIMAL were significant (P < 0.002) demonstrating that AtamaiWarp, in addition to being over 60 times faster than ANIMAL, also provides more accurate results. From the second method, both algorithms treated the interior of homogeneous regions in an appropriate manner.

  8. Confocal laser scanning microscopy and 3-D reconstructions of neuronal structures in human brain cortex.

    PubMed

    Belichenko, P V; Dahlström, A

    1995-09-01

    Human brain material was studied with Lucifer yellow (LY) microinjections, indirect Texas red immunofluorescence, and confocal laser scanning microscopy (CLSM). The scanned images were transferred to a Silicon Graphics (SG) IRIS computer equipped with software for reconstructing the 3-D architecture of cells. By employing dual channel CLSM (Bio-Rad MRC 600), LY-injected cells and Texas red immunofluorescence could be studied simultaneously. Autopsy material with 2- to 48-h postmortem delays (6 control and 2 Rett's syndrome cases) as well as biopsy material (14 cases with therapy-resistant partial epilepsy--TRPE--undergoing neurosurgery) were used. In each specimen, 100-200 pyramidal and nonpyramidal neurons were visualized by LY microinjection. Single neurons were imaged and 2-D reconstructions of each neuron were made using z-projections of serial optical images; 3-D reconstructions and rotations were computed using the SG workstation, with VoxelView software from Vital Images (UK), and stored in a "neuronal library" on laser or magnetic optical disks. In Ret's syndrome cases and in patients with TRPE various abnormalities in the dendritic geometry of pyramidal and nonpyramidal cells have been found. The combination of LY injections with immunofluorescence allows the investigation of transmitter-related substances around the LY-injected cells. Using antibodies to synaptic vesicle proteins, presynaptic elements docking onto individual spines have been demonstrated. This approach may contribute to the understanding of different neurological and psychiatric disorders and may be useful in the Mapping of the Human Brain project. It may also be integrated with functional imaging by PET scan and with the human genome project.

  9. Integrating histology and MRI in the first digital brain of common squirrel monkey, Saimiri sciureus.

    PubMed

    Sun, Peizhen; Parvathaneni, Prasanna; Schilling, Kurt G; Gao, Yurui; Janve, Vaibhav; Anderson, Adam; Landman, Bennett A

    2015-03-17

    This effort is a continuation of development of a digital brain atlas of the common squirrel monkey, Saimiri sciureus, a New World monkey with functional and microstructural organization of central nervous system similar to that of humans. Here, we present the integration of histology with multi-modal magnetic resonance imaging (MRI) atlas constructed from the brain of an adult female squirrel monkey. The central concept of this work is to use block face photography to establish an intermediate common space in coordinate system which preserves the high resolution in-plane resolution of histology while enabling 3-D correspondence with MRI. In vivo MRI acquisitions include high resolution T2 structural imaging (300 µm isotropic) and low resolution diffusion tensor imaging (600 um isotropic). Ex vivo MRI acquisitions include high resolution T2 structural imaging and high resolution diffusion tensor imaging (both 300 µm isotropic). Cortical regions were manually annotated on the co-registered volumes based on published histological sections in-plane. We describe mapping of histology and MRI based data of the common squirrel monkey and construction of a viewing tool that enable online viewing of these datasets. The previously descried atlas MRI is used for its deformation to provide accurate conformation to the MRI, thus adding information at the histological level to the MRI volume. This paper presents the mapping of single 2D image slice in block face as a proof of concept and this can be extended to map the atlas space in 3D coordinate system as part of the future work and can be loaded to an XNAT system for further use.

  10. Integrating histology and MRI in the first digital brain of common squirrel monkey, Saimiri sciureus

    NASA Astrophysics Data System (ADS)

    Sun, Peizhen; Parvathaneni, Prasanna; Schilling, Kurt G.; Gao, Yurui; Janve, Vaibhav; Anderson, Adam; Landman, Bennett A.

    2015-03-01

    This effort is a continuation of development of a digital brain atlas of the common squirrel monkey, Saimiri sciureus, a New World monkey with functional and microstructural organization of central nervous system similar to that of humans. Here, we present the integration of histology with multi-modal magnetic resonance imaging (MRI) atlas constructed from the brain of an adult female squirrel monkey. The central concept of this work is to use block face photography to establish an intermediate common space in coordinate system which preserves the high resolution in-plane resolution of histology while enabling 3-D correspondence with MRI. In vivo MRI acquisitions include high resolution T2 structural imaging (300 μm isotropic) and low resolution diffusion tensor imaging (600 um isotropic). Ex vivo MRI acquisitions include high resolution T2 structural imaging and high resolution diffusion tensor imaging (both 300 μm isotropic). Cortical regions were manually annotated on the co-registered volumes based on published histological sections in-plane. We describe mapping of histology and MRI based data of the common squirrel monkey and construction of a viewing tool that enable online viewing of these datasets. The previously descried atlas MRI is used for its deformation to provide accurate conformation to the MRI, thus adding information at the histological level to the MRI volume. This paper presents the mapping of single 2D image slice in block face as a proof of concept and this can be extended to map the atlas space in 3D coordinate system as part of the future work and can be loaded to an XNAT system for further use.

  11. Dosimetry in brain tumor phantom at 15 MV 3D conformal radiation therapy

    PubMed Central

    2013-01-01

    Glioblastoma multiforme (GBM) is the most common, aggressive, highly malignant and infiltrative of all brain tumors with low rate of control. The main goal of this work was to evaluate the spatial dose distribution into a GBM simulator inside a head phantom exposed to a 15 MV 3D conformal radiation therapy in order to validate internal doses. A head and neck phantom developed by the Ionizing Radiation Research Group (NRI) was used on the experiments. Such phantom holds the following synthetic structures: brain and spinal cord, skull, cervical and thoracic vertebrae, jaw, hyoid bone, laryngeal cartilages, head and neck muscles and skin. Computer tomography (CT) of the simulator was taken, capturing a set of contrasted references. Therapy Radiation planning (TPS) was performed based on those CT images, satisfying a 200 cGy prescribed dose split in three irradiation fields. The TPS assumed 97% of prescribed dose cover the prescribed treatment volume (PTV). Radiochromic films in a solid water phantom provided dose response as a function of optical density. Spatial dosimetric distribution was generated by radiochromic film samples at coronal, sagittal-anterior and sagittal-posterior positions, inserted into tumor simulator and brain. The spatial dose profiles held 70 to 120% of the prescribed dose. In spite of the stratified profile, as opposed to the smooth dose profile from TPS, the tumor internal doses were within a 5% deviation from 214.4 cGy evaluated by TPS. 83.2% of the points with a gamma value of less than 1 (3%/3mm) for TPS and experimental values, respectively. At the tumor, measured at coronal section, a few dark spots in the film caused the appearance of outlier points in 13-15% of dose deviation percentage. And, as final conclusion, such dosimeter choice and the physical anthropomorphic and anthropometric phantom provided an efficient method for validating radiotherapy protocols. PMID:23829593

  12. Computer-based vertebral tumor cryoablation planning and procedure simulation involving two cases using MRI-visible 3D printing and advanced visualization

    PubMed Central

    Guenette, Jeffrey P.; Himes, Nathan; Giannopoulos, Andreas A.; Kelil, Tatiana; Mitsouras, Dimitris; Lee, Thomas C.

    2016-01-01

    We report the development and use of MRI-compatible and MRI-visible 3D printed models in conjunction with advanced visualization software models to plan and simulate safe access routes to achieve a theoretical zone of cryoablation for percutaneous image-guided treatment of a C7 pedicle osteoid osteoma and an L1 lamina osteoblastoma. Both models altered procedural planning and patient care. Patient-specific MRI-visible models can be helpful in planning complex percutaneous image-guided cryoablation procedures. PMID:27505064

  13. 3D MRI-based anisotropic FSI models with cyclic bending for human coronary atherosclerotic plaque mechanical analysis.

    PubMed

    Tang, Dalin; Yang, Chun; Kobayashi, Shunichi; Zheng, Jie; Woodard, Pamela K; Teng, Zhongzhao; Billiar, Kristen; Bach, Richard; Ku, David N

    2009-06-01

    Heart attack and stroke are often caused by atherosclerotic plaque rupture, which happens without warning most of the time. Magnetic resonance imaging (MRI)-based atherosclerotic plaque models with fluid-structure interactions (FSIs) have been introduced to perform flow and stress/strain analysis and identify possible mechanical and morphological indices for accurate plaque vulnerability assessment. For coronary arteries, cyclic bending associated with heart motion and anisotropy of the vessel walls may have significant influence on flow and stress/strain distributions in the plaque. FSI models with cyclic bending and anisotropic vessel properties for coronary plaques are lacking in the current literature. In this paper, cyclic bending and anisotropic vessel properties were added to 3D FSI coronary plaque models so that the models would be more realistic for more accurate computational flow and stress/strain predictions. Six computational models using one ex vivo MRI human coronary plaque specimen data were constructed to assess the effects of cyclic bending, anisotropic vessel properties, pulsating pressure, plaque structure, and axial stretch on plaque stress/strain distributions. Our results indicate that cyclic bending and anisotropic properties may cause 50-800% increase in maximum principal stress (Stress-P1) values at selected locations. The stress increase varies with location and is higher when bending is coupled with axial stretch, nonsmooth plaque structure, and resonant pressure conditions (zero phase angle shift). Effects of cyclic bending on flow behaviors are more modest (9.8% decrease in maximum velocity, 2.5% decrease in flow rate, 15% increase in maximum flow shear stress). Inclusion of cyclic bending, anisotropic vessel material properties, accurate plaque structure, and axial stretch in computational FSI models should lead to a considerable improvement of accuracy of computational stress/strain predictions for coronary plaque vulnerability

  14. Real-time motion- and B0-correction for LASER-localized spiral-accelerated 3D-MRSI of the brain at 3T.

    PubMed

    Bogner, Wolfgang; Hess, Aaron T; Gagoski, Borjan; Tisdall, M Dylan; van der Kouwe, Andre J W; Trattnig, Siegfried; Rosen, Bruce; Andronesi, Ovidiu C

    2014-03-01

    The full potential of magnetic resonance spectroscopic imaging (MRSI) is often limited by localization artifacts, motion-related artifacts, scanner instabilities, and long measurement times. Localized adiabatic selective refocusing (LASER) provides accurate B1-insensitive spatial excitation even at high magnetic fields. Spiral encoding accelerates MRSI acquisition, and thus, enables 3D-coverage without compromising spatial resolution. Real-time position- and shim/frequency-tracking using MR navigators correct motion- and scanner instability-related artifacts. Each of these three advanced MRI techniques provides superior MRSI data compared to commonly used methods. In this work, we integrated in a single pulse sequence these three promising approaches. Real-time correction of motion, shim, and frequency-drifts using volumetric dual-contrast echo planar imaging-based navigators were implemented in an MRSI sequence that uses low-power gradient modulated short-echo time LASER localization and time efficient spiral readouts, in order to provide fast and robust 3D-MRSI in the human brain at 3T. The proposed sequence was demonstrated to be insensitive to motion- and scanner drift-related degradations of MRSI data in both phantoms and volunteers. Motion and scanner drift artifacts were eliminated and excellent spectral quality was recovered in the presence of strong movement. Our results confirm the expected benefits of combining a spiral 3D-LASER-MRSI sequence with real-time correction. The new sequence provides accurate, fast, and robust 3D metabolic imaging of the human brain at 3T. This will further facilitate the use of 3D-MRSI for neuroscience and clinical applications.

  15. Continuous table acquisition MRI for radiotherapy treatment planning: Distortion assessment with a new extended 3D volumetric phantom

    SciTech Connect

    Walker, Amy Metcalfe, Peter; Liney, Gary; Holloway, Lois; Dowling, Jason; Rivest-Henault, David

    2015-04-15

    Purpose: Accurate geometry is required for radiotherapy treatment planning (RTP). When considering the use of magnetic resonance imaging (MRI) for RTP, geometric distortions observed in the acquired images should be considered. While scanner technology and vendor supplied correction algorithms provide some correction, large distortions are still present in images, even when considering considerably smaller scan lengths than those typically acquired with CT in conventional RTP. This study investigates MRI acquisition with a moving table compared with static scans for potential geometric benefits for RTP. Methods: A full field of view (FOV) phantom (diameter 500 mm; length 513 mm) was developed for measuring geometric distortions in MR images over volumes pertinent to RTP. The phantom consisted of layers of refined plastic within which vitamin E capsules were inserted. The phantom was scanned on CT to provide the geometric gold standard and on MRI, with differences in capsule location determining the distortion. MRI images were acquired with two techniques. For the first method, standard static table acquisitions were considered. Both 2D and 3D acquisition techniques were investigated. With the second technique, images were acquired with a moving table. The same sequence was acquired with a static table and then with table speeds of 1.1 mm/s and 2 mm/s. All of the MR images acquired were registered to the CT dataset using a deformable B-spline registration with the resulting deformation fields providing the distortion information for each acquisition. Results: MR images acquired with the moving table enabled imaging of the whole phantom length while images acquired with a static table were only able to image 50%–70% of the phantom length of 513 mm. Maximum distortion values were reduced across a larger volume when imaging with a moving table. Increased table speed resulted in a larger contribution of distortion from gradient nonlinearities in the through

  16. 3D documentation and visualization of external injury findings by integration of simple photography in CT/MRI data sets (IprojeCT).

    PubMed

    Campana, Lorenzo; Breitbeck, Robert; Bauer-Kreuz, Regula; Buck, Ursula

    2016-05-01

    This study evaluated the feasibility of documenting patterned injury using three dimensions and true colour photography without complex 3D surface documentation methods. This method is based on a generated 3D surface model using radiologic slice images (CT) while the colour information is derived from photographs taken with commercially available cameras. The external patterned injuries were documented in 16 cases using digital photography as well as highly precise photogrammetry-supported 3D structured light scanning. The internal findings of these deceased were recorded using CT and MRI. For registration of the internal with the external data, two different types of radiographic markers were used and compared. The 3D surface model generated from CT slice images was linked with the photographs, and thereby digital true-colour 3D models of the patterned injuries could be created (Image projection onto CT/IprojeCT). In addition, these external models were merged with the models of the somatic interior. We demonstrated that 3D documentation and visualization of external injury findings by integration of digital photography in CT/MRI data sets is suitable for the 3D documentation of individual patterned injuries to a body. Nevertheless, this documentation method is not a substitution for photogrammetry and surface scanning, especially when the entire bodily surface is to be recorded in three dimensions including all external findings, and when precise data is required for comparing highly detailed injury features with the injury-inflicting tool.

  17. 2D-3D registration for brain radiation therapy using a 3D CBCT and a single limited field-of-view 2D kV radiograph

    NASA Astrophysics Data System (ADS)

    Munbodh, R.; Moseley, D. J.

    2014-03-01

    We report results of an intensity-based 2D-3D rigid registration framework for patient positioning and monitoring during brain radiotherapy. We evaluated two intensity-based similarity measures, the Pearson Correlation Coefficient (ICC) and Maximum Likelihood with Gaussian noise (MLG) derived from the statistics of transmission images. A useful image frequency band was identified from the bone-to-no-bone ratio. Validation was performed on gold-standard data consisting of 3D kV CBCT scans and 2D kV radiographs of an anthropomorphic head phantom acquired at 23 different poses with parameter variations along six degrees of freedom. At each pose, a single limited field of view kV radiograph was registered to the reference CBCT. The ground truth was determined from markers affixed to the phantom and visible in the CBCT images. The mean (and standard deviation) of the absolute errors in recovering each of the six transformation parameters along the x, y and z axes for ICC were varphix: 0.08(0.04)°, varphiy: 0.10(0.09)°, varphiz: 0.03(0.03)°, tx: 0.13(0.11) mm, ty: 0.08(0.06) mm and tz: 0.44(0.23) mm. For MLG, the corresponding results were varphix: 0.10(0.04)°, varphiy: 0.10(0.09)°, varphiz: 0.05(0.07)°, tx: 0.11(0.13) mm, ty: 0.05(0.05) mm and tz: 0.44(0.31) mm. It is feasible to accurately estimate all six transformation parameters from a 3D CBCT of the head and a single 2D kV radiograph within an intensity-based registration framework that incorporates the physics of transmission images.

  18. MRI Segmentation of the Human Brain: Challenges, Methods, and Applications

    PubMed Central

    Despotović, Ivana

    2015-01-01

    Image segmentation is one of the most important tasks in medical image analysis and is often the first and the most critical step in many clinical applications. In brain MRI analysis, image segmentation is commonly used for measuring and visualizing the brain's anatomical structures, for analyzing brain changes, for delineating pathological regions, and for surgical planning and image-guided interventions. In the last few decades, various segmentation techniques of different accuracy and degree of complexity have been developed and reported in the literature. In this paper we review the most popular methods commonly used for brain MRI segmentation. We highlight differences between them and discuss their capabilities, advantages, and limitations. To address the complexity and challenges of the brain MRI segmentation problem, we first introduce the basic concepts of image segmentation. Then, we explain different MRI preprocessing steps including image registration, bias field correction, and removal of nonbrain tissue. Finally, after reviewing different brain MRI segmentation methods, we discuss the validation problem in brain MRI segmentation. PMID:25945121

  19. Clinical Correlation between Perverted Nystagmus and Brain MRI Abnormal Findings

    PubMed Central

    Han, Won-Gue; Yoon, Hee-Chul; Kim, Tae-Min; Rah, Yoon Chan

    2016-01-01

    Background and Objectives To analyze the clinical correlation between perverted nystagmus and brain magnetic resonance imaging (MRI) abnormal findings and to evaluate whether perverted nystagmus is clinically significant results of brain abnormal lesions or not. Subjects and Methods We performed medical charts review from January 2008 to July 2014, retrospectively. Patients who were suspected central originated vertigo at Frenzel goggles test were included among patients who visited our hospital. To investigate the correlation with nystagmus suspected central originated vertigo and brain MRI abnormal findings, we confirmed whether performing brain MRI or not. Then we exclude that patients not performed brain MRI. Results The number of patients with perverted nystagmus was 15, upbeating was 1 and down-beating was 14. Among these patients, 5 patients have brain MRI abnormal findings. However, 2 patients with MRI abnormal findings were not associated correctly with perverted nystagmus and only 3 patients with perverted nystagmus were considered central originated vertigo and further evaluation and treatment was performed by the department of neurology. Conclusions Perverted nystagmus was considered to the abnormalities at brain lesions, especially cerebellum, but neurologic symptoms and further evaluation were needed for exact diagnosis of central originated vertigo. PMID:27626081

  20. The Ultrasound Brain Helmet: Simultaneous Multi-transducer 3D Transcranial Ultrasound Imaging

    NASA Astrophysics Data System (ADS)

    Lindsey, Brooks D.

    In this work, I examine the problem of rapid imaging of stroke and present ultrasound-based approaches for addressing it. Specifically, this dissertation discusses aberration and attenuation due to the skull as sources of image degradation and presents a prototype system for simultaneous 3D bilateral imaging via both temporal acoustic windows. This system uses custom sparse array transducers built on flexible multilayer circuits that can be positioned for simultaneous imaging via both temporal acoustic windows, allowing for registration and fusion of multiple real-time 3D scans of cerebral vasculature. I examine hardware considerations for new matrix arrays—transducer design and interconnects—in this application. Specifically, it is proposed that signal-to-noise ratio (SNR) may be increased by reducing the length of probe cables. This claim is evaluated as part of the presented system through simulation, experimental data, and in vivo imaging. Ultimately, gains in SNR of 7 dB are realized by replacing a standard probe cable with a much shorter flex interconnect; higher gains may be possible using ribbon-based probe cables. In vivo images are presented depicting cerebral arteries with and without the use of microbubble contrast agent that have been registered and fused using a search algorithm which maximizes normalized cross-correlation. The scanning geometry of a brain helmet-type system is also utilized to allow each matrix array to serve as a correction source for the opposing array. Aberration is estimated using cross-correlation of RF channel signals followed by least mean squares solution of the resulting overdetermined system. Delay maps are updated and real-time 3D scanning resumes. A first attempt is made at using multiple arrival time maps to correct multiple unique aberrators within a single transcranial imaging volume, i.e. several isoplanatic patches. This adaptive imaging technique, which uses steered unfocused waves transmitted by the opposing or

  1. Intensity-based 2D 3D registration for lead localization in robot guided deep brain stimulation.

    PubMed

    Hunsche, Stefan; Sauner, Dieter; Majdoub, Faycal El; Neudorfer, Clemens; Poggenborg, Jörg; Goßmann, Axel; Maarouf, Mohammad

    2017-03-21

    Intraoperative assessment of lead localization has become a standard procedure during deep brain stimulation surgery in many centers, allowing immediate verification of targeting accuracy and, if necessary, adjustment of the trajectory. The most suitable imaging modality to determine lead positioning, however, remains controversially discussed. Current approaches entail the implementation of computed tomography and magnetic resonance imaging. In the present study, we adopted the technique of intensity-based 2D 3D registration that is commonly employed in stereotactic radiotherapy and spinal surgery. For this purpose, intraoperatively acquired 2D x-ray images were fused with preoperative 3D computed tomography (CT) data to verify lead placement during stereotactic robot assisted surgery. Accuracy of lead localization determined from 2D 3D registration was compared to conventional 3D 3D registration in a subsequent patient study. The mean Euclidian distance of lead coordinates estimated from intensity-based 2D 3D registration versus flat-panel detector CT 3D 3D registration was 0.7 mm  ±  0.2 mm. Maximum values of these distances amounted to 1.2 mm. To further investigate 2D 3D registration a simulation study was conducted, challenging two observers to visually assess artificially generated 2D 3D registration errors. 95% of deviation simulations, which were visually assessed as sufficient, had a registration error below 0.7 mm. In conclusion, 2D 3D intensity-based registration revealed high accuracy and reliability during robot guided stereotactic neurosurgery and holds great potential as a low dose, cost effective means for intraoperative lead localization.

  2. Intensity-based 2D 3D registration for lead localization in robot guided deep brain stimulation

    NASA Astrophysics Data System (ADS)

    Hunsche, Stefan; Sauner, Dieter; El Majdoub, Faycal; Neudorfer, Clemens; Poggenborg, Jörg; Goßmann, Axel; Maarouf, Mohammad

    2017-03-01

    Intraoperative assessment of lead localization has become a standard procedure during deep brain stimulation surgery in many centers, allowing immediate verification of targeting accuracy and, if necessary, adjustment of the trajectory. The most suitable imaging modality to determine lead positioning, however, remains controversially discussed. Current approaches entail the implementation of computed tomography and magnetic resonance imaging. In the present study, we adopted the technique of intensity-based 2D 3D registration that is commonly employed in stereotactic radiotherapy and spinal surgery. For this purpose, intraoperatively acquired 2D x-ray images were fused with preoperative 3D computed tomography (CT) data to verify lead placement during stereotactic robot assisted surgery. Accuracy of lead localization determined from 2D 3D registration was compared to conventional 3D 3D registration in a subsequent patient study. The mean Euclidian distance of lead coordinates estimated from intensity-based 2D 3D registration versus flat-panel detector CT 3D 3D registration was 0.7 mm  ±  0.2 mm. Maximum values of these distances amounted to 1.2 mm. To further investigate 2D 3D registration a simulation study was conducted, challenging two observers to visually assess artificially generated 2D 3D registration errors. 95% of deviation simulations, which were visually assessed as sufficient, had a registration error below 0.7 mm. In conclusion, 2D 3D intensity-based registration revealed high accuracy and reliability during robot guided stereotactic neurosurgery and holds great potential as a low dose, cost effective means for intraoperative lead localization.

  3. 4D Magnetic Resonance Velocimetry in a 3D printed brain aneurysm

    NASA Astrophysics Data System (ADS)

    Amili, Omid; Schiavazzi, Daniele; Coletti, Filippo

    2016-11-01

    Cerebral aneurysms are of great clinical importance. It is believed that hemodynamics play a critical role in the development, growth, and rupture of brain arteries with such condition. The flow structure in the aneurysm sac is complex, unsteady, and three-dimensional. Therefore the time-resolved measurement of the three-dimensional three-component velocity field is crucial to predict the clinical outcome. In this study magnetic resonance velocimetry is used to assess the fluid dynamics inside a 3D printed model of a giant intracranial aneurysm. We reach sub-millimeter resolution while resolving sixteen instances within the cardiac cycle. The physiological flow waveform is imposed using an in-house built pump in a flow circuit where the cardiovascular impedance is matched. The flow evolution over time is reconstructed in detail. The complex flow structure is characterized by vortical and helical motions that reside in the aneurysm for most part of the cycle. The 4D pressured distribution is also reconstructed from the velocity field. The present case study was used in a previous CFD challenge, therefore these results may provide useful experimental comparison for simulations performed by other research groups.

  4. 3D quantification of brain microvessels exposed to heavy particle radiation

    NASA Astrophysics Data System (ADS)

    Hintermüller, C.; Coats, J. S.; Obenaus, A.; Nelson, G.; Krucker, T.; Stampanoni, M.

    2009-09-01

    Space radiation with high energy particles and cosmic rays presents a significant hazard to spaceflight crews. Recent reviews of the health risk to astronauts from ionizing radiation concluded to establish a level of risk which may indicate the possible performance decrements and decreased latency of late dysfunction syndromes (LDS) of the brain. A hierarchical imaging approach developed at ETH Zürich and PSI, which relies on synchrotron based X-ray Tomographic Microscopy (SRXTM), was used to visualize and analyze 3D vascular structures down to the capillary level in their precise anatomical context. Various morphological parameters, such as overall vessel volume, vessel thickness and spacing, are extracted to characterize the vascular structure within a region of interest. For a first quantification of the effect of high energy particles on the vasculature we scanned a set of 6 animals, all of same age. The animals were irradiated with 1 Gy, 2 Gy and 4 Gy of 600MeV 56Fe heavy particles simulating the space radiation environment. We found that with increasing dose the diameter of vessels and the overall vessel volume are decreased whereas the vessel spacing is increased. As these parameters reflect blood flow in three-dimensional space they can be used as indicators for the degree of vascular efficiency which can have an impact on the function and development of lung tissue or tumors.

  5. Quantitative 3D Ultrashort Time-to-Echo (UTE) MRI and Micro-CT (μCT) Evaluation of the Temporomandibular Joint (TMJ) Condylar Morphology

    PubMed Central

    Geiger, Daniel; Bae, Won C.; Statum, Sheronda; Du, Jiang; Chung, Christine B.

    2014-01-01

    Objective Temporomandibular dysfunction involves osteoarthritis of the TMJ, including degeneration and morphologic changes of the mandibular condyle. Purpose of this study was to determine accuracy of novel 3D-UTE MRI versus micro-CT (μCT) for quantitative evaluation of mandibular condyle morphology. Material & Methods Nine TMJ condyle specimens were harvested from cadavers (2M, 3F; Age 85 ± 10 yrs., mean±SD). 3D-UTE MRI (TR=50ms, TE=0.05 ms, 104 μm isotropic-voxel) was performed using a 3-T MR scanner and μCT (18 μm isotropic-voxel) was performed. MR datasets were spatially-registered with μCT dataset. Two observers segmented bony contours of the condyles. Fibrocartilage was segmented on MR dataset. Using a custom program, bone and fibrocartilage surface coordinates, Gaussian curvature, volume of segmented regions and fibrocartilage thickness were determined for quantitative evaluation of joint morphology. Agreement between techniques (MRI vs. μCT) and observers (MRI vs. MRI) for Gaussian curvature, mean curvature and segmented volume of the bone were determined using intraclass correlation correlation (ICC) analyses. Results Between MRI and μCT, the average deviation of surface coordinates was 0.19±0.15 mm, slightly higher than spatial resolution of MRI. Average deviation of the Gaussian curvature and volume of segmented regions, from MRI to μCT, was 5.7±6.5% and 6.6±6.2%, respectively. ICC coefficients (MRI vs. μCT) for Gaussian curvature, mean curvature and segmented volumes were respectively 0.892, 0.893 and 0.972. Between observers (MRI vs. MRI), the ICC coefficients were 0.998, 0.999 and 0.997 respectively. Fibrocartilage thickness was 0.55±0.11 mm, as previously described in literature for grossly normal TMJ samples. Conclusion 3D-UTE MR quantitative evaluation of TMJ condyle morphology ex-vivo, including surface, curvature and segmented volume, shows high correlation against μCT and between observers. In addition, UTE MRI allows

  6. 3D pulmonary perfusion MRI and MR angiography of pulmonary embolism in pigs after a single injection of a blood pool MR contrast agent.

    PubMed

    Fink, Christian; Ley, Sebastian; Puderbach, Michael; Plathow, Christian; Bock, Michael; Kauczor, Hans-Ulrich

    2004-07-01

    The purpose of this study was to assess the feasibility of contrast-enhanced 3D perfusion MRI and MR angiography (MRA) of pulmonary embolism (PE) in pigs using a single injection of the blood pool contrast Gadomer. PE was induced in five domestic pigs by injection of autologous blood thrombi. Contrast-enhanced first-pass 3D perfusion MRI (TE/TR/FA: 1.0 ms/2.2 ms/40 degrees; voxel size: 1.3 x 2.5 x 4.0 mm3; TA: 1.8 s per data set) and high-resolution 3D MRA (TE/TR/FA: 1.4 ms/3.4 ms/40 degrees; voxel size: 0.8 x 1.0 x 1.6 mm3) was performed during and after a single injection of 0.1 mmol/kg body weight of Gadomer. Image data were compared to pre-embolism Gd-DTPA-enhanced MRI and post-embolism thin-section multislice CT (n = 2). SNR measurements were performed in the pulmonary arteries and lung. One animal died after induction of PE. In all other animals, perfusion MRI and MRA could be acquired after a single injection of Gadomer. At perfusion MRI, PE could be detected by typical wedge-shaped perfusion defects. While the visualization of central PE at MRA correlated well with the CT, peripheral PE were only visualized by CT. Gadomer achieved a higher peak SNR of the lungs compared to Gd-DTPA (21 +/- 8 vs. 13 +/- 3). Contrast-enhanced 3D perfusion MRI and MRA of PE can be combined using a single injection of the blood pool contrast agent Gadomer.

  7. Velocity Measurement in Carotid Artery: Quantitative Comparison of Time-Resolved 3D Phase-Contrast MRI and Image-based Computational Fluid Dynamics

    PubMed Central

    Sarrami-Foroushani, Ali; Nasr Esfahany, Mohsen; Nasiraei Moghaddam, Abbas; Saligheh Rad, Hamidreza; Firouznia, Kavous; Shakiba, Madjid; Ghanaati, Hossein; Wilkinson, Iain David; Frangi, Alejandro Federico

    2015-01-01

    Background: Understanding hemodynamic environment in vessels is important for realizing the mechanisms leading to vascular pathologies. Objectives: Three-dimensional velocity vector field in carotid bifurcation is visualized using TR 3D phase-contrast magnetic resonance imaging (TR 3D PC MRI) and computational fluid dynamics (CFD). This study aimed to present a qualitative and quantitative comparison of the velocity vector field obtained by each technique. Subjects and Methods: MR imaging was performed on a 30-year old male normal subject. TR 3D PC MRI was performed on a 3 T scanner to measure velocity in carotid bifurcation. 3D anatomical model for CFD was created using images obtained from time-of-flight MR angiography. Velocity vector field in carotid bifurcation was predicted using CFD and PC MRI techniques. A statistical analysis was performed to assess the agreement between the two methods. Results: Although the main flow patterns were the same for the both techniques, CFD showed a greater resolution in mapping the secondary and circulating flows. Overall root mean square (RMS) errors for all the corresponding data points in PC MRI and CFD were 14.27% in peak systole and 12.91% in end diastole relative to maximum velocity measured at each cardiac phase. Bland-Altman plots showed a very good agreement between the two techniques. However, this study was not aimed to validate any of methods, instead, the consistency was assessed to accentuate the similarities and differences between Time-resolved PC MRI and CFD. Conclusion: Both techniques provided quantitatively consistent results of in vivo velocity vector fields in right internal carotid artery (RCA). PC MRI represented a good estimation of main flow patterns inside the vasculature, which seems to be acceptable for clinical use. However, limitations of each technique should be considered while interpreting results. PMID:26793288

  8. Transvaginal 3-d power Doppler ultrasound evaluation of the fetal brain at 10-13 weeks' gestation.

    PubMed

    Hata, Toshiyuki; Tanaka, Hirokazu; Noguchi, Junko

    2012-03-01

    The objective of this study was to measure the fetal brain volume (FBV) and vascularization and blood flow using transvaginal 3-D power Doppler (3DPD) ultrasound late in the first trimester of pregnancy. 3DPD ultrasound examinations with the VOCAL imaging analysis program were performed on 36 normal fetuses from 10-13 weeks' gestation. FBV and 3DPD indices related to the fetal brain vascularization (vascularization index [VI], flow index [FI] and vascularization flow index [VFI]) were calculated in each fetus. Intra- and interclass correlation coefficients and intra- and interobserver agreements of measurements were assessed. FBV was curvilinearly correlated well with the gestational age (R2 = 0.861, p < 0.0001). All 3-D power Doppler indices (VI, FI and VFI) showed no change at 10-13 weeks' gestation. FBV and all 3-D power Doppler indices (VI, FI and VFI) showed a correlation > 0.82, with good intra- and interobserver agreement. Our findings suggest that 3-D ultrasound is a superior means of evaluating the FBV in utero, and that 3-D power Doppler ultrasound histogram analysis may provide new information on the assessment of fetal brain perfusion.

  9. Real-time classification of activated brain areas for fMRI-based human-brain-interfaces

    NASA Astrophysics Data System (ADS)

    Moench, Tobias; Hollmann, Maurice; Grzeschik, Ramona; Mueller, Charles; Luetzkendorf, Ralf; Baecke, Sebastian; Luchtmann, Michael; Wagegg, Daniela; Bernarding, Johannes

    2008-03-01

    Functional MR imaging (fMRI) enables to detect different activated brain areas according to the performed tasks. However, data are usually evaluated after the experiment, which prohibits intra-experiment optimization or more sophisticated applications such as biofeedback experiments. Using a human-brain-interface (HBI), subjects are able to communicate with external programs, e.g. to navigate through virtual scenes, or to experience and modify their own brain activation. These applications require the real-time analysis and classification of activated brain areas. Our paper presents first results of different strategies for real-time pattern analysis and classification realized within a flexible experiment control system that enables the volunteers to move through a 3D virtual scene in real-time using finger tapping tasks, and alternatively only thought-based tasks.

  10. A stereotaxic MRI template set for the rat brain with tissue class distribution maps and co-registered anatomical atlas: application to pharmacological MRI.

    PubMed

    Schwarz, Adam J; Danckaert, Anne; Reese, Torsten; Gozzi, Alessandro; Paxinos, George; Watson, Charles; Merlo-Pich, Emilio V; Bifone, Angelo

    2006-08-15

    We describe a stereotaxic rat brain MRI template set with a co-registered digital anatomical atlas and illustrate its application to the analysis of a pharmacological MRI (phMRI) study of apomorphine. The template set includes anatomical images and tissue class probability maps for brain parenchyma and cerebrospinal fluid (CSF). These facilitate the use of standard fMRI software for spatial normalisation and tissue segmentation of rat brain data. A volumetric reconstruction of the Paxinos and Watson rat brain atlas is also co-localised with the template, enabling the atlas structure and stereotaxic coordinates corresponding to a feature within a statistical map to be interactively reported, facilitating the localisation of functional effects. Moreover, voxels falling within selected brain structures can be combined to define anatomically based 3D volumes of interest (VOIs), free of operator bias. As many atlas structures are small relative to the typical resolution of phMRI studies, a mechanism for defining composite structures as agglomerations of individual atlas structures is also described. This provides a simple and robust means of interrogating structures that are otherwise difficult to delineate and an objective framework for comparing and classifying compounds based on an anatomical profile of their activity. These developments allow a closer alignment of pre-clinical and clinical analysis techniques.

  11. 3D BrainCV: simultaneous visualization and analysis of cells and capillaries in a whole mouse brain with one-micron voxel resolution.

    PubMed

    Wu, Jingpeng; He, Yong; Yang, Zhongqin; Guo, Congdi; Luo, Qingming; Zhou, Wei; Chen, Shangbin; Li, Anan; Xiong, Benyi; Jiang, Tao; Gong, Hui

    2014-02-15

    Systematic cellular and vascular configurations are essential for understanding fundamental brain anatomy and metabolism. We demonstrated a 3D brainwide cellular and vascular (called 3D BrainCV) visualization and quantitative protocol for a whole mouse brain. We developed a modified Nissl staining method that quickly labeled the cells and blood vessels simultaneously in an entire mouse brain. Terabytes 3D datasets of the whole mouse brains, with unprecedented details of both individual cells and blood vessels, including capillaries, were simultaneously imaged at 1-μm voxel resolution using micro-optical sectioning tomography (MOST). For quantitative analysis, we proposed an automatic image-processing pipeline to perform brainwide vectorization and analysis of cells and blood vessels. Six representative brain regions from the cortex to the deep, including FrA, M1, PMBSF, V1, striatum, and amygdala, and six parameters, including cell number density, vascular length density, fractional vascular volume, distance from the cells to the nearest microvessel, microvascular length density, and fractional microvascular volume, had been quantitatively analyzed. The results showed that the proximity of cells to blood vessels was linearly correlated with vascular length density, rather than the cell number density. The 3D BrainCV made overall snapshots of the detailed picture of the whole brain architecture, which could be beneficial for the state comparison of the developing and diseased brain.

  12. PCA and level set based non-rigid image registration for MRI and Paxinos-Watson atlas of rat brain

    NASA Astrophysics Data System (ADS)

    Cai, Chao; Liu, Ailing; Ding, Mingyue; Zhou, Chengping

    2007-12-01

    Image registration provides the ability to geometrically align one dataset with another. It is a basic task in a great variety of biomedical imaging applications. This paper introduced a novel three-dimensional registration method for Magnetic Resonance Image (MRI) and Paxinos-Watson Atlas of rat brain. For the purpose of adapting to a large range and non-linear deformation between MRI and atlas in higher registration accuracy, based on the segmentation of rat brain, we chose the principle components analysis (PCA) automatically performing the linear registration, and then, a level set based nonlinear registration correcting some small distortions. We implemented this registration method in a rat brain 3D reconstruction and analysis system. Experiments have demonstrated that this method can be successfully applied to registering the low resolution and noise affection MRI with Paxinos-Watson Atlas of rat brain.

  13. Design and evaluation of an MRI compatible axial compression device for 3D assessment of spinal deformity and flexibility in AIS.

    PubMed

    Adam, Clayton; Izatt, Maree; Askin, Geoffrey

    2010-01-01

    Magnetic Resonance Imaging (MRI) offers a valuable research tool for the assessment of 3D spinal deformity in AIS, however the horizontal patient position imposed by conventional scanners removes the axial compressive loading on the spine. The objective of this study was to design, construct and test an MRI compatible compression device for research into the effect of axial loading on spinal deformity using supine MRI scans. The device was evaluated by performing unloaded and loaded supine MRI scans on a series of 10 AIS patients. The patient group had a mean initial (unloaded) major Cobb angle of 43+/-7 degrees, which increased to 50+/-9 degrees on application of the compressive load. The 7 degrees increase in mean Cobb angle is consistent with that reported by a previous study comparing standing versus supine posture in scoliosis patients (Torell et al, 1985. Spine 10:425-7).

  14. Magnetic Resonance, Functional (fMRI) -- Brain

    MedlinePlus

    ... thought, speech, movement and sensation, which is called brain mapping. help assess the effects of stroke, trauma or degenerative disease (such as Alzheimer's) on brain function. monitor the growth and function of brain ...

  15. A Non-Local Fuzzy Segmentation Method: Application to Brain MRI

    NASA Astrophysics Data System (ADS)

    Caldairou, Benoît; Rousseau, François; Passat, Nicolas; Habas, Piotr; Studholme, Colin; Heinrich, Christian

    The Fuzzy C-Means algorithm is a widely used and flexible approach for brain tissue segmentation from 3D MRI. Despite its recent enrichment by addition of a spatial dependency to its formulation, it remains quite sensitive to noise. In order to improve its reliability in noisy contexts, we propose a way to select the most suitable example regions for regularisation. This approach inspired by the Non-Local Mean strategy used in image restoration is based on the computation of weights modelling the grey-level similarity between the neighbourhoods being compared. Experiments were performed on MRI data and results illustrate the usefulness of the approach in the context of brain tissue classification.

  16. Evaluation of image quality of MRI data for brain tumor surgery

    NASA Astrophysics Data System (ADS)

    Heckel, Frank; Arlt, Felix; Geisler, Benjamin; Zidowitz, Stephan; Neumuth, Thomas

    2016-03-01

    3D medical images are important components of modern medicine. Their usefulness for the physician depends on their quality, though. Only high-quality images allow accurate and reproducible diagnosis and appropriate support during treatment. We have analyzed 202 MRI images for brain tumor surgery in a retrospective study. Both an experienced neurosurgeon and an experienced neuroradiologist rated each available image with respect to its role in the clinical workflow, its suitability for this specific role, various image quality characteristics, and imaging artifacts. Our results show that MRI data acquired for brain tumor surgery does not always fulfill the required quality standards and that there is a significant disagreement between the surgeon and the radiologist, with the surgeon being more critical. Noise, resolution, as well as the coverage of anatomical structures were the most important criteria for the surgeon, while the radiologist was mainly disturbed by motion artifacts.

  17. MRI Brain Tumor Segmentation and Necrosis Detection Using Adaptive Sobolev Snakes

    PubMed Central

    Nakhmani, Arie; Kikinis, Ron; Tannenbaum, Allen

    2014-01-01

    Brain tumor segmentation in brain MRI volumes is used in neurosurgical planning and illness staging. It is important to explore the tumor shape and necrosis regions at different points of time to evaluate the disease progression. We propose an algorithm for semi-automatic tumor segmentation and necrosis detection. Our algorithm consists of three parts: conversion of MRI volume to a probability space based on the on-line learned model, tumor probability density estimation, and adaptive segmentation in the probability space. We use manually selected acceptance and rejection classes on a single MRI slice to learn the background and foreground statistical models. Then, we propagate this model to all MRI slices to compute the most probable regions of the tumor. Anisotropic 3D diffusion is used to estimate the probability density. Finally, the estimated density is segmented by the Sobolev active contour (snake) algorithm to select smoothed regions of the maximum tumor probability. The segmentation approach is robust to noise and not very sensitive to the manual initialization in the volumes tested. Also, it is appropriate for low contrast imagery. The irregular necrosis regions are detected by using the outliers of the probability distribution inside the segmented region. The necrosis regions of small width are removed due to a high probability of noisy measurements. The MRI volume segmentation results obtained by our algorithm are very similar to expert manual segmentation. PMID:25302005

  18. Application of contrast-enhanced T1-weighted MRI-based 3D reconstruction of the dural tail sign in meningioma resection.

    PubMed

    You, Binsheng; Cheng, Yanhao; Zhang, Jian; Song, Qimin; Dai, Chao; Heng, Xueyuan; Fei, Chang

    2016-07-01

    OBJECT The goal of this study was to investigate the significance of contrast-enhanced T1-weighted (T1W) MRI-based 3D reconstruction of dural tail sign (DTS) in meningioma resection. METHODS Between May 2013 and August 2014, 18 cases of convexity and parasagittal meningiomas showing DTS on contrast-enhanced T1W MRI were selected. Contrast-enhanced T1W MRI-based 3D reconstruction of DTS was conducted before surgical treatment. The vertical and anteroposterior diameters of DTS on the contrast-enhanced T1W MR images and 3D reconstruction images were measured and compared. Surgical incisions were designed by referring to the 3D reconstruction and MR images, and then the efficiency of the 2 methods was evaluated with assistance of neuronavigation. RESULTS Three-dimensional reconstruction of DTS can reveal its overall picture. In most cases, the DTS around the tumor is uneven, whereas the DTS around the dural vessels presents longer extensions. There was no significant difference (p > 0.05) between the vertical and anteroposterior diameters of DTS measured on the contrast-enhanced T1W MR and 3D reconstruction images. The 3D images of DTS were more intuitive, and the overall picture of DTS could be revealed in 1 image, which made it easier to design the incision than by using the MR images. Meanwhile, assessment showed that the incisions designed using 3D images were more accurate than those designed using MR images (ridit analysis by SAS, F = 7.95; p = 0.008). Pathological examination showed that 34 dural specimens (except 2 specimens from 1 tumor) displayed tumor invasion. The distance of tumor cell invasion was 1.0-21.6 mm (5.4 ± 4.41 mm [mean ± SD]). Tumor cell invasion was not observed at the dural resection margin in all 36 specimens. CONCLUSIONS Contrast-enhanced T1W MRI-based 3D reconstruction can intuitively and accurately reveal the size and shape of DTS, and thus provides guidance for designing meningioma incisions.

  19. The ultrasound brain helmet: early human feasibility study of multiple simultaneous 3D scans of cerebral vasculature

    NASA Astrophysics Data System (ADS)

    Lindsey, Brooks D.; Ivancevich, Nikolas M.; Whitman, John; Light, Edward; Fronheiser, Matthew; Nicoletto, Heather A.; Laskowitz, Daniel T.; Smith, Stephen W.

    2009-02-01

    We describe early stage experiments to test the feasibility of an ultrasound brain helmet to produce multiple simultaneous real-time 3D scans of the cerebral vasculature from temporal and suboccipital acoustic windows of the skull. The transducer hardware and software of the Volumetrics Medical Imaging real-time 3D scanner were modified to support dual 2.5 MHz matrix arrays of 256 transmit elements and 128 receive elements which produce two simultaneous 64° pyramidal scans. The real-time display format consists of two coronal B-mode images merged into a 128° sector, two simultaneous parasagittal images merged into a 128° × 64° C-mode plane, and a simultaneous 64° axial image. Real-time 3D color Doppler images acquired in initial clinical studies after contrast injection demonstrate flow in several representative blood vessels. An offline Doppler rendering of data from two transducers simultaneously scanning via the temporal windows provides an early visualization of the flow in vessels on both sides of the brain. The long-term goal is to produce real-time 3D ultrasound images of the cerebral vasculature from a portable unit capable of internet transmission, thus enabling interactive 3D imaging, remote diagnosis and earlier therapeutic intervention. We are motivated by the urgency for rapid diagnosis of stroke due to the short time window of effective therapeutic intervention.

  20. Tracking brain arousal fluctuations with fMRI

    PubMed Central

    Chang, Catie; Leopold, David A.; Schölvinck, Marieke Louise; Mandelkow, Hendrik; Picchioni, Dante; Liu, Xiao; Ye, Frank Q.; Turchi, Janita N.; Duyn, Jeff H.

    2016-01-01

    Changes in brain activity accompanying shifts in vigilance and arousal can interfere with the study of other intrinsic and task-evoked characteristics of brain function. However, the difficulty of tracking and modeling the arousal state during functional MRI (fMRI) typically precludes the assessment of arousal-dependent influences on fMRI signals. Here we combine fMRI, electrophysiology, and the monitoring of eyelid behavior to demonstrate an approach for tracking continuous variations in arousal level from fMRI data. We first characterize the spatial distribution of fMRI signal fluctuations that track a measure of behavioral arousal; taking this pattern as a template, and using the local field potential as a simultaneous and independent measure of cortical activity, we observe that the time-varying expression level of this template in fMRI data provides a close approximation of electrophysiological arousal. We discuss the potential benefit of these findings for increasing the sensitivity of fMRI as a cognitive and clinical biomarker. PMID:27051064

  1. MRI-detectable changes in mouse brain structure induced by voluntary exercise.

    PubMed

    Cahill, Lindsay S; Steadman, Patrick E; Jones, Carly E; Laliberté, Christine L; Dazai, Jun; Lerch, Jason P; Stefanovic, Bojana; Sled, John G

    2015-06-01

    Physical exercise, besides improving cognitive and mental health, is known to cause structural changes in the brain. Understanding the structural changes that occur with exercise as well as the neuroanatomical correlates of a predisposition for exercise is important for understanding human health. This study used high-resolution 3D MR imaging, in combination with deformation-based morphometry, to investigate the macroscopic changes in brain structure that occur in healthy adult mice following four weeks of voluntary exercise. We found that exercise induced changes in multiple brain structures that are involved in motor function and learning and memory including the hippocampus, dentate gyrus, stratum granulosum of the dentate gyrus, cingulate cortex, olivary complex, inferior cerebellar peduncle and regions of the cerebellum. In addition, a number of brain structures, including the hippocampus, striatum and pons, when measured on MRI prior to the start of exercise were highly predictive of subsequent exercise activity. Exercise tended to normalize these pre-existing differences between mice.

  2. Use of High Resolution 3D Diffusion Tensor Imaging to Study Brain White Matter Development in Live Neonatal Rats

    PubMed Central

    Cai, Yu; McMurray, Matthew S.; Oguz, Ipek; Yuan, Hong; Styner, Martin A.; Lin, Weili; Johns, Josephine M.; An, Hongyu

    2011-01-01

    High resolution diffusion tensor imaging (DTI) can provide important information on brain development, yet it is challenging in live neonatal rats due to the small size of neonatal brain and motion-sensitive nature of DTI. Imaging in live neonatal rats has clear advantages over fixed brain scans, as longitudinal and functional studies would be feasible to understand neuro-developmental abnormalities. In this study, we developed imaging strategies that can be used to obtain high resolution 3D DTI images in live neonatal rats at postnatal day 5 (PND5) and PND14, using only 3 h of imaging acquisition time. An optimized 3D DTI pulse sequence and appropriate animal setup to minimize physiological motion artifacts are the keys to successful high resolution 3D DTI imaging. Thus, a 3D rapid acquisition relaxation enhancement DTI sequence with twin navigator echoes was implemented to accelerate imaging acquisition time and minimize motion artifacts. It has been suggested that neonatal mammals possess a unique ability to tolerate mild-to-moderate hypothermia and hypoxia without long term impact. Thus, we additionally utilized this ability to minimize motion artifacts in magnetic resonance images by carefully suppressing the respiratory rate to around 15/min for PND5 and 30/min for PND14 using mild-to-moderate hypothermia. These imaging strategies have been successfully implemented to study how the effect of cocaine exposure in dams might affect brain development in their rat pups. Image quality resulting from this in vivo DTI study was comparable to ex vivo scans. fractional anisotropy values were also similar between the live and fixed brain scans. The capability of acquiring high quality in vivo DTI imaging offers a valuable opportunity to study many neurological disorders in brain development in an authentic living environment. PMID:22013426

  3. A multiscale approach for the reconstruction of the fiber architecture of the human brain based on 3D-PLI

    PubMed Central

    Reckfort, Julia; Wiese, Hendrik; Pietrzyk, Uwe; Zilles, Karl; Amunts, Katrin; Axer, Markus

    2015-01-01

    Structural connectivity of the brain can be conceptionalized as a multiscale organization. The present study is built on 3D-Polarized Light Imaging (3D-PLI), a neuroimaging technique targeting the reconstruction of nerve fiber orientations and therefore contributing to the analysis of brain connectivity. Spatial orientations of the fibers are derived from birefringence measurements of unstained histological sections that are interpreted by means of a voxel-based analysis. This implies that a single fiber orientation vector is obtained for each voxel, which reflects the net effect of all comprised fibers. We have utilized two polarimetric setups providing an object space resolution of 1.3 μm/px (microscopic setup) and 64 μm/px (macroscopic setup) to carry out 3D-PLI and retrieve fiber orientations of the same tissue samples, but at complementary voxel sizes (i.e., scales). The present study identifies the main sources which cause a discrepancy of the measured fiber orientations observed when measuring the same sample with the two polarimetric systems. As such sources the differing optical resolutions and diverging retardances of the implemented waveplates were identified. A methodology was implemented that enables the compensation of measured different systems' responses to the same birefringent sample. This opens up new ways to conduct multiscale analysis in brains by means of 3D-PLI and to provide a reliable basis for the transition between different scales of the nerve fiber architecture. PMID:26388744

  4. Magnetic Resonance Imaging (MRI): Brain (For Parents)

    MedlinePlus

    ... cause a problem near a strong magnetic field. Electronic devices aren't permitted in the MRI room. ... child may be given headphones to listen to music or earplugs to block the noise, and will ...

  5. Technical Note: Immunohistochemical evaluation of mouse brain irradiation targeting accuracy with 3D-printed immobilization device

    SciTech Connect

    Zarghami, Niloufar Jensen, Michael D.; Talluri, Srikanth; Dick, Frederick A.; Foster, Paula J.; Chambers, Ann F.; Wong, Eugene

    2015-11-15

    Purpose: Small animal immobilization devices facilitate positioning of animals for reproducible imaging and accurate focal radiation therapy. In this study, the authors demonstrate the use of three-dimensional (3D) printing technology to fabricate a custom-designed mouse head restraint. The authors evaluate the accuracy of this device for the purpose of mouse brain irradiation. Methods: A mouse head holder was designed for a microCT couch using CAD software and printed in an acrylic based material. Ten mice received half-brain radiation while positioned in the 3D-printed head holder. Animal placement was achieved using on-board image guidance and computerized asymmetric collimators. To evaluate the precision of beam localization for half-brain irradiation, mice were sacrificed approximately 30 min after treatment and brain sections were stained for γ-H2AX, a marker for DNA breaks. The distance and angle of the γ-H2AX radiation beam border to longitudinal fissure were measured on histological samples. Animals were monitored for any possible trauma from the device. Results: Visualization of the radiation beam on ex vivo brain sections with γ-H2AX immunohistochemical staining showed a sharp radiation field within the tissue. Measurements showed a mean irradiation targeting error of 0.14 ± 0.09 mm (standard deviation). Rotation between the beam axis and mouse head was 1.2° ± 1.0° (standard deviation). The immobilization device was easily adjusted to accommodate different sizes of mice. No signs of trauma to the mice were observed from the use of tooth block and ear bars. Conclusions: The authors designed and built a novel 3D-printed mouse head holder with many desired features for accurate and reproducible radiation targeting. The 3D printing technology was found to be practical and economical for producing a small animal imaging and radiation restraint device and allows for customization for study specific needs.

  6. A hybrid approach for fusing 4D-MRI temporal information with 3D-CT for the study of lung and lung tumor motion

    SciTech Connect

    Yang, Y. X.; Van Reeth, E.; Poh, C. L.; Teo, S.-K.; Tan, C. H.; Tham, I. W. K.

    2015-08-15

    Purpose: Accurate visualization of lung motion is important in many clinical applications, such as radiotherapy of lung cancer. Advancement in imaging modalities [e.g., computed tomography (CT) and MRI] has allowed dynamic imaging of lung and lung tumor motion. However, each imaging modality has its advantages and disadvantages. The study presented in this paper aims at generating synthetic 4D-CT dataset for lung cancer patients by combining both continuous three-dimensional (3D) motion captured by 4D-MRI and the high spatial resolution captured by CT using the authors’ proposed approach. Methods: A novel hybrid approach based on deformable image registration (DIR) and finite element method simulation was developed to fuse a static 3D-CT volume (acquired under breath-hold) and the 3D motion information extracted from 4D-MRI dataset, creating a synthetic 4D-CT dataset. Results: The study focuses on imaging of lung and lung tumor. Comparing the synthetic 4D-CT dataset with the acquired 4D-CT dataset of six lung cancer patients based on 420 landmarks, accurate results (average error <2 mm) were achieved using the authors’ proposed approach. Their hybrid approach achieved a 40% error reduction (based on landmarks assessment) over using only DIR techniques. Conclusions: The synthetic 4D-CT dataset generated has high spatial resolution, has excellent lung details, and is able to show movement of lung and lung tumor over multiple breathing cycles.

  7. Automatic MRI 2D brain segmentation using graph searching technique.

    PubMed

    Pedoia, Valentina; Binaghi, Elisabetta

    2013-09-01

    Accurate and efficient segmentation of the whole brain in magnetic resonance (MR) images is a key task in many neuroscience and medical studies either because the whole brain is the final anatomical structure of interest or because the automatic extraction facilitates further analysis. The problem of segmenting brain MRI images has been extensively addressed by many researchers. Despite the relevant achievements obtained, automated segmentation of brain MRI imagery is still a challenging problem whose solution has to cope with critical aspects such as anatomical variability and pathological deformation. In the present paper, we describe and experimentally evaluate a method for segmenting brain from MRI images basing on two-dimensional graph searching principles for border detection. The segmentation of the whole brain over the entire volume is accomplished slice by slice, automatically detecting frames including eyes. The method is fully automatic and easily reproducible by computing the internal main parameters directly from the image data. The segmentation procedure is conceived as a tool of general applicability, although design requirements are especially commensurate with the accuracy required in clinical tasks such as surgical planning and post-surgical assessment. Several experiments were performed to assess the performance of the algorithm on a varied set of MRI images obtaining good results in terms of accuracy and stability.

  8. MRI Evaluation and Safety in the Developing Brain

    PubMed Central

    Tocchio, Shannon; Kline-Fath, Beth; Kanal, Emanuel; Schmithorst, Vincent J.; Panigrahy, Ashok

    2015-01-01

    Magnetic resonance imaging (MRI) evaluation of the developing brain has dramatically increased over the last decade. Faster acquisitions and the development of advanced MRI sequences such as magnetic resonance spectroscopy (MRS), diffusion tensor imaging (DTI), perfusion imaging, functional MR imaging (fMRI), and susceptibility weighted imaging (SWI), as well as the use of higher magnetic field strengths has made MRI an invaluable tool for detailed evaluation of the developing brain. This article will provide an overview of the use and challenges associated with 1.5T and 3T static magnetic fields for evaluation of the developing brain. This review will also summarize the advantages, clinical challenges and safety concerns specifically related to MRI in the fetus and newborn, including the implications of increased magnetic field strength, logistics related to transporting and monitoring of neonates during scanning, sedation considerations and a discussion of current technologies such as MRI-conditional neonatal incubators and dedicated small-foot print neonatal intensive care unit (NICU) scanners. PMID:25743582

  9. Leptomeningeal metastasis from gynecologic cancers diagnosed by brain MRI.

    PubMed

    Toyoshima, Masafumi; Tsuji, Keita; Shigeta, Shogo; Tokunaga, Hideki; Ito, Kiyoshi; Watanabe, Yoh; Yoshinaga, Kosuke; Otsuki, Takeo; Niikura, Hitoshi; Yaegashi, Nobuo

    Leptomeningeal metastasis (LM) is rarely observed in gynecologic cancers. As gadolinium-enhanced magnetic resonance imaging (Gd-MRI) is highly effective for diagnosing LM, the aim of this study is to describe the clinical behaviors and outcomes of LM patients who were diagnosed by Gd-MRI. After securing institutional review board approvals, we retrospectively reviewed patient records. Eight patients were found to have LM from gynecological malignancies. Primary tumors included three ovarian cancers, one tubal cancer, one peritoneal cancer, two endometrial cancers, and one cervical cancer. Gd-MRI of the brain and the spine is indicated as the high-priority inspection for the diagnosis of this devastating complication.

  10. Accuracy of UTE-MRI-based patient setup for brain cancer radiation therapy

    SciTech Connect

    Yang, Yingli; Cao, Minsong; Kaprealian, Tania; Sheng, Ke; Gao, Yu; Gomez, Caitlin; Santhanam, Anand; Tenn, Stephen; Agazaryan, Nzhde; Low, Daniel A.; Han, Fei; Hu, Peng

    2016-01-15

    Purpose: Radiation therapy simulations solely based on MRI have advantages compared to CT-based approaches. One feature readily available from computed tomography (CT) that would need to be reproduced with MR is the ability to compute digitally reconstructed radiographs (DRRs) for comparison against on-board radiographs commonly used for patient positioning. In this study, the authors generate MR-based bone images using a single ultrashort echo time (UTE) pulse sequence and quantify their 3D and 2D image registration accuracy to CT and radiographic images for treatments in the cranium. Methods: Seven brain cancer patients were scanned at 1.5 T using a radial UTE sequence. The sequence acquired two images at two different echo times. The two images were processed using an in-house software to generate the UTE bone images. The resultant bone images were rigidly registered to simulation CT data and the registration error was determined using manually annotated landmarks as references. DRRs were created based on UTE-MRI and registered to simulated on-board images (OBIs) and actual clinical 2D oblique images from ExacTrac™. Results: UTE-MRI resulted in well visualized cranial, facial, and vertebral bones that quantitatively matched the bones in the CT images with geometric measurement errors of less than 1 mm. The registration error between DRRs generated from 3D UTE-MRI and the simulated 2D OBIs or the clinical oblique x-ray images was also less than 1 mm for all patients. Conclusions: UTE-MRI-based DRRs appear to be promising for daily patient setup of brain cancer radiotherapy with kV on-board imaging.

  11. More IMPATIENT: A Gridding-Accelerated Toeplitz-based Strategy for Non-Cartesian High-Resolution 3D MRI on GPUs

    PubMed Central

    Gai, Jiading; Obeid, Nady; Holtrop, Joseph L.; Wu, Xiao-Long; Lam, Fan; Fu, Maojing; Haldar, Justin P.; Hwu, Wen-mei W.; Liang, Zhi-Pei; Sutton, Bradley P.

    2013-01-01

    Several recent methods have been proposed to obtain significant speed-ups in MRI image reconstruction by leveraging the computational power of GPUs. Previously, we implemented a GPU-based image reconstruction technique called the Illinois Massively Parallel Acquisition Toolkit for Image reconstruction with ENhanced Throughput in MRI (IMPATIENT MRI) for reconstructing data collected along arbitrary 3D trajectories. In this paper, we improve IMPATIENT by removing computational bottlenecks by using a gridding approach to accelerate the computation of various data structures needed by the previous routine. Further, we enhance the routine with capabilities for off-resonance correction and multi-sensor parallel imaging reconstruction. Through implementation of optimized gridding into our iterative reconstruction scheme, speed-ups of more than a factor of 200 are provided in the improved GPU implementation compared to the previous accelerated GPU code. PMID:23682203

  12. More IMPATIENT: A Gridding-Accelerated Toeplitz-based Strategy for Non-Cartesian High-Resolution 3D MRI on GPUs.

    PubMed

    Gai, Jiading; Obeid, Nady; Holtrop, Joseph L; Wu, Xiao-Long; Lam, Fan; Fu, Maojing; Haldar, Justin P; Hwu, Wen-Mei W; Liang, Zhi-Pei; Sutton, Bradley P

    2013-05-01

    Several recent methods have been proposed to obtain significant speed-ups in MRI image reconstruction by leveraging the computational power of GPUs. Previously, we implemented a GPU-based image reconstruction technique called the Illinois Massively Parallel Acquisition Toolkit for Image reconstruction with ENhanced Throughput in MRI (IMPATIENT MRI) for reconstructing data collected along arbitrary 3D trajectories. In this paper, we improve IMPATIENT by removing computational bottlenecks by using a gridding approach to accelerate the computation of various data structures needed by the previous routine. Further, we enhance the routine with capabilities for off-resonance correction and multi-sensor parallel imaging reconstruction. Through implementation of optimized gridding into our iterative reconstruction scheme, speed-ups of more than a factor of 200 are provided in the improved GPU implementation compared to the previous accelerated GPU code.

  13. In Vivo/Ex Vivo MRI-Based 3D Non-Newtonian FSI Models for Human Atherosclerotic Plaques Compared with Fluid/Wall-Only Models.

    PubMed

    Yang, Chun; Tang, Dalin; Yuan, Chun; Hatsukami, Thomas S; Zheng, Jie; Woodard, Pamela K

    2007-01-01

    It has been recognized that fluid-structure interactions (FSI) play an important role in cardiovascular disease initiation and development. However, in vivo MRI multi-component FSI models for human carotid atherosclerotic plaques with bifurcation and quantitative comparisons of FSI models with fluid-only or structure-only models are currently lacking in the literature. A 3D non-Newtonian multi-component FSI model based on in vivo/ex vivo MRI images for human atherosclerotic plaques was introduced to investigate flow and plaque stress/strain behaviors which may be related to plaque progression and rupture. Both artery wall and plaque components were assumed to be hyperelastic, isotropic, incompressible and homogeneous. Blood flow was assumed to be laminar, non-Newtonian, viscous and incompressible. In vivo/ex vivo MRI images were acquired using histologically-validated multi-spectral MRI protocols. The 3D FSI models were solved and results were compared with those from a Newtonian FSI model and wall-only/fluid-only models. A 145% difference in maximum principal stresses (Stress-P(1)) between the FSI and wall-only models and 40% difference in flow maximum shear stress (MSS) between the FSI and fluid-only models were found at the throat of the plaque using a severe plaque sample (70% severity by diameter). Flow maximum shear stress (MSS) from the rigid wall model is much higher (20-40% in maximum MSS values, 100-150% in stagnation region) than those from FSI models.

  14. Computer-aided diagnosis of mass-like lesion in breast MRI: differential analysis of the 3-D morphology between benign and malignant tumors.

    PubMed

    Huang, Yan-Hao; Chang, Yeun-Chung; Huang, Chiun-Sheng; Wu, Tsung-Ju; Chen, Jeon-Hor; Chang, Ruey-Feng

    2013-12-01

    This study aimed to evaluate the value of using 3-D breast MRI morphologic features to differentiate benign and malignant breast lesions. The 3-D morphological features extracted from breast MRI were used to analyze the malignant likelihood of tumor from ninety-five solid breast masses (44 benign and 51 malignant) of 82 patients. Each mass-like lesion was examined with regards to three categories of morphologic features, including texture-based gray-level co-occurrence matrix (GLCM) feature, shape, and ellipsoid fitting features. For obtaining a robust combination of features from different categories, the biserial correlation coefficient (|r(pb)|)≧0.4 was used as the feature selection criterion. Receiver operating characteristic (ROC) curve was used to evaluate performance and Student's t-test to verify the classification accuracy. The combination of the selected 3-D morphological features, including conventional compactness, radius, spiculation, surface ratio, volume covering ratio, number of inside angular regions, sum of number of inside and outside angular regions, showed an accuracy of 88.42% (84/95), sensitivity of 88.24% (45/51), and specificity of 88.64% (39/44), respectively. The AZ value was 0.8926 for these seven combined morphological features. In conclusion, 3-D MR morphological features specified by GLCM, tumor shape and ellipsoid fitting were useful for differentiating benign and malignant breast masses.

  15. Time efficiency and diagnostic agreement of 2-D versus 3-D ultrasound acquisition of the neonatal brain.

    PubMed

    Romero, Javier M; Madan, Neil; Betancur, Ilda; Ciobanu, Adrian; Murphy, Erin; McCullough, Danielle; Grant, P Ellen

    2014-08-01

    The purpose of this study was to compare acquisition time efficiency and diagnostic agreement of neonatal brain ultrasound (US) scans obtained with a 3-D volume US acquisition protocol and the conventional 2-D acquisition protocol. Ninety-one consecutive premature neonatal brain ultrasound scans were prospectively performed on 59 neonates with the conventional 2-D acquisition protocol. Immediately after the 2-D study, a coronal 3-D ultrasound volume was acquired and later reconstructed into axial and sagittal planes. All 59 neonates were imaged in the neonatal intensive care unit to rule out intracranial hemorrhage. Total time for 2-D and 3-D acquisition protocols was recorded, and a two-tailed t-test was used to determine if study durations differed significantly. One pediatric neuroradiologist reviewed the reformatted 3-D images, tomographic ultrasound images. Results were compared with the clinical interpretation of the 2-D conventional study. The mean scanning time for the 2-D US acquisition protocol was 10.56 min (standard deviation [SD] = 7.11), and that for the 3-D volume US acquisition protocol was 1.48 min (SD = 0.59) (p ≤ 0.001). Inter-observer agreement revealed k values of 0.84 for hydrocephalus, 0.80 for germinal matrix hemorrhage/intraventricular hemorrhage, 0.74 for periventricular leukomalacia and 0.91 for subdural collection, hence near-perfect to substantial agreement between imaging protocols. There was a significant decrease in acquisition time for the 3-D volume ultrasound acquisition protocol compared with the conventional 2-D US protocol (p = <0.001), without compromising the diagnostic quality compared with a conventional 2-D US imaging protocol.

  16. 3D watershed-based segmentation of internal structures within MR brain images

    NASA Astrophysics Data System (ADS)

    Bueno, Gloria; Musse, Olivier; Heitz, Fabrice; Armspach, Jean-Paul

    2000-06-01

    In this paper an image-based method founded on mathematical morphology is presented in order to facilitate the segmentation of cerebral structures on 3D magnetic resonance images (MRIs). The segmentation is described as an immersion simulation, applied to the modified gradient image, modeled by a generated 3D region adjacency graph (RAG). The segmentation relies on two main processes: homotopy modification and contour decision. The first one is achieved by a marker extraction stage where homogeneous 3D regions are identified in order to attribute an influence zone only to relevant minima of the image. This stage uses contrasted regions from morphological reconstruction and labeled flat regions constrained by the RAG. The goal of the decision stage is to precisely locate the contours of regions detected by the marker extraction. This decision is performed by a 3D extension of the watershed transform. Upon completion of the segmentation, the outcome of the preceding process is presented to the user for manual selection of the structures of interest (SOI). Results of this approach are described and illustrated with examples of segmented 3D MRIs of the human head.

  17. The Relationship of 3D Human Skull Motion to Brain Tissue Deformation in Magnetic Resonance Elastography Studies.

    PubMed

    Badachhape, Andrew A; Okamoto, Ruth J; Durham, Ramona S; Efron, Brent D; Nadell, Sam J; Johnson, Curtis L; Bayly, Philip V

    2017-03-07

    In traumatic brain injury (TBI), membranes such as the dura mater, arachnoid mater, and pia mater play a vital role in transmitting motion from the skull to brain tissue. Magnetic Resonance Elastography (MRE) is an imaging technique developed for non-invasive estimation of soft tissue material parameters. In MRE, dynamic deformation of brain tissue is induced by skull vibrations; however skull motion and its mode of transmission to the brain remain largely uncharacterized. In this study, displacements of points in the skull, reconstructed using data from an array of MRI-safe accelerometers, were compared to displacements of neighboring material points in brain tissue, estimated from MRE measurements. Comparison of the relative amplitudes, directions, and temporal phases of harmonic motion in the skulls and brains of six human subjects shows that the skull-brain interface significantly attenuates and delays transmission of motion from skull to brain. In contrast, in a cylindrical gelatin "phantom", displacements of the rigid case (reconstructed from accelerometer data) were transmitted to the gelatin inside (estimated from MRE data) with little attenuation or phase lag. This quantitative characterization of the skull-brain interface will be valuable in the parameterization and validation of computer models of TBI.

  18. Optimization of PET activation studies based on the SNR measured in the 3-D Hoffman brain phantom.

    PubMed

    Li, H H; Votaw, J R

    1998-08-01

    This work investigates the noise properties of O-15 water PET images in an attempt to increase the sensitivity of activation studies. A method for computing the amount of noise within a region of interest (ROI) from the uncertainty in the raw data was implemented for three-dimensional (3-D) positron emission tomography (PET). The method was used to study the signal-to-noise ratio (SNR) of regions-of-interest (ROI's) inside a 3-D Hoffman brain phantom. Saturation occurs at an activity concentration of 2.2 mCi/l which corresponds to a 75-mCi O-15 water injection into a normal person of average weight. This establishes the upper limit for injections for human brain studies using 3-D PET on the Siemens ECAT 921 EXACT scanner. Data from human brain activation studies on four normal volunteers using two-dimensional (2-D) PET were analyzed. The biological variation was found to be 5% in 1-ml ROI's. The variance for a complete activation study was calculated, for a variety of protocols, by combining the Poisson noise propagated from the raw data in the phantom experiments with the biological variation. A protocol that is predicted to maximize the SNR in dual-condition activation experiments while remaining below the radiation safety limit is: ten scans with 45 mCi per injection. The data should not be corrected for random or scatter events since they do not help in the identification of activation sites while they do add noise to the image. Due to the lower noise level of 3-D PET, the threshold for detecting a true change in activity concentration is 10%-20% lower than 2-D PET. Because of this, a 3-D activation experiment using the Siemens 921 scanner requires fewer subjects for equal statistical power.

  19. MRI virtual biopsy and treatment of brain metastatic tumors with targeted nanobioconjugates: nanoclinic in the brain.

    PubMed

    Patil, Rameshwar; Ljubimov, Alexander V; Gangalum, Pallavi R; Ding, Hui; Portilla-Arias, Jose; Wagner, Shawn; Inoue, Satoshi; Konda, Bindu; Rekechenetskiy, Arthur; Chesnokova, Alexandra; Markman, Janet L; Ljubimov, Vladimir A; Li, Debiao; Prasad, Ravi S; Black, Keith L; Holler, Eggehard; Ljubimova, Julia Y

    2015-05-26

    Differential diagnosis of brain magnetic resonance imaging (MRI) enhancement(s) remains a significant problem, which may be difficult to resolve without biopsy, which can be often dangerous or even impossible. Such MRI enhancement(s) can result from metastasis of primary tumors such as lung or breast, radiation necrosis, infections, or a new primary brain tumor (glioma, meningioma). Neurological symptoms are often the same on initial presentation. To develop a more precise noninvasive MRI diagnostic method, we have engineered a new class of poly(β-l-malic acid) polymeric nanoimaging agents (NIAs). The NIAs carrying attached MRI tracer are able to pass through the blood-brain barrier (BBB) and specifically target cancer cells for efficient imaging. A qualitative/quantitative "MRI virtual biopsy" method is based on a nanoconjugate carrying MRI contrast agent gadolinium-DOTA and antibodies recognizing tumor-specific markers and extravasating through the BBB. In newly developed double tumor xenogeneic mouse models of brain metastasis this noninvasive method allowed differential diagnosis of HER2- and EGFR-expressing brain tumors. After MRI diagnosis, breast and lung cancer brain metastases were successfully treated with similar tumor-targeted nanoconjugates carrying molecular inhibitors of EGFR or HER2 instead of imaging contrast agent. The treatment resulted in a significant increase in animal survival and markedly reduced immunostaining for several cancer stem cell markers. Novel NIAs could be useful for brain diagnostic MRI in the clinic without currently performed brain biopsies. This technology shows promise for differential MRI diagnosis and treatment of brain metastases and other pathologies when biopsies are difficult to perform.

  20. 3D ultrasound in assessment of growth and development of frontal lobes in children with perinatal brain injury.

    PubMed

    Liu, Yunfeng; Zhou, Congle; Wang, Hongmei; Tang, Zezhong; Ding, Haiyan

    2009-01-01

    To investigate the functions of cranial 3D ultrasound in the assessment of growth and development of the volume of frontal lobes in children with perinatal brain injury, 226 neonates of different gestational ages and 86 full term with perinatal brain injury were selected as subjects. The volume of frontal lobe of neonate increased with gestational age within 7 days after birth (r=0.676, P<0.05). The volume of frontal lobe in the 33 children with serious brain injury was lower than that in the control group at 1 month and the difference was significant at 3 and 6 months (P<0.01). There was a correlation between the long-term nervous system dysplasia and the slow increase of frontal lobe volume. The volume of frontal lobe increases with gestational age. The brain injury during the perinatal period affects the development of frontal lobe and is related with neural dysplasia. 3D ultrasound is useful for evaluating the normal and abnormal brain development.

  1. Comparing 3D Gyrification Index and area-independent curvature-based measures in quantifying neonatal brain folding

    NASA Astrophysics Data System (ADS)

    Rodriguez-Carranza, Claudia E.; Mukherjee, P.; Vigneron, Daniel; Barkovich, James; Studholme, Colin

    2007-03-01

    In this work we compare 3D Gyrification Index and our recently proposed area-independent curvature-based surface measures [26] for the in-vivo quantification of brain surface folding in clinically acquired neonatal MR image data. A meaningful comparison of gyrification across brains of different sizes and their subregions will only be possible through the quantification of folding with measures that are independent of the area of the region of analysis. This work uses a 3D implementation of the classical Gyrification Index, a 2D measure that quantifies folding based on the ratio of the inner and outer contours of the brain and which has been used to study gyral patterns in adults with schizophrenia, among other conditions. The new surface curvature-based measures and the 3D Gyrification Index were calculated on twelve premature infants (age 28-37 weeks) from which surfaces of cerebrospinal fluid/gray matter (CSF/GM) interface and gray matter/white matter (GM/WM) interface were extracted. Experimental results show that our measures better quantify folding on the CSF/GM interface than Gyrification Index, and perform similarly on the GM/WM interface.

  2. [Clinical features of NMO according to brain MRI findings].

    PubMed

    Shimizu, Yuko

    2010-09-01

    Neuromyelitis optica (NMO) is a severe inflammatory, demyelinating disease, and its clinical characteristics include recurrent optic neuritis and longitudinally extensive transverse myelitis. The NMO-immunoglobulin (Ig) G auto-antibody (Ab), which binds to the aquaporin-4 (AQP4) water channel protein, is a marker for NMO. These clinical and immunological features have been used to distinguish NMO from multiple sclerosis (MS). In 1999, Wingerchuk et al. broadened the clinical criteria for diagnosing NMO to include "negative brain magnetic resonance imaging (MRI) at onset." However, after NMO-IgG/AQP4-Ab became a supportive criterion for diagnosing NMO, patients with NMO were frequently found to have symptomatic or asymptomatic brain lesions. In 2006, Pittock et al. reported that asymptomatic brain lesions were common in NMO, and that NMO brain lesions characteristically occurred in the hypothalamus and periventricular areas, which correspond to brain regions with high levels of AQP4 expression. Furthermore, Nakashima et al. detected abnormalities on brain MRI in 71% of NMO-IgG-positive Japanese patients. Patients with NMO have unique brain lesions that are clearly different from the lesions of patients with MS. In patients with NMO, involvement of the dorsal portion of the medulla oblongata causes intractable hiccups and nausea. Some studies described a hypothalamic lesion, and hypothalamic dysfunction could cause symptomatic hypersomnia, narcolepsy, and endocrinopathies. In some patients with NMO and NMO spectrum disorder who experience blood pressure fluctuations, vasogenic edema, manifesting as posterior reversible encephalopathy syndrome, may occur. In a recent report highlighting brain MRI with contrast enhancement, the most prominent feature that appeared to be a specific finding in NMO was "cloud-like enhancement" with multiple patchy enhancing lesions with a blurred margin. Another report showed that acute, large, edematous callosal lesions with

  3. Head MRI

    MedlinePlus

    ... the head; MRI - cranial; NMR - cranial; Cranial MRI; Brain MRI; MRI - brain; MRI - head ... the test, tell your provider if you have: Brain aneurysm clips An artificial heart valves Heart defibrillator ...

  4. Spatial correspondence of brain alpha activity component in fMRI and EEG

    NASA Astrophysics Data System (ADS)

    Jeong, Jeong-Won; Kim, Sung-Heon; Singh, Manbir

    2005-04-01

    This paper presents a new approach to investigate the spatial correlation of brain alpha activity in functional magnetic resonance imaging (fMRI) and electroencephalography (EEG). To avoid potential problems of simultaneous fMRI and EEG acquisitions in imaging brain alpha activity, data from each modality were acquired separately under a "three conditions" setup where one of the conditions involved closing eyes and relaxing, thus making it conducive to generation of alpha activity. The other two conditions -- eyes open in a lighted room or engaged in a mental arithmetic task, were designed to attenuate alpha activity. Using the Mixture Density Independent Component Analysis (MD-ICA) that incorporates flexible non-linearity functions into the conventional ICA framework, we could identify the spatiotemporal components of fMRI activations and EEG activities associated with the alpha rhythm. The sources of the individual EEG alpha activity component were localized by a Maximum Entropy (ME) method that solves an inverse problem in the framework of a classical four-sphere head model. The resulting dipole sources of EEG alpha activity were spatially transformed to 3D MRIs of the subject and compared to fMRI ICA-determined alpha activity maps.

  5. [Brain development of infant and MRI by diffusion tensor imaging].

    PubMed

    Dubois, J; Dehaene-Lambertz, G; Mangin, J-F; Le Bihan, D; Hüppi, P S; Hertz-Pannier, L

    2012-01-01

    Studying how the brain develops and becomes functional is important to understand how the man has been able to develop specific cognitive abilities, and to comprehend the complexity of some developmental pathologies. Thanks to magnetic resonance imaging (MRI), it is now possible to image the baby's immature brain and to consider subtle correlations between the brain anatomical development and the early acquisition of cognitive functions. Dedicated methodologies for image acquisition and post-treatment must then be used because the size of cerebral structures and the image contrast are very different in comparison with the adult brain, and because the examination length is a major constraint. Two recent studies have evaluated the developing brain under an original perspective. The first one has focused on cortical folding in preterm newborns, from 6 to 8 months of gestational age, assessed with T2-weighted conventional MRI. The second study has mapped the organization and maturation of white matter fiber bundles in 1- to 4-month-old healthy infants with diffusion tensor imaging (DTI). Both studies have enabled to highlight spatio-temporal differences in the brain regions' maturation, as well as early anatomical asymmetries between cerebral hemispheres. These studies emphasize the potential of MRI to evaluate brain development compared with the infant's psychomotor acquisitions after birth.

  6. Joint brain connectivity estimation from diffusion and functional MRI data

    NASA Astrophysics Data System (ADS)

    Chu, Shu-Hsien; Lenglet, Christophe; Parhi, Keshab K.

    2015-03-01

    Estimating brain wiring patterns is critical to better understand the brain organization and function. Anatomical brain connectivity models axonal pathways, while the functional brain connectivity characterizes the statistical dependencies and correlation between the activities of various brain regions. The synchronization of brain activity can be inferred through the variation of blood-oxygen-level dependent (BOLD) signal from functional MRI (fMRI) and the neural connections can be estimated using tractography from diffusion MRI (dMRI). Functional connections between brain regions are supported by anatomical connections, and the synchronization of brain activities arises through sharing of information in the form of electro-chemical signals on axon pathways. Jointly modeling fMRI and dMRI data may improve the accuracy in constructing anatomical connectivity as well as functional connectivity. Such an approach may lead to novel multimodal biomarkers potentially able to better capture functional and anatomical connectivity variations. We present a novel brain network model which jointly models the dMRI and fMRI data to improve the anatomical connectivity estimation and extract the anatomical subnetworks associated with specific functional modes by constraining the anatomical connections as structural supports to the functional connections. The key idea is similar to a multi-commodity flow optimization problem that minimizes the cost or maximizes the efficiency for flow configuration and simultaneously fulfills the supply-demand constraint for each commodity. In the proposed network, the nodes represent the grey matter (GM) regions providing brain functionality, and the links represent white matter (WM) fiber bundles connecting those regions and delivering information. The commodities can be thought of as the information corresponding to brain activity patterns as obtained for instance by independent component analysis (ICA) of fMRI data. The concept of information

  7. Prediction of standard-dose brain PET image by using MRI and low-dose brain [{sup 18}F]FDG PET images

    SciTech Connect

    Kang, Jiayin; Gao, Yaozong; Shi, Feng; Lalush, David S.; Lin, Weili; Shen, Dinggang

    2015-09-15

    Purpose: Positron emission tomography (PET) is a nuclear medical imaging technology that produces 3D images reflecting tissue metabolic activity in human body. PET has been widely used in various clinical applications, such as in diagnosis of brain disorders. High-quality PET images play an essential role in diagnosing brain diseases/disorders. In practice, in order to obtain high-quality PET images, a standard-dose radionuclide (tracer) needs to be used and injected into a living body. As a result, it will inevitably increase the patient’s exposure to radiation. One solution to solve this problem is predicting standard-dose PET images using low-dose PET images. As yet, no previous studies with this approach have been reported. Accordingly, in this paper, the authors propose a regression forest based framework for predicting a standard-dose brain [{sup 18}F]FDG PET image by using a low-dose brain [{sup 18}F]FDG PET image and its corresponding magnetic resonance imaging (MRI) image. Methods: The authors employ a regression forest for predicting the standard-dose brain [{sup 18}F]FDG PET image by low-dose brain [{sup 18}F]FDG PET and MRI images. Specifically, the proposed method consists of two main steps. First, based on the segmented brain tissues (i.e., cerebrospinal fluid, gray matter, and white matter) in the MRI image, the authors extract features for each patch in the brain image from both low-dose PET and MRI images to build tissue-specific models that can be used to initially predict standard-dose brain [{sup 18}F]FDG PET images. Second, an iterative refinement strategy, via estimating the predicted image difference, is used to further improve the prediction accuracy. Results: The authors evaluated their algorithm on a brain dataset, consisting of 11 subjects with MRI, low-dose PET, and standard-dose PET images, using leave-one-out cross-validations. The proposed algorithm gives promising results with well-estimated standard-dose brain [{sup 18}F]FDG PET

  8. Diffusion MRI at 25: Exploring brain tissue structure and function

    PubMed Central

    Bihan, Denis Le; Johansen-Berg, Heidi

    2013-01-01

    Diffusion MRI (or dMRI) came into existence in the mid-1980s. During the last 25 years, diffusion MRI has been extraordinarily successful (with more than 300,000 entries on Google Scholar for diffusion MRI). Its main clinical domain of application has been neurological disorders, especially for the management of patients with acute stroke. It is also rapidly becoming a standard for white matter disorders, as diffusion tensor imaging (DTI) can reveal abnormalities in white matter fiber structure and provide outstanding maps of brain connectivity. The ability to visualize anatomical connections between different parts of the brain, non-invasively and on an individual basis, has emerged as a major breakthrough for neurosciences. The driving force of dMRI is to monitor microscopic, natural displacements of water molecules that occur in brain tissues as part of the physical diffusion process. Water molecules are thus used as a probe that can reveal microscopic details about tissue architecture, either normal or in a diseased state. PMID:22120012

  9. Virtual Brain Bank a public collection of classified head MRI

    NASA Astrophysics Data System (ADS)

    Barrios, Fernando A.

    2000-10-01

    In this work I present the effort at the Neurobiology Center for creating a digital Brain Bank, a collection of well classified human brains that are used for teaching and research, this bank will be based in a collection of high resolution three dimensional head MRI. For this reason this bank is being named "virtual" and eventually will be of public access though a WEB page in the INTERNET.

  10. Monitoring of brain potassium with rubidium flame photometry and MRI.

    PubMed

    Yushmanov, Victor E; Kharlamov, Alexander; Boada, Fernando E; Jones, Stephen C

    2007-03-01

    An animal model was developed to monitor [K(+)] in the brain using partial K(+) replacement with Rb(+) and (87)Rb MRI. Fifty-one rats were given 0-80 mM of RbCl in the drinking water for up to 90 days. Focal cerebral ischemia was produced in 15 of the animals. Na, K, and Rb content in precision-guided submilligram samples of cortical brain were determined by emission flame photometry. Multinuclear (87)Rb/(23)Na/(1)H MRI was performed on phantoms and rats at 3T using a twisted projection imaging (TPI) scheme for (87)Rb/(23)Na, and custom-built surface or parallel cosine transmit/receive coils. Brain [Rb(+)] was safely brought up to 17-25 mEq/kg within 2-3 weeks of feeding. The characteristic patterns of [K(+)] decrease (with a sharp drop at 3-4 hr of ischemia) and [Na(+)] increase (at a rate of 31%/hr) observed previously in animals without Rb/K substitution were reproduced in ischemic cortex. The Rb/(Rb+K) ratio increased over time in ischemic areas (R = 0.91, P < 0.001), suggesting an additional index of ischemia progression. Preliminary (87)Rb MRI gave an estimate of 20-25 mEq Rb/kg brain weight (N = 2). In conclusion, brain Rb(+) is detectable by (87)Rb MRI and does not significantly interfere with ion dynamics in ischemic brain, which enables (87)Rb MRI studies of K(+) in ischemia.

  11. Diagnostic performance of 3D TSE MRI versus 2D TSE MRI of the knee at 1.5 T, with prompt arthroscopic correlation, in the detection of meniscal and cruciate ligament tears*

    PubMed Central

    Chagas-Neto, Francisco Abaeté; Nogueira-Barbosa, Marcello Henrique; Lorenzato, Mário Müller; Salim, Rodrigo; Kfuri-Junior, Maurício; Crema, Michel Daoud

    2016-01-01

    Objective To compare the diagnostic performance of the three-dimensional turbo spin-echo (3D TSE) magnetic resonance imaging (MRI) technique with the performance of the standard two-dimensional turbo spin-echo (2D TSE) protocol at 1.5 T, in the detection of meniscal and ligament tears. Materials and Methods Thirty-eight patients were imaged twice, first with a standard multiplanar 2D TSE MR technique, and then with a 3D TSE technique, both in the same 1.5 T MRI scanner. The patients underwent knee arthroscopy within the first three days after the MRI. Using arthroscopy as the reference standard, we determined the diagnostic performance and agreement. Results For detecting anterior cruciate ligament tears, the 3D TSE and routine 2D TSE techniques showed similar values for sensitivity (93% and 93%, respectively) and specificity (80% and 85%, respectively). For detecting medial meniscal tears, the two techniques also had similar sensitivity (85% and 83%, respectively) and specificity (68% and 71%, respectively). In addition, for detecting lateral meniscal tears, the two techniques had similar sensitivity (58% and 54%, respectively) and specificity (82% and 92%, respectively). There was a substantial to almost perfect intraobserver and interobserver agreement when comparing the readings for both techniques. Conclusion The 3D TSE technique has a diagnostic performance similar to that of the routine 2D TSE protocol for detecting meniscal and anterior cruciate ligament tears at 1.5 T, with the advantage of faster acquisition. PMID:27141127

  12. Volume estimation of brain abnormalities in MRI data

    NASA Astrophysics Data System (ADS)

    Suprijadi, Pratama, S. H.; Haryanto, F.

    2014-02-01

    The abnormality of brain tissue always becomes a crucial issue in medical field. This medical condition can be recognized through segmentation of certain region from medical images obtained from MRI dataset. Image processing is one of computational methods which very helpful to analyze the MRI data. In this study, combination of segmentation and rendering image were used to isolate tumor and stroke. Two methods of thresholding were employed to segment the abnormality occurrence, followed by filtering to reduce non-abnormality area. Each MRI image is labeled and then used for volume estimations of tumor and stroke-attacked area. The algorithms are shown to be successful in isolating tumor and stroke in MRI images, based on thresholding parameter and stated detection accuracy.

  13. 3D volume reconstruction of a mouse brain histological sections using warp filtering

    SciTech Connect

    Ju, Tao; Warren, Joe; Carson, James P.; Bello, Musodiq; Kakadiaris, Ioannis; Chiu, Wah; Thaller, Christina; Eichele, Gregor

    2006-09-30

    Sectioning tissues for optical microscopy often introduces upon the resulting sections distortions that make 3D reconstruction difficult. Here we present an automatic method for producing a smooth 3D volume from distorted 2D sections in the absence of any undistorted references. The method is based on pairwise elastic image warps between successive tissue sections, which can be computed by 2D image registration. Using a Gaussian filter, an average warp is computed for each section from the pairwise warps in a group of its neighboring sections. The average warps deform each section to match its neighboring sections, thus creating a smooth volume where corresponding features on successive sections lie close to each other. The proposed method can be used with any existing 2D image registration method for 3D reconstruction. In particular, we present a novel image warping algorithm based on dynamic programming that extends Dynamic Time Warping in 1D speech recognition to compute pairwise warps between high-resolution 2D images. The warping algorithm efficiently computes a restricted class of 2D local deformations that are characteristic between successive tissue sections. Finally, a validation framework is proposed and applied to evaluate the quality of reconstruction using both real sections and a synthetic volume.

  14. 3D volume reconstruction of a mouse brain from histological sections using warp filtering.

    PubMed

    Ju, Tao; Warren, Joe; Carson, James; Bello, Musodiq; Kakadiaris, Ioannis; Chiu, Wah; Thaller, Christina; Eichele, Gregor

    2006-09-30

    Sectioning tissues for optical microscopy often introduces upon the resulting sections distortions that make 3D reconstruction difficult. Here we present an automatic method for producing a smooth 3D volume from distorted 2D sections in the absence of any undistorted references. The method is based on pairwise elastic image warps between successive tissue sections, which can be computed by 2D image registration. Using a Gaussian filter, an average warp is computed for each section from the pairwise warps in a group of its neighboring sections. The average warps deform each section to match its neighboring sections, thus creating a smooth volume where corresponding features on successive sections lie close to each other. The proposed method can be used with any existing 2D image registration method for 3D reconstruction. In particular, we present a novel image warping algorithm based on dynamic programming that extends Dynamic Time Warping in 1D speech recognition to compute pairwise warps between high-resolution 2D images. The warping algorithm efficiently computes a restricted class of 2D local deformations that are characteristic between successive tissue sections. Finally, a validation framework is proposed and applied to evaluate the quality of reconstruction using both real sections and a synthetic volume.

  15. Simultaneous MRI and PET imaging of a rat brain

    NASA Astrophysics Data System (ADS)

    Raylman, Raymond R.; Majewski, Stan; Lemieux, Susan K.; Sendhil Velan, S.; Kross, Brian; Popov, Vladimir; Smith, Mark F.; Weisenberger, Andrew G.; Zorn, Carl; Marano, Gary D.

    2006-12-01

    Multi-modality imaging is rapidly becoming a valuable tool in the diagnosis of disease and in the development of new drugs. Functional images produced with PET fused with anatomical structure images created by MRI will allow the correlation of form with function. Our group is developing a system to acquire MRI and PET images contemporaneously. The prototype device consists of two opposed detector heads, operating in coincidence mode. Each MRI-PET detector module consists of an array of LSO detector elements coupled through a long fibre optic light guide to a single Hamamatsu flat panel position-sensitive photomultiplier tube (PSPMT). The use of light guides allows the PSPMTs to be positioned outside the bore of a 3T MRI scanner where the magnetic field is relatively small. To test the device, simultaneous MRI and PET images of the brain of a male Sprague Dawley rat injected with FDG were successfully obtained. The images revealed no noticeable artefacts in either image set. Future work includes the construction of a full ring PET scanner, improved light guides and construction of a specialized MRI coil to permit higher quality MRI imaging.

  16. Automating measurement of subtle changes in articular cartilage from MRI of the knee by combining 3D image registration and segmentation

    NASA Astrophysics Data System (ADS)

    Lynch, John A.; Zaim, Souhil; Zhao, Jenny; Peterfy, Charles G.; Genant, Harry K.

    2001-07-01

    In osteoarthritis, articular cartilage loses integrity and becomes thinned. This usually occurs at sites which bear weight during normal use. Measurement of such loss from MRI scans, requires precise and reproducible techniques, which can overcome the difficulties of patient repositioning within the scanner. In this study, we combine a previously described technique for segmentation of cartilage from MRI of the knee, with a technique for 3D image registration that matches localized regions of interest at followup and baseline. Two patients, who had recently undergone meniscal surgery, and developed lesions during the 12 month followup period were examined. Image registration matched regions of interest (ROI) between baseline and followup, and changes within the cartilage lesions were estimate to be about a 16% reduction in cartilage volume within each ROI. This was more than 5 times the reproducibility of the measurement, but only represented a change of between 1 and 2% in total femoral cartilage volume. Changes in total cartilage volume may be insensitive for quantifying changes in cartilage morphology. A combined used of automated image segmentation, with 3D image registration could be a useful tool for the precise and sensitive measurement of localized changes in cartilage from MRI of the knee.

  17. MRI-based Preplanning Using CT and MRI Data Fusion in Patients With Cervical Cancer Treated With 3D-based Brachytherapy: Feasibility and Accuracy Study

    SciTech Connect

    Dolezel, Martin; Odrazka, Karel; Zizka, Jan; Vanasek, Jaroslav; Kohlova, Tereza; Kroulik, Tomas; Spitzer, Dusan; Ryska, Pavel; Tichy, Michal; Kostal, Milan; Jalcova, Lubica

    2012-09-01

    Purpose: Magnetic resonance imaging (MRI)-assisted radiation treatment planning enables enhanced target contouring. The purpose of this study is to analyze the feasibility and accuracy of computed tomography (CT) and MRI data fusion for MRI-based treatment planning in an institution where an MRI scanner is not available in the radiotherapy department. Methods and Materials: The registration inaccuracy of applicators and soft tissue was assessed in 42 applications with CT/MRI data fusion. The absolute positional difference of the center of the applicators was measured in four different planes from the top of the tandem to the cervix. Any inaccuracy of registration of soft tissue in relation to the position of applicators was determined and dose-volume parameters for MRI preplans and for CT/MRI fusion plans with or without target and organs at risk (OAR) adaptation were evaluated. Results: We performed 6,132 measurements in 42 CT/MRI image fusions. Median absolute difference of the center of tandem on CT and MRI was 1.1 mm. Median distance between the center of the right ovoid on CT and MRI was 1.7 and 1.9 mm in the laterolateral and anteroposterior direction, respectively. Corresponding values for the left ovoid were 1.6 and 1.8 mm. Rotation of applicators was 3.1 Degree-Sign . Median absolute difference in position of applicators in relation to soft tissue was 1.93, 1.50, 1.05, and 0.84 mm in the respective transverse planes, and 1.17, 1.28, 1.27, and 1.17 mm in selected angular directions. The dosimetric parameters for organs at risk on CT/MRI fusion plans without OAR adaptation were significantly impaired whereas the target coverage was not influenced. Planning without target adaptation led to overdosing of the target volume, especially high-risk clinical target volume - D{sub 90} 88.2 vs. 83.1 (p < 0.05). Conclusions: MRI-based preplanning with consecutive CT/MRI data fusion can be safe and feasible, with an acceptable inaccuracy of soft tissue registration.

  18. Systolic and diastolic assessment by 3D-ASM segmentation of gated-SPECT Studies: a comparison with MRI

    NASA Astrophysics Data System (ADS)

    Tobon-Gomez, C.; Bijnens, B. H.; Huguet, M.; Sukno, F.; Moragas, G.; Frangi, A. F.

    2009-02-01

    Gated single photon emission tomography (gSPECT) is a well-established technique used routinely in clinical practice. It can be employed to evaluate global left ventricular (LV) function of a patient. The purpose of this study is to assess LV systolic and diastolic function from gSPECT datasets in comparison with cardiac magnetic resonance imaging (CMR) measurements. This is achieved by applying our recently implemented 3D active shape model (3D-ASM) segmentation approach for gSPECT studies. This methodology allows for generation of 3D LV meshes for all cardiac phases, providing volume time curves and filling rate curves. Both systolic and diastolic functional parameters can be derived from these curves for an assessment of patient condition even at early stages of LV dysfunction. Agreement of functional parameters, with respect to CMR measurements, were analyzed by means of Bland-Altman plots. The analysis included subjects presenting either LV hypertrophy, dilation or myocardial infarction.

  19. Brain palpation from physiological vibrations using MRI

    PubMed Central

    Zorgani, Ali; Souchon, Rémi; Dinh, Au-Hoang; Chapelon, Jean-Yves; Ménager, Jean-Michel; Lounis, Samir; Rouvière, Olivier; Catheline, Stefan

    2015-01-01

    We present a magnetic resonance elastography approach for tissue characterization that is inspired by seismic noise correlation and time reversal. The idea consists of extracting the elasticity from the natural shear waves in living tissues that are caused by cardiac motion, blood pulsatility, and any muscle activity. In contrast to other magnetic resonance elastography techniques, this noise-based approach is, thus, passive and broadband and does not need any synchronization with sources. The experimental demonstration is conducted in a calibrated phantom and in vivo in the brain of two healthy volunteers. Potential applications of this “brain palpation” approach for characterizing brain anomalies and diseases are foreseen. PMID:26438877

  20. Brain palpation from physiological vibrations using MRI.

    PubMed

    Zorgani, Ali; Souchon, Rémi; Dinh, Au-Hoang; Chapelon, Jean-Yves; Ménager, Jean-Michel; Lounis, Samir; Rouvière, Olivier; Catheline, Stefan

    2015-10-20

    We present a magnetic resonance elastography approach for tissue characterization that is inspired by seismic noise correlation and time reversal. The idea consists of extracting the elasticity from the natural shear waves in living tissues that are caused by cardiac motion, blood pulsatility, and any muscle activity. In contrast to other magnetic resonance elastography techniques, this noise-based approach is, thus, passive and broadband and does not need any synchronization with sources. The experimental demonstration is conducted in a calibrated phantom and in vivo in the brain of two healthy volunteers. Potential applications of this "brain palpation" approach for characterizing brain anomalies and diseases are foreseen.

  1. MRI Helps Assess Fetal Brain Abnormalities

    MedlinePlus

    ... decisions about their pregnancy," said lead author Paul Griffiths. He's a professor of radiology at the University ... the fetus may have a suspected brain abnormality," Griffiths said in a journal news release. In this ...

  2. REGULARIZED 3D FUNCTIONAL REGRESSION FOR BRAIN IMAGE DATA VIA HAAR WAVELETS.

    PubMed

    Wang, Xuejing; Nan, Bin; Zhu, Ji; Koeppe, Robert

    2014-06-01

    The primary motivation and application in this article come from brain imaging studies on cognitive impairment in elderly subjects with brain disorders. We propose a regularized Haar wavelet-based approach for the analysis of three-dimensional brain image data in the framework of functional data analysis, which automatically takes into account the spatial information among neighboring voxels. We conduct extensive simulation studies to evaluate the prediction performance of the proposed approach and its ability to identify related regions to the outcome of interest, with the underlying assumption that only few relatively small subregions are truly predictive of the outcome of interest. We then apply the proposed approach to searching for brain subregions that are associated with cognition using PET images of patients with Alzheimer's disease, patients with mild cognitive impairment, and normal controls.

  3. Culturing thick brain slices: an interstitial 3D microperfusion system for enhanced viability.

    PubMed

    Rambani, Komal; Vukasinovic, Jelena; Glezer, Ari; Potter, Steve M

    2009-06-15

    Brain slice preparations are well-established models for a wide spectrum of in vitro investigations in the neuroscience discipline. However, these investigations are limited to acute preparations or thin organotypic culture preparations due to the lack of a successful method that allows culturing of thick organotypic brain slices. Thick brain slice cultures suffer necrosis due to ischemia deep in the tissue resulting from a destroyed circulatory system and subsequent diffusion-limited supply of nutrients and oxygen. Although thin organotypic brain slice cultures can be successfully cultured using a well-established roller-tube method (a monolayer organotypic culture) (Gahwiler B H. Organotypic monolayer cultures of nervous tissue. J Neurosci Methods. 1981; 4: 329-342) or a membrane-insert method (up to 1-4 cell layers, <150 microm) (Stoppini L, Buchs PA, Muller D. A simple method for organotypic cultures of neural tissue. J Neurosci Methods 1991; 37: 173-182), these methods fail to support thick tissue preparations. A few perfusion methods (using submerged or interface/microfluidic chambers) have been reported to enhance the longevity (up to few hours) of acute slice preparations (up to 600 microm thick) (Hass HL, Schaerer B, Vosmansky M. A simple perfusion chamber for study of nervous tissue slices in vitro. J Neurosci Methods 1979; 1: 323-325; Nicoll RA, Alger BE. A simple chamber for recording from submerged brain slices. J Neurosci Methods 1981; 4: 153-156; Passeraub PA, Almeida AC, Thakor NV. Design, microfabrication and characterization of a microfluidic chamber for the perfusion of brain tissue slices. J Biomed Dev 2003; 5: 147-155). Here, we report a unique interstitial microfluidic perfusion technique to culture thick (700 microm) organotypic brain slices. The design of the custom-made microperfusion chamber facilitates laminar, interstitial perfusion of oxygenated nutrient medium throughout the tissue thickness with concomitant removal of depleted medium

  4. Segmentation of brain blood vessels using projections in 3-D CT angiography images.

    PubMed

    Babin, Danilo; Vansteenkiste, Ewout; Pizurica, Aleksandra; Philips, Wilfried

    2011-01-01

    Segmenting cerebral blood vessels is of great importance in diagnostic and clinical applications, especially in quantitative diagnostics and surgery on aneurysms and arteriovenous malformations (AVM). Segmentation of CT angiography images requires algorithms robust to high intensity noise, while being able to segment low-contrast vessels. Because of this, most of the existing methods require user intervention. In this work we propose an automatic algorithm for efficient segmentation of 3-D CT angiography images of cerebral blood vessels. Our method is robust to high intensity noise and is able to accurately segment blood vessels with high range of luminance values, as well as low-contrast vessels.

  5. Scalable fluidic injector arrays for viral targeting of intact 3-D brain circuits.

    PubMed

    Chan, Stephanie; Bernstein, Jacob; Boyden, Edward

    2010-01-21

    Our understanding of neural circuits--how they mediate the computations that subserve sensation, thought, emotion, and action, and how they are corrupted in neurological and psychiatric disorders--would be greatly facilitated by a technology for rapidly targeting genes to complex 3-dimensional neural circuits, enabling fast creation of "circuit-level transgenics." We have recently developed methods in which viruses encoding for light-sensitive proteins can sensitize specific cell types to millisecond-timescale activation and silencing in the intact brain. We here present the design and implementation of an injector array capable of delivering viruses (or other fluids) to dozens of defined points within the 3-dimensional structure of the brain (Figure. 1A, 1B). The injector array comprises one or more displacement pumps that each drive a set of syringes, each of which feeds into a polyimide/fused-silica capillary via a high-pressure-tolerant connector. The capillaries are sized, and then inserted into, desired locations specified by custom-milling a stereotactic positioning board, thus allowing viruses or other reagents to be delivered to the desired set of brain regions. To use the device, the surgeon first fills the fluidic subsystem entirely with oil, backfills the capillaries with the virus, inserts the device into the brain, and infuses reagents slowly (<0.1 microliters/min). The parallel nature of the injector array facilitates rapid, accurate, and robust labeling of entire neural circuits with viral payloads such as optical sensitizers to enable light-activation and silencing of defined brain circuits. Along with other technologies, such as optical fiber arrays for light delivery to desired sets of brain regions, we hope to create a toolbox that enables the systematic probing of causal neural functions in the intact brain. This technology may not only open up such systematic approaches to circuit-focused neuroscience in mammals, and facilitate labeling of

  6. Digital preservation of anatomical variation: 3D-modeling of embalmed and plastinated cadaveric specimens using uCT and MRI.

    PubMed

    Moore, Colin W; Wilson, Timothy D; Rice, Charles L

    2017-01-01

    Anatomy educators have an opportunity to teach anatomical variations as a part of medical and allied health curricula using both cadaveric and three-dimensional (3D) digital models of these specimens. Beyond published cadaveric case reports, anatomical variations identified during routine gross anatomy dissection can be powerful teaching tools and a medium to discuss several anatomical sub-disciplines from embryology to medical imaging. The purpose of this study is to document how cadaveric anatomical variation identified during routine dissection can be scanned using medical imaging techniques to create two-dimensional axial images and interactive 3D models for teaching and learning of anatomical variations. Three cadaveric specimens (2 formalin embalmed, 1 plastinated) depicting anatomical variations and an embryological malformation were scanned using magnetic resonance imaging (MRI) and micro-computed tomography (μCT) for visualization in cross-section and for creation of 3D volumetric models. Results provide educational options to enable visualization and facilitate learning of anatomical variations from cross-sectional scans. Furthermore, the variations can be highlighted, digitized, modeled and manipulated using 3D imaging software and viewed in the anatomy laboratory in conjunction with traditional anatomical dissection. This study provides an example for anatomy educators to teach and describe anatomical variations in the undergraduate medical curriculum.

  7. A biofidelic 3D culture model to study the development of brain cellular systems.

    PubMed

    Ren, M; Du, C; Herrero Acero, E; Tang-Schomer, M D; Özkucur, N

    2016-04-26

    Little is known about how cells assemble as systems during corticogenesis to generate collective functions. We built a neurobiology platform that consists of fetal rat cerebral cortical cells grown within 3D silk scaffolds (SF). Ivermectin (Ivm), a glycine receptor (GLR) agonist, was used to modulate cell resting membrane potential (Vmem) according to methods described in a previous work that implicated Ivm in the arrangement and connectivity of cortical cell assemblies. The cells developed into distinct populations of neuroglial stem/progenitor cells, mature neurons or epithelial-mesenchymal cells. Importantly, the synchronized electrical activity in the newly developed cortical assemblies could be recorded as local field potential (LFP) measurements. This study therefore describes the first example of the development of a biologically relevant cortical plate assembly outside of the body. This model provides i) a preclinical basis for engineering cerebral cortex tissue autografts and ii) a biofidelic 3D culture model for investigating biologically relevant processes during the functional development of cerebral cortical cellular systems.

  8. A biofidelic 3D culture model to study the development of brain cellular systems

    PubMed Central

    Ren, M.; Du, C.; Herrero Acero, E.; Tang-Schomer, M. D.; Özkucur, N.

    2016-01-01

    Little is known about how cells assemble as systems during corticogenesis to generate collective functions. We built a neurobiology platform that consists of fetal rat cerebral cortical cells grown within 3D silk scaffolds (SF). Ivermectin (Ivm), a glycine receptor (GLR) agonist, was used to modulate cell resting membrane potential (Vmem) according to methods described in a previous work that implicated Ivm in the arrangement and connectivity of cortical cell assemblies. The cells developed into distinct populations of neuroglial stem/progenitor cells, mature neurons or epithelial-mesenchymal cells. Importantly, the synchronized electrical activity in the newly developed cortical assemblies could be recorded as local field potential (LFP) measurements. This study therefore describes the first example of the development of a biologically relevant cortical plate assembly outside of the body. This model provides i) a preclinical basis for engineering cerebral cortex tissue autografts and ii) a biofidelic 3D culture model for investigating biologically relevant processes during the functional development of cerebral cortical cellular systems. PMID:27112667

  9. Detection of infarct lesions from single MRI modality using inconsistency between voxel intensity and spatial location--a 3-D automatic approach.

    PubMed

    Shen, Shan; Szameitat, André J; Sterr, Annette

    2008-07-01

    Detection of infarct lesions using traditional segmentation methods is always problematic due to intensity similarity between lesions and normal tissues, so that multispectral MRI modalities were often employed for this purpose. However, the high costs of MRI scan and the severity of patient conditions restrict the collection of multiple images. Therefore, in this paper, a new 3-D automatic lesion detection approach was proposed, which required only a single type of anatomical MRI scan. It was developed on a theory that, when lesions were present, the voxel-intensity-based segmentation and the spatial-location-based tissue distribution should be inconsistent in the regions of lesions. The degree of this inconsistency was calculated, which indicated the likelihood of tissue abnormality. Lesions were identified when the inconsistency exceeded a defined threshold. In this approach, the intensity-based segmentation was implemented by the conventional fuzzy c-mean (FCM) algorithm, while the spatial location of tissues was provided by prior tissue probability maps. The use of simulated MRI lesions allowed us to quantitatively evaluate the performance of the proposed method, as the size and location of lesions were prespecified. The results showed that our method effectively detected lesions with 40-80% signal reduction compared to normal tissues (similarity index > 0.7). The capability of the proposed method in practice was also demonstrated on real infarct lesions from 15 stroke patients, where the lesions detected were in broad agreement with true lesions. Furthermore, a comparison to a statistical segmentation approach presented in the literature suggested that our 3-D lesion detection approach was more reliable. Future work will focus on adapting the current method to multiple sclerosis lesion detection.

  10. The Implications of Brain MRI in Autism Spectrum Disorder.

    PubMed

    Cooper, Alison S; Friedlaender, Eron; Levy, Susan E; Shekdar, Karuna V; Bradford, Andrea Bennett; Wells, Kimberly E; Mollen, Cynthia

    2016-12-01

    Our objective was to describe the types of providers who refer children with autism spectrum disorder (ASD) for brain magnetic resonance imaging (MRI), the referral reason, and MRI results. The most common referral reasons were autism spectrum disorder with seizures (33.7%), autism spectrum disorder alone (26.3%), and autism spectrum disorder with abnormal neurologic examination or preexisting finding (24%). Neurology (62.5%), general pediatric (22.3%), and developmental/behavioral practitioners (8.9%) referred the most patients. The prevalence of definite pathology was highest in children referred for autism spectrum disorder with abnormal neurologic examination/preexisting finding (26.2%, 95% CI: 16.8%-36%), headaches (25.7%, 95% CI: 11.2%-40.2%), or seizures (22%, 95% CI: 14.6%-29.5%), and was lowest in children referred for autism spectrum disorder alone (6.5%, 95% CI: 1.5%-11.6%). We concluded that there is a low prevalence of definite pathology in children with autism spectrum disorder undergoing brain MRI. In children with abnormal neurologic examination or preexisting finding, seizures, or headaches, one may consider performing brain MRI given the higher prevalence of pathology.

  11. Culturing thick brain slices: An interstitial 3D microperfusion system for enhanced viability

    PubMed Central

    Rambani, Komal; Vukasinovic, Jelena; Glezer, Ari; Potter, Steve M.

    2009-01-01

    Brain slice preparations are well-established models for a wide spectrum of in vitro investigations in the neuroscience discipline. However, these investigations are limited to acute preparations or thin organotypic culture preparations due to the lack of a successful method that allows culturing of thick organotypic brain slices. Thick brain slice cultures suffer necrosis due to ischemia deep in the tissue resulting from a destroyed circulatory system and subsequent diffusion-limited supply of nutrients and oxygen. Although thin organotypic brain slice cultures can be successfully cultured using a well established roller tube method (a monolayer organotypic culture) (Gahwiler B H, 1981) or a membrane insert method (up to 1–4 cell layers, <150μm)(Stoppini L et al., 1991), these methods fail to support thick tissue preparations. A few perfusion methods (using submerged or interface/microfluidic chambers) have been reported to enhance the longevity (up to few hours) of acute slice preparations (up to 600μm thick) (Hass H L et al., 1979; Nicoll R A and Alger B E, 1981; Passeraub P A et al., 2003). Here, we report a unique interstitial microfluidic perfusion technique to culture thick (700μm) organotypic brain slices. The design of the custom-made micro-perfusion chamber facilitates laminar, interstitial perfusion of oxygenated nutrient medium throughout the tissue thickness with concomitant removal of depleted medium and catabolites. We examined the utility of this perfusion method to enhance the viability of the thick organotypic brain slice cultures after 2 days and 5 days in vitro (DIV). We investigated the range of amenable flow rates that enhance the viability of 700μm thick organotypic brain slices compared to the unperfused control cultures. Our perfusion method allows up to 84.6% viability (P<0.01) and up to 700μm thickness, even after 5 DIV. Our results also confirm that these cultures are functionally active and have their in vivo cytoarchitecture

  12. Audio-visual perception of 3D cinematography: an fMRI study using condition-based and computation-based analyses.

    PubMed

    Ogawa, Akitoshi; Bordier, Cecile; Macaluso, Emiliano

    2013-01-01

    The use of naturalistic stimuli to probe sensory functions in the human brain is gaining increasing interest. Previous imaging studies examined brain activity associated with the processing of cinematographic material using both standard "condition-based" designs, as well as "computational" methods based on the extraction of time-varying features of the stimuli (e.g. motion). Here, we exploited both approaches to investigate the neural correlates of complex visual and auditory spatial signals in cinematography. In the first experiment, the participants watched a piece of a commercial movie presented in four blocked conditions: 3D vision with surround sounds (3D-Surround), 3D with monaural sound (3D-Mono), 2D-Surround, and 2D-Mono. In the second experiment, they watched two different segments of the movie both presented continuously in 3D-Surround. The blocked presentation served for standard condition-based analyses, while all datasets were submitted to computation-based analyses. The latter assessed where activity co-varied with visual disparity signals and the complexity of auditory multi-sources signals. The blocked analyses associated 3D viewing with the activation of the dorsal and lateral occipital cortex and superior parietal lobule, while the surround sounds activated the superior and middle temporal gyri (S/MTG). The computation-based analyses revealed the effects of absolute disparity in dorsal occipital and posterior parietal cortices and of disparity gradients in the posterior middle temporal gyrus plus the inferior frontal gyrus. The complexity of the surround sounds was associated with activity in specific sub-regions of S/MTG, even after accounting for changes of sound intensity. These results demonstrate that the processing of naturalistic audio-visual signals entails an extensive set of visual and auditory areas, and that computation-based analyses can track the contribution of complex spatial aspects characterizing such life-like stimuli.

  13. Audio-Visual Perception of 3D Cinematography: An fMRI Study Using Condition-Based and Computation-Based Analyses

    PubMed Central

    Ogawa, Akitoshi; Bordier, Cecile; Macaluso, Emiliano

    2013-01-01

    The use of naturalistic stimuli to probe sensory functions in the human brain is gaining increasing interest. Previous imaging studies examined brain activity associated with the processing of cinematographic material using both standard “condition-based” designs, as well as “computational” methods based on the extraction of time-varying features of the stimuli (e.g. motion). Here, we exploited both approaches to investigate the neural correlates of complex visual and auditory spatial signals in cinematography. In the first experiment, the participants watched a piece of a commercial movie presented in four blocked conditions: 3D vision with surround sounds (3D-Surround), 3D with monaural sound (3D-Mono), 2D-Surround, and 2D-Mono. In the second experiment, they watched two different segments of the movie both presented continuously in 3D-Surround. The blocked presentation served for standard condition-based analyses, while all datasets were submitted to computation-based analyses. The latter assessed where activity co-varied with visual disparity signals and the complexity of auditory multi-sources signals. The blocked analyses associated 3D viewing with the activation of the dorsal and lateral occipital cortex and superior parietal lobule, while the surround sounds activated the superior and middle temporal gyri (S/MTG). The computation-based analyses revealed the effects of absolute disparity in dorsal occipital and posterior parietal cortices and of disparity gradients in the posterior middle temporal gyrus plus the inferior frontal gyrus. The complexity of the surround sounds was associated with activity in specific sub-regions of S/MTG, even after accounting for changes of sound intensity. These results demonstrate that the processing of naturalistic audio-visual signals entails an extensive set of visual and auditory areas, and that computation-based analyses can track the contribution of complex spatial aspects characterizing such life-like stimuli

  14. Accurate high-resolution measurements of 3-D tissue dynamics with registration-enhanced displacement encoded MRI.

    PubMed

    Gomez, Arnold D; Merchant, Samer S; Hsu, Edward W

    2014-06-01

    Displacement fields are important to analyze deformation, which is associated with functional and material tissue properties often used as indicators of health. Magnetic resonance imaging (MRI) techniques like DENSE and image registration methods like Hyperelastic Warping have been used to produce pixel-level deformation fields that are desirable in high-resolution analysis. However, DENSE can be complicated by challenges associated with image phase unwrapping, in particular offset determination. On the other hand, Hyperelastic Warping can be hampered by low local image contrast. The current work proposes a novel approach for measuring tissue displacement with both DENSE and Hyperelastic Warping, incorporating physically accurate displacements obtained by the latter to improve phase characterization in DENSE. The validity of the proposed technique is demonstrated using numerical and physical phantoms, and in vivo small animal cardiac MRI.

  15. Efficient global optimization based 3D carotid AB-LIB MRI segmentation by simultaneously evolving coupled surfaces.

    PubMed

    Ukwatta, Eranga; Yuan, Jing; Rajchl, Martin; Fenster, Aaron

    2012-01-01

    Magnetic resonance (MR) imaging of carotid atherosclerosis biomarkers are increasingly being investigated for the risk assessment of vulnerable plaques. A fast and robust 3D segmentation of the carotid adventitia (AB) and lumen-intima (LIB) boundaries can greatly alleviate the measurement burden of generating quantitative imaging biomarkers in clinical research. In this paper, we propose a novel global optimization-based approach to segment the carotid AB and LIB from 3D T1-weighted black blood MR images, by simultaneously evolving two coupled surfaces with enforcement of anatomical consistency of the AB and LIB. We show that the evolution of two surfaces at each discrete time-frame can be optimized exactly and globally by means of convex relaxation. Our continuous max-flow based algorithm is implemented in GPUs to achieve high computational performance. The experiment results from 16 carotid MR images show that the algorithm obtained high agreement with manual segmentations and achieved high repeatability in segmentation.

  16. 3D shape analysis of the brain's third ventricle using a midplane encoded symmetric template model

    PubMed Central

    Kim, Jaeil; Valdés Hernández, Maria del C.; Royle, Natalie A.; Maniega, Susana Muñoz; Aribisala, Benjamin S.; Gow, Alan J.; Bastin, Mark E.; Deary, Ian J.; Wardlaw, Joanna M.; Park, Jinah

    2016-01-01

    Background Structural changes of the brain's third ventricle have been acknowledged as an indicative measure of the brain atrophy progression in neurodegenerative and endocrinal diseases. To investigate the ventricular enlargement in relation to the atrophy of the surrounding structures, shape analysis is a promising approach. However, there are hurdles in modeling the third ventricle shape. First, it has topological variations across individuals due to the inter-thalamic adhesion. In addition, as an interhemispheric structure, it needs to be aligned to the midsagittal plane to assess its asymmetric and regional deformation. Method To address these issues, we propose a model-based shape assessment. Our template model of the third ventricle consists of a midplane and a symmetric mesh of generic shape. By mapping the template's midplane to the individuals’ brain midsagittal plane, we align the symmetric mesh on the midline of the brain before quantifying the third ventricle shape. To build the vertex-wise correspondence between the individual third ventricle and the template mesh, we employ a minimal-distortion surface deformation framework. In addition, to account for topological variations, we implement geometric constraints guiding the template mesh to have zero width where the inter-thalamic adhesion passes through, preventing vertices crossing between left and right walls of the third ventricle. The individual shapes are compared using a vertex-wise deformity from the symmetric template. Results Experiments on imaging and demographic data from a study of aging showed that our model was sensitive in assessing morphological differences between individuals in relation to brain volume (i.e. proxy for general brain atrophy), gender and the fluid intelligence at age 72. It also revealed that the proposed method can detect the regional and asymmetrical deformation unlike the conventional measures: volume (median 1.95 ml, IQR 0.96 ml) and width of the third

  17. Single breath hold 3D cardiac cine MRI using kat-ARC: preliminary results at 1.5T.

    PubMed

    Jeong, Daniel; Schiebler, Mark L; Lai, Peng; Wang, Kang; Vigen, Karl K; François, Christopher J

    2015-04-01

    Validation of a new single breath-hold, three-dimensional, cine balanced steady-state free precession (3D cine bSSFP) cardiac magnetic resonance (CMR) sequence for left ventricular function. CMR examinations were performed on fifteen patients and three healthy volunteers on a clinical 1.5T scanner using a two-dimensional (2D) cine balanced SSFP CMR sequence (2D cine bSSFP) followed by an investigational 3D cine bSSFP pulse sequence acquired within a single breath hold. Left ventricular end diastolic volume (LVEDV), end systolic volume (LVESV), ejection fraction (LVEF), and myocardial mass were independently segmented on a workstation by two experienced radiologists. Blood pool to myocardial contrast was evaluated in consensus using a Likert scale. Bland-Altman analysis was used to compare these quantitative and nominal measurements for the two sequences. The average acquisition time was significantly shorter for the 3D cine bSSFP than for 2D cine bSSFP (0.36 ± 0.03 vs. 8.5 ± 2.3 min) p = 0.0002. Bland-Altman analyses [bias and (limits of agreement)] of the data derived from these two methods revealed that the LVEF 0.9% (-4.7, 6.4), LVEDV 4.9 ml (-23.0, 32.8), LVESV -0.2 ml (-22.4, 21.9), and myocardial mass -0.4 g (-23.8, 23.0) were not significantly different. There was excellent intraclass correlation for intra-observer variability (0.981, 0.989, 0.997, 0.985) and inter-observer variability (0.903, 0.954, 0.970, 0.842) for LVEF, LVEDV, LVESV, and myocardial mass respectively. 3D cine bSSFP allows for accurate single breath-hold volumetric cine CMR which enables substantial improvements in scanner time efficiency without sacrificing diagnostic accuracy.

  18. Toward a 3D model of human brain development for studying gene/environment interactions.

    PubMed

    Hogberg, Helena T; Bressler, Joseph; Christian, Kimberly M; Harris, Georgina; Makri, Georgia; O'Driscoll, Cliona; Pamies, David; Smirnova, Lena; Wen, Zhexing; Hartung, Thomas

    2013-01-01

    This project aims to establish and characterize an in vitro model of the developing human brain for the purpose of testing drugs and chemicals. To accurately assess risk, a model needs to recapitulate the complex interactions between different types of glial cells and neurons in a three-dimensional platform. Moreover, human cells are preferred over cells from rodents to eliminate cross-species differences in sensitivity to chemicals. Previously, we established conditions to culture rat primary cells as three-dimensional aggregates, which will be humanized and evaluated here with induced pluripotent stem cells (iPSCs). The use of iPSCs allows us to address gene/environment interactions as well as the potential of chemicals to interfere with epigenetic mechanisms. Additionally, iPSCs afford us the opportunity to study the effect of chemicals during very early stages of brain development. It is well recognized that assays for testing toxicity in the developing brain must consider differences in sensitivity and susceptibility that arise depending on the time of exposure. This model will reflect critical developmental processes such as proliferation, differentiation, lineage specification, migration, axonal growth, dendritic arborization and synaptogenesis, which will probably display differences in sensitivity to different types of chemicals. Functional endpoints will evaluate the complex cell-to-cell interactions that are affected in neurodevelopment through chemical perturbation, and the efficacy of drug intervention to prevent or reverse phenotypes. The model described is designed to assess developmental neurotoxicity effects on unique processes occurring during human brain development by leveraging human iPSCs from diverse genetic backgrounds, which can be differentiated into different cell types of the central nervous system. Our goal is to demonstrate the feasibility of the personalized model using iPSCs derived from individuals with neurodevelopmental disorders

  19. A comparison study of atlas-based 3D cardiac MRI segmentation: global versus global and local transformations

    NASA Astrophysics Data System (ADS)

    Daryanani, Aditya; Dangi, Shusil; Ben-Zikri, Yehuda Kfir; Linte, Cristian A.

    2016-03-01

    Magnetic Resonance Imaging (MRI) is a standard-of-care imaging modality for cardiac function assessment and guidance of cardiac interventions thanks to its high image quality and lack of exposure to ionizing radiation. Cardiac health parameters such as left ventricular volume, ejection fraction, myocardial mass, thickness, and strain can be assessed by segmenting the heart from cardiac MRI images. Furthermore, the segmented pre-operative anatomical heart models can be used to precisely identify regions of interest to be treated during minimally invasive therapy. Hence, the use of accurate and computationally efficient segmentation techniques is critical, especially for intra-procedural guidance applications that rely on the peri-operative segmentation of subject-specific datasets without delaying the procedure workflow. Atlas-based segmentation incorporates prior knowledge of the anatomy of interest from expertly annotated image datasets. Typically, the ground truth atlas label is propagated to a test image using a combination of global and local registration. The high computational cost of non-rigid registration motivated us to obtain an initial segmentation using global transformations based on an atlas of the left ventricle from a population of patient MRI images and refine it using well developed technique based on graph cuts. Here we quantitatively compare the segmentations obtained from the global and global plus local atlases and refined using graph cut-based techniques with the expert segmentations according to several similarity metrics, including Dice correlation coefficient, Jaccard coefficient, Hausdorff distance, and Mean absolute distance error.

  20. Alpha shape theory for 3D visualization and volumetric measurement of brain tumor progression using magnetic resonance images.

    PubMed

    Hamoud Al-Tamimi, Mohammed Sabbih; Sulong, Ghazali; Shuaib, Ibrahim Lutfi

    2015-07-01

    Resection of brain tumors is a tricky task in surgery due to its direct influence on the patients' survival rate. Determining the tumor resection extent for its complete information via-à-vis volume and dimensions in pre- and post-operative Magnetic Resonance Images (MRI) requires accurate estimation and comparison. The active contour segmentation technique is used to segment brain tumors on pre-operative MR images using self-developed software. Tumor volume is acquired from its contours via alpha shape theory. The graphical user interface is developed for rendering, visualizing and estimating the volume of a brain tumor. Internet Brain Segmentation Repository dataset (IBSR) is employed to analyze and determine the repeatability and reproducibility of tumor volume. Accuracy of the method is validated by comparing the estimated volume using the proposed method with that of gold-standard. Segmentation by active contour technique is found to be capable of detecting the brain tumor boundaries. Furthermore, the volume description and visualization enable an interactive examination of tumor tissue and its surrounding. Admirable features of our results demonstrate that alpha shape theory in comparison to other existing standard methods is superior for precise volumetric measurement of tumor.

  1. High-throughput, high-frequency 3-D ultrasound for in utero analysis of embryonic mouse brain development.

    PubMed

    Aristizábal, Orlando; Mamou, Jonathan; Ketterling, Jeffrey A; Turnbull, Daniel H

    2013-12-01

    With the emergence of the mouse as the predominant model system for studying mammalian brain development, in utero imaging methods are urgently required to analyze the dynamics of brain growth and patterning in mouse embryos. To address this need, we combined synthetic focusing with a high-frequency (38-MHz) annular-array ultrasound imaging system for extended depth-of-field, coded excitation for improved penetration and respiratory-gated transmit/receive. This combination allowed non-invasive in utero acquisition of motion-free 3-D data from individual embryos in approximately 2 min, and data from four or more embryos in a pregnant mouse in less than 30 min. Data were acquired from 148 embryos spanning 5 d of early to mid-gestational stages of brain development. The results indicated that brain anatomy and cerebral vasculature can be imaged with this system and that quantitative analyses of segmented cerebral ventricles can be used to characterize volumetric changes associated with mouse brain development.

  2. Texture anisotropy of the brain's white matter as revealed by anatomical MRI.

    PubMed

    Kovalev, Vassili; Kruggel, Frithjof

    2007-05-01

    The purpose of this work was to study specific texture properties of the brain's white matter (WM) based on conventional high-resolution T1-weighted magnetic resonance imaging (MRI) datasets. Quantitative parameters anisotropy and laminarity were derived from 3-D texture analysis. Differences in WM texture associated with gender were evaluated on an age-matched sample of 210 young healthy subjects (mean age 24.8, SD 3.97 years, 103 males and 107 females). Changes of WM texture with age were studied using 112 MRI-T1 datasets of healthy subjects aged 16 to 70 years (57 males and 55 females). Both texture measures indicated a "more regular" WM structure in females (p < 10(-6)). An age-related deterioration of WM structure manifests itself as a remarkable decline of both parameters (p < 10(-6)) that is more prominent in females (p < 10(-6)) than in males (p = 0.02). Texture analysis of anatomical MRI-T1 brain datasets provides quantitative information about macroscopic WM characteristics and helps discriminating between normal and pathological aging.

  3. Classification of normal and pathological aging processes based on brain MRI morphology measures

    NASA Astrophysics Data System (ADS)

    Perez-Gonzalez, J. L.; Yanez-Suarez, O.; Medina-Bañuelos, V.

    2014-03-01

    Reported studies describing normal and abnormal aging based on anatomical MRI analysis do not consider morphological brain changes, but only volumetric measures to distinguish among these processes. This work presents a classification scheme, based both on size and shape features extracted from brain volumes, to determine different aging stages: healthy control (HC) adults, mild cognitive impairment (MCI), and Alzheimer's disease (AD). Three support vector machines were optimized and validated for the pair-wise separation of these three classes, using selected features from a set of 3D discrete compactness measures and normalized volumes of several global and local anatomical structures. Our analysis show classification rates of up to 98.3% between HC and AD; of 85% between HC and MCI and of 93.3% for MCI and AD separation. These results outperform those reported in the literature and demonstrate the viability of the proposed morphological indexes to classify different aging stages.

  4. Tl-201 and Tc-99m-Sestamibi SPECT for brain tumor detection: Comparison using MRI coregistration

    SciTech Connect

    Darcourt, J.; Itti, L.; Chang, L.

    1994-05-01

    Tl-201 (Tl) brain SPECT has been validated for the differential diagnosis of high versus low grade gliomas and recurrence versus radiation necrosis. We compared this technique to Tc-99m-Sestamibi (MIBI) SPECT in 9 patients (pts) with brain tumors using MRI coregistration. Pts were injected with 4 mCi of Tl and brain SPECT was performed using a dedicated brain system. This was immediately following by an injection of 20 mCi of MIBI and a brain SPECT using the same camera and with the pt in the same position. Four pts were studied for the diagnosis of radiation necrosis vs. tumor recurrence (2 had biopsy proven recurrence); 5 pts were studied for primary tumor evaluation: 2 meningiomas, 1 oligodendroglioma, 1 low-grade astrocytoma, 1 cysticercosis. Coregistration was performed for every pt by 3D surface fitting of the inner skull MIBI contour to the MRI brain surface extracted automatically. ROIs were drawn on the MRI and applied to the coregistered MIBI and Tl images for tumor to non-tumor ratios T/NT calculations. There was a tight correlation between MIBI and Tl T/NT (r-0.96) and a 1.5 threshold separated radiation necrosis from recurrence and low from high grade primary tumors. Therefore, the data already available on Tl brain tumor imaging can be used with MIBI SPECT with the advantage of a better image quality (2.5 to 4 times more counts).

  5. Mapping motion from 4D-MRI to 3D-CT for use in 4D dose calculations: A technical feasibility study

    SciTech Connect

    Boye, Dirk; Lomax, Tony; Knopf, Antje

    2013-06-15

    Purpose: Target sites affected by organ motion require a time resolved (4D) dose calculation. Typical 4D dose calculations use 4D-CT as a basis. Unfortunately, 4D-CT images have the disadvantage of being a 'snap-shot' of the motion during acquisition and of assuming regularity of breathing. In addition, 4D-CT acquisitions involve a substantial additional dose burden to the patient making many, repeated 4D-CT acquisitions undesirable. Here the authors test the feasibility of an alternative approach to generate patient specific 4D-CT data sets. Methods: In this approach motion information is extracted from 4D-MRI. Simulated 4D-CT data sets [which the authors call 4D-CT(MRI)] are created by warping extracted deformation fields to a static 3D-CT data set. The employment of 4D-MRI sequences for this has the advantage that no assumptions on breathing regularity are made, irregularities in breathing can be studied and, if necessary, many repeat imaging studies (and consequently simulated 4D-CT data sets) can be performed on patients and/or volunteers. The accuracy of 4D-CT(MRI)s has been validated by 4D proton dose calculations. Our 4D dose algorithm takes into account displacements as well as deformations on the originating 4D-CT/4D-CT(MRI) by calculating the dose of each pencil beam based on an individual time stamp of when that pencil beam is applied. According to corresponding displacement and density-variation-maps the position and the water equivalent range of the dose grid points is adjusted at each time instance. Results: 4D dose distributions, using 4D-CT(MRI) data sets as input were compared to results based on a reference conventional 4D-CT data set capturing similar motion characteristics. Almost identical 4D dose distributions could be achieved, even though scanned proton beams are very sensitive to small differences in the patient geometry. In addition, 4D dose calculations have been performed on the same patient, but using 4D-CT(MRI) data sets based on

  6. Cardiac-induced physiological noise in 3D gradient echo brain imaging: Effect of k -space sampling scheme

    NASA Astrophysics Data System (ADS)

    Kristoffersen, Anders; Goa, Pål Erik

    2011-09-01

    The physiological noise in 3D image acquisition is shown to depend strongly on the sampling scheme. Five sampling schemes are considered: Linear, Centric, Segmented, Random and Tuned. Tuned acquisition means that data acquisition at k-space positions k and - k are separated with a specific time interval. We model physiological noise as a periodic temporal oscillation with arbitrary spatial amplitude in the physical object and develop a general framework to describe how this is rendered in the reconstructed image. Reconstructed noise can be decomposed in one component that is in phase with the signal (parallel) and one that is 90° out of phase (orthogonal). Only the former has a significant influence on the magnitude of the signal. The study focuses on fMRI using 3D EPI. Each k-space plane is acquired in a single shot in a time much shorter than the period of the physiological noise. The above mentioned sampling schemes are applied in the slow k-space direction and noise propagates almost exclusively in this direction. The problem then, is effectively one-dimensional. Numerical simulations and analytical expressions are presented. 3D noise measurements and 2D measurements with high temporal resolution are conducted. The measurements are performed under breath-hold to isolate the effect of cardiac-induced pulsatile motion. We compare the time-course stability of the sampling schemes and the extent to which noise propagates from a localized source into other parts of the imaging volume. Tuned and Linear acquisitions perform better than Centric, Segmented and Random.

  7. Optimization of 3-D MP-RAGE sequences for structural brain imaging.

    PubMed

    Deichmann, R; Good, C D; Josephs, O; Ashburner, J; Turner, R

    2000-07-01

    An optimized MR sequence for structural three-dimensional brain scans is presented, giving good T(1) contrast and excellent white matter/gray matter segmentation. Modification of the usual linear phase encoding order to centric phase encoding restores the contrast loss, which usually occurs after magnetization preparation during the acquisition process when large volumes are imaged. The deleterious effects on the point-spread function are compensated by means of an appropriate k-space filter. RF coil inhomogeneities are corrected by means of shaped excitation pulses. High contrast-to-noise images of the entire brain with 1 mm isotropic resolution can be obtained in 12 min. The contrast-to-noise-ratio is about 100% higher than for sequences based on linear phase encoding.

  8. Fast, Accurate and Precise Mid-Sagittal Plane Location in 3D MR Images of the Brain

    NASA Astrophysics Data System (ADS)

    Bergo, Felipe P. G.; Falcão, Alexandre X.; Yasuda, Clarissa L.; Ruppert, Guilherme C. S.

    Extraction of the mid-sagittal plane (MSP) is a key step for brain image registration and asymmetry analysis. We present a fast MSP extraction method for 3D MR images, based on automatic segmentation of the brain and on heuristic maximization of the cerebro-spinal fluid within the MSP. The method is robust to severe anatomical asymmetries between the hemispheres, caused by surgical procedures and lesions. The method is also accurate with respect to MSP delineations done by a specialist. The method was evaluated on 64 MR images (36 pathological, 20 healthy, 8 synthetic), and it found a precise and accurate approximation of the MSP in all of them with a mean time of 60.0 seconds per image, mean angular variation within a same image (precision) of 1.26o and mean angular difference from specialist delineations (accuracy) of 1.64o.

  9. Hemorrhage detection in MRI brain images using images features

    NASA Astrophysics Data System (ADS)

    Moraru, Luminita; Moldovanu, Simona; Bibicu, Dorin; Stratulat (Visan), Mirela

    2013-11-01

    The abnormalities appear frequently on Magnetic Resonance Images (MRI) of brain in elderly patients presenting either stroke or cognitive impairment. Detection of brain hemorrhage lesions in MRI is an important but very time-consuming task. This research aims to develop a method to extract brain tissue features from T2-weighted MR images of the brain using a selection of the most valuable texture features in order to discriminate between normal and affected areas of the brain. Due to textural similarity between normal and affected areas in brain MR images these operation are very challenging. A trauma may cause microstructural changes, which are not necessarily perceptible by visual inspection, but they could be detected by using a texture analysis. The proposed analysis is developed in five steps: i) in the pre-processing step: the de-noising operation is performed using the Daubechies wavelets; ii) the original images were transformed in image features using the first order descriptors; iii) the regions of interest (ROIs) were cropped from images feature following up the axial symmetry properties with respect to the mid - sagittal plan; iv) the variation in the measurement of features was quantified using the two descriptors of the co-occurrence matrix, namely energy and homogeneity; v) finally, the meaningful of the image features is analyzed by using the t-test method. P-value has been applied to the pair of features in order to measure they efficacy.

  10. 3D active shape models of human brain structures: application to patient-specific mesh generation

    NASA Astrophysics Data System (ADS)

    Ravikumar, Nishant; Castro-Mateos, Isaac; Pozo, Jose M.; Frangi, Alejandro F.; Taylor, Zeike A.

    2015-03-01

    The use of biomechanics-based numerical simulations has attracted growing interest in recent years for computer-aided diagnosis and treatment planning. With this in mind, a method for automatic mesh generation of brain structures of interest, using statistical models of shape (SSM) and appearance (SAM), for personalised computational modelling is presented. SSMs are constructed as point distribution models (PDMs) while SAMs are trained using intensity profiles sampled from a training set of T1-weighted magnetic resonance images. The brain structures of interest are, the cortical surface (cerebrum, cerebellum & brainstem), lateral ventricles and falx-cerebri membrane. Two methods for establishing correspondences across the training set of shapes are investigated and compared (based on SSM quality): the Coherent Point Drift (CPD) point-set registration method and B-spline mesh-to-mesh registration method. The MNI-305 (Montreal Neurological Institute) average brain atlas is used to generate the template mesh, which is deformed and registered to each training case, to establish correspondence over the training set of shapes. 18 healthy patients' T1-weightedMRimages form the training set used to generate the SSM and SAM. Both model-training and model-fitting are performed over multiple brain structures simultaneously. Compactness and generalisation errors of the BSpline-SSM and CPD-SSM are evaluated and used to quantitatively compare the SSMs. Leave-one-out cross validation is used to evaluate SSM quality in terms of these measures. The mesh-based SSM is found to generalise better and is more compact, relative to the CPD-based SSM. Quality of the best-fit model instance from the trained SSMs, to test cases are evaluated using the Hausdorff distance (HD) and mean absolute surface distance (MASD) metrics.

  11. Lossless 3-D reconstruction and registration of semi-quantitative gene expression data in the mouse brain

    PubMed Central

    Enlow, Matthew A.; Ju, Tao; Kakadiaris, Ioannis A.; Carson, James P.

    2012-01-01

    As imaging, computing, and data storage technologies improve, there is an increasing opportunity for multiscale analysis of three-dimensional datasets (3-D). Such analysis enables, for example, microscale elements of multiple macroscale specimens to be compared throughout the entire macroscale specimen. Spatial comparisons require bringing datasets into co-alignment. One approach for co-alignment involves elastic deformations of data in addition to rigid alignments. The elastic deformations distort space, and if not accounted for, can distort the information at the microscale. The algorithms developed in this work address this issue by allowing multiple data points to be encoded into a single image pixel, appropriately tracking each data point to ensure lossless data mapping during elastic spatial deformation. This approach was developed and implemented for both 2-D and 3-D registration of images. Lossless reconstruction and registration was applied to semi-quantitative cellular gene expression data in the mouse brain, enabling comparison of multiple spatially registered 3-D datasets without any augmentation of the cellular data. Standard reconstruction and registration without the lossless approach resulted in errors in cellular quantities of ~ 8%. PMID:22256218

  12. Lossless 3-D reconstruction and registration of semi-quantitative gene expression data in the mouse brain.

    PubMed

    Enlow, Matthew A; Ju, Tao; Kakadiaris, Ioannis A; Carson, James P

    2011-01-01

    As imaging, computing, and data storage technologies improve, there is an increasing opportunity for multiscale analysis of three-dimensional datasets (3-D). Such analysis enables, for example, microscale elements of multiple macroscale specimens to be compared throughout the entire macroscale specimen. Spatial comparisons require bringing datasets into co-alignment. One approach for co-alignment involves elastic deformations of data in addition to rigid alignments. The elastic deformations distort space, and if not accounted for, can distort the information at the microscale. The algorithms developed in this work address this issue by allowing multiple data points to be encoded into a single image pixel, appropriately tracking each data point to ensure lossless data mapping during elastic spatial deformation. This approach was developed and implemented for both 2-D and 3D registration of images. Lossless reconstruction and registration was applied to semi-quantitative cellular gene expression data in the mouse brain, enabling comparison of multiple spatially registered 3-D datasets without any augmentation of the cellular data. Standard reconstruction and registration without the lossless approach resulted in errors in cellular quantities of ∼ 8%.

  13. Real-time 3D motion tracking for small animal brain PET

    NASA Astrophysics Data System (ADS)

    Kyme, A. Z.; Zhou, V. W.; Meikle, S. R.; Fulton, R. R.

    2008-05-01

    High-resolution positron emission tomography (PET) imaging of conscious, unrestrained laboratory animals presents many challenges. Some form of motion correction will normally be necessary to avoid motion artefacts in the reconstruction. The aim of the current work was to develop and evaluate a motion tracking system potentially suitable for use in small animal PET. This system is based on the commercially available stereo-optical MicronTracker S60 which we have integrated with a Siemens Focus-220 microPET scanner. We present measured performance limits of the tracker and the technical details of our implementation, including calibration and synchronization of the system. A phantom study demonstrating motion tracking and correction was also performed. The system can be calibrated with sub-millimetre accuracy, and small lightweight markers can be constructed to provide accurate 3D motion data. A marked reduction in motion artefacts was demonstrated in the phantom study. The techniques and results described here represent a step towards a practical method for rigid-body motion correction in small animal PET. There is scope to achieve further improvements in the accuracy of synchronization and pose measurements in future work.

  14. Advanced MRI for Pediatric Brain Tumors with Emphasis on Clinical Benefits

    PubMed Central

    Ra, Young-Shin

    2017-01-01

    Conventional anatomic brain MRI is often limited in evaluating pediatric brain tumors, the most common solid tumors and a leading cause of death in children. Advanced brain MRI techniques have great potential to improve diagnostic performance in children with brain tumors and overcome diagnostic pitfalls resulting from diverse tumor pathologies as well as nonspecific or overlapped imaging findings. Advanced MRI techniques used for evaluating pediatric brain tumors include diffusion-weighted imaging, diffusion tensor imaging, functional MRI, perfusion imaging, spectroscopy, susceptibility-weighted imaging, and chemical exchange saturation transfer imaging. Because pediatric brain tumors differ from adult counterparts in various aspects, MRI protocols should be designed to achieve maximal clinical benefits in pediatric brain tumors. In this study, we review advanced MRI techniques and interpretation algorithms for pediatric brain tumors. PMID:28096729

  15. Longitudinal stability of MRI for mapping brain change using tensor-based morphometry.

    PubMed

    Leow, Alex D; Klunder, Andrea D; Jack, Clifford R; Toga, Arthur W; Dale, Anders M; Bernstein, Matt A; Britson, Paula J; Gunter, Jeffrey L; Ward, Chadwick P; Whitwell, Jennifer L; Borowski, Bret J; Fleisher, Adam S; Fox, Nick C; Harvey, Danielle; Kornak, John; Schuff, Norbert; Studholme, Colin; Alexander, Gene E; Weiner, Michael W; Thompson, Paul M

    2006-06-01

    Measures of brain change can be computed from sequential MRI scans, providing valuable information on disease progression, e.g., for patient monitoring and drug trials. Tensor-based morphometry (TBM) creates maps of these brain changes, visualizing the 3D profile and rates of tissue growth or atrophy, but its sensitivity depends on the contrast and geometric stability of the images. As part of the Alzheimer's Disease Neuroimaging Initiative (ADNI), 17 normal elderly subjects were scanned twice (at a 2-week interval) with several 3D 1.5 T MRI pulse sequences: high and low flip angle SPGR/FLASH (from which Synthetic T1 images were generated), MP-RAGE, IR-SPGR (N = 10) and MEDIC (N = 7) scans. For each subject and scan type, a 3D deformation map aligned baseline and follow-up scans, computed with a nonlinear, inverse-consistent elastic registration algorithm. Voxelwise statistics, in ICBM stereotaxic space, visualized the profile of mean absolute change and its cross-subject variance; these maps were then compared using permutation testing. Image stability depended on: (1) the pulse sequence; (2) the transmit/receive coil type (birdcage versus phased array); (3) spatial distortion corrections (using MEDIC sequence information); (4) B1-field intensity inhomogeneity correction (using N3). SPGR/FLASH images acquired using a birdcage coil had least overall deviation. N3 correction reduced coil type and pulse sequence differences and improved scan reproducibility, except for Synthetic T1 images (which were intrinsically corrected for B1-inhomogeneity). No strong evidence favored B0 correction. Although SPGR/FLASH images showed least deviation here, pulse sequence selection for the ADNI project was based on multiple additional image analyses, to be reported elsewhere.

  16. 3-D diffusion tensor MRI anisotropy content-adaptive finite element head model generation for bioelectromagnetic imaging.

    PubMed

    Lee, W H; Kim, T S; Kim, Andrew T; Lee, S Y

    2008-01-01

    Realistic finite element (FE) head models have been successfully applied to bioelectromagnetic problems due to a realistic representation of arbitrary head geometry with inclusion of anisotropic material properties. In this paper, we propose a new automatic FE mesh generation scheme to generate a diffusion tensor MRI (DT-MRI) white matter anisotropy content-adaptive FE head model. We term this kind of mesh as wMesh. With this meshing technique, the anisotropic electrical conductivities derived from DT-MRIs can be best incorporated into the model. The influence of the white matter anisotropy on the EEG forward solutions has been studied via our wMesh head models. The scalp potentials computed from the anisotropic wMesh models against those of the isotropic models have been compared. The results describe that there are substantial changes in the scalp electrical potentials between the isotropic and anisotropic models, indicating that the inclusion of the white matter anisotropy is critical for accurate computation of E/MEG forward and inverse solutions. This fully automatic anisotropy-adaptive wMesh meshing scheme could be useful for modeling of individual-specific FE head models with better incorporation of the white matter anisotropic property towards bioelectromagnetic imaging.

  17. A Real-Time Magnetoencephalography Brain-Computer Interface Using Interactive 3D Visualization and the Hadoop Ecosystem.

    PubMed

    McClay, Wilbert A; Yadav, Nancy; Ozbek, Yusuf; Haas, Andy; Attias, Hagaii T; Nagarajan, Srikantan S

    2015-09-30

    Ecumenically, the fastest growing segment of Big Data is human biology-related data and the annual data creation is on the order of zetabytes. The implications are global across industries, of which the treatment of brain related illnesses and trauma could see the most significant and immediate effects. The next generation of health care IT and sensory devices are acquiring and storing massive amounts of patient related data. An innovative Brain-Computer Interface (BCI) for interactive 3D visualization is presented utilizing the Hadoop Ecosystem for data analysis and storage. The BCI is an implementation of Bayesian factor analysis algorithms that can distinguish distinct thought actions using magneto encephalographic (MEG) brain signals. We have collected data on five subjects yielding 90% positive performance in MEG mid- and post-movement activity. We describe a driver that substitutes the actions of the BCI as mouse button presses for real-time use in visual simulations. This process has been added into a flight visualization demonstration. By thinking left or right, the user experiences the aircraft turning in the chosen direction. The driver components of the BCI can be compiled into any software and substitute a user's intent for specific keyboard strikes or mouse button presses. The BCI's data analytics OPEN ACCESS Brain. Sci. 2015, 5 420 of a subject's MEG brainwaves and flight visualization performance are stored and analyzed using the Hadoop Ecosystem as a quick retrieval data warehouse.

  18. Non-spin-echo 3D transverse hadamard encoded proton spectroscopic imaging in the human brain.

    PubMed

    Cohen, Ouri; Tal, Assaf; Goelman, Gadi; Gonen, Oded

    2013-07-01

    A non-spin-echo multivoxel proton MR localization method based on three-dimensional transverse Hadamard spectroscopic imaging is introduced and demonstrated in a phantom and the human brain. Spatial encoding is achieved with three selective 90° radiofrequency pulses along perpendicular axes: The first two create a longitudinal ±M(Z) Hadamard order in the volume of interest. The third pulse spatially Hadamard-encodes the ±M(Z)s in the volume of interest in the third direction while bringing them to the transverse plane to be acquired immediately. The approaching-ideal point spread function of Hadamard encoding and very short acquisition delay yield signal-to-noise-ratios of 20 ± 8, 23 ± 9, and 31 ± 10 for choline, creatine, and N-acetylaspartate in the human brain at 1.5 T from 1 cm(3) voxels in 21 min. The advantages of transverse Hadamard spectroscopic imaging are that unlike gradient (Fourier) phase-encoding: (i) the volume of interest does not need to be smaller than the field of view to prevent aliasing; (ii) the number of partitions in each direction can be small, 8, 4, or even 2 at no cost in point spread function; (iii) the volume of interest does not have to be contiguous; and (iv) the voxel profile depends on the available B1 and pulse synthesis paradigm and can, therefore, at least theoretically, approach "ideal" "1" inside and "0" elsewhere.

  19. Classification of mathematics deficiency using shape and scale analysis of 3D brain structures

    NASA Astrophysics Data System (ADS)

    Kurtek, Sebastian; Klassen, Eric; Gore, John C.; Ding, Zhaohua; Srivastava, Anuj

    2011-03-01

    We investigate the use of a recent technique for shape analysis of brain substructures in identifying learning disabilities in third-grade children. This Riemannian technique provides a quantification of differences in shapes of parameterized surfaces, using a distance that is invariant to rigid motions and re-parameterizations. Additionally, it provides an optimal registration across surfaces for improved matching and comparisons. We utilize an efficient gradient based method to obtain the optimal re-parameterizations of surfaces. In this study we consider 20 different substructures in the human brain and correlate the differences in their shapes with abnormalities manifested in deficiency of mathematical skills in 106 subjects. The selection of these structures is motivated in part by the past links between their shapes and cognitive skills, albeit in broader contexts. We have studied the use of both individual substructures and multiple structures jointly for disease classification. Using a leave-one-out nearest neighbor classifier, we obtained a 62.3% classification rate based on the shape of the left hippocampus. The use of multiple structures resulted in an improved classification rate of 71.4%.

  20. A Novel Brain Stimulation Technology Provides Compatibility with MRI

    PubMed Central

    Serano, Peter; Angelone, Leonardo M.; Katnani, Husam; Eskandar, Emad; Bonmassar, Giorgio

    2015-01-01

    Clinical electrical stimulation systems — such as pacemakers and deep brain stimulators (DBS) — are an increasingly common therapeutic option to treat a large range of medical conditions. Despite their remarkable success, one of the significant limitations of these medical devices is the limited compatibility with magnetic resonance imaging (MRI), a standard diagnostic tool in medicine. During an MRI exam, the leads used with these devices, implanted in the body of the patient, act as an electric antenna potentially causing a large amount of energy to be absorbed in the tissue, which can lead to serious heat-related injury. This study presents a novel lead design that reduces the antenna effect and allows for decreased tissue heating during MRI. The optimal parameters of the wire design were determined by a combination of computational modeling and experimental measurements. The results of these simulations were used to build a prototype, which was tested in a gel phantom during an MRI scan. Measurement results showed a three-fold decrease in heating when compared to a commercially available DBS lead. Accordingly, the proposed design may allow a significantly increased number of patients with medical implants to have safe access to the diagnostic benefits of MRI. PMID:25924189

  1. Comprehensive brain MRI segmentation in high risk preterm newborns.

    PubMed

    Yu, Xintian; Zhang, Yanjie; Lasky, Robert E; Datta, Sushmita; Parikh, Nehal A; Narayana, Ponnada A

    2010-11-08

    Most extremely preterm newborns exhibit cerebral atrophy/growth disturbances and white matter signal abnormalities on MRI at term-equivalent age. MRI brain volumes could serve as biomarkers for evaluating the effects of neonatal intensive care and predicting neurodevelopmental outcomes. This requires detailed, accurate, and reliable brain MRI segmentation methods. We describe our efforts to develop such methods in high risk newborns using a combination of manual and automated segmentation tools. After intensive efforts to accurately define structural boundaries, two trained raters independently performed manual segmentation of nine subcortical structures using axial T2-weighted MRI scans from 20 randomly selected extremely preterm infants. All scans were re-segmented by both raters to assess reliability. High intra-rater reliability was achieved, as assessed by repeatability and intra-class correlation coefficients (ICC range: 0.97 to 0.99) for all manually segmented regions. Inter-rater reliability was slightly lower (ICC range: 0.93 to 0.99). A semi-automated segmentation approach was developed that combined the parametric strengths of the Hidden Markov Random Field Expectation Maximization algorithm with non-parametric Parzen window classifier resulting in accurate white matter, gray matter, and CSF segmentation. Final manual correction of misclassification errors improved accuracy (similarity index range: 0.87 to 0.89) and facilitated objective quantification of white matter signal abnormalities. The semi-automated and manual methods were seamlessly integrated to generate full brain segmentation within two hours. This comprehensive approach can facilitate the evaluation of large cohorts to rigorously evaluate the utility of regional brain volumes as biomarkers of neonatal care and surrogate endpoints for neurodevelopmental outcomes.

  2. DLP technology application: 3D head tracking and motion correction in medical brain imaging

    NASA Astrophysics Data System (ADS)

    Olesen, Oline V.; Wilm, Jakob; Paulsen, Rasmus R.; Højgaard, Liselotte; Larsen, Rasmus

    2014-03-01

    In this paper we present a novel sensing system, robust Near-infrared Structured Light Scanning (NIRSL) for three-dimensional human model scanning application. Human model scanning due to its nature of various hair and dress appearance and body motion has long been a challenging task. Previous structured light scanning methods typically emitted visible coded light patterns onto static and opaque objects to establish correspondence between a projector and a camera for triangulation. In the success of these methods rely on scanning objects with proper reflective surface for visible light, such as plaster, light colored cloth. Whereas for human model scanning application, conventional methods suffer from low signal to noise ratio caused by low contrast of visible light over the human body. The proposed robust NIRSL, as implemented with the near infrared light, is capable of recovering those dark surfaces, such as hair, dark jeans and black shoes under visible illumination. Moreover, successful structured light scan relies on the assumption that the subject is static during scanning. Due to the nature of body motion, it is very time sensitive to keep this assumption in the case of human model scan. The proposed sensing system, by utilizing the new near-infrared capable high speed LightCrafter DLP projector, is robust to motion, provides accurate and high resolution three-dimensional point cloud, making our system more efficient and robust for human model reconstruction. Experimental results demonstrate that our system is effective and efficient to scan real human models with various dark hair, jeans and shoes, robust to human body motion and produces accurate and high resolution 3D point cloud.

  3. Functional MRI during Hippocampal Deep Brain Stimulation in the Healthy Rat Brain

    PubMed Central

    Van Den Berge, Nathalie; Vanhove, Christian; Descamps, Benedicte; Dauwe, Ine; van Mierlo, Pieter; Vonck, Kristl; Keereman, Vincent; Raedt, Robrecht; Boon, Paul; Van Holen, Roel

    2015-01-01

    Deep Brain Stimulation (DBS) is a promising treatment for neurological and psychiatric disorders. The mechanism of action and the effects of electrical fields administered to the brain by means of an electrode remain to be elucidated. The effects of DBS have been investigated primarily by electrophysiological and neurochemical studies, which lack the ability to investigate DBS-related responses on a whole-brain scale. Visualization of whole-brain effects of DBS requires functional imaging techniques such as functional Magnetic Resonance Imaging (fMRI), which reflects changes in blood oxygen level dependent (BOLD) responses throughout the entire brain volume. In order to visualize BOLD responses induced by DBS, we have developed an MRI-compatible electrode and an acquisition protocol to perform DBS during BOLD fMRI. In this study, we investigate whether DBS during fMRI is valuable to study local and whole-brain effects of hippocampal DBS and to investigate the changes induced by different stimulation intensities. Seven rats were stereotactically implanted with a custom-made MRI-compatible DBS-electrode in the right hippocampus. High frequency Poisson distributed stimulation was applied using a block-design paradigm. Data were processed by means of Independent Component Analysis. Clusters were considered significant when p-values were <0.05 after correction for multiple comparisons. Our data indicate that real-time hippocampal DBS evokes a bilateral BOLD response in hippocampal and other mesolimbic structures, depending on the applied stimulation intensity. We conclude that simultaneous DBS and fMRI can be used to detect local and whole-brain responses to circuit activation with different stimulation intensities, making this technique potentially powerful for exploration of cerebral changes in response to DBS for both preclinical and clinical DBS. PMID:26193653

  4. 3D-Reconstructions and Virtual 4D-Visualization to Study Metamorphic Brain Development in the Sphinx Moth Manduca Sexta.

    PubMed

    Huetteroth, Wolf; El Jundi, Basil; El Jundi, Sirri; Schachtner, Joachim

    2010-01-01

    DURING METAMORPHOSIS, THE TRANSITION FROM THE LARVA TO THE ADULT, THE INSECT BRAIN UNDERGOES CONSIDERABLE REMODELING: new neurons are integrated while larval neurons are remodeled or eliminated. One well acknowledged model to study metamorphic brain development is the sphinx moth Manduca sexta. To further understand mechanisms involved in the metamorphic transition of the brain we generated a 3D standard brain based on selected brain areas of adult females and 3D reconstructed the same areas during defined stages of pupal development. Selected brain areas include for example mushroom bodies, central complex, antennal- and optic lobes. With this approach we eventually want to quantify developmental changes in neuropilar architecture, but also quantify changes in the neuronal complement and monitor the development of selected neuronal populations. Furthermore, we used a modeling software (Cinema 4D) to create a virtual 4D brain, morphing through its developmental stages. Thus the didactical advantages of 3D visualization are expanded to better comprehend complex processes of neuropil formation and remodeling during development. To obtain datasets of the M. sexta brain areas, we stained whole brains with an antiserum against the synaptic vesicle protein synapsin. Such labeled brains were then scanned with a confocal laser scanning microscope and selected neuropils were reconstructed with the 3D software AMIRA 4.1.

  5. Gender and age effects in structural brain asymmetry as measured by MRI texture analysis.

    PubMed

    Kovalev, Vassili A; Kruggel, Frithjof; von Cramon, D Yves

    2003-07-01

    Effects of gender and age on structural brain asymmetry were studied by 3D texture analysis in 380 adults. Asymmetry is detected by comparing the complex 3D gray-scale image patterns in the left and right cerebral hemispheres as revealed by anatomical T1-weighted MRI datasets. The Talairach and Tournoux parcellation system was applied to study the asymmetry on five levels: the whole cerebrum, nine coronal sections, 12 axial sections, boxes resulting from both coronal and axial subdivisions, and by a sliding spherical window of 9 mm diameter. The analysis revealed that the brain asymmetry increases in the anterior-posterior direction starting from the central region onward. Male brains were found to be more asymmetric than female. This gender-related effect is noticeable in all brain areas but is most significant in the superior temporal gyrus, Heschl's gyrus, the adjacent white matter regions in the temporal stem and the knee of the optic radiation, the thalamus, and the posterior cingulate. The brain asymmetry increases significantly with age in the inferior frontal gyrus, anterior insula, anterior cingulate, parahippocampal gyrus, retrosplenial cortex, coronal radiata, and knee region of the internal capsule. Asymmetry decreases with age in the optic radiation, precentral gyrus, and angular gyrus. The texture-based method reported here is based on extended multisort cooccurrence matrices that employ intensity, gradient, and anisotropy features in a uniform way. It is sensitive, simple to reproduce, robust, and unbiased in the sense that segmentation of brain compartments and spatial transformations are not necessary. Thus, it should be considered as another tool for digital morphometry in neuroscience.

  6. 3-D reconstruction of tissue components for atherosclerotic human arteries using ex vivo high-resolution MRI.

    PubMed

    Auer, Martin; Stollberger, Rudolf; Regitnig, Peter; Ebner, Franz; Holzapfel, Gerhard A

    2006-03-01

    Automatic computer-based methods are well suited for the image analysis of the different components in atherosclerotic plaques. Although several groups work on such analysis some of the methods used are oversimplified and require improvements when used within a computational framework for predicting meaningful stress and strain distributions in the heterogeneous arterial wall under various loading conditions. Based on high-resolution magnetic resonance imaging of excised atherosclerotic human arteries and a series of two-dimensional (2-D) contours we present a segmentation tool that permits a three-dimensional (3-D) reconstruction of the most important tissue components of atherosclerotic arteries. The underlying principle of the proposed approach is a model-based snake algorithm for identifying 2-D contours, which uses information about the plaque composition and geometric data of the tissue layers. Validation of the computer-generated tissue boundaries is performed with 100 MR images, which are compared with the results of a manual segmentation performed by four experts. Based on the Hausdorff distance and the average distance for computer-to-expert differences and the interexpert differences for the outer boundary of the adventitia, the adventitia-media, media-intima, intima-lumen and calcification boundaries are less than 1 pixel (0.234 mm). The percentage statistic shows similar results to the modified Williams index in terms of accuracy. Except for the identification of lipid-rich regions the proposed algorithm is automatic. The nonuniform rational B-spline-based computer-generated 3-D models of the individual tissue components provide a basis for clinical and computational analysis.

  7. Superfast elastic registration of histologic images of a whole rat brain for 3D reconstruction

    NASA Astrophysics Data System (ADS)

    Wirtz, Stefan; Fischer, Bernd; Modersitzki, Jan; Schmitt, Oliver

    2004-05-01

    We present a super-fast and parameter-free algorithm for non-rigid elastic registration of images of a serially sectioned whole rat brain. The purpose is to produce a three-dimensional high-resolution reconstruction. The registration is modelled as a minimization problem of a functional consisting of a distance measure and a regularizer based on the elastic potential of the displacement field. The minimization of the functional leads to a system of non-linear partial differential equations, the so-called Navier-Lame equations (NLE). Discretization of the NLE and a fixed point type iteration method lead to a linear system of equations, which has to be solved at each iteration step. We not only present a super-fast solution technique for this system, but also come up with sound strategies for accelerating the outer iteration. This does include a multi-scale approach based on a Gaussian pyramid as well as a clever estimation of the material constants for the elastic potential. The results of the registration process were controlled by an expert who was able to recognize histological details like laminations which was not possible before. Therefore, it is essential to apply elastic registration to this kind of imaging problem. Finally, the visually pleasing results were quantified by a distance measure leading to an improvement of about 79% after just 35 iteration steps.

  8. volBrain: An Online MRI Brain Volumetry System.

    PubMed

    Manjón, José V; Coupé, Pierrick

    2016-01-01

    The amount of medical image data produced in clinical and research settings is rapidly growing resulting in vast amount of data to analyze. Automatic and reliable quantitative analysis tools, including segmentation, allow to analyze brain development and to understand specific patterns of many neurological diseases. This field has recently experienced many advances with successful techniques based on non-linear warping and label fusion. In this work we present a novel and fully automatic pipeline for volumetric brain analysis based on multi-atlas label fusion technology that is able to provide accurate volumetric information at different levels of detail in a short time. This method is available through the volBrain online web interface (http://volbrain.upv.es), which is publically and freely accessible to the scientific community. Our new framework has been compared with current state-of-the-art methods showing very competitive results.

  9. volBrain: An Online MRI Brain Volumetry System

    PubMed Central

    Manjón, José V.; Coupé, Pierrick

    2016-01-01

    The amount of medical image data produced in clinical and research settings is rapidly growing resulting in vast amount of data to analyze. Automatic and reliable quantitative analysis tools, including segmentation, allow to analyze brain development and to understand specific patterns of many neurological diseases. This field has recently experienced many advances with successful techniques based on non-linear warping and label fusion. In this work we present a novel and fully automatic pipeline for volumetric brain analysis based on multi-atlas label fusion technology that is able to provide accurate volumetric information at different levels of detail in a short time. This method is available through the volBrain online web interface (http://volbrain.upv.es), which is publically and freely accessible to the scientific community. Our new framework has been compared with current state-of-the-art methods showing very competitive results. PMID:27512372

  10. Human brain diffusion tensor imaging at submillimeter isotropic resolution on a 3Tesla clinical MRI scanner.

    PubMed

    Chang, Hing-Chiu; Sundman, Mark; Petit, Laurent; Guhaniyogi, Shayan; Chu, Mei-Lan; Petty, Christopher; Song, Allen W; Chen, Nan-kuei

    2015-09-01

    The advantages of high-resolution diffusion tensor imaging (DTI) have been demonstrated in a recent post-mortem human brain study (Miller et al., NeuroImage 2011;57(1):167-181), showing that white matter fiber tracts can be much more accurately detected in data at a submillimeter isotropic resolution. To our knowledge, in vivo human brain DTI at a submillimeter isotropic resolution has not been routinely achieved yet because of the difficulty in simultaneously achieving high resolution and high signal-to-noise ratio (SNR) in DTI scans. Here we report a 3D multi-slab interleaved EPI acquisition integrated with multiplexed sensitivity encoded (MUSE) reconstruction, to achieve high-quality, high-SNR and submillimeter isotropic resolution (0.85×0.85×0.85mm(3)) in vivo human brain DTI on a 3Tesla clinical MRI scanner. In agreement with the previously reported post-mortem human brain DTI study, our in vivo data show that the structural connectivity networks of human brains can be mapped more accurately and completely with high-resolution DTI as compared with conventional DTI (e.g., 2×2×2mm(3)).

  11. Semi-automated 3D segmentation of major tracts in the rat brain: comparing DTI with standard histological methods.

    PubMed

    Gyengesi, Erika; Calabrese, Evan; Sherrier, Matthew C; Johnson, G Allan; Paxinos, George; Watson, Charles

    2014-03-01

    Researchers working with rodent models of neurological disease often require an accurate map of the anatomical organization of the white matter of the rodent brain. With the increasing popularity of small animal MRI techniques, including diffusion tensor imaging (DTI), there is considerable interest in rapid segmentation methods of neurological structures for quantitative comparisons. DTI-derived tractography allows simple and rapid segmentation of major white matter tracts, but the anatomic accuracy of these computer-generated fibers is open to question and has not been rigorously evaluated in the rat brain. In this study, we examine the anatomic accuracy of tractography-based segmentation in the adult rat brain. We analysed 12 major white matter pathways using semi-automated tractography-based segmentation alongside manual segmentation of Gallyas silver-stained histology sections. We applied four fiber-tracking algorithms to the DTI data-two integration methods and two deflection methods. In many cases, tractography-based segmentation closely matched histology-based segmentation; however different tractography algorithms produced dramatically different results. Results suggest that certain white matter pathways are more amenable to tractography-based segmentation than others. We believe that these data will help researchers decide whether it is appropriate to use tractography-based segmentation of white matter structures for quantitative DTI-based analysis of neurologic disease models.

  12. A Real-Time Magnetoencephalography Brain-Computer Interface Using Interactive 3D Visualization and the Hadoop Ecosystem

    PubMed Central

    McClay, Wilbert A.; Yadav, Nancy; Ozbek, Yusuf; Haas, Andy; Attias, Hagaii T.; Nagarajan, Srikantan S.

    2015-01-01

    Ecumenically, the fastest growing segment of Big Data is human biology-related data and the annual data creation is on the order of zetabytes. The implications are global across industries, of which the treatment of brain related illnesses and trauma could see the most significant and immediate effects. The next generation of health care IT and sensory devices are acquiring and storing massive amounts of patient related data. An innovative Brain-Computer Interface (BCI) for interactive 3D visualization is presented utilizing the Hadoop Ecosystem for data analysis and storage. The BCI is an implementation of Bayesian factor analysis algorithms that can distinguish distinct thought actions using magneto encephalographic (MEG) brain signals. We have collected data on five subjects yielding 90% positive performance in MEG mid- and post-movement activity. We describe a driver that substitutes the actions of the BCI as mouse button presses for real-time use in visual simulations. This process has been added into a flight visualization demonstration. By thinking left or right, the user experiences the aircraft turning in the chosen direction. The driver components of the BCI can be compiled into any software and substitute a user’s intent for specific keyboard strikes or mouse button presses. The BCI’s data analytics of a subject’s MEG brainwaves and flight visualization performance are stored and analyzed using the Hadoop Ecosystem as a quick retrieval data warehouse. PMID:26437432

  13. Structural and functional correlates of visual field asymmetry in the human brain by diffusion kurtosis MRI and functional MRI.

    PubMed

    O'Connell, Caitlin; Ho, Leon C; Murphy, Matthew C; Conner, Ian P; Wollstein, Gadi; Cham, Rakie; Chan, Kevin C

    2016-11-09

    Human visual performance has been observed to show superiority in localized regions of the visual field across many classes of stimuli. However, the underlying neural mechanisms remain unclear. This study aims to determine whether the visual information processing in the human brain is dependent on the location of stimuli in the visual field and the corresponding neuroarchitecture using blood-oxygenation-level-dependent functional MRI (fMRI) and diffusion kurtosis MRI, respectively, in 15 healthy individuals at 3 T. In fMRI, visual stimulation to the lower hemifield showed stronger brain responses and larger brain activation volumes than the upper hemifield, indicative of the differential sensitivity of the human brain across the visual field. In diffusion kurtosis MRI, the brain regions mapping to the lower visual field showed higher mean kurtosis, but not fractional anisotropy or mean diffusivity compared with the upper visual field. These results suggested the different distributions of microstructural organization across visual field brain representations. There was also a strong positive relationship between diffusion kurtosis and fMRI responses in the lower field brain representations. In summary, this study suggested the structural and functional brain involvements in the asymmetry of visual field responses in humans, and is important to the neurophysiological and psychological understanding of human visual information processing.

  14. Automated detection of periventricular veins on 7 T brain MRI

    NASA Astrophysics Data System (ADS)

    Kuijf, Hugo J.; Bouvy, Willem H.; Zwanenburg, Jaco J. M.; Viergever, Max A.; Biessels, Geert Jan; Vincken, Koen L.

    2015-03-01

    Cerebral small vessel disease is common in elderly persons and a leading cause of cognitive decline, dementia, and acute stroke. With the introduction of ultra-high field strength 7.0T MRI, it is possible to visualize small vessels in the brain. In this work, a proof-of-principle study is conducted to assess the feasibility of automatically detecting periventricular veins. Periventricular veins are organized in a fan-pattern and drain venous blood from the brain towards the caudate vein of Schlesinger, which is situated along the lateral ventricles. Just outside this vein, a region-of- interest (ROI) through which all periventricular veins must cross is defined. Within this ROI, a combination of the vesselness filter, tubular tracking, and hysteresis thresholding is applied to locate periventricular veins. All detected locations were evaluated by an expert human observer. The results showed a positive predictive value of 88% and a sensitivity of 95% for detecting periventricular veins. The proposed method shows good results in detecting periventricular veins in the brain on 7.0T MR images. Compared to previous works, that only use a 1D or 2D ROI and limited image processing, our work presents a more comprehensive definition of the ROI, advanced image processing techniques to detect periventricular veins, and a quantitative analysis of the performance. The results of this proof-of-principle study are promising and will be used to assess periventricular veins on 7.0T brain MRI.

  15. 3D He-3 diffusion MRI as a local in vivo morphometric tool to evaluate emphysematous rat lungs

    SciTech Connect

    Jacob, Rick E.; Minard, Kevin R.; Laicher, Gernot J.; Timchalk, Charles

    2008-08-21

    In this work, we validate 3He magnetic resonance imaging as a non-invasive morphometric tool to assess emphysematous disease state on a local level. Emphysema was induced intratracheally in rats with 25U/100g body weight of porcine pancreatic elastase dissolved in 200 μL saline. Rats were then paired with saline-dosed controls. Nine three-dimensional 3He diffusion-weighted images were acquired at one-, two-, or three-weeks post-dose, after which the lungs were harvested and prepared for histological analysis. Recently introduced indices sensitive to the heterogeneity of the airspace size distribution were calculated. These indices, D1 and D2, were derived from the moments of the mean equivalent airway diameters. Averaged over the entire lung, it is shown that the 3He diffusivity (Dave) and anisotropy (Dan) both correlate with histology (R = 0.85, p < 0.0001 and R = 0.88, p < 0.0001, respectively). By matching small (0.046 cm2) regions in 3He images with corresponding regions in histological slices, Dave and Dan each correlate significantly with both D1 and D2 (R = 0.93, p < 0.0001). It is concluded that 3He MRI is a viable non-invasive morphometric tool for localized in vivo emphysema assessment.

  16. Endolymphatic Hydrops Reversal following Acetazolamide Therapy: Demonstration with Delayed Intravenous Contrast-Enhanced 3D-FLAIR MRI.

    PubMed

    Sepahdari, A R; Vorasubin, N; Ishiyama, G; Ishiyama, A

    2016-01-01

    Endolymphatic hydrops, the primary pathologic alteration in Menière disease, can be visualized by using delayed intravenous contrast-enhanced 3D-FLAIR MR imaging. It is not known whether MR imaging-demonstrable changes of hydrops fluctuate with disease activity or are fixed. We describe the results of baseline and posttreatment MR imaging studies in a group of subjects with Menière disease with hydrops who were treated with acetazolamide. Seven subjects with untreated Menière disease with MR imaging evidence of hydrops had repeat MR imaging during acetazolamide treatment. Symptoms and imaging findings were assessed at each time point. Five subjects showed symptom improvement, of whom 3 had improvement or resolution of hydrops. One subject had recurrent symptoms with recurrent hydrops after discontinuing therapy. Two had unchanged hydrops despite symptom improvement. Subjects with unchanged symptoms had unchanged hydrops. Hydrops reversal may be seen with acetazolamide treatment in Menière disease. MR imaging may provide an additional biomarker of disease.

  17. Comprehensive 3D Model of Shock Wave-Brain Interactions in Blast-Induced Traumatic Brain Injuries

    DTIC Science & Technology

    2009-10-01

    waves can cause brain damage by other mechanisms including excess pressure (leading to contusions), excess strain (leading to subdural ... hematomas and/or diffuse axonal injuries), and, in particular, cavitation effects (leading to subcellular damage). This project aims at the development of a

  18. Ultra-low-cost 3D gaze estimation: an intuitive high information throughput compliment to direct brain-machine interfaces

    NASA Astrophysics Data System (ADS)

    Abbott, W. W.; Faisal, A. A.

    2012-08-01

    Eye movements are highly correlated with motor intentions and are often retained by patients with serious motor deficiencies. Despite this, eye tracking is not widely used as control interface for movement in impaired patients due to poor signal interpretation and lack of control flexibility. We propose that tracking the gaze position in 3D rather than 2D provides a considerably richer signal for human machine interfaces by allowing direct interaction with the environment rather than via computer displays. We demonstrate here that by using mass-produced video-game hardware, it is possible to produce an ultra-low-cost binocular eye-tracker with comparable performance to commercial systems, yet 800 times cheaper. Our head-mounted system has 30 USD material costs and operates at over 120 Hz sampling rate with a 0.5-1 degree of visual angle resolution. We perform 2D and 3D gaze estimation, controlling a real-time volumetric cursor essential for driving complex user interfaces. Our approach yields an information throughput of 43 bits s-1, more than ten times that of invasive and semi-invasive brain-machine interfaces (BMIs) that are vastly more expensive. Unlike many BMIs our system yields effective real-time closed loop control of devices (10 ms latency), after just ten minutes of training, which we demonstrate through a novel BMI benchmark—the control of the video arcade game ‘Pong’.

  19. Ultra-low-cost 3D gaze estimation: an intuitive high information throughput compliment to direct brain-machine interfaces.

    PubMed

    Abbott, W W; Faisal, A A

    2012-08-01

    Eye movements are highly correlated with motor intentions and are often retained by patients with serious motor deficiencies. Despite this, eye tracking is not widely used as control interface for movement in impaired patients due to poor signal interpretation and lack of control flexibility. We propose that tracking the gaze position in 3D rather than 2D provides a considerably richer signal for human machine interfaces by allowing direct interaction with the environment rather than via computer displays. We demonstrate here that by using mass-produced video-game hardware, it is possible to produce an ultra-low-cost binocular eye-tracker with comparable performance to commercial systems, yet 800 times cheaper. Our head-mounted system has 30 USD material costs and operates at over 120 Hz sampling rate with a 0.5-1 degree of visual angle resolution. We perform 2D and 3D gaze estimation, controlling a real-time volumetric cursor essential for driving complex user interfaces. Our approach yields an information throughput of 43 bits s(-1), more than ten times that of invasive and semi-invasive brain-machine interfaces (BMIs) that are vastly more expensive. Unlike many BMIs our system yields effective real-time closed loop control of devices (10 ms latency), after just ten minutes of training, which we demonstrate through a novel BMI benchmark--the control of the video arcade game 'Pong'.

  20. QuickBrain MRI for the detection of acute pediatric traumatic brain injury.

    PubMed

    Sheridan, David C; Newgard, Craig D; Selden, Nathan R; Jafri, Mubeen A; Hansen, Matthew L

    2017-02-01

    OBJECTIVE The current gold-standard imaging modality for pediatric traumatic brain injury (TBI) is CT, but it confers risks associated with ionizing radiation. QuickBrain MRI (qbMRI) is a rapid brain MRI protocol that has been studied in the setting of hydrocephalus, but its ability to detect traumatic injuries is unknown. METHODS The authors performed a retrospective cohort study of pediatric patients with TBI who were undergoing evaluation at a single Level I trauma center between February 2010 and December 2013. Patients who underwent CT imaging of the head and qbMRI during their acute hospitalization were included. Images were reviewed independently by 2 neuroradiology fellows blinded to patient identifiers. Image review consisted of identifying traumatic mass lesions and their intracranial compartment and the presence or absence of midline shift. CT imaging was used as the reference against which qbMRI was measured. RESULTS A total of 54 patients met the inclusion criteria; the median patient age was 3.24 years, 65% were male, and 74% were noted to have a Glasgow Coma Scale score of 14 or greater. The sensitivity and specificity of qbMRI to detect any lesion were 85% (95% CI 73%-93%) and 100% (95% CI 61%-100%), respectively; the sensitivity increased to 100% (95% CI 89%-100%) for clinically important TBIs as previously defined. The mean interval between CT and qbMRI was 27.5 hours, and approximately half of the images were obtained within 12 hours. CONCLUSIONS In this retrospective pilot study, qbMRI demonstrated reasonable sensitivity and specificity for detecting a lesion or injury seen with neuroimaging (radiographic TBI) and clinically important acute pediatric TBI.

  1. Steady-State VEP-Based Brain-Computer Interface Control in an Immersive 3D Gaming Environment

    NASA Astrophysics Data System (ADS)

    Lalor, E. C.; Kelly, S. P.; Finucane, C.; Burke, R.; Smith, R.; Reilly, R. B.; McDarby, G.

    2005-12-01

    This paper presents the application of an effective EEG-based brain-computer interface design for binary control in a visually elaborate immersive 3D game. The BCI uses the steady-state visual evoked potential (SSVEP) generated in response to phase-reversing checkerboard patterns. Two power-spectrum estimation methods were employed for feature extraction in a series of offline classification tests. Both methods were also implemented during real-time game play. The performance of the BCI was found to be robust to distracting visual stimulation in the game and relatively consistent across six subjects, with 41 of 48 games successfully completed. For the best performing feature extraction method, the average real-time control accuracy across subjects was 89%. The feasibility of obtaining reliable control in such a visually rich environment using SSVEPs is thus demonstrated and the impact of this result is discussed.

  2. MRI magnetic field stimulates rotational sensors of the brain.

    PubMed

    Roberts, Dale C; Marcelli, Vincenzo; Gillen, Joseph S; Carey, John P; Della Santina, Charles C; Zee, David S

    2011-10-11

    Vertigo in and around magnetic resonance imaging (MRI) machines has been noted for years [1, 2]. Several mechanisms have been suggested to explain these sensations [3, 4], yet without direct, objective measures, the cause is unknown. We found that all of our healthy human subjects developed a robust nystagmus while simply lying in the static magnetic field of an MRI machine. Patients lacking labyrinthine function did not. We use the pattern of eye movements as a measure of vestibular stimulation to show that the stimulation is static (continuous, proportional to static magnetic field strength, requiring neither head movement nor dynamic change in magnetic field strength) and directional (sensitive to magnetic field polarity and head orientation). Our calculations and geometric model suggest that magnetic vestibular stimulation (MVS) derives from a Lorentz force resulting from interaction between the magnetic field and naturally occurring ionic currents in the labyrinthine endolymph fluid. This force pushes on the semicircular canal cupula, leading to nystagmus. We emphasize that the unique, dual role of endolymph in the delivery of both ionic current and fluid pressure, coupled with the cupula's function as a pressure sensor, makes magnetic-field-induced nystagmus and vertigo possible. Such effects could confound functional MRI studies of brain behavior, including resting-state brain activity.

  3. MRI Magnetic Field Stimulates Rotational Sensors of the Brain

    PubMed Central

    Roberts, Dale C.; Marcelli, Vincenzo; Gillen, Joseph S.; Carey, John P.; Santina, Charles C. Della; Zee, David S.

    2012-01-01

    SUMMARY Vertigo in and around MRI machines has been noted for years [1, 2]. Several mechanisms have been suggested to explain these sensations [3, 4], yet without direct, objective measures, the cause is unknown. We found that all healthy human subjects lying in the static magnetic field of an MRI machine develop a robust nystagmus. Patients lacking labyrinthine function do not. Here we use the pattern of eye movements as a measure of vestibular stimulation to show that the stimulation is static (continuous, proportional to static magnetic field strength, requiring neither head movement nor dynamic change in magnetic field strength) and directional (sensitive to magnetic field polarity and head orientation). Our calculations and geometric model suggest that magnetic vestibular stimulation derives from a Lorentz force due to interaction between the magnetic field and naturally-occurring ionic currents in the labyrinthine endolymph fluid. This force pushes on the semicircular canal cupula, leading to nystagmus. We emphasize that the unique, dual role of endolymph in the delivery of both ionic current and fluid pressure, coupled with the cupula’s function as a pressure sensor, makes magnetic field induced nystagmus and vertigo possible. Such effects could confound fMRI studies of brain behavior, including resting-state brain activity. PMID:21945276

  4. Brain Tumor Segmentation Using Convolutional Neural Networks in MRI Images.

    PubMed

    Pereira, Sergio; Pinto, Adriano; Alves, Victor; Silva, Carlos A

    2016-05-01

    Among brain tumors, gliomas are the most common and aggressive, leading to a very short life expectancy in their highest grade. Thus, treatment planning is a key stage to improve the quality of life of oncological patients. Magnetic resonance imaging (MRI) is a widely used imaging technique to assess these tumors, but the large amount of data produced by MRI prevents manual segmentation in a reasonable time, limiting the use of precise quantitative measurements in the clinical practice. So, automatic and reliable segmentation methods are required; however, the large spatial and structural variability among brain tumors make automatic segmentation a challenging problem. In this paper, we propose an automatic segmentation method based on Convolutional Neural Networks (CNN), exploring small 3 ×3 kernels. The use of small kernels allows designing a deeper architecture, besides having a positive effect against overfitting, given the fewer number of weights in the network. We also investigated the use of intensity normalization as a pre-processing step, which though not common in CNN-based segmentation methods, proved together with data augmentation to be very effective for brain tumor segmentation in MRI images. Our proposal was validated in the Brain Tumor Segmentation Challenge 2013 database (BRATS 2013), obtaining simultaneously the first position for the complete, core, and enhancing regions in Dice Similarity Coefficient metric (0.88, 0.83, 0.77) for the Challenge data set. Also, it obtained the overall first position by the online evaluation platform. We also participated in the on-site BRATS 2015 Challenge using the same model, obtaining the second place, with Dice Similarity Coefficient metric of 0.78, 0.65, and 0.75 for the complete, core, and enhancing regions, respectively.

  5. Brain Tumor Segmentation using Convolutional Neural Networks in MRI Images.

    PubMed

    Pereira, Sergio; Pinto, Adriano; Alves, Victor; Silva, Carlos A

    2016-03-04

    Among brain tumors, gliomas are the most common and aggressive, leading to a very short life expectancy in their highest grade. Thus, treatment planning is a key stage to improve the quality of life of oncological patients. Magnetic Resonance Imaging (MRI) is a widely used imaging technique to assess these tumors, but the large amount of data produced by MRI prevents manual segmentation in a reasonable time, limiting the use of precise quantitative measurements in the clinical practice. So, automatic and reliable segmentation methods are required; however, the large spatial and structural variability among brain tumors make automatic segmentation a challenging problem. In this paper, we propose an automatic segmentation method based on Convolutional Neural Networks (CNN), exploring small 33 kernels. The use of small kernels allows designing a deeper architecture, besides having a positive effect against overfitting, given the fewer number of weights in the network. We also investigated the use of intensity normalization as a pre-processing step, which though not common in CNN-based segmentation methods, proved together with data augmentation to be very effective for brain tumor segmentation in MRI images. Our proposal was validated in the Brain Tumor Segmentation Challenge 2013 database (BRATS 2013), obtaining simultaneously the first position for the complete, core, and enhancing regions in Dice Similarity Coefficient metric (0:88, 0:83, 0:77) for the Challenge data set. Also, it obtained the overall first position by the online evaluation platform. We also participated in the on-site BRATS 2015 Challenge using the same model, obtaining the second place, with Dice Similarity Coefficient metric of 0:78, 0:65, and 0:75 for the complete, core, and enhancing regions, respectively.

  6. Quantitative analysis of brain pathology based on MRI and brain atlases--applications for cerebral palsy.

    PubMed

    Faria, Andreia V; Hoon, Alexander; Stashinko, Elaine; Li, Xin; Jiang, Hangyi; Mashayekh, Ameneh; Akhter, Kazi; Hsu, John; Oishi, Kenichi; Zhang, Jiangyang; Miller, Michael I; van Zijl, Peter C M; Mori, Susumu

    2011-02-01

    We have developed a new method to provide a comprehensive quantitative analysis of brain anatomy in cerebral palsy patients, which makes use of two techniques: diffusion tensor imaging and automated 3D whole brain segmentation based on our brain atlas and a nonlinear normalization technique (large-deformation diffeomorphic metric mapping). This method was applied to 13 patients and normal controls. The reliability of the automated segmentation revealed close agreement with the manual segmentation. We illustrate some potential applications for individual characterization and group comparison. This technique also provides a framework for determining the impact of various neuroanatomic features on brain functions.

  7. High-Resolution 3D Proton MRI of Hyperpolarized Gas Enabled by Parahydrogen and Rh/TiO2 Heterogeneous Catalyst

    PubMed Central

    Barskiy, Danila A.; Coffey, Aaron M.; Truong, Milton L.; Salnikov, Oleg G.; Khudorozhkov, Alexander K.; Inozemtseva, Elizaveta A.; Prosvirin, Igor P.; Bukhtiyarov, Valery I.; Waddell, Kevin W.; Koptyug, Igor V.

    2015-01-01

    Several supported metal catalysts were synthesized, characterized, and tested in heterogeneous hydrogenation of propene with parahydrogen to maximize nuclear spin hyperpolarization of propane gas using parahydrogen induced polarization (PHIP). The Rh/TiO2 catalyst with a metal particle size of 1.6 nm was found to be the most active and effective in the pairwise hydrogen addition and robust, demonstrating reproducible results with multiple hydrogenation experiments and stability for ≥1.5 years. 3D 1H magnetic resonance imaging (MRI) of 1 % hyperpolarized flowing gas with microscale spatial resolution (625 × 625 × 625 μm3) and large imaging matrix (128 × 128 × 32) was demonstrated by using a preclinical 4.7 T scanner and 17.4 s imaging scan time. PMID:24961814

  8. A New Method to Explore the Spectral Impact of the Piriform Fossae on the Singing Voice: Benchmarking Using MRI-Based 3D-Printed Vocal Tracts

    PubMed Central

    Delvaux, Bertrand; Howard, David

    2014-01-01

    The piriform fossae are the 2 pear-shaped cavities lateral to the laryngeal vestibule at the lower end of the vocal tract. They act acoustically as side-branches to the main tract, resulting in a spectral zero in the output of the human voice. This study investigates their spectral role by comparing numerical and experimental results of MRI-based 3D printed Vocal Tracts, for which a new experimental method (based on room acoustics) is introduced. The findings support results in the literature: the piriform fossae create a spectral trough in the region 4–5 kHz and act as formants repellents. Moreover, this study extends those results by demonstrating numerically and perceptually the impact of having large piriform fossae on the sung output. PMID:25048199

  9. A new method to explore the spectral impact of the piriform fossae on the singing voice: benchmarking using MRI-based 3D-printed vocal tracts.

    PubMed

    Delvaux, Bertrand; Howard, David

    2014-01-01

    The piriform fossae are the 2 pear-shaped cavities lateral to the laryngeal vestibule at the lower end of the vocal tract. They act acoustically as side-branches to the main tract, resulting in a spectral zero in the output of the human voice. This study investigates their spectral role by comparing numerical and experimental results of MRI-based 3D printed Vocal Tracts, for which a new experimental method (based on room acoustics) is introduced. The findings support results in the literature: the piriform fossae create a spectral trough in the region 4-5 kHz and act as formants repellents. Moreover, this study extends those results by demonstrating numerically and perceptually the impact of having large piriform fossae on the sung output.

  10. Functional MRI and intraoperative brain mapping to evaluate brain plasticity in patients with brain tumours and hemiparesis

    PubMed Central

    Roux, F; Boulanouar, K; Ibarrola, D; Tremoulet, M; Chollet, F; Berry, I

    2000-01-01

    OBJECTIVE—To support the hypothesis about the potential compensatory role of ipsilateral corticofugal pathways when the contralateral pathways are impaired by brain tumours.
METHODS—Retrospective analysis was carried out on the results of functional MRI (fMRI) of a selected group of five paretic patients with Rolandic brain tumours who exhibited an abnormally high ipsilateral/contralateral ratio of activation—that is, movements of the paretic hand activated predominately the ipsilateral cortex. Brain activation was achieved with a flexion extension of the fingers. Statistical parametric activation was obtained using a t test and a threshold of p<0.001. These patients, candidates for tumour resection, also underwent cortical intraoperative stimulation that was correlated to the fMRI spatial data using three dimensional reconstructions of the brain. Three patients also had postoperative control fMRI.
RESULTS—The absence of fMRI activation of the primary sensorimotor cortex normally innervating the paretic hand for the threshold chosen, was correlated with completely negative cortical responses of the cortical hand area during the operation. The preoperative fMRI activation of these patients predominantly found in the ipsilateral frontal and primary sensorimotor cortices could be related to the residual ipsilateral hand function. Postoperatively, the fMRI activation returned to more classic patterns of activation, reflecting the consequences of therapy.
CONCLUSION—In paretic patients with brain tumours, ipsilateral control could be implicated in the residual hand function, when the normal primary pathways are impaired. The possibility that functional tissue still remains in the peritumorous sensorimotor cortex even when the preoperative fMRI and the cortical intraoperative stimulations are negative, should be taken into account when planning the tumour resection and during the operation.

 PMID:10990503

  11. Inverse Planning Approach for 3-D MRI-Based Pulse-Dose Rate Intracavitary Brachytherapy in Cervix Cancer

    SciTech Connect

    Chajon, Enrique; Dumas, Isabelle; Touleimat, Mahmoud B.Sc.; Magne, Nicolas; Coulot, Jeremy; Verstraet, Rodolfe; Lefkopoulos, Dimitri; Haie-Meder, Christine

    2007-11-01

    Purpose: The purpose of this study was to evaluate the inverse planning simulated annealing (IPSA) software for the optimization of dose distribution in patients with cervix carcinoma treated with MRI-based pulsed-dose rate intracavitary brachytherapy. Methods and Materials: Thirty patients treated with a technique using a customized vaginal mold were selected. Dose-volume parameters obtained using the IPSA method were compared with the classic manual optimization method (MOM). Target volumes and organs at risk were delineated according to the Gynecological Brachytherapy Group/European Society for Therapeutic Radiology and Oncology recommendations. Because the pulsed dose rate program was based on clinical experience with low dose rate, dwell time values were required to be as homogeneous as possible. To achieve this goal, different modifications of the IPSA program were applied. Results: The first dose distribution calculated by the IPSA algorithm proposed a heterogeneous distribution of dwell time positions. The mean D90, D100, and V100 calculated with both methods did not differ significantly when the constraints were applied. For the bladder, doses calculated at the ICRU reference point derived from the MOM differed significantly from the doses calculated by the IPSA method (mean, 58.4 vs. 55 Gy respectively; p = 0.0001). For the rectum, the doses calculated at the ICRU reference point were also significantly lower with the IPSA method. Conclusions: The inverse planning method provided fast and automatic solutions for the optimization of dose distribution. However, the straightforward use of IPSA generated significant heterogeneity in dwell time values. Caution is therefore recommended in the use of inverse optimization tools with clinical relevance study of new dosimetric rules.

  12. Prior knowledge driven multiscale segmentation of brain MRI.

    PubMed

    Akselrod-Ballin, Ayelet; Galun, Meirav; Gomori, John Moshe; Brandt, Achi; Basri, Ronen

    2007-01-01

    We present a novel automatic multiscale algorithm applied to segmentation of anatomical structures in brain MRI. The algorithm which is derived from algebraic multigrid, uses a graph representation of the image and performs a coarsening process that produces a full hierarchy of segments. Our main contribution is the incorporation of prior knowledge information into the multiscale framework through a Bayesian formulation. The probabilistic information is based on an atlas prior and on a likelihood function estimated from a manually labeled training set. The significance of our new approach is that the constructed pyramid, reflects the prior knowledge formulated. This leads to an accurate and efficient methodology for detection of various anatomical structures simultaneously. Quantitative validation results on gold standard MRI show the benefit of our approach.

  13. Automated selection of brain regions for real-time fMRI brain-computer interfaces

    NASA Astrophysics Data System (ADS)

    Lührs, Michael; Sorger, Bettina; Goebel, Rainer; Esposito, Fabrizio

    2017-02-01

    Objective. Brain-computer interfaces (BCIs) implemented with real-time functional magnetic resonance imaging (rt-fMRI) use fMRI time-courses from predefined regions of interest (ROIs). To reach best performances, localizer experiments and on-site expert supervision are required for ROI definition. To automate this step, we developed two unsupervised computational techniques based on the general linear model (GLM) and independent component analysis (ICA) of rt-fMRI data, and compared their performances on a communication BCI. Approach. 3 T fMRI data of six volunteers were re-analyzed in simulated real-time. During a localizer run, participants performed three mental tasks following visual cues. During two communication runs, a letter-spelling display guided the subjects to freely encode letters by performing one of the mental tasks with a specific timing. GLM- and ICA-based procedures were used to decode each letter, respectively using compact ROIs and whole-brain distributed spatio-temporal patterns of fMRI activity, automatically defined from subject-specific or group-level maps. Main results. Letter-decoding performances were comparable to supervised methods. In combination with a similarity-based criterion, GLM- and ICA-based approaches successfully decoded more than 80% (average) of the letters. Subject-specific maps yielded optimal performances. Significance. Automated solutions for ROI selection may help accelerating the translation of rt-fMRI BCIs from research to clinical applications.

  14. Joint Design of Excitation k-Space Trajectory and RF Pulse for Small-Tip 3D Tailored Excitation in MRI.

    PubMed

    Hao, Sun; Fessler, Jeffrey A; Noll, Douglas C; Nielsen, Jon-Fredrik

    2016-02-01

    We propose a new method for the joint design of k-space trajectory and RF pulse in 3D small-tip tailored excitation. Designing time-varying RF and gradient waveforms for a desired 3D target excitation pattern in MRI poses a non-linear, non-convex, constrained optimization problem with relatively large problem size that is difficult to solve directly. Existing joint pulse design approaches are therefore typically restricted to predefined trajectory types such as EPI or stack-of-spirals that intrinsically satisfy the gradient maximum and slew rate constraints and reduce the problem size (dimensionality) dramatically, but lead to suboptimal excitation accuracy for a given pulse duration. Here we use a 2nd-order B-spline basis that can be fitted to an arbitrary k-space trajectory, and allows the gradient constraints to be implemented efficiently. We show that this allows the joint optimization problem to be solved with quite general k-space trajectories. Starting from an arbitrary initial trajectory, we first approximate the trajectory using B-spline basis, and then optimize the corresponding coefficients. We evaluate our method in simulation using four different k-space initializations: stack-of-spirals, SPINS, KT-points, and a new method based on KT-points. In all cases, our approach leads to substantial improvement in excitation accuracy for a given pulse duration. We also validated our method for inner-volume excitation using phantom experiments. The computation is fast enough for online applications.

  15. Postmortem examination of patient H.M.’s brain based on histological sectioning and digital 3D reconstruction

    NASA Astrophysics Data System (ADS)

    Annese, Jacopo; Schenker-Ahmed, Natalie M.; Bartsch, Hauke; Maechler, Paul; Sheh, Colleen; Thomas, Natasha; Kayano, Junya; Ghatan, Alexander; Bresler, Noah; Frosch, Matthew P.; Klaming, Ruth; Corkin, Suzanne

    2014-01-01

    Modern scientific knowledge of how memory functions are organized in the human brain originated from the case of Henry G. Molaison (H.M.), an epileptic patient whose amnesia ensued unexpectedly following a bilateral surgical ablation of medial temporal lobe structures, including the hippocampus. The neuroanatomical extent of the 1953 operation could not be assessed definitively during H.M.’s life. Here we describe the results of a procedure designed to reconstruct a microscopic anatomical model of the whole brain and conduct detailed 3D measurements in the medial temporal lobe region. This approach, combined with cellular-level imaging of stained histological slices, demonstrates a significant amount of residual hippocampal tissue with distinctive cytoarchitecture. Our study also reveals diffuse pathology in the deep white matter and a small, circumscribed lesion in the left orbitofrontal cortex. The findings constitute new evidence that may help elucidate the consequences of H.M.’s operation in the context of the brain’s overall pathology.

  16. Postmortem examination of patient H.M.’s brain based on histological sectioning and digital 3D reconstruction

    PubMed Central

    Annese, Jacopo; Schenker-Ahmed, Natalie M.; Bartsch, Hauke; Maechler, Paul; Sheh, Colleen; Thomas, Natasha; Kayano, Junya; Ghatan, Alexander; Bresler, Noah; Frosch, Matthew P.; Klaming, Ruth; Corkin, Suzanne

    2014-01-01

    Modern scientific knowledge of how memory functions are organized in the human brain originated from the case of Henry G. Molaison (H.M.), an epileptic patient whose amnesia ensued unexpectedly following a bilateral surgical ablation of medial temporal lobe structures, including the hippocampus. The neuroanatomical extent of the 1953 operation could not be assessed definitively during H.M.’s life. Here we describe the results of a procedure designed to reconstruct a microscopic anatomical model of the whole brain and conduct detailed 3D measurements in the medial temporal lobe region. This approach, combined with cellular-level imaging of stained histological slices, demonstrates a significant amount of residual hippocampal tissue with distinctive cytoarchitecture. Our study also reveals diffuse pathology in the deep white matter and a small, circumscribed lesion in the left orbitofrontal cortex. The findings constitute new evidence that may help elucidate the consequences of H.M.’s operation in the context of the brain’s overall pathology. PMID:24473151

  17. SU-E-T-678: Response Calibration Using Electron Depth-Dose Data for MRI-Based 3D Polymer Gel Dosimetry

    SciTech Connect

    Watanabe, Y; Warmington, L; Gopishankar, N

    2015-06-15

    Purpose: To evaluate a calibration method using the depth-dose data of an electron beam for MRI-based polymer gel dosimetry. Methods: MAGAT was manufactured in-house to fill two 400mL-cylindrical phantoms and nine 22mL-glass vials. Phantom-A was irradiated along the cylinder axis with a 9MeV electron beam of 6 cm x 6 cm field size (FS). Phantom-B was irradiated with a 6MV photon beam of 3 cm x 3 cm FS by a 360-degree arc technique. Eight vials were irradiated in a water-bath to various doses with a 20 cm x 20 cm FS 6MV photon beam. All irradiated phantoms and one un-irradiated vial were scanned with a 3T MRI scanner to obtain the spin-spin relaxation rate (R2) distributions. By comparing the measured R2-to-depth data with the known depth-dose data for Phantom-A, R2-to-dose calibration data were obtained (e-beam method). Another calibration data were obtained from the 9 vials data (9-vial method). We tested two regression equations, i.e., third-order polynomial and tangent functions, and two dose normalization methods, i.e., one-point and two-point methods. Then, these two calibration methods were used to obtain the 3D dose distribution of Phantom-B and evaluated by comparing the measured data with the dose distribution from a treatment planning system. The comparison was made with gamma passing rate (2%/2mm criteria). Results: We did not observe a clear advantage of the e-beam method over the 9-vial method for the 3D dose comparison with the test case. Nevertheless, we found that the e-beam method required a smaller dose scaling for the dose comparison. Furthermore, the tangent function showed better data fitting than the polynomial function with smaller uncertainty of the estimated coefficients. Conclusions: Considering the overall superior performance, we recommend the e-beam method with the tangent function as the regression equation and one-point dose normalization for the MRI-based polymer gel dosimetry.

  18. A unified approach to diffusion direction sensitive slice registration and 3-D DTI reconstruction from moving fetal brain anatomy.

    PubMed

    Fogtmann, Mads; Seshamani, Sharmishtaa; Kroenke, Christopher; Xi Cheng; Chapman, Teresa; Wilm, Jakob; Rousseau, Francois; Studholme, Colin

    2014-02-01

    This paper presents an approach to 3-D diffusion tensor image (DTI) reconstruction from multi-slice diffusion weighted (DW) magnetic resonance imaging acquisitions of the moving fetal brain. Motion scatters the slice measurements in the spatial and spherical diffusion domain with respect to the underlying anatomy. Previous image registration techniques have been described to estimate the between slice fetal head motion, allowing the reconstruction of 3D a diffusion estimate on a regular grid using interpolation. We propose Approach to Unified Diffusion Sensitive Slice Alignment and Reconstruction (AUDiSSAR) that explicitly formulates a process for diffusion direction sensitive DW-slice-to-DTI-volume alignment. This also incorporates image resolution modeling to iteratively deconvolve the effects of the imaging point spread function using the multiple views provided by thick slices acquired in different anatomical planes. The algorithm is implemented using a multi-resolution iterative scheme and multiple real and synthetic data are used to evaluate the performance of the technique. An accuracy experiment using synthetically created motion data of an adult head and an experiment using synthetic motion added to sedated fetal monkey dataset show a significant improvement in motion-trajectory estimation compared to current state-of-the-art approaches. The performance of the method is then evaluated on challenging but clinically typical in utero fetal scans of four different human cases, showing improved rendition of cortical anatomy and extraction of white matter tracts. While the experimental work focuses on DTI reconstruction (second-order tensor model), the proposed reconstruction framework can employ any 5-D diffusion volume model that can be represented by the spatial parameterizations of an orientation distribution function.

  19. A Unified Approach to Diffusion Direction Sensitive Slice Registration and 3-D DTI Reconstruction From Moving Fetal Brain Anatomy

    PubMed Central

    Fogtmann, Mads; Seshamani, Sharmishtaa; Kroenke, Christopher; Cheng, Xi; Chapman, Teresa; Wilm, Jakob; Rousseau, François

    2014-01-01

    This paper presents an approach to 3-D diffusion tensor image (DTI) reconstruction from multi-slice diffusion weighted (DW) magnetic resonance imaging acquisitions of the moving fetal brain. Motion scatters the slice measurements in the spatial and spherical diffusion domain with respect to the underlying anatomy. Previous image registration techniques have been described to estimate the between slice fetal head motion, allowing the reconstruction of 3-D a diffusion estimate on a regular grid using interpolation. We propose Approach to Unified Diffusion Sensitive Slice Alignment and Reconstruction (AUDiSSAR) that explicitly formulates a process for diffusion direction sensitive DW-slice-to-DTI-volume alignment. This also incorporates image resolution modeling to iteratively deconvolve the effects of the imaging point spread function using the multiple views provided by thick slices acquired in different anatomical planes. The algorithm is implemented using a multi-resolution iterative scheme and multiple real and synthetic data are used to evaluate the performance of the technique. An accuracy experiment using synthetically created motion data of an adult head and a experiment using synthetic motion added to sedated fetal monkey dataset show a significant improvement in motion-trajectory estimation compared to a state-of-the-art approaches. The performance of the method is then evaluated on challenging but clinically typical in utero fetal scans of four different human cases, showing improved rendition of cortical anatomy and extraction of white matter tracts. While the experimental work focuses on DTI reconstruction (second-order tensor model), the proposed reconstruction framework can employ any 5-D diffusion volume model that can be represented by the spatial parameterizations of an orientation distribution function. PMID:24108711

  20. Simple Fully Automated Group Classification on Brain fMRI

    SciTech Connect

    Honorio, J.; Goldstein, R.; Honorio, J.; Samaras, D.; Tomasi, D.; Goldstein, R.Z.

    2010-04-14

    We propose a simple, well grounded classification technique which is suited for group classification on brain fMRI data sets that have high dimensionality, small number of subjects, high noise level, high subject variability, imperfect registration and capture subtle cognitive effects. We propose threshold-split region as a new feature selection method and majority voteas the classification technique. Our method does not require a predefined set of regions of interest. We use average acros ssessions, only one feature perexperimental condition, feature independence assumption, and simple classifiers. The seeming counter-intuitive approach of using a simple design is supported by signal processing and statistical theory. Experimental results in two block design data sets that capture brain function under distinct monetary rewards for cocaine addicted and control subjects, show that our method exhibits increased generalization accuracy compared to commonly used feature selection and classification techniques.

  1. Predicting aphasia type from brain damage measured with structural MRI.

    PubMed

    Yourganov, Grigori; Smith, Kimberly G; Fridriksson, Julius; Rorden, Chris

    2015-12-01

    Chronic aphasia is a common consequence of a left-hemisphere stroke. Since the early insights by Broca and Wernicke, studying the relationship between the loci of cortical damage and patterns of language impairment has been one of the concerns of aphasiology. We utilized multivariate classification in a cross-validation framework to predict the type of chronic aphasia from the spatial pattern of brain damage. Our sample consisted of 98 patients with five types of aphasia (Broca's, Wernicke's, global, conduction, and anomic), classified based on scores on the Western Aphasia Battery (WAB). Binary lesion maps were obtained from structural MRI scans (obtained at least 6 months poststroke, and within 2 days of behavioural assessment); after spatial normalization, the lesions were parcellated into a disjoint set of brain areas. The proportion of damage to the brain areas was used to classify patients' aphasia type. To create this parcellation, we relied on five brain atlases; our classifier (support vector machine - SVM) could differentiate between different kinds of aphasia using any of the five parcellations. In our sample, the best classification accuracy was obtained when using a novel parcellation that combined two previously published brain atlases, with the first atlas providing the segmentation of grey matter, and the second atlas used to segment the white matter. For each aphasia type, we computed the relative importance of different brain areas for distinguishing it from other aphasia types; our findings were consistent with previously published reports of lesion locations implicated in different types of aphasia. Overall, our results revealed that automated multivariate classification could distinguish between aphasia types based on damage to atlas-defined brain areas.

  2. Automatic brain tumor detection in MRI: methodology and statistical validation

    NASA Astrophysics Data System (ADS)

    Iftekharuddin, Khan M.; Islam, Mohammad A.; Shaik, Jahangheer; Parra, Carlos; Ogg, Robert

    2005-04-01

    Automated brain tumor segmentation and detection are immensely important in medical diagnostics because it provides information associated to anatomical structures as well as potential abnormal tissue necessary to delineate appropriate surgical planning. In this work, we propose a novel automated brain tumor segmentation technique based on multiresolution texture information that combines fractal Brownian motion (fBm) and wavelet multiresolution analysis. Our wavelet-fractal technique combines the excellent multiresolution localization property of wavelets to texture extraction of fractal. We prove the efficacy of our technique by successfully segmenting pediatric brain MR images (MRIs) from St. Jude Children"s Research Hospital. We use self-organizing map (SOM) as our clustering tool wherein we exploit both pixel intensity and multiresolution texture features to obtain segmented tumor. Our test results show that our technique successfully segments abnormal brain tissues in a set of T1 images. In the next step, we design a classifier using Feed-Forward (FF) neural network to statistically validate the presence of tumor in MRI using both the multiresolution texture and the pixel intensity features. We estimate the corresponding receiver operating curve (ROC) based on the findings of true positive fractions and false positive fractions estimated from our classifier at different threshold values. An ROC, which can be considered as a gold standard to prove the competence of a classifier, is obtained to ascertain the sensitivity and specificity of our classifier. We observe that at threshold 0.4 we achieve true positive value of 1.0 (100%) sacrificing only 0.16 (16%) false positive value for the set of 50 T1 MRI analyzed in this experiment.

  3. A System for True and False Memory Prediction Based on 2D and 3D Educational Contents and EEG Brain Signals

    PubMed Central

    2016-01-01

    We studied the impact of 2D and 3D educational contents on learning and memory recall using electroencephalography (EEG) brain signals. For this purpose, we adopted a classification approach that predicts true and false memories in case of both short term memory (STM) and long term memory (LTM) and helps to decide whether there is a difference between the impact of 2D and 3D educational contents. In this approach, EEG brain signals are converted into topomaps and then discriminative features are extracted from them and finally support vector machine (SVM) which is employed to predict brain states. For data collection, half of sixty-eight healthy individuals watched the learning material in 2D format whereas the rest watched the same material in 3D format. After learning task, memory recall tasks were performed after 30 minutes (STM) and two months (LTM), and EEG signals were recorded. In case of STM, 97.5% prediction accuracy was achieved for 3D and 96.6% for 2D and, in case of LTM, it was 100% for both 2D and 3D. The statistical analysis of the results suggested that for learning and memory recall both 2D and 3D materials do not have much difference in case of STM and LTM. PMID:26819593

  4. A System for True and False Memory Prediction Based on 2D and 3D Educational Contents and EEG Brain Signals.

    PubMed

    Bamatraf, Saeed; Hussain, Muhammad; Aboalsamh, Hatim; Qazi, Emad-Ul-Haq; Malik, Amir Saeed; Amin, Hafeez Ullah; Mathkour, Hassan; Muhammad, Ghulam; Imran, Hafiz Muhammad

    2016-01-01

    We studied the impact of 2D and 3D educational contents on learning and memory recall using electroencephalography (EEG) brain signals. For this purpose, we adopted a classification approach that predicts true and false memories in case of both short term memory (STM) and long term memory (LTM) and helps to decide whether there is a difference between the impact of 2D and 3D educational contents. In this approach, EEG brain signals are converted into topomaps and then discriminative features are extracted from them and finally support vector machine (SVM) which is employed to predict brain states. For data collection, half of sixty-eight healthy individuals watched the learning material in 2D format whereas the rest watched the same material in 3D format. After learning task, memory recall tasks were performed after 30 minutes (STM) and two months (LTM), and EEG signals were recorded. In case of STM, 97.5% prediction accuracy was achieved for 3D and 96.6% for 2D and, in case of LTM, it was 100% for both 2D and 3D. The statistical analysis of the results suggested that for learning and memory recall both 2D and 3D materials do not have much difference in case of STM and LTM.

  5. Evaluation of MRI and cannabinoid type 1 receptor PET templates constructed using DARTEL for spatial normalization of rat brains

    SciTech Connect

    Kronfeld, Andrea; Müller-Forell, Wibke; Buchholz, Hans-Georg; Maus, Stephan; Reuss, Stefan; Schreckenberger, Mathias; Miederer, Isabelle; Lutz, Beat

    2015-12-15

    Purpose: Image registration is one prerequisite for the analysis of brain regions in magnetic-resonance-imaging (MRI) or positron-emission-tomography (PET) studies. Diffeomorphic anatomical registration through exponentiated Lie algebra (DARTEL) is a nonlinear, diffeomorphic algorithm for image registration and construction of image templates. The goal of this small animal study was (1) the evaluation of a MRI and calculation of several cannabinoid type 1 (CB1) receptor PET templates constructed using DARTEL and (2) the analysis of the image registration accuracy of MR and PET images to their DARTEL templates with reference to analytical and iterative PET reconstruction algorithms. Methods: Five male Sprague Dawley rats were investigated for template construction using MRI and [{sup 18}F]MK-9470 PET for CB1 receptor representation. PET images were reconstructed using the algorithms filtered back-projection, ordered subset expectation maximization in 2D, and maximum a posteriori in 3D. Landmarks were defined on each MR image, and templates were constructed under different settings, i.e., based on different tissue class images [gray matter (GM), white matter (WM), and GM + WM] and regularization forms (“linear elastic energy,” “membrane energy,” and “bending energy”). Registration accuracy for MRI and PET templates was evaluated by means of the distance between landmark coordinates. Results: The best MRI template was constructed based on gray and white matter images and the regularization form linear elastic energy. In this case, most distances between landmark coordinates were <1 mm. Accordingly, MRI-based spatial normalization was most accurate, but results of the PET-based spatial normalization were quite comparable. Conclusions: Image registration using DARTEL provides a standardized and automatic framework for small animal brain data analysis. The authors were able to show that this method works with high reliability and validity. Using DARTEL

  6. Functional Brain Activation Differences in Stuttering Identified with a Rapid fMRI Sequence

    ERIC Educational Resources Information Center

    Loucks, Torrey; Kraft, Shelly Jo; Choo, Ai Leen; Sharma, Harish; Ambrose, Nicoline G.

    2011-01-01

    The purpose of this study was to investigate whether brain activity related to the presence of stuttering can be identified with rapid functional MRI (fMRI) sequences that involved overt and covert speech processing tasks. The long-term goal is to develop sensitive fMRI approaches with developmentally appropriate tasks to identify deviant speech…

  7. Brain Activity Associated with Emoticons: An fMRI Study

    NASA Astrophysics Data System (ADS)

    Yuasa, Masahide; Saito, Keiichi; Mukawa, Naoki

    In this paper, we describe that brain activities associated with emoticons by using fMRI. In communication over a computer network, we use abstract faces such as computer graphics (CG) avatars and emoticons. These faces convey users' emotions and enrich their communications. However, the manner in which these faces influence the mental process is as yet unknown. The human brain may perceive the abstract face in an entirely different manner, depending on its level of reality. We conducted an experiment using fMRI in order to investigate the effects of emoticons. The results show that right inferior frontal gyrus, which associated with nonverbal communication, is activated by emoticons. Since the emoticons were created to reflect the real human facial expressions as accurately as possible, we believed that they would activate the right fusiform gyrus. However, this region was not found to be activated during the experiment. This finding is useful in understanding how abstract faces affect our behaviors and decision-making in communication over a computer network.

  8. ‘Extra-operatve’ MRI (eoMRI) for Brain Tumor Surgery – Initial Results at a Single Institution

    PubMed Central

    Abd-El-Barr, Muhammad M.; Santos, Seth M.; Aglio, Linda S.; Young, Geoffrey S.; Mukundan, Srinivasan; Golby, Alexandra J.; Gormley, William B.; Dunn, Ian F.

    2015-01-01

    Background There is accumulating evidence that extent of resection (EOR) in intrinsic brain tumor surgery prolongs overall survival (OS) and progression-free survival (PFS). One of the strategies to increase EOR is the use of intraoperative MRI (ioMRI). However, considerable infrastructure investment is needed to establish and maintain a sophisticated ioMRI. We report the preliminary results of an extra-operative (eoMRI) protocol, with a focus on safety, feasibility and EOR in intrinsic brain tumor surgery. Methods Ten patients underwent an eoMRI protocol consisting of surgical resection in a conventional operating room followed by an immediate MRI in a clinical MRI scanner while the patient was still under anesthesia. If MRI suggested residual safely resectable tumor, the patient was returned to the operating room. Retrospective volumetric analysis was undertaken to investigate the percentage of tumor resected after first resection and if applicable, after further resection. Results 6 out of 10 (60%) patients were felt to require no further resection after eoMRI. The EOR in these patients was 97.8±1.8%. In the 4 patients who underwent further resection, the EOR during the original surgery was 88.5±9.5% (p =0.04). There was an average of 10.1 % more tumor removed between the first and second surgery. In 3/4 (75%) of patients who returned for further resection, gross total resection of was achieved. Conclusion An eoMRI protocol appears to be a safe and practical method to ensure maximum safe resections in patients with brain tumors and can be performed readily in all centers with MRI capability. PMID:25700968

  9. MRI of the human brain at 130 microtesla

    PubMed Central

    Inglis, Ben; Buckenmaier, Kai; SanGiorgio, Paul; Pedersen, Anders F.; Nichols, Matthew A.; Clarke, John

    2013-01-01

    We present in vivo images of the human brain acquired with an ultralow field MRI (ULFMRI) system operating at a magnetic field B0 ∼ 130 μT. The system features prepolarization of the proton spins at Bp ∼ 80 mT and detection of the NMR signals with a superconducting, second-derivative gradiometer inductively coupled to a superconducting quantum interference device (SQUID). We report measurements of the longitudinal relaxation time T1 of brain tissue, blood, and scalp fat at B0 and Bp, and cerebrospinal fluid at B0. We use these T1 values to construct inversion recovery sequences that we combine with Carr–Purcell–Meiboom–Gill echo trains to obtain images in which one species can be nulled and another species emphasized. In particular, we show an image in which only blood is visible. Such techniques greatly enhance the already high intrinsic T1 contrast obtainable at ULF. We further present 2D images of T1 and the transverse relaxation time T2 of the brain and show that, as expected at ULF, they exhibit similar contrast. Applications of brain ULFMRI include integration with systems for magnetoencephalography. More generally, these techniques may be applicable, for example, to the imaging of tumors without the need for a contrast agent and to modalities recently demonstrated with T1ρ contrast imaging (T1 in the rotating frame) at fields of 1.5 T and above. PMID:24255111

  10. MRI of the human brain at 130 microtesla.

    PubMed

    Inglis, Ben; Buckenmaier, Kai; Sangiorgio, Paul; Pedersen, Anders F; Nichols, Matthew A; Clarke, John

    2013-11-26

    We present in vivo images of the human brain acquired with an ultralow field MRI (ULFMRI) system operating at a magnetic field B0 ~ 130 μT. The system features prepolarization of the proton spins at Bp ~ 80 mT and detection of the NMR signals with a superconducting, second-derivative gradiometer inductively coupled to a superconducting quantum interference device (SQUID). We report measurements of the longitudinal relaxation time T1 of brain tissue, blood, and scalp fat at B0 and Bp, and cerebrospinal fluid at B0. We use these T1 values to construct inversion recovery sequences that we combine with Carr-Purcell-Meiboom-Gill echo trains to obtain images in which one species can be nulled and another species emphasized. In particular, we show an image in which only blood is visible. Such techniques greatly enhance the already high intrinsic T1 contrast obtainable at ULF. We further present 2D images of T1 and the transverse relaxation time T2 of the brain and show that, as expected at ULF, they exhibit similar contrast. Applications of brain ULFMRI include integration with systems for magnetoencephalography. More generally, these techniques may be applicable, for example, to the imaging of tumors without the need for a contrast agent and to modalities recently demonstrated with T1ρ contrast imaging (T1 in the rotating frame) at fields of 1.5 T and above.

  11. Automated Template-based Brain Localization and Extraction for Fetal Brain MRI Reconstruction.

    PubMed

    Tourbier, Sébastien; Velasco-Annis, Clemente; Taimouri, Vahid; Hagmann, Patric; Meuli, Reto; Warfield, Simon K; Cuadra, Meritxell Bach; Gholipour, Ali

    2017-04-10

    Most fetal brain MRI reconstruction algorithms rely only on brain tissue-relevant voxels of low-resolution (LR) images to enhance the quality of inter-slice motion correction and image reconstruction. Consequently the fetal brain needs to be localized and extracted as a first step, which is usually a laborious and time consuming manual or semi-automatic task. We have proposed in this work to use age-matched template images as prior knowledge to automatize brain localization and extraction. This has been achieved through a novel automatic brain localization and extraction method based on robust template-to-slice block matching and deformable slice-to-template registration. Our template-based approach has also enabled the reconstruction of fetal brain images in standard radiological anatomical planes in a common coordinate space. We have integrated this approach into our new reconstruction pipeline that involves intensity normalization, inter-slice motion correction, and super-resolution (SR) reconstruction. To this end we have adopted a novel approach based on projection of every slice of the LR brain masks into the template space using a fusion strategy. This has enabled the refinement of brain masks in the LR images at each motion correction iteration. The overall brain localization and extraction algorithm has shown to produce brain masks that are very close to manually drawn brain masks, showing an average Dice overlap measure of 94.5%. We have also demonstrated that adopting a slice-to-template registration and propagation of the brain mask slice-by-slice leads to a significant improvement in brain extraction performance compared to global rigid brain extraction and consequently in the quality of the final reconstructed images. Ratings performed by two expert observers show that the proposed pipeline can achieve similar reconstruction quality to reference reconstruction based on manual slice-by-slice brain extraction. The proposed brain mask refinement and

  12. Brain MRI volumetry in a single patient with mild traumatic brain injury.

    PubMed

    Ross, David E; Castelvecchi, Cody; Ochs, Alfred L

    2013-01-01

    This letter to the editor describes the case of a 42 year old man with mild traumatic brain injury and multiple neuropsychiatric symptoms which persisted for a few years after the injury. Initial CT scans and MRI scans of the brain showed no signs of atrophy. Brain volume was measured using NeuroQuant®, an FDA-approved, commercially available software method. Volumetric cross-sectional (one point in time) analysis also showed no atrophy. However, volumetric longitudinal (two points in time) analysis showed progressive atrophy in several brain regions. This case illustrated in a single patient the principle discovered in multiple previous group studies, namely that the longitudinal design is more powerful than the cross-sectional design for finding atrophy in patients with traumatic brain injury.

  13. A methodology to accurately quantify patellofemoral cartilage contact kinematics by combining 3D image shape registration and cine-PC MRI velocity data.

    PubMed

    Borotikar, Bhushan S; Sipprell, William H; Wible, Emily E; Sheehan, Frances T

    2012-04-05

    Patellofemoral osteoarthritis and its potential precursor patellofemoral pain syndrome (PFPS) are common, costly, and debilitating diseases. PFPS has been shown to be associated with altered patellofemoral joint mechanics; however, an actual variation in joint contact stresses has not been established due to challenges in accurately quantifying in vivo contact kinematics (area and location). This study developed and validated a method for tracking dynamic, in vivo cartilage contact kinematics by combining three magnetic resonance imaging (MRI) techniques, cine-phase contrast (CPC), multi-plane cine (MPC), and 3D high-resolution static imaging. CPC and MPC data were acquired from 12 healthy volunteers while they actively extended/flexed their knee within the MRI scanner. Since no gold standard exists for the quantification of in vivo dynamic cartilage contact kinematics, the accuracy of tracking a single point (patellar origin relative to the femur) represented the accuracy of tracking the kinematics of an entire surface. The accuracy was determined by the average absolute error between the PF kinematics derived through registration of MPC images to a static model and those derived through integration of the CPC velocity data. The accuracy ranged from 0.47 mm to 0.77 mm for the patella and femur and from 0.68 mm to 0.86 mm for the patellofemoral joint. For purely quantifying joint kinematics, CPC remains an analytically simpler and more accurate (accuracy <0.33 mm) technique. However, for application requiring the tracking of an entire surface, such as quantifying cartilage contact kinematics, this combined imaging approach produces accurate results with minimal operator intervention.

  14. Joint design of excitation k-space trajectory and RF pulse for small-tip 3D tailored excitation in MRI

    PubMed Central

    Fessler, Jeffrey A.; Noll, Douglas C.; Nielsen, Jon-Fredrik

    2015-01-01

    We propose a new method for the joint design of k-space trajectory and RF pulse in 3D small-tip tailored excitation. Designing time-varying RF and gradient waveforms for a desired 3D target excitation pattern in MRI poses a non-linear, non-convex, constrained optimization problem with relatively large problem size that is difficult to solve directly. Existing joint pulse design approaches are therefore typically restricted to predefined trajectory types such as EPI or stack-of-spirals that intrinsically satisfy the gradient maximum and slew rate constraints and reduce the problem size (dimensionality) dramatically, but lead to suboptimal excitation accuracy for a given pulse duration. Here we use a 2nd-order B-spline basis that can be fitted to an arbitrary k-space trajectory, and allows the gradient constraints to be implemented efficiently. We show that this allows the joint optimization problem to be solved with quite general k-space trajectories. Starting from an arbitrary initial trajectory, we first approximate the trajectory using B-spline basis, and then optimize the corresponding coefficients. We evaluate our method in simulation using four different k-space initializations: stack-of-spirals, SPINS, KT-points, and a new method based on KT-points. In all cases, our approach leads to substantial improvement in excitation accuracy for a given pulse duration. We also validated our method for inner-volume excitation using phantom experiments. The computation is fast enough for online applications. PMID:26390450

  15. Building an EEG-fMRI Multi-Modal Brain Graph: A Concurrent EEG-fMRI Study

    PubMed Central

    Yu, Qingbao; Wu, Lei; Bridwell, David A.; Erhardt, Erik B.; Du, Yuhui; He, Hao; Chen, Jiayu; Liu, Peng; Sui, Jing; Pearlson, Godfrey; Calhoun, Vince D.

    2016-01-01

    The topological architecture of brain connectivity has been well-characterized by graph theory based analysis. However, previous studies have primarily built brain graphs based on a single modality of brain imaging data. Here we develop a framework to construct multi-modal brain graphs using concurrent EEG-fMRI data which are simultaneously collected during eyes open (EO) and eyes closed (EC) resting states. FMRI data are decomposed into independent components with associated time courses by group independent component analysis (ICA). EEG time series are segmented, and then spectral power time courses are computed and averaged within 5 frequency bands (delta; theta; alpha; beta; low gamma). EEG-fMRI brain graphs, with EEG electrodes and fMRI brain components serving as nodes, are built by computing correlations within and between fMRI ICA time courses and EEG spectral power time courses. Dynamic EEG-fMRI graphs are built using a sliding window method, versus static ones treating the entire time course as stationary. In global level, static graph measures and properties of dynamic graph measures are different across frequency bands and are mainly showing higher values in eyes closed than eyes open. Nodal level graph measures of a few brain components are also showing higher values during eyes closed in specific frequency bands. Overall, these findings incorporate fMRI spatial localization and EEG frequency information which could not be obtained by examining only one modality. This work provides a new approach to examine EEG-fMRI associations within a graph theoretic framework with potential application to many topics. PMID:27733821

  16. Building an EEG-fMRI Multi-Modal Brain Graph: A Concurrent EEG-fMRI Study.

    PubMed

    Yu, Qingbao; Wu, Lei; Bridwell, David A; Erhardt, Erik B; Du, Yuhui; He, Hao; Chen, Jiayu; Liu, Peng; Sui, Jing; Pearlson, Godfrey; Calhoun, Vince D

    2016-01-01

    The topological architecture of brain connectivity has been well-characterized by graph theory based analysis. However, previous studies have primarily built brain graphs based on a single modality of brain imaging data. Here we develop a framework to construct multi-modal brain graphs using concurrent EEG-fMRI data which are simultaneously collected during eyes open (EO) and eyes closed (EC) resting states. FMRI data are decomposed into independent components with associated time courses by group independent component analysis (ICA). EEG time series are segmented, and then spectral power time courses are computed and averaged within 5 frequency bands (delta; theta; alpha; beta; low gamma). EEG-fMRI brain graphs, with EEG electrodes and fMRI brain components serving as nodes, are built by computing correlations within and between fMRI ICA time courses and EEG spectral power time courses. Dynamic EEG-fMRI graphs are built using a sliding window method, versus static ones treating the entire time course as stationary. In global level, static graph measures and properties of dynamic graph measures are different across frequency bands and are mainly showing higher values in eyes closed than eyes open. Nodal level graph measures of a few brain components are also showing higher values during eyes closed in specific frequency bands. Overall, these findings incorporate fMRI spatial localization and EEG frequency information which could not be obtained by examining only one modality. This work provides a new approach to examine EEG-fMRI associations within a graph theoretic framework with potential application to many topics.

  17. Strain and rate-dependent neuronal injury in a 3D in vitro compression model of traumatic brain injury.

    PubMed

    Bar-Kochba, Eyal; Scimone, Mark T; Estrada, Jonathan B; Franck, Christian

    2016-08-02

    In the United States over 1.7 million cases of traumatic brain injury are reported yearly, but predictive correlation of cellular injury to impact tissue strain is still lacking, particularly for neuronal injury resulting from compression. Given the prevalence of compressive deformations in most blunt head trauma, this information is critically important for the development of future mitigation and diagnosis strategies. Using a 3D in vitro neuronal compression model, we investigated the role of impact strain and strain rate on neuronal lifetime, viability, and pathomorphology. We find that strain magnitude and rate have profound, yet distinctively different effects on the injury pathology. While strain magnitude affects the time of neuronal death, strain rate influences the pathomorphology and extent of population injury. Cellular injury is not initiated through localized deformation of the cytoskeleton but rather driven by excess strain on the entire cell. Furthermore we find that, mechanoporation, one of the key pathological trigger mechanisms in stretch and shear neuronal injuries, was not observed under compression.

  18. Strain and rate-dependent neuronal injury in a 3D in vitro compression model of traumatic brain injury

    NASA Astrophysics Data System (ADS)

    Bar-Kochba, Eyal; Scimone, Mark T.; Estrada, Jonathan B.; Franck, Christian

    2016-08-01

    In the United States over 1.7 million cases of traumatic brain injury are reported yearly, but predictive correlation of cellular injury to impact tissue strain is still lacking, particularly for neuronal injury resulting from compression. Given the prevalence of compressive deformations in most blunt head trauma, this information is critically important for the development of future mitigation and diagnosis strategies. Using a 3D in vitro neuronal compression model, we investigated the role of impact strain and strain rate on neuronal lifetime, viability, and pathomorphology. We find that strain magnitude and rate have profound, yet distinctively different effects on the injury pathology. While strain magnitude affects the time of neuronal death, strain rate influences the pathomorphology and extent of population injury. Cellular injury is not initiated through localized deformation of the cytoskeleton but rather driven by excess strain on the entire cell. Furthermore we find that, mechanoporation, one of the key pathological trigger mechanisms in stretch and shear neuronal injuries, was not observed under compression.

  19. Strain and rate-dependent neuronal injury in a 3D in vitro compression model of traumatic brain injury

    PubMed Central

    Bar-Kochba, Eyal; Scimone, Mark T.; Estrada, Jonathan B.; Franck, Christian

    2016-01-01

    In the United States over 1.7 million cases of traumatic brain injury are reported yearly, but predictive correlation of cellular injury to impact tissue strain is still lacking, particularly for neuronal injury resulting from compression. Given the prevalence of compressive deformations in most blunt head trauma, this information is critically important for the development of future mitigation and diagnosis strategies. Using a 3D in vitro neuronal compression model, we investigated the role of impact strain and strain rate on neuronal lifetime, viability, and pathomorphology. We find that strain magnitude and rate have profound, yet distinctively different effects on the injury pathology. While strain magnitude affects the time of neuronal death, strain rate influences the pathomorphology and extent of population injury. Cellular injury is not initiated through localized deformation of the cytoskeleton but rather driven by excess strain on the entire cell. Furthermore we find that, mechanoporation, one of the key pathological trigger mechanisms in stretch and shear neuronal injuries, was not observed under compression. PMID:27480807

  20. A brief report on MRI investigation of experimental traumatic brain injury

    PubMed Central

    Duong, Timothy Q.; Watts, Lora T.

    2016-01-01

    Traumatic brain injury is a major cause of death and disability. This is a brief report based on a symposium presentation to the 2014 Chinese Neurotrauma Association Meeting in San Francisco, USA. It covers the work from our laboratory in applying multimodal MRI to study experimental traumatic brain injury in rats with comparisons made to behavioral tests and histology. MRI protocols include structural, perfusion, manganese-enhanced, diffusion-tensor MRI, and MRI of blood-brain barrier integrity and cerebrovascular reactivity. PMID:26981069

  1. 3D reconstruction of tensors and vectors

    SciTech Connect

    Defrise, Michel; Gullberg, Grant T.

    2005-02-17

    Here we have developed formulations for the reconstruction of 3D tensor fields from planar (Radon) and line-integral (X-ray) projections of 3D vector and tensor fields. Much of the motivation for this work is the potential application of MRI to perform diffusion tensor tomography. The goal is to develop a theory for the reconstruction of both Radon planar and X-ray or line-integral projections because of the flexibility of MRI to obtain both of these type of projections in 3D. The development presented here for the linear tensor tomography problem provides insight into the structure of the nonlinear MRI diffusion tensor inverse problem. A particular application of tensor imaging in MRI is the potential application of cardiac diffusion tensor tomography for determining in vivo cardiac fiber structure. One difficulty in the cardiac application is the motion of the heart. This presents a need for developing future theory for tensor tomography in a motion field. This means developing a better understanding of the MRI signal for diffusion processes in a deforming media. The techniques developed may allow the application of MRI tensor tomography for the study of structure of fiber tracts in the brain, atherosclerotic plaque, and spine in addition to fiber structure in the heart. However, the relations presented are also applicable to other fields in medical imaging such as diffraction tomography using ultrasound. The mathematics presented can also be extended to exponential Radon transform of tensor fields and to other geometric acquisitions such as cone beam tomography of tensor fields.

  2. Real-time fMRI brain computer interfaces: self-regulation of single brain regions to networks.

    PubMed

    Ruiz, Sergio; Buyukturkoglu, Korhan; Rana, Mohit; Birbaumer, Niels; Sitaram, Ranganatha

    2014-01-01

    With the advent of brain computer interfaces based on real-time fMRI (rtfMRI-BCI), the possibility of performing neurofeedback based on brain hemodynamics has become a reality. In the early stage of the development of this field, studies have focused on the volitional control of activity in circumscribed brain regions. However, based on the understanding that the brain functions by coordinated activity of spatially distributed regions, there have recently been further developments to incorporate real-time feedback of functional connectivity and spatio-temporal patterns of brain activity. The present article reviews the principles of rtfMRI neurofeedback, its applications, benefits and limitations. A special emphasis is given to the discussion of novel developments that have enabled the use of this methodology to achieve self-regulation of the functional connectivity between different brain areas and of distributed brain networks, anticipating new and exciting applications for cognitive neuroscience and for the potential alleviation of neuropsychiatric disorders.

  3. An example-based brain MRI simulation framework

    NASA Astrophysics Data System (ADS)

    He, Qing; Roy, Snehashis; Jog, Amod; Pham, Dzung L.

    2015-03-01

    The simulation of magnetic resonance (MR) images plays an important role in the validation of image analysis algorithms such as image segmentation, due to lack of sufficient ground truth in real MR images. Previous work on MRI simulation has focused on explicitly modeling the MR image formation process. However, because of the overwhelming complexity of MR acquisition these simulations must involve simplifications and approximations that can result in visually unrealistic simulated images. In this work, we describe an example-based simulation framework, which uses an "atlas" consisting of an MR image and its anatomical models derived from the hard segmentation. The relationships between the MR image intensities and its anatomical models are learned using a patch-based regression that implicitly models the physics of the MR image formation. Given the anatomical models of a new brain, a new MR image can be simulated using the learned regression. This approach has been extended to also simulate intensity inhomogeneity artifacts based on the statistical model of training data. Results show that the example based MRI simulation method is capable of simulating different image contrasts and is robust to different choices of atlas. The simulated images resemble real MR images more than simulations produced by a physics-based model.

  4. Collimator design for a multipinhole brain SPECT insert for MRI

    SciTech Connect

    Van Audenhaege, Karen; Van Holen, Roel; Vanhove, Christian; Vandenberghe, Stefaan

    2015-11-15

    Purpose: Brain single photon emission computed tomography (SPECT) imaging is an important clinical tool, with unique tracers for studying neurological diseases. Nowadays, most commercial SPECT systems are combined with x-ray computed tomography (CT) in so-called SPECT/CT systems to obtain an anatomical background for the functional information. However, while CT images have a high spatial resolution, they have a low soft-tissue contrast, which is an important disadvantage for brain imaging. Magnetic resonance imaging (MRI), on the other hand, has a very high soft-tissue contrast and does not involve extra ionizing radiation. Therefore, the authors designed a brain SPECT insert that can operate inside a clinical MRI. Methods: The authors designed and simulated a compact stationary multipinhole SPECT insert based on digital silicon photomultiplier detector modules, which have shown to be MR-compatible and have an excellent intrinsic resolution (0.5 mm) when combined with a monolithic 2 mm thick LYSO crystal. First, the authors optimized the different parameters of the SPECT system to maximize sensitivity for a given target resolution of 7.2 mm in the center of the field-of-view, given the spatial constraints of the MR system. Second, the authors performed noiseless simulations of two multipinhole configurations to evaluate sampling and reconstructed resolution. Finally, the authors performed Monte Carlo simulations and compared the SPECT insert with a clinical system with ultrahigh-resolution (UHR) fan beam collimators, based on contrast-to-noise ratio and a visual comparison of a Hoffman phantom with a 9 mm cold lesion. Results: The optimization resulted in a stationary multipinhole system with a collimator radius of 150.2 mm and a detector radius of 172.67 mm, which corresponds to four rings of 34 diSPM detector modules. This allows the authors to include eight rings of 24 pinholes, which results in a system volume sensitivity of 395 cps/MBq. Noiseless simulations

  5. Motion-Correction Enabled Ultra-High Resolution In-Vivo 7T-MRI of the Brain

    PubMed Central

    Federau, Christian

    2016-01-01

    Objectives To demonstrate the image quality that can be obtained for multiple contrasts using ultra-high resolution MRI (highest nominal resolution: 350 μm isotropic) at 7T using appropriate motion-correction. Materials and Methods An MRI-based fat-excitation motion navigator (which requires no additional hardware) was incorporated into T1-weighted (MP2RAGE, 350 μm nominal isotropic resolution, total scan time 124 mins over 2 sessions. The MP2RAGE also provides quantitative T1-maps), 3D-TSE (380 μm nominal isotropic resolution, total scan time 58 mins) and T2*-weighted protocols (3D-GRE, 380 μm nominal isotropic resolution, total scan time 42 mins) on a 7T MR system. Images from each contrast are presented from a single healthy adult male volunteer (34 years) for direct comparison. The subject provided written consent in accordance with the local review board. Results Images of various brain structures are revealed at unprecedented quality for in-vivo MRI. The presented images permit, for example, to delimit the internal structure of the basal ganglia and thalamus. The single digitationes of the hippocampus are visible, and the gyrus dentatus can be visualized. Intracortical contrast was also observed in the neocortex, including the stria of Gennari of the primary visual cortex. Conclusions Appropriate motion-correction allows MRI scans to be performed with extended scan times enabling exceptionally high resolution scans with high image quality, with the use of a 7T scanner allowing large brain coverage for 350–380 μm isotropic voxels with total scan times for each contrast ranging from 42 to 124 minutes. PMID:27159492

  6. Monitoring brain tumor response to therapy using MRI segmentation.

    PubMed

    Vaidyanathan, M; Clarke, L P; Hall, L O; Heidtman, C; Velthuizen, R; Gosche, K; Phuphanich, S; Wagner, H; Greenberg, H; Silbiger, M L

    1997-01-01

    The performance evaluation of a semi-supervised fuzzy c-means (SFCM) clustering method for monitoring brain tumor volume changes during the course of routine clinical radiation-therapeutic and chemo-therapeutic regimens is presented. The tumor volume determined using the SFCM method was compared with the volume estimates obtained using three other methods: (a) a k nearest neighbor (kNN) classifier, b) a grey level thresholding and seed growing (ISG-SG) method and c) a manual pixel labeling (GT) method for ground truth estimation. The SFCM and kNN methods are applied to the multispectral, contrast enhanced T1, proton density, and T2 weighted, magnetic resonance images (MRI) whereas the ISG-SG and GT methods are applied only to the contrast enhanced T1 weighted image. Estimations of tumor volume were made on eight patient cases with follow-up MRI scans performed over a 32 week interval during treatment. The tumor cases studied include one meningioma, two brain metastases and five gliomas. Comparisons with manually labeled ground truth estimations showed that there is a limited agreement between the segmentation methods for absolute tumor volume measurements when using images of patients after treatment. The average intraobserver reproducibility for the SFCM, kNN and ISG-SG methods was found to be 5.8%, 6.6% and 8.9%, respectively. The average of the interobserver reproducibility of these methods was found to be 5.5%, 6.5% and 11.4%, respectively. For the measurement of relative change of tumor volume as required for the response assessment, the multi-spectral methods kNN and SFCM are therefore preferred over the seedgrowing method.

  7. Simultaneous fMRI-PET of the opioidergic pain system in human brain.

    PubMed

    Wey, Hsiao-Ying; Catana, Ciprian; Hooker, Jacob M; Dougherty, Darin D; Knudsen, Gitte M; Wang, Danny J J; Chonde, Daniel B; Rosen, Bruce R; Gollub, Randy L; Kong, Jian

    2014-11-15

    MRI and PET provide complementary information for studying brain function. While the potential use of simultaneous MRI/PET for clinical diagnostic and disease staging has been demonstrated recently; the biological relevance of concurrent functional MRI-PET brain imaging to dissect neurochemically distinct components of the blood oxygenation level dependent (BOLD) fMRI signal has not yet been shown. We obtained sixteen fMRI-PET data sets from eight healthy volunteers. Each subject participated in randomized order in a pain scan and a control (nonpainful pressure) scan on the same day. Dynamic PET data were acquired with an opioid radioligand, [(11)C]diprenorphine, to detect endogenous opioid releases in response to pain. BOLD fMRI data were collected at the same time to capture hemodynamic responses. In this simultaneous human fMRI-PET imaging study, we show co-localized responses in thalamus and striatum related to pain processing, while modality specific brain networks were also found. Co-localized fMRI and PET signal changes in the thalamus were positively correlated suggesting that pain-induced changes in opioid neurotransmission contribute a significant component of the fMRI signal change in this region. Simultaneous fMRI-PET provides unique opportunities allowing us to relate specific neurochemical events to functional hemodynamic activation and to investigate the impacts of neurotransmission on neurovascular coupling of the human brain in vivo.

  8. TU-F-17A-04: Respiratory Phase-Resolved 3D MRI with Isotropic High Spatial Resolution: Determination of the Average Breathing Motion Pattern for Abdominal Radiotherapy Planning

    SciTech Connect

    Deng, Z; Pang, J; Yang, W; Yue, Y; Tuli, R; Fraass, B; Li, D; Fan, Z

    2014-06-15

    Purpose: To develop a retrospective 4D-MRI technique (respiratory phase-resolved 3D-MRI) for providing an accurate assessment of tumor motion secondary to respiration. Methods: A 3D projection reconstruction (PR) sequence with self-gating (SG) was developed for 4D-MRI on a 3.0T MRI scanner. The respiration-induced shift of the imaging target was recorded by SG signals acquired in the superior-inferior direction every 15 radial projections (i.e. temporal resolution 98 ms). A total of 73000 radial projections obtained in 8-min were retrospectively sorted into 10 time-domain evenly distributed respiratory phases based on the SG information. Ten 3D image sets were then reconstructed offline. The technique was validated on a motion phantom (gadolinium-doped water-filled box, frequency of 10 and 18 cycles/min) and humans (4 healthy and 2 patients with liver tumors). Imaging protocol included 8-min 4D-MRI followed by 1-min 2D-realtime (498 ms/frame) MRI as a reference. Results: The multiphase 3D image sets with isotropic high spatial resolution (1.56 mm) permits flexible image reformatting and visualization. No intra-phase motion-induced blurring was observed. Comparing to 2D-realtime, 4D-MRI yielded similar motion range (phantom: 10.46 vs. 11.27 mm; healthy subject: 25.20 vs. 17.9 mm; patient: 11.38 vs. 9.30 mm), reasonable displacement difference averaged over the 10 phases (0.74mm; 3.63mm; 1.65mm), and excellent cross-correlation (0.98; 0.96; 0.94) between the two displacement series. Conclusion: Our preliminary study has demonstrated that the 4D-MRI technique can provide high-quality respiratory phase-resolved 3D images that feature: a) isotropic high spatial resolution, b) a fixed scan time of 8 minutes, c) an accurate estimate of average motion pattern, and d) minimal intra-phase motion artifact. This approach has the potential to become a viable alternative solution to assess the impact of breathing on tumor motion and determine appropriate treatment margins

  9. Functional MRI and diffusion tensor imaging of brain reorganization after experimental stroke.

    PubMed

    Dijkhuizen, Rick M; van der Marel, Kajo; Otte, Willem M; Hoff, Erik I; van der Zijden, Jet P; van der Toorn, Annette; van Meer, Maurits P A

    2012-03-01

    The potential of the adult brain to reorganize after ischemic injury is critical for functional recovery and provides a significant target for therapeutic strategies to promote brain repair. Despite the accumulating evidence of brain plasticity, the interaction and significance of morphological and physiological modifications in post-stroke brain tissue remain mostly unclear. Neuroimaging techniques such as functional MRI (fMRI) and diffusion tensor imaging (DTI) enable in vivo assessment of the spatial and temporal pattern of functional and structural changes inside and outside ischemic lesion areas. This can contribute to the elucidation of critical aspects in post-stroke brain remodeling. Task/stimulus-related fMRI, resting-state fMRI, or pharmacological MRI enables direct or indirect measurement of neuronal activation, functional connectivity, or neurotransmitter system responses, respectively. DTI allows estimation of the structural integrity and connectivity of white matter tracts. Together, these MRI methods provide an unprecedented means to (a) measure longitudinal changes in tissue structure and function close by and remote from ischemic lesion areas, (b) evaluate the organizational profile of neural networks after stroke, and (c) identify degenerative and restorative processes that affect post-stroke functional outcome. Besides, the availability of MRI in clinical institutions as well as research laboratories provides an optimal basis for translational research on stroke recovery. This review gives an overview of the current status and perspectives of fMRI and DTI applications to study brain reorganization in experimental stroke models.

  10. Transplantation of marrow stromal cells restores cerebral blood flow and reduces cerebral atrophy in rats with traumatic brain injury: in vivo MRI study.

    PubMed

    Li, Lian; Jiang, Quan; Qu, Chang Sheng; Ding, Guang Liang; Li, Qing Jiang; Wang, Shi Yang; Lee, Ji Hyun; Lu, Mei; Mahmood, Asim; Chopp, Michael

    2011-04-01

    Cell therapy promotes brain remodeling and improves functional recovery after various central nervous system disorders, including traumatic brain injury (TBI). We tested the hypothesis that treatment of TBI with intravenous administration of human marrow stromal cells (hMSCs) provides therapeutic benefit in modifying hemodynamic and structural abnormalities, which are detectable by in vivo MRI. hMSCs were labeled with superparamagnetic iron oxide (SPIO) nanoparticles. Male Wistar rats (300-350 g, n=18) subjected to controlled cortical impact TBI were intravenously injected with 1 mL of saline (n=9) or hMSCs in suspension (n=9, approximately 3 × 10(6) SPIO-labeled hMSCs) 5 days post-TBI. In vivo MRI measurements consisting of cerebral blood flow (CBF), T2-weighted imaging, and 3D gradient echo imaging were performed for all animals 2 days post-TBI and weekly for 6 weeks. Functional outcome was evaluated with modified neurological severity score and Morris water maze test. Cell engraftment was detected in vivo by 3D MRI and confirmed by double staining. Ventricle and lesion volumetric alterations were measured using T2 maps, and hemodynamic abnormality was tracked by MRI CBF measurements. Our data demonstrate that treatment with hMSCs following TBI diminishes hemodynamic abnormalities by early restoration and preservation of CBF in the brain regions adjacent to and remote from the impact site, and reduces generalized cerebral atrophy, all of which may contribute to the observed improvement of functional outcome.

  11. Brain tissue classification from MRI data by means of texture analysis

    NASA Astrophysics Data System (ADS)

    Lachmann, Frederic; Barillot, Christian

    1992-06-01

    The new magnetic resonance imaging systems (MRI) are able to perform a brain scan with fairly good three-dimensional resolution. In order to allow the physician, and especially the neuroanatomist, to deal with the prime information borne by the images, the prevalent data have to be enhanced with regards to the medical objective. The aim of the work presented in this paper is to recognize and to label the head structures from MR images. This is done by computing probabilities for a pixel to belong to pre-specified head structures (i.e., skin, bone, CSF, ventricular system, grey and white matter, and brain). Several ways are presented and discussed in this paper, including the computation of statistical properties like `Markov parameters' and `fractal dimension.' From these statistical parameters, computed from a single MR image or a 3-D isotropic MR database, clustering and classification processes are used to issue fuzzy membership coefficients representing the probabilities for a pixel to belong to a particular structure. Improvements are proposed with regard to the expressed choices and examples are presented.

  12. Bioengineered 3D brain tumor model to elucidate the effects of matrix stiffness on glioblastoma cell behavior using PEG-based hydrogels.

    PubMed

    Wang, Christine; Tong, Xinming; Yang, Fan

    2014-07-07

    Glioblastoma (GBM) is the most common and aggressive form of primary brain tumor with a median survival of 12-15 months, and the mechanisms underlying GBM tumor progression remain largely elusive. Given the importance of tumor niche signaling in driving GBM progression, there is a strong need to develop in vitro models to facilitate analysis of brain tumor cell-niche interactions in a physiologically relevant and controllable manner. Here we report the development of a bioengineered 3D brain tumor model to help elucidate the effects of matrix stiffness on GBM cell fate using poly(ethylene-glycol) (PEG)-based hydrogels with brain-mimicking biochemical and mechanical properties. We have chosen PEG given its bioinert nature and tunable physical property, and the resulting hydrogels allow tunable matrix stiffness without changing the biochemical contents. To facilitate cell proliferation and migration, CRGDS and a MMP-cleavable peptide were chemically incorporated. Hyaluronic acid (HA) was also incorporated to mimic the concentration in the brain extracellular matrix. Using U87 cells as a model GBM cell line, we demonstrate that such biomimetic hydrogels support U87 cell growth, spreading, and migration in 3D over the course of 3 weeks in culture. Gene expression analyses showed U87 cells actively deposited extracellular matrix and continued to upregulate matrix remodeling genes. To examine the effects of matrix stiffness on GBM cell fate in 3D, we encapsulated U87 cells in soft (1 kPa) or stiff (26 kPa) hydrogels, which respectively mimics the matrix stiffness of normal brain or GBM tumor tissues. Our results suggest that changes in matrix stiffness induce differential GBM cell proliferation, morphology, and migration modes in 3D. Increasing matrix stiffness led to delayed U87 cell proliferation inside hydrogels, but cells formed denser spheroids with extended cell protrusions. Cells cultured in stiff hydrogels also showed upregulation of HA synthase 1 and matrix

  13. Advanced human carotid plaque progression correlates positively with flow shear stress using follow-up scan data: an in vivo MRI multi-patient 3D FSI study.

    PubMed

    Yang, Chun; Canton, Gador; Yuan, Chun; Ferguson, Marina; Hatsukami, Thomas S; Tang, Dalin

    2010-09-17

    Although it has been well-accepted that atherosclerosis initiation and early progression correlate negatively with flow wall shear stresses (FSS), increasing evidence suggests mechanisms governing advanced plaque progression are not well understood. Fourteen patients were scanned 2-4 times at 18 month intervals using a histologically validated multi-contrast magnetic resonance imaging (MRI) protocol to acquire carotid plaque progression data. Thirty-two scan pairs (baseline and follow-up scans) were formed with slices matched for model construction and analysis. 3D fluid-structure interaction (FSI) models were constructed and plaque wall stress (PWS) and flow shear stress (FSS) were obtained from all matching lumen data points (400-1000 per plaque; 100 points per matched slice) to quantify correlations with plaque progression measured by vessel wall thickness increase (WTI). Using FSS and PWS data from follow-up scan, 21 out of 32 scan pairs showed a significant positive correlation between WTI and FSS (positive/negative/no significance ratio=21/8/3), and 26 out of 32 scan pairs showed a significant negative correlation between WTI and PWS (positive/negative/no significance ratio=2/26/4). The mean FSS value of lipid core nodes (n=5294) from all 47 plaque models was 63.5dyn/cm(2), which was 45% higher than that from all normal vessel nodes (n=27553, p<0.00001). The results from this intensive FSI study indicate that flow shear stress from follow-up scan correlates positively with advanced plaque progression which is different from what has been observed in plaque initiation and early-stage progression. It should be noted that the correlation results do not automatically lead to any causality conclusions.

  14. High resolution MRI anatomy of the cat brain at 3 Tesla

    PubMed Central

    Gray-Edwards, Heather L.; Salibi, Nouha; Josephson, Eleanor M.; Hudson, Judith A.; Cox, Nancy R.; Randle, Ashley N.; McCurdy, Victoria J.; Bradbury, Allison M.; Wilson, Diane U.; Beyers, Ronald J.; Denney, Thomas S.; Martin, Douglas R.

    2014-01-01

    Background Feline models of neurologic diseases, such as lysosomal storage diseases, leukodystrophies, Parkinson’s disease, stroke and NeuroAIDS, accurately recreate many aspects of human disease allowing for comparative study of neuropathology and the testing of novel therapeutics. Here we describe in vivo visualization of fine structures within the feline brain that were previously only visible post mortem. New Method 3 Tesla MR images were acquired using T1-weighted (T1w) 3D magnetization-prepared rapid gradient echo (MPRAGE) sequence (0.4mm isotropic resolution) and T2-weighted (T2w) turbo spin echo (TSE) images (0.3×0.3×1 mm3 resolution). Anatomic structures were identified based on feline and canine histology. Results T2w high resolution MR images with detailed structural identification are provided in transverse, sagittal and dorsal planes. T1w MR images are provided electronically in three dimensions for unrestricted spatial evaluation. Comparison with Existing Methods Many areas of the feline brain previously unresolvable on MRI are clearly visible in three orientations, including the dentate, interpositus and fastigial cerebellar nuclei, cranial nerves, lateral geniculate nucleus, optic radiation, cochlea, caudal colliculus, temporal lobe, precuneus, spinocerebellar tract, vestibular nuclei, reticular formation, pyramids and rostral and middle cerebral arteries. Additionally, the feline brain is represented in 3 dimensions for the first time. Conclusions These data establish normal appearance of detailed anatomical structures of the feline brain, which provide reference when evaluating neurologic disease or testing efficacy of novel therapeutics in animal models. PMID:24525327

  15. High-resolution whole-brain DCE-MRI using constrained reconstruction: Prospective clinical evaluation in brain tumor patients

    PubMed Central

    Guo, Yi; Lebel, R. Marc; Zhu, Yinghua; Lingala, Sajan Goud; Shiroishi, Mark S.; Law, Meng; Nayak, Krishna

    2016-01-01

    Purpose: To clinically evaluate a highly accelerated T1-weighted dynamic contrast-enhanced (DCE) MRI technique that provides high spatial resolution and whole-brain coverage via undersampling and constrained reconstruction with multiple sparsity constraints. Methods: Conventional (rate-2 SENSE) and experimental DCE-MRI (rate-30) scans were performed 20 minutes apart in 15 brain tumor patients. The conventional clinical DCE-MRI had voxel dimensions 0.9 × 1.3 × 7.0 mm3, FOV 22 × 22 × 4.2 cm3, and the experimental DCE-MRI had voxel dimensions 0.9 × 0.9 × 1.9 mm3, and broader coverage 22 × 22 × 19 cm3. Temporal resolution was 5 s for both protocols. Time-resolved images and blood–brain barrier permeability maps were qualitatively evaluated by two radiologists. Results: The experimental DCE-MRI scans showed no loss of qualitative information in any of the cases, while achieving substantially higher spatial resolution and whole-brain spatial coverage. Average qualitative scores (from 0 to 3) were 2.1 for the experimental scans and 1.1 for the conventional clinical scans. Conclusions: The proposed DCE-MRI approach provides clinically superior image quality with higher spatial resolution and coverage than currently available approaches. These advantages may allow comprehensive permeability mapping in the brain, which is especially valuable in the setting of large lesions or multiple lesions spread throughout the brain. PMID:27147313

  16. Localizing the site of magnetic brain stimulation by functional MRI.

    PubMed

    Terao, Y; Ugawa, Y; Sakai, K; Miyauchi, S; Fukuda, H; Sasaki, Y; Takino, R; Hanajima, R; Furubayashi, T; Pütz, B; Kanazawa, I

    1998-07-01

    In order to locate the site of action of transcranial magnetic stimulation (TMS) within the human motor cortices, we investigated how the optimal positions for evoking motor responses over the scalp corresponded to the hand and leg primary-motor areas. TMS was delivered with a figure-8 shaped coil over each point of a grid system constructed on the skull surface, each separated by 1 cm, to find the optimal site for obtaining motor-evoked potentials (MEPs) in the contralateral first dorsal interosseous (FDI) and tibialis anterior (TA) muscles. Magnetic resonance imaging scans of the brain were taken for each subject with markers placed over these sites, the positions of which were projected onto the cortical region just beneath. On the other hand, cortical areas where blood flow increased during finger tapping or leg movements were identified on functional magnetic resonance images (fMRI), which should include the hand and leg primary-motor areas. The optimal location for eliciting MEPs in FDI, regardless of their latency, lay just above the bank of the precentral gyrus, which coincided with the activated region during finger tapping in fMRI studies. The direction of induced current preferentially eliciting MEPs with the shortest latency in each subject was nearly perpendicular to the course of the precentral gyrus at this position. The optimal site for evoking motor responses in TA was also located just above the activated area during leg movements identified within the anterior portion of the paracentral lobule. The results suggest that, for magnetic stimulation, activation occurs in the primary hand and leg motor area (Brodmann area 4), which is closest in distance to the optimal scalp position for evoking motor responses.

  17. Assessment of C-phycocyanin effect on astrocytes-mediated neuroprotection against oxidative brain injury using 2D and 3D astrocyte tissue model

    PubMed Central

    Min, Seul Ki; Park, Jun Sang; Luo, Lidan; Kwon, Yeo Seon; Lee, Hoo Cheol; Jung Shim, Hyun; Kim, Il-Doo; Lee, Ja-Kyeong; Shin, Hwa Sung

    2015-01-01

    Drugs are currently being developed to attenuate oxidative stress as a treatment for brain injuries. C-phycocyanin (C-Pc) is an antioxidant protein of green microalgae known to exert neuroprotective effects against oxidative brain injury. Astrocytes, which compose many portions of the brain, exert various functions to overcome oxidative stress; however, little is known about how C-Pc mediates the antioxidative effects of astrocytes. In this study, we revealed that C-Pc intranasal administration to the middle cerebral artery occlusion (MCAO) rats ensures neuroprotection of ischemic brain by reducing infarct size and improving behavioral deficits. C-Pc also enhanced viability and proliferation but attenuated apoptosis and reactive oxygen species (ROS) of oxidized astrocytes, without cytotoxicity to normal astrocytes and neurons. To elucidate how C-Pc leads astrocytes to enhance neuroprotection and repair of ischemia brain, we firstly developed 3D oxidized astrocyte model. C-Pc had astrocytes upregulate antioxidant enzymes such as SOD and catalase and neurotrophic factors BDNF and NGF, while alleviating inflammatory factors IL-6 and IL-1β and glial scar. Additionally, C-Pc improved viability of 3D oxidized neurons. In summary, C-Pc was concluded to activate oxidized astrocytes to protect and repair the ischemic brain with the combinatorial effects of improved antioxidative, neurotrophic, and anti-inflammatory mechanisms. PMID:26399322

  18. Assessment of C-phycocyanin effect on astrocytes-mediated neuroprotection against oxidative brain injury using 2D and 3D astrocyte tissue model.

    PubMed

    Min, Seul Ki; Park, Jun Sang; Luo, Lidan; Kwon, Yeo Seon; Lee, Hoo Cheol; Shim, Hyun Jung; Kim, Il-Doo; Lee, Ja-Kyeong; Shin, Hwa Sung

    2015-09-24

    Drugs are currently being developed to attenuate oxidative stress as a treatment for brain injuries. C-phycocyanin (C-Pc) is an antioxidant protein of green microalgae known to exert neuroprotective effects against oxidative brain injury. Astrocytes, which compose many portions of the brain, exert various functions to overcome oxidative stress; however, little is known about how C-Pc mediates the antioxidative effects of astrocytes. In this study, we revealed that C-Pc intranasal administration to the middle cerebral artery occlusion (MCAO) rats ensures neuroprotection of ischemic brain by reducing infarct size and improving behavioral deficits. C-Pc also enhanced viability and proliferation but attenuated apoptosis and reactive oxygen species (ROS) of oxidized astrocytes, without cytotoxicity to normal astrocytes and neurons. To elucidate how C-Pc leads astrocytes to enhance neuroprotection and repair of ischemia brain, we firstly developed 3D oxidized astrocyte model. C-Pc had astrocytes upregulate antioxidant enzymes such as SOD and catalase and neurotrophic factors BDNF and NGF, while alleviating inflammatory factors IL-6 and IL-1β and glial scar. Additionally, C-Pc improved viability of 3D oxidized neurons. In summary, C-Pc was concluded to activate oxidized astrocytes to protect and repair the ischemic brain with the combinatorial effects of improved antioxidative, neurotrophic, and anti-inflammatory mechanisms.

  19. Localization of Metal Electrodes in the Intact Rat Brain Using Registration of 3D Microcomputed Tomography Images to a Magnetic Resonance Histology Atlas1,2,3

    PubMed Central

    Borg, Jana Schaich; Vu, Mai-Anh; Badea, Cristian; Badea, Alexandra; Johnson, G. Allan

    2015-01-01

    Abstract Simultaneous neural recordings taken from multiple areas of the rodent brain are garnering growing interest because of the insight they can provide about spatially distributed neural circuitry. The promise of such recordings has inspired great progress in methods for surgically implanting large numbers of metal electrodes into intact rodent brains. However, methods for localizing the precise location of these electrodes have remained severely lacking. Traditional histological techniques that require slicing and staining of physical brain tissue are cumbersome and become increasingly impractical as the number of implanted electrodes increases. Here we solve these problems by describing a method that registers 3D computed tomography (CT) images of intact rat brains implanted with metal electrode bundles to a magnetic resonance imaging histology (MRH) atlas. Our method allows accurate visualization of each electrode bundle’s trajectory and location without removing the electrodes from the brain or surgically implanting external markers. In addition, unlike physical brain slices, once the 3D images of the electrode bundles and the MRH atlas are registered, it is possible to verify electrode placements from many angles by “reslicing” the images along different planes of view. Furthermore, our method can be fully automated and easily scaled to applications with large numbers of specimens. Our digital imaging approach to efficiently localizing metal electrodes offers a substantial addition to currently available methods, which, in turn, may help accelerate the rate at which insights are gleaned from rodent network neuroscience. PMID:26322331

  20. [Brain functional MRI: physiological, technical, and methodological bases, and clinical applications].

    PubMed

    Hertz-Pannier, L; Lehéricy, S; Cordoliani, Y; Le Bihan, D; Marsault, C; Brunelle, F

    2000-06-01

    Brain functional MRI (fMRI) provides an indirect mapping of cerebral activity, based on the detection of the local blood flow and oxygenation changes following neuronal activity (BOLD contrast, Blood Oxygenation Level Dependent). fMRI allows us to study non invasively the normal and pathological aspects of cortical functional organization. Each fMRI study compares two different states of activity. Echo-Planar Imaging (EPI) is the technic of choice that makes it possible to study the whole brain at a rapid pace. Activation maps are calculated from a statistical analysis of the local signal changes. Functional MRI is now becoming an essential tool in the neurofunctional work-up of many neurosurgery patients, as well as the reference method to image normal or pathologic functional brain organization in adults and children.

  1. The future of ultra-high field MRI and fMRI for study of the human brain

    PubMed Central

    Duyn, Jeff H.

    2011-01-01

    MRI and fMRI have been used for about three and two decades respectively and much has changed over this time period, both in the quality of the data and in the range of applications for studying the brain. Apart from resolution improvements from around 4 mm in the early days to below 0.5 mm with modern technology, novel uses of contrast have led to the ability to sensitize images to some of the brain’s structural properties at the cellular scale as well as study the localization and organization of brain function at the level of cortical columns. These developments have in part been facilitated by a continuing drive to increase the magnetic field strength. Will the next few decades see similar improvements? Here we will discuss current state of high field MRI, expected further increases in field strength, and improvements expected with these increases. PMID:22063093

  2. Would gestational age and presence of brain anomalies affect interobserver reliability of fetal head biometry? Using off-line analysis of 3-D dataset.

    PubMed

    Salman, Mona S M; Mousa, Hatem A; Twining, Peter; Jones, Nia W; James, David; Momtaz, Mohamed; Aboulghar, Mona; El-Sheikhah, Ahmad; Bugg, George

    2012-01-01

    The objective was to assess interobserver reliability of fetal head biometry using archived three-dimensional (3-D) volumes and the impact of gestational age and presence of brain anomalies on examiners' performance. Seventy nine 3-D volume datasets of fetal head were examined: 27 were normal and 52 had brain abnormalities. Off-line analysis was done by three fetal medicine experts (E1, E2 and E2), all were blinded to history and patient details. Measurements of the biparietal diameter (BPD), head circumference (HC), lateral ventricle (Vp) and transcerebellar diameter (TCD) were compared between examiners and to two-dimensional (2-D) measurements. Comparisons were made at two gestational age groups (≤22 and >22 weeks) and in presence and absence of brain anomalies. The intraclass coefficient showed a significantly high level of measurement agreement between 3-D examiners and 2-D, with values >0.9 throughout (p < 0.001). Bias was evident between 3-D examiners. E2 produced smaller measurements. The mean percentage difference between this examiner and the other two in BPD, HC, Vp and TCD measurements was significant, of 1.6%, 1%, 4.9% and 1.8%, respectively. E1 measured statistically larger for HC and TCD. E3 measured significantly larger for only BPD. The presence of anomalies was of no influence on the 3-D examiners' performance except for E3 who showed bias in BPD measurements only in cases with brain anomalies. Unlike other examiners, bias of E2 was only seen at gestational age group ≤22 weeks. Limits of agreement in measurements between observers were narrow for all parameters but were widest for the Vp measurements, being ±23% of the mean difference. Despite the above bias, the actual mean difference between examiners was small and unlikely to be of any clinical significance. Off-line measurement of fetal head biometry using 3-D volumes is reliable. In our study, presence of brain anomalies was unlikely to influence the reproducibility of measurements

  3. Outcome Classification of Preschool Children with Autism Spectrum Disorders Using Mri Brain Measures.

    ERIC Educational Resources Information Center

    Akshoomoff, Natacha; Lord, Catherine; Lincoln, Alan J.; Courchesne, Rachel Y.; Carper, Ruth A.; Townsend, Jeanne; Courchesne, Eric

    2004-01-01

    Objective: To test the hypothesis that a combination of magnetic resonance imaging (MRI) brain measures obtained during early childhood distinguish children with autism spectrum disorders (ASD) from typically developing children and is associated with functional outcome. Method: Quantitative MRI technology was used to measure gray and white matter…

  4. Relating resting-state fMRI and EEG whole-brain connectomes across frequency bands.

    PubMed

    Deligianni, Fani; Centeno, Maria; Carmichael, David W; Clayden, Jonathan D

    2014-01-01

    Whole brain functional connectomes hold promise for understanding human brain activity across a range of cognitive, developmental and pathological states. So called resting-state (rs) functional MRI studies have contributed to the brain being considered at a macroscopic scale as a set of interacting regions. Interactions are defined as correlation-based signal measurements driven by blood oxygenation level dependent (BOLD) contrast. Understanding the neurophysiological basis of these measurements is important in conveying useful information about brain function. Local coupling between BOLD fMRI and neurophysiological measurements is relatively well defined, with evidence that gamma (range) frequency EEG signals are the closest correlate of BOLD fMRI changes during cognitive processing. However, it is less clear how whole-brain network interactions relate during rest where lower frequency signals have been suggested to play a key role. Simultaneous EEG-fMRI offers the opportunity to observe brain network dynamics with high spatio-temporal resolution. We utilize these measurements to compare the connectomes derived from rs-fMRI and EEG band limited power (BLP). Merging this multi-modal information requires the development of an appropriate statistical framework. We relate the covariance matrices of the Hilbert envelope of the source localized EEG signal across bands to the covariance matrices derived from rs-fMRI with the means of statistical prediction based on sparse Canonical Correlation Analysis (sCCA). Subsequently, we identify the most prominent connections that contribute to this relationship. We compare whole-brain functional connectomes based on their geodesic distance to reliably estimate the performance of the prediction. The performance of predicting fMRI from EEG connectomes is considerably better than predicting EEG from fMRI across all bands, whereas the connectomes derived in low frequency EEG bands resemble best rs-fMRI connectivity.

  5. Abnormality of spontaneous brain activities in patients with chronic neck and shoulder pain: A resting-state fMRI study.

    PubMed

    Yu, Cheng-Xin; Ji, Ting-Ting; Song, Hao; Li, Bo; Han, Qiang; Li, Liang; Zhuo, Zhi-Zheng

    2017-02-01

    Objectives Chronic gneck and shoulder pain (CNSP) is a common clinical symptom of cervical spondylotic radiculopathy. Several studies using resting-state functional magnetic resonance imaging (rs-fMRI) have reported that most chronic pain diseases are accompanied by structural and functional changes in the brain. However, few rs-fMRI studies have examined CNSP. The current study investigated cerebral structural and functional changes in CNSP patients. Methods In total, 25 CNSP patients and 20 healthy volunteers participated in the study. 3D-T1W and rs-fMRI images were acquired. Voxel-based morphometry analysis was applied to structural images, and regional homogeneity (ReHo) was extracted from rs-fMRI. Statistical analysis was performed on post-processing images and ReHo parameter maps. Results The results revealed no significant differences in brain structure between the two groups. In the patient group, ReHo values were significantly increased in the bilateral middle frontal gyrus and decreased in the left insula, superior frontal gyrus, middle cingulate gyrus, supplementary motor area, right postcentral gyrus, and superior parietal lobule. Conclusions This initial structural and rs-fMRI study of CNSP revealed characteristic features of spontaneous brain activity of CNSP patients. These findings may be helpful for increasing our understanding of the neuropathology of CNSP.

  6. Measurement of blood-brain barrier permeability with t1-weighted dynamic contrast-enhanced MRI in brain tumors: a comparative study with two different algorithms.

    PubMed

    Bergamino, Maurizio; Saitta, Laura; Barletta, Laura; Bonzano, Laura; Mancardi, Giovanni Luigi; Castellan, Lucio; Ravetti, Jean Louis; Roccatagliata, Luca

    2013-01-01

    The purpose of this study was to assess the feasibility of measuring different permeability parameters with T1-weighted dynamic contrast-enhanced (DCE) magnetic resonance imaging (MRI) in order to investigate the blood brain-barrier permeability associated with different brain tumors. The Patlak algorithm and the extended Tofts-Kety model were used to this aim. Twenty-five adult patients with tumors of different histological grades were enrolled in this study. MRI examinations were performed at 1.5 T. Multiflip angle, fast low-angle shot, and axial 3D T1-weighted images were acquired to calculate T1 maps, followed by a DCE acquisition. A region of interest was placed within the tumor of each patient to calculate the mean value of different permeability parameters. Differences in permeability measurements were found between different tumor grades, with higher histological grades characterized by higher permeability values. A significant difference in transfer constant (K (trans)) values was found between the two methods on high-grade tumors; however, both techniques revealed a significant correlation between the histological grade of tumors and their K (trans) values. Our results suggest that DCE acquisition is feasible in patients with brain tumors and that K (trans) maps can be easily obtained by these two algorithms, even if the theoretical model adopted could affect the final results.

  7. Distinct Contributions of Astrocytes and Pericytes to Neuroinflammation Identified in a 3D Human Blood-Brain Barrier on a Chip.

    PubMed

    Herland, Anna; van der Meer, Andries D; FitzGerald, Edward A; Park, Tae-Eun; Sleeboom, Jelle J F; Ingber, Donald E

    2016-01-01

    Neurovascular inflammation is a major contributor to many neurological disorders, but modeling these processes in vitro has proven to be difficult. Here, we microengineered a three-dimensional (3D) model of the human blood-brain barrier (BBB) within a microfluidic chip by creating a cylindrical collagen gel containing a central hollow lumen inside a microchannel, culturing primary human brain microvascular endothelial cells on the gel's inner surface, and flowing medium through the lumen. Studies were carried out with the engineered microvessel containing endothelium in the presence or absence of either primary human brain pericytes beneath the endothelium or primary human brain astrocytes within the surrounding collagen gel to explore the ability of this simplified model to identify distinct contributions of these supporting cells to the neuroinflammatory response. This human 3D BBB-on-a-chip exhibited barrier permeability similar to that observed in other in vitro BBB models created with non-human cells, and when stimulated with the inflammatory trigger, tumor necrosis factor-alpha (TNF-α), different secretion profiles for granulocyte colony-stimulating factor (G-CSF) and interleukin-6 (IL-6) were observed depending on the presence of astrocytes or pericytes. Importantly, the levels of these responses detected in the 3D BBB chip were significantly greater than when the same cells were co-cultured in static Transwell plates. Thus, as G-CSF and IL-6 have been reported to play important roles in neuroprotection and neuroactivation in vivo, this 3D BBB chip potentially offers a new method to study human neurovascular function and inflammation in vitro, and to identify physiological contributions of individual cell types.

  8. Distinct Contributions of Astrocytes and Pericytes to Neuroinflammation Identified in a 3D Human Blood-Brain Barrier on a Chip

    PubMed Central

    FitzGerald, Edward A.; Park, Tae-Eun; Sleeboom, Jelle J. F.; Ingber, Donald E.

    2016-01-01

    Neurovascular inflammation is a major contributor to many neurological disorders, but modeling these processes in vitro has proven to be difficult. Here, we microengineered a three-dimensional (3D) model of the human blood-brain barrier (BBB) within a microfluidic chip by creating a cylindrical collagen gel containing a central hollow lumen inside a microchannel, culturing primary human brain microvascular endothelial cells on the gel’s inner surface, and flowing medium through the lumen. Studies were carried out with the engineered microvessel containing endothelium in the presence or absence of either primary human brain pericytes beneath the endothelium or primary human brain astrocytes within the surrounding collagen gel to explore the ability of this simplified model to identify distinct contributions of these supporting cells to the neuroinflammatory response. This human 3D BBB-on-a-chip exhibited barrier permeability similar to that observed in other in vitro BBB models created with non-human cells, and when stimulated with the inflammatory trigger, tumor necrosis factor-alpha (TNF-α), different secretion profiles for granulocyte colony-stimulating factor (G-CSF) and interleukin-6 (IL-6) were observed depending on the presence of astrocytes or pericytes. Importantly, the levels of these responses detected in the 3D BBB chip were significantly greater than when the same cells were co-cultured in static Transwell plates. Thus, as G-CSF and IL-6 have been reported to play important roles in neuroprotection and neuroactivation in vivo, this 3D BBB chip potentially offers a new method to study human neurovascular function and inflammation in vitro, and to identify physiological contributions of individual cell types. PMID:26930059

  9. Object categories specific brain activity classification with simultaneous EEG-fMRI.

    PubMed

    Ahmad, Rana Fayyaz; Malik, Aamir Saeed; Kamel, Nidal; Reza, Faruque

    2015-01-01

    Any kind of visual information is encoded in terms of patterns of neural activity occurring inside the brain. Decoding neural patterns or its classification is a challenging task. Functional magnetic resonance imaging (fMRI) and Electroencephalography (EEG) are non-invasive neuroimaging modalities to capture the brain activity pattern in term of images and electric potential respectively. To get higher spatiotemporal resolution of human brain from these two complementary neuroimaging modalities, simultaneous EEG-fMRI can be helpful. In this paper, we proposed a framework for classifying the brain activity patterns with simultaneous EEG-fMRI. We have acquired five human participants' data with simultaneous EEG-fMRI by showing different object categories. Further, combined analysis of EEG and fMRI data was carried out. Extracted information through combine analysis is passed to support vector machine (SVM) classifier for classification purpose. We have achieved better classification accuracy using simultaneous EEG-fMRI i.e., 81.8% as compared to fMRI data standalone. This shows that multimodal neuroimaging can improve the classification accuracy of brain activity patterns as compared to individual modalities reported in literature.

  10. Clinical outcome of protocol based image (MRI) guided adaptive brachytherapy combined with 3D conformal radiotherapy with or without chemotherapy in patients with locally advanced cervical cancer

    PubMed Central

    Pötter, Richard; Georg, Petra; Dimopoulos, Johannes C.A.; Grimm, Magdalena; Berger, Daniel; Nesvacil, Nicole; Georg, Dietmar; Schmid, Maximilian P.; Reinthaller, Alexander; Sturdza, Alina; Kirisits, Christian

    2011-01-01

    survival at 3 years was in total 68%, 72% for tumours 2–5 cm, 65% for tumours >5 cm, 74% for IB, 78% for IIB, 45% for IIIB. In regard to late morbidity in total 188 grade 1 + 2 and 11 grade 3 + 4 late events were observed in 143 patients. G1 + 2/G3 + 4 events for bladder were n = 32/3, for rectum n = 14/5, for bowel (including sigmoid) n = 3/0, for vagina n = 128/2, respectively. Interpretation 3D conformal radiotherapy ± chemotherapy plus image (MRI) guided adaptive intracavitary brachytherapy including needle insertion in advanced disease results in local control rates of 95–100% at 3 years in limited/favourable (IB/IIB) and 85–90% in large/poor response (IIB/III/IV) cervix cancer patients associated with a moderate rate of treatment related morbidity. Compared to the historical Vienna series there is relative reduction in pelvic recurrence by 65–70% and reduction in major morbidity. The local control improvement seems to have impact on CSS and OS. Prospective clinical multi-centre studies are mandatory to evaluate these challenging mono-institutional findings. PMID:21821305

  11. Comparison of manual vs. automated multimodality (CT-MRI) image registration for brain tumors

    SciTech Connect

    Sarkar, Abhirup; Santiago, Roberto J.; Smith, Ryan; Kassaee, Alireza . E-mail: Kassaee@xrt.upenn.edu

    2005-03-31

    Computed tomgoraphy-magnetic resonance imaging (CT-MRI) registrations are routinely used for target-volume delineation of brain tumors. We clinically use 2 software packages based on manual operation and 1 automated package with 2 different algorithms: chamfer matching using bony structures, and mutual information using intensity patterns. In all registration algorithms, a minimum of 3 pairs of identical anatomical and preferably noncoplanar landmarks is used on each of the 2 image sets. In manual registration, the program registers these points and links the image sets using a 3-dimensional (3D) transformation. In automated registration, the 3 landmarks are used as an initial starting point and further processing is done to complete the registration. Using our registration packages, registration of CT and MRI was performed on 10 patients. We scored the results of each registration set based on the amount of time spent, the accuracy reported by the software, and a final evaluation. We evaluated each software program by measuring the residual error between 'matched' points on the right and left globes and the posterior fossa for fused image slices. In general, manual registration showed higher misalignment between corresponding points compared to automated registration using intensity matching. This error had no directional dependence and was, most of the time, larger for a larger structure in both registration techniques. Automated algorithm based on intensity matching also gave the best results in terms of registration accuracy, irrespective of whether or not the initial landmarks were chosen carefully, when compared to that done using bone matching algorithm. Intensity-matching algorithm required the least amount of user-time and provided better accuracy.

  12. A systematic pipeline for the objective comparison of whole-brain spectroscopic MRI with histology in biopsy specimens from grade III glioma

    PubMed Central

    Cordova, J. Scott; Gurbani, Saumya S.; Olson, Jeffrey J.; Liang, Zhongxing; Cooper, Lee A. D.; Shu, Hui-Kuo G.; Schreibmann, Eduard; Neill, Stewart G.; Hadjipanayis, Constantinos G.; Holder, Chad A.; Shim, Hyunsuk

    2016-01-01

    The diagnosis, prognosis, and management of patients with gliomas are largely dictated by the pathological analysis of tissue biopsied from a selected region within the lesion. However, due to the heterogeneous and infiltrative nature of gliomas, identifying the optimal region for biopsy with conventional magnetic resonance imaging (MRI) can be quite difficult. This is especially true for low grade gliomas, which often are non-enhancing tumors. To improve the management of patients with these tumors, the field of neuro-oncology requires an imaging modality that can specifically identify a tumor’s most anaplastic/aggressive region(s) for biopsy targeting. The addition of metabolic mapping using spectroscopic MRI (sMRI) to supplement conventional MRI could improve biopsy targeting and, ultimately, diagnostic accuracy. Here, we describe a pipeline for the integration of state-of-the-art, high-resolution whole-brain 3D sMRI maps into a stereotactic neuronavigation system for guiding biopsies in gliomas with nonenhancing components. We also outline a machine-learning method for automated histology analysis that generates normalized, quantitative metrics describing tumor infiltration in immunohistochemically-stained tissue specimens. As a proof of concept, we describe the combination of these two techniques in a small cohort of grade III glioma patients. In this work, we aim to set forth a systematic pipeline to stimulate histopathology-image validation of advanced MRI techniques, such as sMRI. PMID:27489883

  13. A normative spatiotemporal MRI atlas of the fetal brain for automatic segmentation and analysis of early brain growth.

    PubMed

    Gholipour, Ali; Rollins, Caitlin K; Velasco-Annis, Clemente; Ouaalam, Abdelhakim; Akhondi-Asl, Alireza; Afacan, Onur; Ortinau, Cynthia M; Clancy, Sean; Limperopoulos, Catherine; Yang, Edward; Estroff, Judy A; Warfield, Simon K

    2017-03-28

    Longitudinal characterization of early brain growth in-utero has been limited by a number of challenges in fetal imaging, the rapid change in size, shape and volume of the developing brain, and the consequent lack of suitable algorithms for fetal brain image analysis. There is a need for an improved digital brain atlas of the spatiotemporal maturation of the fetal brain extending over the key developmental periods. We have developed an algorithm for construction of an unbiased four-dimensional atlas of the developing fetal brain by integrating symmetric diffeomorphic deformable registration in space with kernel regression in age. We applied this new algorithm to construct a spatiotemporal atlas from MRI of 81 normal fetuses scanned between 19 and 39 weeks of gestation and labeled the structures of the developing brain. We evaluated the use of this atlas and additional individual fetal brain MRI atlases for completely automatic multi-atlas segmentation of fetal brain MRI. The atlas is available online as a reference for anatomy and for registration and segmentation, to aid in connectivity analysis, and for groupwise and longitudinal analysis of early brain growth.

  14. Brain-stem Listeriosis: A Comparison of SPECT and MRI Findings

    PubMed Central

    Sahin, Sevki; Arisoy, Ayse S.; Topkaya, Aynur E.; Karsidag, Sibel

    2006-01-01

    Abstract and Introduction Abstract Listeria monocytogenes, although uncommon as a cause of illness in the general population, can result in serious illness when it affects pregnant women, neonates, the elderly, and immunocompromised individuals. Typically, it is a food-borne organism. This report describes a case of brain-stem listeriosis in a previously healthy 51-year-old woman. The diagnosis was based on clinical findings, the results of cerebrospinal fluid (CSF) analysis, CSF culture, and magnetic resonance imaging (MRI) findings. MRI demonstrated upper brain stem and cerebellar peduncle involvement. In addition, Tc-99m exametazime (HMPAO)-labeled single photon emission computed tomography (SPECT) of the brain revealed bilateral cerebellar hypoperfusion. Antibiotic therapy resulted in partial clinical recovery after 3 weeks. At the end of 6 months, brain-stem findings had nearly resolved. However, although minimal residual findings were observed on MRI at 6 months, bilateral diffuse cerebellar hypoperfusion remained on Tc-99m HMPAO brain SPECT. PMID:17415328

  15. Guiding Brain-Tumor Surgery via Blood-Brain-Barrier-Permeable Gold Nanoprobes with Acid-Triggered MRI/SERRS Signals.

    PubMed

    Gao, Xihui; Yue, Qi; Liu, Zining; Ke, Mengjing; Zhou, Xingyu; Li, Sihan; Zhang, Jianping; Zhang, Ren; Chen, Liang; Mao, Ying; Li, Cong

    2017-03-15

    Surgical resection is a mainstay in the treatment of malignant brain tumors. Surgeons, however, face great challenges in distinguishing tumor margins due to their infiltrated nature. Here, a pair of gold nanoprobes that enter a brain tumor by crossing the blood-brain barrier is developed. The acidic tumor environment triggers their assembly with the concomitant activation of both magnetic resonance (MR) and surface-enhanced resonance Raman spectroscopy (SERRS) signals. While the bulky aggregates continuously trap into the tumor interstitium, the intact nanoprobes in normal brain tissue can be transported back into the blood stream in a timely manner. Experimental results show that physiological acidity triggers nanoparticle assembly by forming 3D spherical nanoclusters with remarkable MR and SERRS signal enhancements. The nanoprobes not only preoperatively define orthotopic glioblastoma xenografts by magnetic resonance imaging (MRI) with high sensitivity and durability in vivo, but also intraoperatively guide tumor excision with the assistance of a handheld Raman scanner. Microscopy studies verify the precisely demarcated tumor margin marked by the assembled nanoprobes. Taking advantage of the nanoprobes' rapid excretion rate and the extracellular acidification as a hallmark of solid tumors, these nanoprobes are promising in improving brain-tumor surgical outcome with high specificity, safety, and universality.

  16. A multi-contrast MRI study of microstructural brain damage in patients with mild cognitive impairment

    PubMed Central

    Granziera, C.; Daducci, A.; Donati, A.; Bonnier, G.; Romascano, D.; Roche, A.; Bach Cuadra, M.; Schmitter, D.; Klöppel, S.; Meuli, R.; von Gunten, A.; Krueger, G.

    2015-01-01

    Objectives The aim of this study was to investigate pathological mechanisms underlying brain tissue alterations in mild cognitive impairment (MCI) using multi-contrast 3 T magnetic resonance imaging (MRI). Methods Forty-two MCI patients and 77 healthy controls (HC) underwent T1/T2* relaxometry as well as Magnetization Transfer (MT) MRI. Between-groups comparisons in MRI metrics were performed using permutation-based tests. Using MRI data, a generalized linear model (GLM) was computed to predict clinical performance and a support-vector machine (SVM) classification was used to classify MCI and HC subjects. Results Multi-parametric MRI data showed microstructural brain alterations in MCI patients vs HC that might be interpreted as: (i) a broad loss of myelin/cellular proteins and tissue microstructure in the hippocampus (p ≤ 0.01) and global white matter (p < 0.05); and (ii) iron accumulation in the pallidus nucleus (p ≤ 0.05). MRI metrics accurately predicted memory and executive performances in patients (p ≤ 0.005). SVM classification reached an accuracy of 75% to separate MCI and HC, and performed best using both volumes and T1/T2*/MT metrics. Conclusion Multi-contrast MRI appears to be a promising approach to infer pathophysiological mechanisms leading to brain tissue alterations in MCI. Likewise, parametric MRI data provide powerful correlates of cognitive deficits and improve automatic disease classification based on morphometric features. PMID:26236628

  17. EEG-fMRI integration for the study of human brain function.

    PubMed

    Jorge, João; van der Zwaag, Wietske; Figueiredo, Patrícia

    2014-11-15

    Electroencephalography (EEG) and functional magnetic resonance imaging (fMRI) have proved to be extremely valuable tools for the non-invasive study of human brain function. Moreover, due to a notable degree of complementarity between the two modalities, the combination of EEG and fMRI data has been actively sought in the last two decades. Although initially focused on epilepsy, EEG-fMRI applications were rapidly extended to the study of healthy brain function, yielding new insights into its underlying mechanisms and pathways. Nevertheless, EEG and fMRI have markedly different spatial and temporal resolutions, and probe neuronal activity through distinct biophysical processes, many aspects of which are still poorly understood. The remarkable conceptual and methodological challenges associated with EEG-fMRI integration have motivated the development of a wide range of analysis approaches over the years, each relying on more or less restrictive assumptions, and aiming to shed further light on the mechanisms of brain function along with those of the EEG-fMRI coupling itself. Here, we present a review of the most relevant EEG-fMRI integration approaches yet proposed for the study of brain function, supported by a general overview of our current understanding of the biophysical mechanisms coupling the signals obtained from the two modalities.

  18. The spatiospectral characterization of brain networks: fusing concurrent EEG spectra and fMRI maps.

    PubMed

    Bridwell, David A; Wu, Lei; Eichele, Tom; Calhoun, Vince D

    2013-04-01

    Different imaging modalities capture different aspects of brain activity. Functional magnetic resonance imaging (fMRI) reveals intrinsic networks whose BOLD signals have periods from 100 s (0.01 Hz) to about 10s (0.1 Hz). Electroencephalographic (EEG) recordings, in contrast, commonly reflect cortical electrical fluctuations with periods up to 20 ms (50 Hz) or above. We examined the correspondence between intrinsic fMRI and EEG network activity at rest in order to characterize brain networks both spatially (with fMRI) and spectrally (with EEG). Brain networks were separately identified within the concurrently recorded fMRI and EEG at the aggregate group level with group independent component analysis and the association between spatial fMRI and frequency by spatial EEG sources was examined by deconvolving their component time courses. The two modalities are considered linked if the estimated impulse response function (IRF) is significantly non-zero at biologically plausible delays. We found that negative associations were primarily present within two of five alpha components, which highlights the importance of considering multiple alpha sources in EEG-fMRI. Positive associations were primarily present within the lower (e.g. delta and theta) and higher (e.g. upper beta and lower gamma) spectral regions, sometimes within the same fMRI components. Collectively, the results demonstrate a promising approach to characterize brain networks spatially and spectrally, and reveal that positive and negative associations appear within partially distinct regions of the EEG spectrum.

  19. Individual 3D region-of-interest atlas of the human brain: knowledge-based class image analysis for extraction of anatomical objects

    NASA Astrophysics Data System (ADS)

    Wagenknecht, Gudrun; Kaiser, Hans-Juergen; Sabri, Osama; Buell, Udalrich

    2000-06-01

    After neural network-based classification of tissue types, the second step of atlas extraction is knowledge-based class image analysis to get anatomically meaningful objects. Basic algorithms are region growing, mathematical morphology operations, and template matching. A special algorithm was designed for each object. The class label of each voxel and the knowledge about the relative position of anatomical objects to each other and to the sagittal midplane of the brain can be utilized for object extraction. User interaction is only necessary to define starting, mid- and end planes for most object extractions and to determine the number of iterations for erosion and dilation operations. Extraction can be done for the following anatomical brain regions: cerebrum; cerebral hemispheres; cerebellum; brain stem; white matter (e.g., centrum semiovale); gray matter [cortex, frontal, parietal, occipital, temporal lobes, cingulum, insula, basal ganglia (nuclei caudati, putamen, thalami)]. For atlas- based quantification of functional data, anatomical objects can be convoluted with the point spread function of functional data to take into account the different resolutions of morphological and functional modalities. This method allows individual atlas extraction from MRI image data of a patient without the need of warping individual data to an anatomical or statistical MRI brain atlas.

  20. Population based MRI and DTI templates of the adult ferret brain and tools for voxelwise analysis.

    PubMed

    Hutchinson, E B; Schwerin, S C; Radomski, K L; Sadeghi, N; Jenkins, J; Komlosh, M E; Irfanoglu, M O; Juliano, S L; Pierpaoli, C

    2017-03-16

    Non-invasive imaging has the potential to play a crucial role in the characterization and translation of experimental animal models to investigate human brain development and disorders, especially when employed to study animal models that more accurately represent features of human neuroanatomy. The purpose of this study was to build and make available MRI and DTI templates and analysis tools for the ferret brain as the ferret is a well-suited species for pre-clinical MRI studies with folded cortical surface, relatively high white matter volume and body dimensions that allow imaging with pre-clinical MRI scanners. Four ferret brain templates were built in this study - in-vivo MRI and DTI and ex-vivo MRI and DTI - using brain images across many ferrets and region of interest (ROI) masks corresponding to established ferret neuroanatomy were generated by semi-automatic and manual segmentation. The templates and ROI masks were used to create a web-based ferret brain viewing software for browsing the MRI and DTI volumes with annotations based on the ROI masks. A second objective of this study was to provide a careful description of the imaging methods used for acquisition, processing, registration and template building and to demonstrate several voxelwise analysis methods including Jacobian analysis of morphometry differences between the female and male brain and bias-free identification of DTI abnormalities in an injured ferret brain. The templates, tools and methodological optimization presented in this study are intended to advance non-invasive imaging approaches for human-similar animal species that will enable the use of pre-clinical MRI studies for understanding and treating brain disorders.

  1. Neurobiological origin of spurious brain morphological changes: A quantitative MRI study.

    PubMed

    Lorio, Sara; Kherif, Ferath; Ruef, Anne; Melie-Garcia, Lester; Frackowiak, Richard; Ashburner, John; Helms, Gunther; Lutti, Antoine; Draganski, Bodgan

    2016-05-01

    The high gray-white matter contrast and spatial resolution provided by T1-weighted magnetic resonance imaging (MRI) has made it a widely used imaging protocol for computational anatomy studies of the brain. While the image intensity in T1-weighted images is predominantly driven by T1, other MRI parameters affect the image contrast, and hence brain morphological measures derived from the data. Because MRI parameters are correlates of different histological properties of brain tissue, this mixed contribution hampers the neurobiological interpretation of morphometry findings, an issue which remains largely ignored in the community. We acquired quantitative maps of the MRI parameters that determine signal intensities in T1-weighted images (R1 (=1/T1), R2 *, and PD) in a large cohort of healthy subjects (n = 120, aged 18-87 years). Synthetic T1-weighted images were calculated from these quantitative maps and used to extract morphometry features-gray matter volume and cortical thickness. We observed significant variations in morphometry measures obtained from synthetic images derived from different subsets of MRI parameters. We also detected a modulation of these variations by age. Our findings highlight the impact of microstructural properties of brain tissue-myelination, iron, and water content-on automated measures of brain morphology and show that microstructural tissue changes might lead to the detection of spurious morphological changes in computational anatomy studies. They motivate a review of previous morphological results obtained from standard anatomical MRI images and highlight the value of quantitative MRI data for the inference of microscopic tissue changes in the healthy and diseased brain. Hum Brain Mapp 37:1801-1815, 2016. © 2016 The Authors. Human Brain Mapping Published by Wiley Periodicals, Inc.

  2. Neurobiological origin of spurious brain morphological changes: A quantitative MRI study

    PubMed Central

    Lorio, Sara; Kherif, Ferath; Ruef, Anne; Melie‐Garcia, Lester; Frackowiak, Richard; Ashburner, John; Helms, Gunther

    2016-01-01

    Abstract The high gray‐white matter contrast and spatial resolution provided by T1‐weighted magnetic resonance imaging (MRI) has made it a widely used imaging protocol for computational anatomy studies of the brain. While the image intensity in T1‐weighted images is predominantly driven by T1, other MRI parameters affect the image contrast, and hence brain morphological measures derived from the data. Because MRI parameters are correlates of different histological properties of brain tissue, this mixed contribution hampers the neurobiological interpretation of morphometry findings, an issue which remains largely ignored in the community. We acquired quantitative maps of the MRI parameters that determine signal intensities in T1‐weighted images (R 1 (=1/T1), R 2*, and PD) in a large cohort of healthy subjects (n = 120, aged 18–87 years). Synthetic T1‐weighted images were calculated from these quantitative maps and used to extract morphometry features—gray matter volume and cortical thickness. We observed significant variations in morphometry measures obtained from synthetic images derived from different subsets of MRI parameters. We also detected a modulation of these variations by age. Our findings highlight the impact of microstructural properties of brain tissue—myelination, iron, and water content—on automated measures of brain morphology and show that microstructural tissue changes might lead to the detection of spurious morphological changes in computational anatomy studies. They motivate a review of previous morphological results obtained from standard anatomical MRI images and highlight the value of quantitative MRI data for the inference of microscopic tissue changes in the healthy and diseased brain. Hum Brain Mapp 37:1801–1815, 2016. © 2016 The Authors. Human Brain Mapping Published by Wiley Periodicals, Inc. PMID:26876452

  3. Diagnostic Value and Surgical Implications of the 3D DW-SSFP MRI On the Management of Patients with Brachial Plexus Injuries

    PubMed Central

    Qin, Ben-Gang; Yang, Jian-Tao; Yang, Yi; Wang, Hong-Gang; Fu, Guo; Gu, Li-Qiang; Li, Ping; Zhu, Qing-Tang; Liu, Xiao-Lin; Zhu, Jia-Kai

    2016-01-01

    Three-dimensional diffusion-weighted steady-state free precession (3D DW-SSFP) of high-resolution magnetic resonance has emerged as a promising method to visualize the peripheral nerves. In this study, the application value of 3D DW-SSFP brachial plexus imaging in the diagnosis of brachial plexus injury (BPI) was investigated. 33 patients with BPI were prospectively examined using 3D DW-SSFP MR neurography (MRN) of brachial plexus. Results of 3D DW-SSFP MRN were compared with intraoperative findings and measurements of electromyogram (EMG) or somatosensory evoked potentials (SEP) for each injured nerve root. 3D DW-SSFP MRN of brachial plexus has enabled good visualization of the small components of the brachial plexus. The postganglionic section of the brachial plexus was clearly visible in 26 patients, while the preganglionic section of the brachial plexus was clearly visible in 22 patients. Pseudomeningoceles were commonly observed in 23 patients. Others finding of MRN of brachial plexus included spinal cord offset (in 16 patients) and spinal cord deformation (in 6 patients). As for the 3D DW-SSFP MRN diagnosis of preganglionic BPI, the sensitivity, the specificity and the accuracy were respectively 96.8%, 90.29%, and 94.18%. 3D DW-SSFP MRN of brachial plexus improve visualization of brachial plexus and benefit to determine the extent of injury. PMID:27782162

  4. Profiles by Sex of Brain MRI and Cognitive Function in The Framingham Offspring Study

    PubMed Central

    Albert, Mark; Massaro, Joseph; DeCarli, Charles; Beiser, Alexa; Seshadri, Sudha; Wolf, Philip A.; Au, Rhoda

    2009-01-01

    Objective To examine whether there are sex-specific associations between brain MRI measures and neuropsychological test performance. Background Differences in cardiovascular risk factors (CVRF) have been linked to decreased total cerebral brain volume (TCBV) and white matter hyperintensities (WMH). Although brain morphology has been related to cognitive performance, few studies have addressed sex-specific effects in this relationship. Methods Framingham Offspring who were stroke and dementia-free underwent a brain MRI scan and neuropsychological (NP) testing (n=2,085; 978 men). Factor analysis identified four domain-specific neuropsychological factors. MRI participants were divided into four MRI subgroups based on measures of TCBV and combinations of the presence of WMH and silent cerebral infarcts (≥3mm; SCI). Results Overall, the relationship between MRI and NP measures was similar between the sexes. The exception was that only men showed a positive relationship between executive function (EF) and cerebrovascular disease defined as large white matter hyperintensity volume plus SCI. This finding was attributed only among men with FSRP scores > 90th percentile range (p=0.0019). Conclusions Measures of brain atrophy and subclinical markers of vascular disease showed that sex does not significantly alter the relationship between MRI and NP, except among men and women who are at high risk for stroke; these men show poorer performance on EF, whereas the women do not. PMID:20505436

  5. Dynamic contrast-enhanced MRI perfusion for differentiating between melanoma and lung cancer brain metastases.

    PubMed

    Hatzoglou, Vaios; Tisnado, Jamie; Mehta, Alpesh; Peck, Kyung K; Daras, Mariza; Omuro, Antonio M; Beal, Kathryn; Holodny, Andrei I

    2017-04-01

    Brain metastases originating from different primary sites overlap in appearance and are difficult to differentiate with conventional MRI. Dynamic contrast-enhanced (DCE)-MRI can assess tumor microvasculature and has demonstrated utility in characterizing primary brain tumors. Our aim was to evaluate the performance of plasma volume (Vp) and volume transfer coefficient (K(trans) ) derived from DCE-MRI in distinguishing between melanoma and nonsmall cell lung cancer (NSCLC) brain metastases. Forty-seven NSCLC and 23 melanoma brain metastases were retrospectively assessed with DCE-MRI. Regions of interest were manually drawn around the metastases to calculate Vpmean and Kmeantrans. The Mann-Whitney U test and receiver operating characteristic analysis (ROC) were performed to compare perfusion parameters between the two groups. The Vpmean of melanoma brain metastases (4.35, standard deviation [SD] = 1.31) was significantly higher (P = 0.03) than Vpmean of NSCLC brain metastases (2.27, SD = 0.96). The Kmeantrans values were higher in melanoma brain metastases, but the difference between the two groups was not significant (P = 0.12). Based on ROC analysis, a cut-off value of 3.02 for Vpmean (area under curve = 0.659 with SD = 0.074) distinguished between melanoma brain metastases and NSCLC brain metastases (P < 0.01) with 72% specificity. Our data show the DCE-MRI parameter Vpmean can differentiate between melanoma and NSCLC brain metastases. The ability to noninvasively predict tumor histology of brain metastases in patients with multiple malignancies can have important clinical implications.

  6. Simultaneous PET-MRI reveals brain function in activated and resting state on metabolic, hemodynamic and multiple temporal scales.

    PubMed

    Wehrl, Hans F; Hossain, Mosaddek; Lankes, Konrad; Liu, Chih-Chieh; Bezrukov, Ilja; Martirosian, Petros; Schick, Fritz; Reischl, Gerald; Pichler, Bernd J

    2013-09-01

    Combined positron emission tomography (PET) and magnetic resonance imaging (MRI) is a new tool to study functional processes in the brain. Here we study brain function in response to a barrel-field stimulus simultaneously using PET, which traces changes in glucose metabolism on a slow time scale, and functional MRI (fMRI), which assesses fast vascular and oxygenation changes during activation. We found spatial and quantitative discrepancies between the PET and the fMRI activation data. The functional connectivity of the rat brain was assessed by both modalities: the fMRI approach determined a total of nine known neural networks, whereas the PET method identified seven glucose metabolism-related networks. These results demonstrate the feasibility of combined PET-MRI for the simultaneous study of the brain at activation and rest, revealing comprehensive and complementary information to further decode brain function and brain networks.

  7. Non-invasive Quantification of Whole-brain Cerebral Metabolic Rate of Oxygen by MRI

    PubMed Central

    Xu, Feng; Ge, Yulin; Lu, Hanzhang

    2009-01-01

    Cerebral metabolic rate of oxygen (CMRO2) is an important marker for brain function and brain health. Existing techniques for quantification of CMRO2 with Positron Emission Tomography (PET) or MRI involve special equipment and/or exogenous agent, and may not be suitable for routine clinical studies. In the present study, a non-invasive method is developed to estimate whole-brain CMRO2 in humans. This method applies phase-contrast MRI for quantitative blood flow measurement and T2-Relaxation-Under-Spin-Tagging (TRUST) MRI for venous oxygenation estimation, and uses the Fick principle of arteriovenous difference for the calculation of CMRO2. Whole-brain averaged CMRO2 values in young, healthy subjects were 132.1±20.0 μmol/100g/min, in good agreement with literature reports using PET. Various acquisition strategies for phase-contrast and TRUST MRI were compared, and it was found that non-gated phase-contrast and sagittal sinus TRUST MRI were able to provide the most efficient and accurate estimation of CMRO2. In addition, blood flow and venous oxygenation were found to be positively correlated across subjects. Owing to the non-invasive nature of this method, it may be a convenient and useful approach for assessment of brain metabolism in brain disorders as well as under various physiologic conditions. PMID:19353674

  8. Comparison of unsupervised classification methods for brain tumor segmentation using multi-parametric MRI.

    PubMed

    Sauwen, N; Acou, M; Van Cauter, S; Sima, D M; Veraart, J; Maes, F; Himmelreich, U; Achten, E; Van Huffel, S

    2016-01-01

    Tumor segmentation is a particularly challenging task in high-grade gliomas (HGGs), as they are among the most heterogeneous tumors in oncology. An accurate delineation of the lesion and its main subcomponents contributes to optimal treatment planning, prognosis and follow-up. Conventional MRI (cMRI) is the imaging modality of choice for manual segmentation, and is also considered in the vast majority of automated segmentation studies. Advanced MRI modalities such as perfusion-weighted imaging (PWI), diffusion-weighted imaging (DWI) and magnetic resonance spectroscopic imaging (MRSI) have already shown their added value in tumor tissue characterization, hence there have been recent suggestions of combining different MRI modalities into a multi-parametric MRI (MP-MRI) approach for brain tumor segmentation. In this paper, we compare the performance of several unsupervised classification methods for HGG segmentation based on MP-MRI data including cMRI, DWI, MRSI and PWI. Two independent MP-MRI datasets with a different acquisition protocol were available from different hospitals. We demonstrate that a hierarchical non-negative matrix factorization variant which was previously introduced for MP-MRI tumor segmentation gives the best performance in terms of mean Dice-scores for the pathologic tissue classes on both datasets.

  9. Repeated BOLD-fMRI Imaging of Deep Brain Stimulation Responses in Rats

    PubMed Central

    Chao, Tzu-Hao Harry; Chen, Jyh-Horng; Yen, Chen-Tung

    2014-01-01

    Functional magnetic resonance imaging (fMRI) provides a picture of the global spatial activation pattern of the brain. Interest is growing regarding the application of fMRI to rodent models to investigate adult brain plasticity. To date, most rodent studies used an electrical forepaw stimulation model to acquire fMRI data, with α-chloralose as the anesthetic. However, α-chloralose is harmful to animals, and not suitable for longitudinal studies. Moreover, peripheral stimulation models enable only a limited number of brain regions to be studied. Processing between peripheral regions and the brain is multisynaptic, and renders interpretation difficult and uncertain. In the present study, we combined the medetomidine-based fMRI protocol (a noninvasive rodent fMRI protocol) with chronic implantation of an MRI-compatible stimulation electrode in the ventroposterior (VP) thalamus to repetitively sample thalamocortical responses in the rat brain. Using this model, we scanned the forebrain responses evoked by the VP stimulation repeatedly of individual rats over 1 week. Cortical BOLD responses were compared between the 2 profiles obtained at day1 and day8. We discovered reproducible frequency- and amplitude-dependent BOLD responses in the ipsilateral somatosensory cortex (S1). The S1 BOLD responses during the 2 sessions were conserved in maximal response amplitude, area size (size ratio from 0.88 to 0.91), and location (overlap ratio from 0.61 to 0.67). The present study provides a long-term chronic brain stimulation protocol for studying the plasticity of specific neural circuits in the rodent brain by BOLD-fMRI. PMID:24825464

  10. Robust volume assessment of brain tissues for 3-dimensional fourier transformation MRI via a novel multispectral technique.

    PubMed

    Chai, Jyh-Wen; Chen, Clayton C; Wu, Yi-Ying; Chen, Hung-Chieh; Tsai, Yi-Hsin; Chen, Hsian-Min; Lan, Tsuo-Hung; Ouyang, Yen-Chieh; Lee, San-Kan

    2015-01-01

    A new TRIO algorithm method integrating three different algorithms is proposed to perform brain MRI segmentation in the native coordinate space, with no need of transformation to a standard coordinate space or the probability maps for segmentation. The method is a simple voxel-based algorithm, derived from multispectral remote sensing techniques, and only requires minimal operator input to depict GM, WM, and CSF tissue clusters to complete classification of a 3D high-resolution multislice-multispectral MRI data. Results showed very high accuracy and reproducibility in classification of GM, WM, and CSF in multislice-multispectral synthetic MRI data. The similarity indexes, expressing overlap between classification results and the ground truth, were 0.951, 0.962, and 0.956 for GM, WM, and CSF classifications in the image data with 3% noise level and 0% non-uniformity intensity. The method particularly allows for classification of CSF with 0.994, 0.961 and 0.996 of accuracy, sensitivity and specificity in images data with 3% noise level and 0% non-uniformity intensity, which had seldom performed well in previous studies. As for clinical MRI data, the quantitative data of brain tissue volumes aligned closely with the brain morphometrics in three different study groups of young adults, elderly volunteers, and dementia patients. The results also showed very low rates of the intra- and extra-operator variability in measurements of the absolute volumes and volume fractions of cerebral GM, WM, and CSF in three different study groups. The mean coefficients of variation of GM, WM, and CSF volume measurements were in the range of 0.03% to 0.30% of intra-operator measurements and 0.06% to 0.45% of inter-operator measurements. In conclusion, the TRIO algorithm exhibits a remarkable ability in robust classification of multislice-multispectral brain MR images, which would be potentially applicable for clinical brain volumetric analysis and explicitly promising in cross

  11. 3D spatially encoded and accelerated TE-averaged echo planar spectroscopic imaging in healthy human brain.

    PubMed

    Iqbal, Zohaib; Wilson, Neil E; Thomas, M Albert

    2016-03-01

    Several different pathologies, including many neurodegenerative disorders, affect the energy metabolism of the brain. Glutamate, a neurotransmitter in the brain, can be used as a biomarker to monitor these metabolic processes. One method that is capable of quantifying glutamate concentration reliably in several regions of the brain is TE-averaged (1) H spectroscopic imaging. However, this type of method requires the acquisition of multiple TE lines, resulting in long scan durations. The goal of this experiment was to use non-uniform sampling, compressed sensing reconstruction and an echo planar readout gradient to reduce the scan time by a factor of eight to acquire TE-averaged spectra in three spatial dimensions. Simulation of glutamate and glutamine showed that the 2.2-2.4 ppm spectral region contained 95% glutamate signal using the TE-averaged method. Peak integration of this spectral range and home-developed, prior-knowledge-based fitting were used for quantitation. Gray matter brain phantom measurements were acquired on a Siemens 3 T Trio scanner. Non-uniform sampling was applied retrospectively to these phantom measurements and quantitative results of glutamate with respect to creatine 3.0 (Glu/Cr) ratios showed a coefficient of variance of 16% for peak integration and 9% for peak fitting using eight-fold acceleration. In vivo scans of the human brain were acquired as well and five different brain regions were quantified using the prior-knowledge-based algorithm. Glu/Cr ratios from these regions agreed with previously reported results in the literature. The method described here, called accelerated TE-averaged echo planar spectroscopic imaging (TEA-EPSI), is a significant methodological advancement and may be a useful tool for categorizing glutamate changes in pathologies where affected brain regions are not known a priori. Copyright © 2016 John Wiley & Sons, Ltd.

  12. A Window into the Brain: Advances in Psychiatric fMRI

    PubMed Central

    Zhan, Xiaoyan; Yu, Rongjun

    2015-01-01

    Functional magnetic resonance imaging (fMRI) plays a key role in modern psychiatric research. It provides a means to assay differences in brain systems that underlie psychiatric illness, treatment response, and properties of brain structure and function that convey risk factor for mental diseases. Here we review recent advances in fMRI methods in general use and progress made in understanding the neural basis of mental illness. Drawing on concepts and findings from psychiatric fMRI, we propose that mental illness may not be associated with abnormalities in specific local regions but rather corresponds to variation in the overall organization of functional communication throughout the brain network. Future research may need to integrate neuroimaging information drawn from different analysis methods and delineate spatial and temporal patterns of brain responses that are specific to certain types of psychiatric disorders. PMID:26413531

  13. Measurement of brain volume using MRI: software, techniques, choices and prerequisites.

    PubMed

    Keller, Simon S; Roberts, Neil

    2009-01-01

    Magnetic resonance imaging (MRI) permits in vivo quantification of brain compartment volume, and has many applications in cognitive, clinical and comparative neuroscience. There dre numerous approaches for obtaining a brain volume estimate from MRI, and the primary focus of this paper is to provide an overview of the methods available to estimate the volume of three brain structures that are of particular interest in the neurosciences: the cerebral hemispheres, hippocampus and Brocas area. We provide information on choice of computer software, hardware compatibility, required user expertise, the application of manual and automated MR image analysis techniques, and anatomical guidelines, providing the reader with enough information to decide on their approach at the outset of a quantitative MRI study. We advocate the use ofstereology in conjunction with point counting for an unbiased and time efficient estimate of brain compartment volume.

  14. MRI-based elastic-mapping method for inter-subject comparison of brain FDG-PET images

    SciTech Connect

    Yang, J.; Huang, S.C.; Lin, K.P.; Small, G.; Phelps, M.E.

    1996-12-31

    Inter-subject anatomic differences prohibits direct image-wise statistical evaluation of brain FDG-PET images of Alzheimer`s disease (AD) patients. In this study, we propose a MRI-based elastic-mapping method which enables image-wise evaluation. The method involves intra-subject MR-PET registration, 3-D elastic mapping of two set of MR images, and elastically transforming the co-registered PET images. The MR-PET registration used simulated PET images, which were based on segmentation of MR images. In the 3-D elastic mapping stage, first a global linear scaling was applied to compensate for brain size difference, then a deformation field was obtained by minimizing the regional sum of squared difference between the two sets of MR images. Two groups (AD patient and normal control), each with three subjects, were included in the current study. After processing, images from all subjects have similar shapes. Averaging the images across all subjects (either within the individual group or for both groups) give images indistinguishable from original single subject FDG images (i.e. without much spatial resolution loss), except with lower image noise level. The method is expected to allow statistical image-wise analysis to be performed across different subjects.

  15. A methodology for generating normal and pathological brain perfusion SPECT images for evaluation of MRI/SPECT fusion methods: application in epilepsy

    NASA Astrophysics Data System (ADS)

    Grova, C.; Jannin, P.; Biraben, A.; Buvat, I.; Benali, H.; Bernard, A. M.; Scarabin, J. M.; Gibaud, B.

    2003-12-01

    Quantitative evaluation of brain MRI/SPECT fusion methods for normal and in particular pathological datasets is difficult, due to the frequent lack of relevant ground truth. We propose a methodology to generate MRI and SPECT datasets dedicated to the evaluation of MRI/SPECT fusion methods and illustrate the method when dealing with ictal SPECT. The method consists in generating normal or pathological SPECT data perfectly aligned with a high-resolution 3D T1-weighted MRI using realistic Monte Carlo simulations that closely reproduce the response of a SPECT imaging system. Anatomical input data for the SPECT simulations are obtained from this 3D T1-weighted MRI, while functional input data result from an inter-individual analysis of anatomically standardized SPECT data. The method makes it possible to control the 'brain perfusion' function by proposing a theoretical model of brain perfusion from measurements performed on real SPECT images. Our method provides an absolute gold standard for assessing MRI/SPECT registration method accuracy since, by construction, the SPECT data are perfectly registered with the MRI data. The proposed methodology has been applied to create a theoretical model of normal brain perfusion and ictal brain perfusion characteristic of mesial temporal lobe epilepsy. To approach realistic and unbiased perfusion models, real SPECT data were corrected for uniform attenuation, scatter and partial volume effect. An anatomic standardization was used to account for anatomic variability between subjects. Realistic simulations of normal and ictal SPECT deduced from these perfusion models are presented. The comparison of real and simulated SPECT images showed relative differences in regional activity concentration of less than 20% in most anatomical structures, for both normal and ictal data, suggesting realistic models of perfusion distributions for evaluation purposes. Inter-hemispheric asymmetry coefficients measured on simulated data were found within

  16. A methodology for generating normal and pathological brain perfusion SPECT images for evaluation of MRI/SPECT fusion methods: application in epilepsy.

    PubMed

    Grova, C; Jannin, P; Biraben, A; Buvat, I; Benali, H; Bernard, A M; Scarabin, J M; Gibaud, B

    2003-12-21

    Quantitative evaluation of brain MRI/SPECT fusion methods for normal and in particular pathological datasets is difficult, due to the frequent lack of relevant ground truth. We propose a methodology to generate MRI and SPECT datasets dedicated to the evaluation of MRI/SPECT fusion methods and illustrate the method when dealing with ictal SPECT. The method consists in generating normal or pathological SPECT data perfectly aligned with a high-resolution 3D T1-weighted MRI using realistic Monte Carlo simulations that closely reproduce the response of a SPECT imaging system. Anatomical input data for the SPECT simulations are obtained from this 3D T1-weighted MRI, while functional input data result from an inter-individual analysis of anatomically standardized SPECT data. The method makes it possible to control the 'brain perfusion' function by proposing a theoretical model of brain perfusion from measurements performed on real SPECT images. Our method provides an absolute gold standard for assessing MRI/SPECT registration method accuracy since, by construction, the SPECT data are perfectly registered with the MRI data. The proposed methodology has been applied to create a theoretical model of normal brain perfusion and ictal brain perfusion characteristic of mesial temporal lobe epilepsy. To approach realistic and unbiased perfusion models, real SPECT data were corrected for uniform attenuation, scatter and partial volume effect. An anatomic standardization was used to account for anatomic variability between subjects. Realistic simulations of normal and ictal SPECT deduced from these perfusion models are presented. The comparison of real and simulated SPECT images showed relative differences in regional activity concentration of less than 20% in most anatomical structures, for both normal and ictal data, suggesting realistic models of perfusion distributions for evaluation purposes. Inter-hemispheric asymmetry coefficients measured on simulated data were found within

  17. A robust framework for soft tissue simulations with application to modeling brain tumor mass effect in 3D MR images

    NASA Astrophysics Data System (ADS)

    Hogea, Cosmina; Biros, George; Abraham, Feby; Davatzikos, Christos

    2007-12-01

    We present a framework for black-box and flexible simulation of soft tissue deformation for medical imaging and surgical planning applications. Our main motivation in the present work is to develop robust algorithms that allow batch processing for registration of brains with tumors to statistical atlases of normal brains and construction of brain tumor atlases. We describe a fully Eulerian formulation able to handle large deformations effortlessly, with a level-set-based approach for evolving fronts. We use a regular grid—fictitious domain method approach, in which we approximate coefficient discontinuities, distributed forces and boundary conditions. This approach circumvents the need for unstructured mesh generation, which is often a bottleneck in the modeling and simulation pipeline. Our framework employs penalty approaches to impose boundary conditions and uses a matrix-free implementation coupled with a multigrid-accelerated Krylov solver. The overall scheme results in a scalable method with minimal storage requirements and optimal algorithmic complexity. We illustrate the potential of our framework to simulate realistic brain tumor mass effects at reduced computational cost, for aiding the registration process towards the construction of brain tumor atlases.

  18. The ultrasound brain helmet: new transducers and volume registration for in vivo simultaneous multi-transducer 3-D transcranial imaging.

    PubMed

    Lindsey, Brooks D; Light, Edward D; Nicoletto, Heather A; Bennett, Ellen R; Laskowitz, Daniel T; Smith, Stephen W

    2011-06-01

    Because stroke remains an important and time-sensitive health concern in developed nations, we present a system capable of fusing 3-D transcranial ultrasound volumes acquired from two sides of the head. This system uses custom sparse array transducers built on flexible multilayer circuits that can be positioned for simultaneous imaging through both temporal acoustic windows, allowing for potential registration of multiple real-time 3-D scans of cerebral vasculature. We examine hardware considerations for new matrix arrays-transducer design and interconnects-in this application. Specifically, it is proposed that SNR may be increased by reducing the length of probe cables. This claim is evaluated as part of the presented system through simulation, experimental data, and in vivo imaging. Ultimately, gains in SNR of 7 dB are realized by replacing a standard probe cable with a much shorter flex interconnect; higher gains may be possible using ribbon-based probe cables. In vivo images are presented, showing cerebral arteries with and without the use of microbubble contrast agent; they have been registered and fused using a simple algorithm which maximizes normalized cross-correlation.

  19. Resting-state fMRI: a window into human brain plasticity.

    PubMed

    Guerra-Carrillo, Belén; Mackey, Allyson P; Bunge, Silvia A

    2014-10-01

    Although brain plasticity is greatest in the first few years of life, the brain continues to be shaped by experience throughout adulthood. Advances in fMRI have enabled us to examine the plasticity of large-scale networks using blood oxygen level-dependent (BOLD) correlations measured at rest. Resting-state functional connectivity analysis makes it possible to measure task-independent changes in brain function and therefore could provide unique insights into experience-dependent brain plasticity in humans. Here, we evaluate the hypothesis that resting-state functional connectivity reflects the repeated history of co-activation between brain regions. To this end, we review resting-state fMRI studies in the sensory, motor, and cognitive learning literature. This body of research provides evidence that the brain's resting-state functional architecture displays dynamic properties in young adulthood.

  20. Phase synchronization in brain networks derived from correlation between probabilities of recurrences in functional MRI data.

    PubMed

    Rangaprakash, D; Hu, Xiaoping; Deshpande, Gopikrishna

    2013-04-01

    It is increasingly being recognized that resting state brain connectivity derived from functional magnetic resonance imaging (fMRI) data is an important marker of brain function both in healthy and clinical populations. Though linear correlation has been extensively used to characterize brain connectivity, it is limited to detecting first order dependencies. In this study, we propose a framework where in phase synchronization (PS) between brain regions is characterized using a new metric "correlation between probabilities of recurrence" (CPR) and subsequent graph-theoretic analysis of the ensuing networks. We applied this method to resting state fMRI data obtained from human subjects with and without administration of propofol anesthetic. Our results showed decreased PS during anesthesia and a biologically more plausible community structure using CPR rather than linear correlation. We conclude that CPR provides an attractive nonparametric method for modeling interactions in brain networks as compared to standard correlation for obtaining physiologically meaningful insights about brain function.

  1. Early development of arterial spin labeling to measure regional brain blood flow by MRI.

    PubMed

    Koretsky, Alan P

    2012-08-15

    Two major avenues of work converged in the late 1980's and early 1990's to give rise to brain perfusion MRI. The development of anatomical brain MRI quickly had as a major goal the generation of angiograms using tricks to label flowing blood in macroscopic vessels. These ideas were aimed at getting information about microcirculatory flow as well. Over the same time course the development of in vivo magnetic resonance spectroscopy had as its primary goal the assessment of tissue function and in particular, tissue energetics. For this the measurement of the delivery of water to tissue was critical for assessing tissue oxygenation and viability. The measurement of the washin/washout of "freely" diffusible tracers by spectroscopic based techniques pointed the way for quantitative approaches to measure regional blood flow by MRI. These two avenues came together in the development of arterial spin labeling (ASL) MRI techniques to measure regional cerebral blood flow. The early use of ASL to measure brain activation to help verify BOLD fMRI led to a rapid development of ASL based perfusion MRI. Today development and applications of regional brain blood flow measurements with ASL continues to be a major area of activity.

  2. Resting State Brain Function Analysis Using Concurrent BOLD in ASL Perfusion fMRI

    PubMed Central

    Zhu, Senhua; Fang, Zhuo; Hu, Siyuan; Wang, Ze; Rao, Hengyi

    2013-01-01

    The past decade has seen astounding discoveries about resting-state brain activity patterns in normal brain as well as their alterations in brain diseases. While the vast majority of resting-state studies are based on the blood-oxygen-level-dependent (BOLD) functional MRI (fMRI), arterial spin labeling (ASL) perfusion fMRI can simultaneously capture BOLD and cerebral blood flow (CBF) signals, providing a unique opportunity for assessing resting brain functions with concurrent BOLD (ccBOLD) and CBF signals. Before taking that benefit, it is necessary to validate the utility of ccBOLD signal for resting-state analysis using conventional BOLD (cvBOLD) signal acquired without ASL modulations. To address this technical issue, resting cvBOLD and ASL perfusion MRI were acquired from a large cohort (n = 89) of healthy subjects. Four widely used resting-state brain function analyses were conducted and compared between the two types of BOLD signal, including the posterior cingulate cortex (PCC) seed-based functional connectivity (FC) analysis, independent component analysis (ICA), analysis of amplitude of low frequency fluctuation (ALFF), and analysis of regional homogeneity (ReHo). Consistent default mode network (DMN) as well as other resting-state networks (RSNs) were observed from cvBOLD and ccBOLD using PCC-FC analysis and ICA. ALFF from both modalities were the same for most of brain regions but were different in peripheral regions suffering from the susceptibility gradients induced signal drop. ReHo showed difference in many brain regions, likely reflecting the SNR and resolution differences between the two BOLD modalities. The DMN and auditory networks showed highest CBF values among all RSNs. These results demonstrated the feasibility of ASL perfusion MRI for assessing resting brain functions using its concurrent BOLD in addition to CBF signal, which provides a potentially useful way to maximize the utility of ASL perfusion MRI. PMID:23750275

  3. Robust brain parcellation using sparse representation on resting-state fMRI.

    PubMed

    Zhang, Yu; Caspers, Svenja; Fan, Lingzhong; Fan, Yong; Song, Ming; Liu, Cirong; Mo, Yin; Roski, Christian; Eickhoff, Simon; Amunts, Katrin; Jiang, Tianzi

    2015-11-01

    Resting-state fMRI (rs-fMRI) has been widely used to segregate the brain into individual modules based on the presence of distinct connectivity patterns. Many parcellation methods have been proposed for brain parcellation using rs-fMRI, but their results have been somewhat inconsistent, potentially due to various types of noise. In this study, we provide a robust parcellation method for rs-fMRI-based brain parcellation, which constructs a sparse similarity graph based on the sparse representation coefficients of each seed voxel and then uses spectral clustering to identify distinct modules. Both the local time-varying BOLD signals and whole-brain connectivity patterns may be used as features and yield similar parcellation results. The robustness of our method was tested on both simulated and real rs-fMRI datasets. In particular, on simulated rs-fMRI data, sparse representation achieved good performance across different noise levels, including high accuracy of parcellation and high robustness to noise. On real rs-fMRI data, stable parcellation of the medial frontal cortex (MFC) and parietal operculum (OP) were achieved on three different datasets, with high reproducibility within each dataset and high consistency across these results. Besides, the parcellation of MFC was little influenced by the degrees of spatial smoothing. Furthermore, the consistent parcellation of OP was also well corresponding to cytoarchitectonic subdivisions and known somatotopic organizations. Our results demonstrate a new promising approach to robust brain parcellation using resting-state fMRI by sparse representation.

  4. Quantitative estimation of 3-D fiber course in gross histological sections of the human brain using polarized light.

    PubMed

    Axer, H; Axer, M; Krings, T; Keyserlingk, D G

    2001-02-15

    Series of polarized light images can be used to achieve quantitative estimates of the angles of inclination (z-direction) and direction (in xy-plane) of central nervous fibers in histological sections of the human brain. (1) The corpus callosum of a formalin-fixed human brain was sectioned at different angles of inclination of nerve fibers and at different thicknesses of the samples. The minimum, and maximum intensities, and their differences revealed a linear relationship to the angle of inclination of fibers. It was demonstrated that sections with a thickness of 80--120 microm are best suited for estimating the angle of inclination. (2) Afterwards the optic tracts of eight formalin-fixed human brains were sliced at different angles of fiber inclination at 100 microm. Measurements of intensity in 30 pixels in each section were used to calculate a linear function of calibration. The maximum intensities and the differences between maximum and minimum values measured with two polars only were best suited for estimation of fiber inclination. (3) Gross histological brain slices of formalin-fixed human brains were digitized under azimuths from 0 to 80 degrees using two polars only. These sequences were used to estimate the inclination of fibers (in z-direction). The same slices were digitized under azimuths from 0 to 160 degrees in steps of 20 degrees using a quarter wave plate additionally. These sequences were used to estimate the direction of the fibers in xy-direction. The method can be used to produce maps of fiber orientation in gross histological sections of the human brain similar to the fiber orientation maps derived by diffusion weighted magnetic resonance imaging.

  5. Optimization of flow-sensitive alternating inversion recovery (FAIR) for perfusion functional MRI of rodent brain.

    PubMed

    Nasrallah, Fatima A; Lee, Eugene L Q; Chuang, Kai-Hsiang

    2012-11-01

    Arterial spin labeling (ASL) MRI provides a noninvasive method to image perfusion, and has been applied to map neural activation in the brain. Although pulsed labeling methods have been widely used in humans, continuous ASL with a dedicated neck labeling coil is still the preferred method in rodent brain functional MRI (fMRI) to maximize the sensitivity and allow multislice acquisition. However, the additional hardware is not readily available and hence its application is limited. In this study, flow-sensitive alternating inversion recovery (FAIR) pulsed ASL was optimized for fMRI of rat brain. A practical challenge of FAIR is the suboptimal global inversion by the transmit coil of limited dimensions, which results in low effective labeling. By using a large volume transmit coil and proper positioning to optimize the body coverage, the perfusion signal was increased by 38.3% compared with positioning the brain at the isocenter. An additional 53.3% gain in signal was achieved using optimized repetition and inversion times compared with a long TR. Under electrical stimulation to the forepaws, a perfusion activation signal change of 63.7 ± 6.3% can be reliably detected in the primary somatosensory cortices using single slice or multislice echo planar imaging at 9.4 T. This demonstrates the potential of using pulsed ASL for multislice perfusion fMRI in functional and pharmacological applications in rat brain.

  6. Preoperative functional MRI localization of language areas in Chinese patients with brain tumors

    PubMed Central

    Xia, Hechun; Huang, Wei; Wu, Liang; Ma, Hui; Wang, Xiaodong; Chen, Xuexin; Sun, Shengyu; Jia, Xiaoxiong

    2012-01-01

    Ten Chinese patients with brain tumors involving language regions were selected. Preoperative functional MRI was performed to locate Broca's or Wernicke's area, and the cortex that was essential for language function was determined by electrocortical mapping. A site-by-site comparison between functional MRI and electrocortical mapping was performed with the