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Sample records for 3d brain mri

  1. In vivo 3D MRI of insect brain: cerebral development during metamorphosis of Manduca sexta.

    PubMed

    Michaelis, Thomas; Watanabe, Takashi; Natt, Oliver; Boretius, Susann; Frahm, Jens; Utz, Sandra; Schachtner, Joachim

    2005-01-15

    High-resolution 3D MRI of male pupae of Manduca sexta was performed at 2.35 T in order to evaluate its potential for an in vivo characterization of insect brain during metamorphosis. T1-weighted 3D FLASH (TR/TE = 20/7.8 ms, 25 degrees flip angle) and T2-weighted 3D fast SE MRI data sets (TR/TEeff = 3000/100 ms) were acquired at different developmental stages with an isotropic resolution of 100 microm. Both T1- and T2-weighted 3D MRI allowed for the identification of cerebral structures such as the antennal nerve, antennal and optical lobe, and central brain. Pronounced developmental alterations of the morphology were observed during metamorphosis. The results demonstrate the feasibility of 3D MRI at nanoliter resolution to identify major brain systems of M. sexta and respective changes during pupal development from caterpillar to sphinx moth. Together with the use of suitable contrast agents, this approach may provide new ways for studying the axonal connectivity and neural function of the developing insect brain.

  2. Reconstruction of the human brain from MRI-T1 using 3-D morphology and snake

    NASA Astrophysics Data System (ADS)

    Lin, Chih-Yang; Ching, Yu-Tai

    2002-04-01

    Accurate reconstruction of the human brain in MRI-T1 images is valuable and important to clinical needs. In this paper, the morphology and snake techniques are proposed to reconstruct a human brain model. First step in our method is to preprocess the volumetric image to remove skull, muscle, fat, and other non-brain tissue. We use a method of 3-d region growing. It has the advantage over thresholding that the resulting objects will be spatially connected, since brain has the connected property. Second, we use clustering method, and than use them to produce an initial estimate of the cortical surface. Third, we propose a novel active contour algorithm to move the snake toward the cortex. Thus we can use the snake to segment the brain. We use a wavelet method to model the external force that significantly increases the capture range of a traditional snake. Afterwards, we render the volumetric image to display the brain from multiple views. Both simulated data and patient data have been use to test the proposed techniques. The proposed method combines various techniques of 3-D morphology, clustering, active contour, wavelet, and volume rendering to accurately, robustly, and automatically reconstruct brain from MRI-T1 images.

  3. 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.

  4. Deep MRI brain extraction: A 3D convolutional neural network for skull stripping.

    PubMed

    Kleesiek, Jens; Urban, Gregor; Hubert, Alexander; Schwarz, Daniel; Maier-Hein, Klaus; Bendszus, Martin; Biller, Armin

    2016-04-01

    Brain extraction from magnetic resonance imaging (MRI) is crucial for many neuroimaging workflows. Current methods demonstrate good results on non-enhanced T1-weighted images, but struggle when confronted with other modalities and pathologically altered tissue. In this paper we present a 3D convolutional deep learning architecture to address these shortcomings. In contrast to existing methods, we are not limited to non-enhanced T1w images. When trained appropriately, our approach handles an arbitrary number of modalities including contrast-enhanced scans. Its applicability to MRI data, comprising four channels: non-enhanced and contrast-enhanced T1w, T2w and FLAIR contrasts, is demonstrated on a challenging clinical data set containing brain tumors (N=53), where our approach significantly outperforms six commonly used tools with a mean Dice score of 95.19. Further, the proposed method at least matches state-of-the-art performance as demonstrated on three publicly available data sets: IBSR, LPBA40 and OASIS, totaling N=135 volumes. For the IBSR (96.32) and LPBA40 (96.96) data set the convolutional neuronal network (CNN) obtains the highest average Dice scores, albeit not being significantly different from the second best performing method. For the OASIS data the second best Dice (95.02) results are achieved, with no statistical difference in comparison to the best performing tool. For all data sets the highest average specificity measures are evaluated, whereas the sensitivity displays about average results. Adjusting the cut-off threshold for generating the binary masks from the CNN's probability output can be used to increase the sensitivity of the method. Of course, this comes at the cost of a decreased specificity and has to be decided application specific. Using an optimized GPU implementation predictions can be achieved in less than one minute. The proposed method may prove useful for large-scale studies and clinical trials. PMID:26808333

  5. Deep MRI brain extraction: A 3D convolutional neural network for skull stripping.

    PubMed

    Kleesiek, Jens; Urban, Gregor; Hubert, Alexander; Schwarz, Daniel; Maier-Hein, Klaus; Bendszus, Martin; Biller, Armin

    2016-04-01

    Brain extraction from magnetic resonance imaging (MRI) is crucial for many neuroimaging workflows. Current methods demonstrate good results on non-enhanced T1-weighted images, but struggle when confronted with other modalities and pathologically altered tissue. In this paper we present a 3D convolutional deep learning architecture to address these shortcomings. In contrast to existing methods, we are not limited to non-enhanced T1w images. When trained appropriately, our approach handles an arbitrary number of modalities including contrast-enhanced scans. Its applicability to MRI data, comprising four channels: non-enhanced and contrast-enhanced T1w, T2w and FLAIR contrasts, is demonstrated on a challenging clinical data set containing brain tumors (N=53), where our approach significantly outperforms six commonly used tools with a mean Dice score of 95.19. Further, the proposed method at least matches state-of-the-art performance as demonstrated on three publicly available data sets: IBSR, LPBA40 and OASIS, totaling N=135 volumes. For the IBSR (96.32) and LPBA40 (96.96) data set the convolutional neuronal network (CNN) obtains the highest average Dice scores, albeit not being significantly different from the second best performing method. For the OASIS data the second best Dice (95.02) results are achieved, with no statistical difference in comparison to the best performing tool. For all data sets the highest average specificity measures are evaluated, whereas the sensitivity displays about average results. Adjusting the cut-off threshold for generating the binary masks from the CNN's probability output can be used to increase the sensitivity of the method. Of course, this comes at the cost of a decreased specificity and has to be decided application specific. Using an optimized GPU implementation predictions can be achieved in less than one minute. The proposed method may prove useful for large-scale studies and clinical trials.

  6. 3D+t brain MRI segmentation using robust 4D Hidden Markov Chain.

    PubMed

    Lavigne, François; Collet, Christophe; Armspach, Jean-Paul

    2014-01-01

    In recent years many automatic methods have been developed to help physicians diagnose brain disorders, but the problem remains complex. In this paper we propose a method to segment brain structures on two 3D multi-modal MR images taken at different times (longitudinal acquisition). A bias field correction is performed with an adaptation of the Hidden Markov Chain (HMC) allowing us to take into account the temporal correlation in addition to spatial neighbourhood information. To improve the robustness of the segmentation of the principal brain structures and to detect Multiple Sclerosis Lesions as outliers the Trimmed Likelihood Estimator (TLE) is used during the process. The method is validated on 3D+t brain MR images. PMID:25571045

  7. In vivo isotropic 3D diffusion tensor mapping of the rat brain using diffusion-weighted 3D MP-RAGE MRI.

    PubMed

    Numano, Tomokazu; Homma, Kazuhiro; Iwasaki, Nobuaki; Hyodo, Koji; Nitta, Naotaka; Hirose, Takeshi

    2006-04-01

    The purpose of this study was to examine the potential of diffusion-weighted (DW) three-dimensional (3D) MP-RAGE MRI for diffusion-tensor mapping of the rat brain in vivo. A DW-3D-MP-RAGE (3D-DWI) sequence was implemented at 2.0 T using six gradient orientations and a b value of 1000 s/mm2. In this sequence, the preparation sequence with a "90 degrees RF-motion proving gradient (MPG): MPG-180 degrees RF-MPG-90 degrees RF" pulse train (DW driven equilibrium Fourier transform) was used to sensitize the magnetization to diffusion. A centric k-space acquisition order was necessary to minimize saturation effects (T1 contamination) from tissues with short relaxation time. The image matrix was 128x128x128 (interpolated from 64x64x64 acquisitions), which resulted in small isotropic DW image data (voxel size: 0.273x0.273x0.273 mm3). Moreover, 3D-DWI-derived maps of the fractional anisotropy (FA), relative anisotropy (RA) and main-diffusion direction were completely free of susceptibility-induced signal losses and geometric distortions. Two well-known commissural fibers, the corpus callosum and anterior commissure, were indicated and shown to be in agreement with the locations of these known stereotaxic atlases. The experiment took 45 min, and shorter times should be possible in clinical application. The 3D-DWI sequence allows for in vivo 3D diffusion-tensor mapping of the rat brain without motion artifacts and susceptibility to distortion. PMID:16563958

  8. Segmentation of the brain from 3D MRI using a hierarchical active surface template

    NASA Astrophysics Data System (ADS)

    Snell, John W.; Merickel, Michael B.; Ortega, James M.; Goble, John C.; Brookeman, James R.; Kassell, Neal F.

    1994-05-01

    The accurate segmentation of the brain from three-dimensional medical imagery is important as the basis for visualization, morphometry, surgical planning and intraoperative navigation. The complex and variable nature of brain anatomy makes recognition of the brain boundaries a difficult problem and frustrates segmentation schemes based solely on local image features. We have developed a deformable surface model of the brain as a mechanism for utilizing a priori anatomical knowledge in the segmentation process. The active surface template uses an energy minimization scheme to find a globally consistent surface configuration given a set of potentially ambiguous image features. Solution of the entire 3D problem at once produces superior results to those achieved using a slice by slice approach. We have achieved good results with MR image volumes of both normal and abnormal subjects. Evaluation of the segmentation results has been performed using cadaver studies.

  9. 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.

  10. 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.

  11. Multidimensional morphometric 3D MRI analyses for detecting brain abnormalities in children: impact of control population.

    PubMed

    Wilke, Marko; Rose, Douglas F; Holland, Scott K; Leach, James L

    2014-07-01

    Automated morphometric approaches are used to detect epileptogenic structural abnormalities in 3D MR images in adults, using the variance of a control population to obtain z-score maps in an individual patient. Due to the substantial changes the developing human brain undergoes, performing such analyses in children is challenging. This study investigated six features derived from high-resolution T1 datasets in four groups: normal children (1.5T or 3T data), normal clinical scans (3T data), and patients with structural brain lesions (3T data), with each n = 10. Normative control data were obtained from the NIH study on normal brain development (n = 401). We show that control group size substantially influences the captured variance, directly impacting the patient's z-scores. Interestingly, matching on gender does not seem to be beneficial, which was unexpected. Using data obtained at higher field scanners produces slightly different base rates of suprathreshold voxels, as does using clinically derived normal studies, suggesting a subtle but systematic effect of both factors. Two approaches for controlling suprathreshold voxels in a multidimensional approach (combining features and requiring a minimum cluster size) were shown to be substantial and effective in reducing this number. Finally, specific strengths and limitations of such an approach could be demonstrated in individual cases. PMID:25050423

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

    PubMed Central

    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 (R2*) 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. PMID:26284778

  13. Automatic ROI selection in structural brain MRI using SOM 3D projection.

    PubMed

    Ortiz, Andrés; Górriz, Juan M; Ramírez, Javier; Martinez-Murcia, Francisco J

    2014-01-01

    This paper presents a method for selecting Regions of Interest (ROI) in brain Magnetic Resonance Imaging (MRI) for diagnostic purposes, using statistical learning and vector quantization techniques. The proposed method models the distribution of GM and WM tissues grouping the voxels belonging to each tissue in ROIs associated to a specific neurological disorder. Tissue distribution of normal and abnormal images is modelled by a Self-Organizing map (SOM), generating a set of representative prototypes, and the receptive field (RF) of each SOM prototype defines a ROI. Moreover, the proposed method computes the relative importance of each ROI by means of its discriminative power. The devised method has been assessed using 818 images from the Alzheimer's disease Neuroimaging Initiative (ADNI) which were previously segmented through Statistical Parametric Mapping (SPM). The proposed algorithm was used over these images to parcel ROIs associated to the Alzheimer's Disease (AD). Additionally, this method can be used to extract a reduced set of discriminative features for classification, since it compresses discriminative information contained in the brain. Voxels marked by ROIs which were computed using the proposed method, yield classification results up to 90% of accuracy for controls (CN) and Alzheimer's disease (AD) patients, and 84% of accuracy for Mild Cognitive Impairment (MCI) and AD patients.

  14. 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

  15. 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.

  16. MRI Volume Fusion Based on 3D Shearlet Decompositions

    PubMed Central

    Duan, Chang; Wang, Shuai; Wang, Xue Gang; Huang, Qi Hong

    2014-01-01

    Nowadays many MRI scans can give 3D volume data with different contrasts, but the observers may want to view various contrasts in the same 3D volume. The conventional 2D medical fusion methods can only fuse the 3D volume data layer by layer, which may lead to the loss of interframe correlative information. In this paper, a novel 3D medical volume fusion method based on 3D band limited shearlet transform (3D BLST) is proposed. And this method is evaluated upon MRI T2* and quantitative susceptibility mapping data of 4 human brains. Both the perspective impression and the quality indices indicate that the proposed method has a better performance than conventional 2D wavelet, DT CWT, and 3D wavelet, DT CWT based fusion methods. PMID:24817880

  17. Creating 3D visualizations of MRI data: A brief guide

    PubMed Central

    Madan, Christopher R.

    2015-01-01

    While magnetic resonance imaging (MRI) data is itself 3D, it is often difficult to adequately present the results papers and slides in 3D. As a result, findings of MRI studies are often presented in 2D instead. A solution is to create figures that include perspective and can convey 3D information; such figures can sometimes be produced by standard functional magnetic resonance imaging (fMRI) analysis packages and related specialty programs. However, many options cannot provide functionality such as visualizing activation clusters that are both cortical and subcortical (i.e., a 3D glass brain), the production of several statistical maps with an identical perspective in the 3D rendering, or animated renderings. Here I detail an approach for creating 3D visualizations of MRI data that satisfies all of these criteria. Though a 3D ‘glass brain’ rendering can sometimes be difficult to interpret, they are useful in showing a more overall representation of the results, whereas the traditional slices show a more local view. Combined, presenting both 2D and 3D representations of MR images can provide a more comprehensive view of the study’s findings. PMID:26594340

  18. Detection of subjects and brain regions related to Alzheimer's disease using 3D MRI scans based on eigenbrain and machine learning

    PubMed Central

    Zhang, Yudong; Dong, Zhengchao; Phillips, Preetha; Wang, Shuihua; Ji, Genlin; Yang, Jiquan; Yuan, Ti-Fei

    2015-01-01

    Purpose: Early diagnosis or detection of Alzheimer's disease (AD) from the normal elder control (NC) is very important. However, the computer-aided diagnosis (CAD) was not widely used, and the classification performance did not reach the standard of practical use. We proposed a novel CAD system for MR brain images based on eigenbrains and machine learning with two goals: accurate detection of both AD subjects and AD-related brain regions. Method: First, we used maximum inter-class variance (ICV) to select key slices from 3D volumetric data. Second, we generated an eigenbrain set for each subject. Third, the most important eigenbrain (MIE) was obtained by Welch's t-test (WTT). Finally, kernel support-vector-machines with different kernels that were trained by particle swarm optimization, were used to make an accurate prediction of AD subjects. Coefficients of MIE with values higher than 0.98 quantile were highlighted to obtain the discriminant regions that distinguish AD from NC. Results: The experiments showed that the proposed method can predict AD subjects with a competitive performance with existing methods, especially the accuracy of the polynomial kernel (92.36 ± 0.94) was better than the linear kernel of 91.47 ± 1.02 and the radial basis function (RBF) kernel of 86.71 ± 1.93. The proposed eigenbrain-based CAD system detected 30 AD-related brain regions (Anterior Cingulate, Caudate Nucleus, Cerebellum, Cingulate Gyrus, Claustrum, Inferior Frontal Gyrus, Inferior Parietal Lobule, Insula, Lateral Ventricle, Lentiform Nucleus, Lingual Gyrus, Medial Frontal Gyrus, Middle Frontal Gyrus, Middle Occipital Gyrus, Middle Temporal Gyrus, Paracentral Lobule, Parahippocampal Gyrus, Postcentral Gyrus, Posterial Cingulate, Precentral Gyrus, Precuneus, Subcallosal Gyrus, Sub-Gyral, Superior Frontal Gyrus, Superior Parietal Lobule, Superior Temporal Gyrus, Supramarginal Gyrus, Thalamus, Transverse Temporal Gyrus, and Uncus). The results were coherent with existing

  19. 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/.

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

    PubMed

    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 21.1T 3D sodium MRI brain images of live rats with spatial resolution of 0.8×0.8×0.8 mm(3) 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/.

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

    PubMed

    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 21.1T 3D sodium MRI brain images of live rats with spatial resolution of 0.8×0.8×0.8 mm(3) 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

  2. 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…

  3. 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

  4. 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.

  5. 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. PMID:26295459

  6. Construction and investigation of 3D vessels net of the brain according to MRI data using the method of variation of scanning plane

    NASA Astrophysics Data System (ADS)

    Cherevko, A. A.; Yankova, G. S.; Maltseva, S. V.; Parshin, D. V.; Akulov, A. E.; Khe, A. K.; Chupakhin, A. P.

    2016-06-01

    The blood realizes the transport of substances, which are necessary for livelihoods, throughout the body. The assumption about the relationship genotype and structure of vasculature (in particular of brain) is natural. In the paper we consider models of vessel net for two genetic lines of laboratory mice. Vascular net obtained as a result of preprocessing MRI data. MRI scanning is realized using the method of variation of slope of scanning plane, i.e. by several sets of parallel planes specified by different normal vectors. The following special processing allowed to construct models of vessel nets without fragmentation. The purpose of the work is to compare the vascular network models of two different genetic lines of laboratory mice.

  7. Viewing 3D MRI data in perspective

    NASA Astrophysics Data System (ADS)

    Liu, Haiying; Chin, Chialei

    2000-10-01

    In medical imaging applications, 3D morphological data set is often presented in 2D format without considering visual perspective. Without perspective, the resulting image can be counterintuitive to natural human visual perception, specially in a setting of MR guided neurosurgical procedure where depth perception is crucial. To address this problem we have developed a new projection scheme that incorporates linear perspective transformation in various image reconstructions, including MR angiographical projection. In the scheme, an imaginary picture plane (PP) can be placed within or immediately in front of a 3D object, and the stand point (SP) of an observer is fixed at a normal viewing distance os 25 cm in front of the picture plane. A clinical 3D angiography data set (TR/TF/Flipequals30/5.4/15) was obtained from a patient head on a 1.5T MR scanner in 4 min 10 sec (87.5% rectangular, 52% scan). The length, width and height of the image volume were 200mm, 200mm and 72.4mm respectively, corresponding to an effective matrix size of 236x512x44 in transverse orientation (512x512x88 after interpolation). Maximum intensity project (MaxIP) algorithm was used along the viewing trace of perspective projection than rather the parallel projection. Consecutive 36 views were obtained at a 10 degree interval azimuthally. When displayed in cine-mode, the new MaxIP images appeared realistic with an improved depth perception.

  8. 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.

  9. 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. PMID:20203478

  10. 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.

  11. Automated Prescription of Oblique Brain 3D MRSI

    PubMed Central

    Ozhinsky, Eugene; Vigneron, Daniel B.; Chang, Susan M.; Nelson, Sarah J.

    2012-01-01

    Two major difficulties encountered in implementing Magnetic Resonance Spectroscopic Imaging (MRSI) in a clinical setting are limited coverage and difficulty in prescription. The goal of this project was to completely automate the process of 3D PRESS MRSI prescription, including placement of the selection box, saturation bands and shim volume, while maximizing the coverage of the brain. The automated prescription technique included acquisition of an anatomical MRI image, optimization of the oblique selection box parameters, optimization of the placement of OVS saturation bands, and loading of the calculated parameters into a customized 3D MRSI pulse sequence. To validate the technique and compare its performance with existing protocols, 3D MRSI data were acquired from 6 exams from 3 healthy volunteers. To assess the performance of the automated 3D MRSI prescription for patients with brain tumors, the data were collected from 16 exams from 8 subjects with gliomas. This technique demonstrated robust coverage of the tumor, high consistency of prescription and very good data quality within the T2 lesion. PMID:22692829

  12. Image segmentation and 3D visualization for MRI mammography

    NASA Astrophysics Data System (ADS)

    Li, Lihua; Chu, Yong; Salem, Angela F.; Clark, Robert A.

    2002-05-01

    MRI mammography has a number of advantages, including the tomographic, and therefore three-dimensional (3-D) nature, of the images. It allows the application of MRI mammography to breasts with dense tissue, post operative scarring, and silicon implants. However, due to the vast quantity of images and subtlety of difference in MR sequence, there is a need for reliable computer diagnosis to reduce the radiologist's workload. The purpose of this work was to develop automatic breast/tissue segmentation and visualization algorithms to aid physicians in detecting and observing abnormalities in breast. Two segmentation algorithms were developed: one for breast segmentation, the other for glandular tissue segmentation. In breast segmentation, the MRI image is first segmented using an adaptive growing clustering method. Two tracing algorithms were then developed to refine the breast air and chest wall boundaries of breast. The glandular tissue segmentation was performed using an adaptive thresholding method, in which the threshold value was spatially adaptive using a sliding window. The 3D visualization of the segmented 2D slices of MRI mammography was implemented under IDL environment. The breast and glandular tissue rendering, slicing and animation were displayed.

  13. Quantification of the accuracy of MRI generated 3D models of long bones compared to CT generated 3D models.

    PubMed

    Rathnayaka, Kanchana; Momot, Konstantin I; Noser, Hansrudi; Volp, Andrew; Schuetz, Michael A; Sahama, Tony; Schmutz, Beat

    2012-04-01

    Orthopaedic fracture fixation implants are increasingly being designed using accurate 3D models of long bones based on computer tomography (CT). Unlike CT, magnetic resonance imaging (MRI) does not involve ionising radiation and is therefore a desirable alternative to CT. This study aims to quantify the accuracy of MRI-based 3D models compared to CT-based 3D models of long bones. The femora of five intact cadaver ovine limbs were scanned using a 1.5 T MRI and a CT scanner. Image segmentation of CT and MRI data was performed using a multi-threshold segmentation method. Reference models were generated by digitising the bone surfaces free of soft tissue with a mechanical contact scanner. The MRI- and CT-derived models were validated against the reference models. The results demonstrated that the CT-based models contained an average error of 0.15 mm while the MRI-based models contained an average error of 0.23 mm. Statistical validation shows that there are no significant differences between 3D models based on CT and MRI data. These results indicate that the geometric accuracy of MRI based 3D models was comparable to that of CT-based models and therefore MRI is a potential alternative to CT for generation of 3D models with high geometric accuracy.

  14. MRI brain imaging.

    PubMed

    Skinner, Sarah

    2013-11-01

    General practitioners (GPs) are expected to be allowed to request MRI scans for adults for selected clinically appropriate indications from November 2013 as part of the expansion of Medicare-funded MRI services announced by the Federal Government in 2011. This article aims to give a brief overview of MRI brain imaging relevant to GPs, which will facilitate explanation of scan findings and management planning with their patients. Basic imaging techniques, common findings and terminology are presented using some illustrative case examples.

  15. 3D MRI volume sizing of knee meniscus cartilage.

    PubMed

    Stone, K R; Stoller, D W; Irving, S G; Elmquist, C; Gildengorin, G

    1994-12-01

    Meniscal replacement by allograft and meniscal regeneration through collagen meniscal scaffolds have been recently reported. To evaluate the effectiveness of a replaced or regrown meniscal cartilage, a method for measuring the size and function of the regenerated tissue in vivo is required. To solve this problem, we developed and evaluated a magnetic resonance imaging (MRI) technique to measure the volume of meniscal tissues. Twenty-one intact fresh cadaver knees were evaluated and scanned with MRI for meniscal volume sizing. The sizing sequence was repeated six times for each of 21 lateral and 12 medial menisci. The menisci were then excised and measured by water volume displacement. Each volume displacement measurement was repeated six times. The MRI technique employed to measure the volume of the menisci was shown to correspond to that of the standard measure of volume and was just as precise. However, the MRI technique consistently underestimated the actual volume. The average of the coefficient of variation for lateral volumes was 0.04 and 0.05 for the water and the MRI measurements, respectively. For medial measurements it was 0.04 and 0.06. The correlation for the lateral menisci was r = 0.45 (p = 0.04) and for the medial menisci it was r = 0.57 (p = 0.05). We conclude that 3D MRI is precise and repeatable but not accurate when used to measure meniscal volume in vivo and therefore may only be useful for evaluating changes in meniscal allografts and meniscal regeneration templates over time.

  16. MRI of the brain (image)

    MedlinePlus

    An MRI (magnetic resonance imaging) of the brain creates a detailed image of the complex structures in the brain. An MRI can give a three-dimensional depiction of the brain, making location of problems such ...

  17. Optimized 3D Ultrashort Echo Time Pulmonary MRI

    PubMed Central

    Johnson, Kevin M.; Fain, Sean B.; Schiebler, Mark L.; Nagle, Scott

    2012-01-01

    Purpose To optimize 3D radial ultrashort echo time MRI for high resolution whole-lung imaging. Methods 3D radial ultrashort echo time was implemented on a 3T scanner to investigate the effects of: (1) limited field-of-view excitation, (2) variable density readouts, and (3) radial oversampling. Improvements in noise performance and spatial resolution were assessed through simulation and phantom studies. Their effects on lung and airway visualization in five healthy male human subjects (mean age 32 years) were compared qualitatively through blinded ordinal scoring by two cardiothoracic radiologists using a nonparametric Friedman test (P < 0.05). Relative signal difference between endobronchial air and adjacent lung tissue, normalized to nearby vessel, was used as a surrogate for lung tissue signal. Quantitative measures were compared using the paired Student's t-test (P < 0.05). Finally, clinical feasibility was investigated in a patient with interstitial fibrosis. Results Simulation and phantom studies showed up to 67% improvement in SNR and reduced blurring for short T2* species using all three optimizations. In vivo images showed decreased artifacts and improved lung tissue and airway visualization both qualitatively and quantitatively. Conclusion The use of limited field-of-view excitation, variable readout gradients, and radial oversampling significantly improve the technical quality of 3D radial ultrashort echo time lung images. PMID:23213020

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

    PubMed

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

    2015-05-01

    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 that

  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. 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.

  2. A 3-D visualization method for image-guided brain surgery.

    PubMed

    Bourbakis, N G; Awad, M

    2003-01-01

    This paper deals with a 3D methodology for brain tumor image-guided surgery. The methodology is based on development of a visualization process that mimics the human surgeon behavior and decision-making. In particular, it originally constructs a 3D representation of a tumor by using the segmented version of the 2D MRI images. Then it develops an optimal path for the tumor extraction based on minimizing the surgical effort and penetration area. A cost function, incorporated in this process, minimizes the damage surrounding healthy tissues taking into consideration the constraints of a new snake-like surgical tool proposed here. The tumor extraction method presented in this paper is compared with the ordinary method used on brain surgery, which is based on a straight-line based surgical tool. Illustrative examples based on real simulations present the advantages of the 3D methodology proposed here.

  3. 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.

  4. 3D thermal medical image visualization tool: Integration between MRI and thermographic images.

    PubMed

    Abreu de Souza, Mauren; Chagas Paz, André Augusto; Sanches, Ionildo Jóse; Nohama, Percy; Gamba, Humberto Remigio

    2014-01-01

    Three-dimensional medical image reconstruction using different images modalities require registration techniques that are, in general, based on the stacking of 2D MRI/CT images slices. In this way, the integration of two different imaging modalities: anatomical (MRI/CT) and physiological information (infrared image), to generate a 3D thermal model, is a new methodology still under development. This paper presents a 3D THERMO interface that provides flexibility for the 3D visualization: it incorporates the DICOM parameters; different color scale palettes at the final 3D model; 3D visualization at different planes of sections; and a filtering option that provides better image visualization. To summarize, the 3D thermographc medical image visualization provides a realistic and precise medical tool. The merging of two different imaging modalities allows better quality and more fidelity, especially for medical applications in which the temperature changes are clinically significant.

  5. 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.

  6. Consistent realignment of 3D diffusion tensor MRI eigenvectors

    NASA Astrophysics Data System (ADS)

    Beg, Mirza Faisal; Dickie, Ryan; Golds, Gregory; Younes, Laurent

    2007-03-01

    Diffusion tensor MR image data gives at each voxel in the image a symmetric, positive definite matrix that is denoted as the diffusion tensor at that voxel location. The eigenvectors of the tensor represent the principal directions of anisotopy in water diffusion. The eigenvector with the largest eigenvalue indicates the local orientation of tissue fibers in 3D as water is expected to diffuse preferentially up and down along the fiber tracts. Although there is no anatomically valid positive or negative direction to these fiber tracts, for many applications, it is of interest to assign an artificial direction to the fiber tract by choosing one of the two signs of the principal eigenvector in such a way that in local neighborhoods the assigned directions are consistent and vary smoothly in space. We demonstrate here an algorithm for realigning the principal eigenvectors by flipping their sign such that it assigns a locally consistent and spatially smooth fiber direction to the eigenvector field based on a Monte-Carlo algorithm adapted from updating clusters of spin systems. We present results that show the success of this algorithm on 11 available unsegmented canine cardiac volumes of both healthy and failing hearts.

  7. Near-infrared optical imaging of human brain based on the semi-3D reconstruction algorithm

    NASA Astrophysics Data System (ADS)

    Liu, Ming; Meng, Wei; Qin, Zhuanping; Zhou, Xiaoqing; Zhao, Huijuan; Gao, Feng

    2013-03-01

    In the non-invasive brain imaging with near-infrared light, precise head model is of great significance to the forward model and the image reconstruction. To deal with the individual difference of human head tissues and the problem of the irregular curvature, in this paper, we extracted head structure with Mimics software from the MRI image of a volunteer. This scheme makes it possible to assign the optical parameters to every layer of the head tissues reasonably and solve the diffusion equation with the finite-element analysis. During the solution of the inverse problem, a semi-3D reconstruction algorithm is adopted to trade off the computation cost and accuracy between the full 3-D and the 2-D reconstructions. In this scheme, the changes in the optical properties of the inclusions are assumed either axially invariable or confined to the imaging plane, while the 3-D nature of the photon migration is still retained. This therefore leads to a 2-D inverse issue with the matched 3-D forward model. Simulation results show that comparing to the 3-D reconstruction algorithm, the Semi-3D reconstruction algorithm cut 27% the calculation time consumption.

  8. Validation of computational fluid dynamics methods with anatomically exact, 3D printed MRI phantoms and 4D pcMRI.

    PubMed

    Anderson, Jeff R; Diaz, Orlando; Klucznik, Richard; Zhang, Y Jonathan; Britz, Gavin W; Grossman, Robert G; Lv, Nan; Huang, Qinghai; Karmonik, Christof

    2014-01-01

    A new concept of rapid 3D prototyping was implemented using cost-effective 3D printing for creating anatomically correct replica of cerebral aneurysms. With a dedicated flow loop set-up in a full body human MRI scanner, flow measurements were performed using 4D phase contrast magnetic resonance imaging to visualize and quantify intra-aneurysmal flow patterns. Ultrashort TE sequences were employed to obtain high-resolution 3D image data to visualize the lumen inside the plastic replica. In-vitro results were compared with retrospectively obtained in-vivo data and results from computational fluid dynamics simulations (CFD). Rapid prototyping of anatomically realistic 3D models may have future impact in treatment planning, design of image acquisition methods for MRI and angiographic systems and for the design and testing of advanced image post-processing technologies.

  9. 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.

  10. Brain surface maps from 3-D medical images

    NASA Astrophysics Data System (ADS)

    Lu, Jiuhuai; Hansen, Eric W.; Gazzaniga, Michael S.

    1991-06-01

    The anatomic and functional localization of brain lesions for neurologic diagnosis and brain surgery is facilitated by labeling the cortical surface in 3D images. This paper presents a method which extracts cortical contours from magnetic resonance (MR) image series and then produces a planar surface map which preserves important anatomic features. The resultant map may be used for manual anatomic localization as well as for further automatic labeling. Outer contours are determined on MR cross-sectional images by following the clear boundaries between gray matter and cerebral-spinal fluid, skipping over sulci. Carrying this contour below the surface by shrinking it along its normal produces an inner contour that alternately intercepts gray matter (sulci) and white matter along its length. This procedure is applied to every section in the set, and the image (grayscale) values along the inner contours are radially projected and interpolated onto a semi-cylindrical surface with axis normal to the slices and large enough to cover the whole brain. A planar map of the cortical surface results by flattening this cylindrical surface. The projection from inner contour to cylindrical surface is unique in the sense that different points on the inner contour correspond to different points on the cylindrical surface. As the outer contours are readily obtained by automatic segmentation, cortical maps can be made directly from an MR series.

  11. 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

  12. 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.

  13. 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.

  14. Optimization of 3D MP-RAGE for neonatal brain imaging at 3.0 T.

    PubMed

    Williams, Lori-Anne; DeVito, Timothy J; Winter, Jeff D; Orr, Timothy N; Thompson, R Terry; Gelman, Neil

    2007-10-01

    Three-dimensional (3D) magnetic resonance imaging (MRI) has shown great potential for studying the impact of prematurity and pathology on brain development. We have investigated the potential of optimized T1-weighted 3D magnetization-prepared rapid gradient-echo imaging (MP-RAGE) for obtaining contrast between white matter (WM) and gray matter (GM) in neonates at 3 T. Using numerical simulations, we predicted that the inversion time (TI) for obtaining strongest contrast at 3 T is approximately 2 s for neonates, whereas for adults, this value is approximately 1.3 s. The optimal neonatal TI value was found to be insensitive to reasonable variations of the assumed T1 relaxation times. The maximum theoretical contrast for neonates was found to be approximately one third of that for adults. Using the optimized TI values, MP-RAGE images were obtained from seven neonates and seven adults at 3 T, and the contrast-to-noise ratio (CNR) was measured for WM versus five GM regions. Compared to adults, neonates exhibited lower CNR between cortical GM and WM and showed a different pattern of regional variation in CNR. These results emphasize the importance of sequence optimization specifically for neonates and demonstrate the challenge in obtaining strong contrast in neonatal brain with T1-weighted 3D imaging. PMID:17391887

  15. 3D active surfaces for liver segmentation in multisequence MRI images.

    PubMed

    Bereciartua, Arantza; Picon, Artzai; Galdran, Adrian; Iriondo, Pedro

    2016-08-01

    Biopsies for diagnosis can sometimes be replaced by non-invasive techniques such as CT and MRI. Surgeons require accurate and efficient methods that allow proper segmentation of the organs in order to ensure the most reliable intervention planning. Automated liver segmentation is a difficult and open problem where CT has been more widely explored than MRI. MRI liver segmentation represents a challenge due to the presence of characteristic artifacts, such as partial volumes, noise and low contrast. In this paper, we present a novel method for multichannel MRI automatic liver segmentation. The proposed method consists of the minimization of a 3D active surface by means of the dual approach to the variational formulation of the underlying problem. This active surface evolves over a probability map that is based on a new compact descriptor comprising spatial and multisequence information which is further modeled by means of a liver statistical model. This proposed 3D active surface approach naturally integrates volumetric regularization in the statistical model. The advantages of the compact visual descriptor together with the proposed approach result in a fast and accurate 3D segmentation method. The method was tested on 18 healthy liver studies and results were compared to a gold standard made by expert radiologists. Comparisons with other state-of-the-art approaches are provided by means of nine well established quality metrics. The obtained results improve these methodologies, achieving a Dice Similarity Coefficient of 98.59. PMID:27282235

  16. 3-D Maps and Compasses in the Brain.

    PubMed

    Finkelstein, Arseny; Las, Liora; Ulanovsky, Nachum

    2016-07-01

    The world has a complex, three-dimensional (3-D) spatial structure, but until recently the neural representation of space was studied primarily in planar horizontal environments. Here we review the emerging literature on allocentric spatial representations in 3-D and discuss the relations between 3-D spatial perception and the underlying neural codes. We suggest that the statistics of movements through space determine the topology and the dimensionality of the neural representation, across species and different behavioral modes. We argue that hippocampal place-cell maps are metric in all three dimensions, and might be composed of 2-D and 3-D fragments that are stitched together into a global 3-D metric representation via the 3-D head-direction cells. Finally, we propose that the hippocampal formation might implement a neural analogue of a Kalman filter, a standard engineering algorithm used for 3-D navigation. PMID:27442069

  17. Imaging and 3-D dosimetry: top tips for MRI and optical CT

    NASA Astrophysics Data System (ADS)

    Doran, Simon J.

    2010-11-01

    The conference "refresher session" associated with this abstract reviews the main principles of the two most important imaging readout modalities for 3-D dosimetry: MRI and optical CT. Best practices for both these techniques are already described in several different places in the literature, but, for the uninitiated, there are a number of pitfalls. Here, I list some of the important considerations required to obtain good results from these methods and point to relevant prior work.

  18. Visualization of 3D geometric models of the breast created from contrast-enhanced MRI

    NASA Astrophysics Data System (ADS)

    Leader, J. Ken, III; Wang, Xiao Hui; Chang, Yuan-Hsiang; Chapman, Brian E.

    2002-05-01

    Contrast enhanced breast MRI is currently used as an adjuvant modality to x-ray mammography because of its ability to resolve ambiguities and determine the extent of malignancy. This study described techniques to create and visualize 3D geometric models of abnormal breast tissue. MRIs were performed on a General Electric 1.5 Tesla scanner using dual phased array breast coils. Image processing tasks included: 1) correction of image inhomogeneity caused by the coils, 2) segmentation of normal and abnormal tissue, and 3) modeling and visualization of the segmented tissue. The models were visualized using object-based surface rendering which revealed characteristics critical to differentiating benign from malignant tissue. Surface rendering illustrated the enhancement distribution and enhancement patterns. The modeling process condensed the multi-slice MRI data information and standardized its interpretation. Visualizing the 3D models should improve the radiologist's and/or surgeon's impression of the 3D shape, extent, and accessibility of the malignancy compared to viewing breast MRI data slice by slice.

  19. Extraction and tracking of MRI tagging sheets using a 3D Gabor filter bank.

    PubMed

    Qian, Zhen; Metaxas, Dimitris N; Axel, Leon

    2006-01-01

    In this paper, we present a novel method for automatically extracting the tagging sheets in tagged cardiac MR images, and tracking their displacement during the heart cycle, using a tunable 3D Gabor filter bank. Tagged MRI is a non-invasive technique for the study of myocardial deformation. We design the 3D Gabor filter bank based on the geometric characteristics of the tagging sheets. The tunable parameters of the Gabor filter bank are used to adapt to the myocardium deformation. The whole 3D image dataset is convolved with each Gabor filter in the filter bank, in the Fourier domain. Then we impose a set of deformable meshes onto the extracted tagging sheets and track them over time. Dynamic estimation of the filter parameters and the mesh internal smoothness are used to help the tracking. Some very encouraging results are shown.

  20. 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.

  1. Multimodal visualization of 3D enhanced MRI and CT of acoustic schwannoma and related structures

    NASA Astrophysics Data System (ADS)

    Kucharski, Tomasz; Kujawinska, Malgorzata; Niemczyk, Kazimierz; Marchel, Andrzej

    2005-09-01

    According to the necessity of supporting vestibular schwannoma surgery, there is a demand to develop a convenient method of medical data visualization. The process of making choice of optimal operating access way has been uncomfortable for a surgeon so far, because there has been a necessity of analyzing two independent 3D images series (CT -bone tissues visible, MRI - soft tissues visible) in the region of ponto-cerebellar angle tumors. The authors propose a solution that will improve this process. The system used is equipped with stereoscopic helmet mounted display. It allows merged CT and MRI data representing tissues in the region of of ponto-cerebellar angle to be visualized in stereoscopic way. The process of data preparation for visualization includes: -automated segmentation algorithms, -different types of 3D images (CT, MRI) fusion. The authors focused on the development of novel algorithms for segmentation of vestibular schwannoma. It is important and difficult task due to different types of tumors and their inhomogeneous character dependent on growth models. The authors propose algorithms based on histogram spectrum and multimodal character of MRI imaging (T1 and T2 modes). However due to a variety of objects the library of algorithms with specific modifications matching to selected types of images is proposed. The applicability and functionality of the algorithms and library was proved on the series of data delivered by Warsaw Central Medical University Hospital.

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

    PubMed

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

    2016-09-27

    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 (1)H 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.

  3. 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

  4. Postmortem Magnetic Resonance Imaging to Guide the Pathological Cut: Individualized, 3D-Printed Cutting Boxes for Fixed Brains

    PubMed Central

    Absinta, Martina; Nair, Govind; Filippi, Massimo; Ray-Chaudhury, Abhik; Reyes-Mantilla, Maria I.; Pardo, Carlos A.; Reich, Daniel S.

    2014-01-01

    Interfacing magnetic resonance imaging (MRI) and pathology is critically important for understanding the pathological basis of MRI signal changes in vivo and for clinicopathological correlations. Postmortem MRI is an intermediate step in this process; unfortunately, however, relating the data to standard pathological sections, which are relatively thick and often non-parallel, is both time consuming and insufficiently accurate. The aim of this project was to develop technology to integrate postmortem, high-resolution, whole-brain MRI into the planning and execution of the pathological analysis through precise localization of the target and coordinates of cut. Compared to standard pathological sectioning, the use of an individualized 3D-printed cutting-box, designed based on postmortem MRI of formalin-fixed whole brains, improved the speed, quality, and accuracy of radiological-pathological correlation and, specifically, the histopathological localization of imaging findings. The technology described herein is easily implemented, applicable to any brain disorder, and potentially extendable to other organs. From the point of view of the pathologist this technique can improve localization of small or subtle abnormalities, whereas from the point of view of the radiologist it has the potential to improve understanding of MRI signal changes observed in disease. PMID:25007244

  5. Meshless deformable models for 3D cardiac motion and strain analysis from tagged MRI.

    PubMed

    Wang, Xiaoxu; Chen, Ting; Zhang, Shaoting; Schaerer, Joël; Qian, Zhen; Huh, Suejung; Metaxas, Dimitris; Axel, Leon

    2015-01-01

    Tagged magnetic resonance imaging (TMRI) provides a direct and noninvasive way to visualize the in-wall deformation of the myocardium. Due to the through-plane motion, the tracking of 3D trajectories of the material points and the computation of 3D strain field call for the necessity of building 3D cardiac deformable models. The intersections of three stacks of orthogonal tagging planes are material points in the myocardium. With these intersections as control points, 3D motion can be reconstructed with a novel meshless deformable model (MDM). Volumetric MDMs describe an object as point cloud inside the object boundary and the coordinate of each point can be written in parametric functions. A generic heart mesh is registered on the TMRI with polar decomposition. A 3D MDM is generated and deformed with MR image tagging lines. Volumetric MDMs are deformed by calculating the dynamics function and minimizing the local Laplacian coordinates. The similarity transformation of each point is computed by assuming its neighboring points are making the same transformation. The deformation is computed iteratively until the control points match the target positions in the consecutive image frame. The 3D strain field is computed from the 3D displacement field with moving least squares. We demonstrate that MDMs outperformed the finite element method and the spline method with a numerical phantom. Meshless deformable models can track the trajectory of any material point in the myocardium and compute the 3D strain field of any particular area. The experimental results on in vivo healthy and patient heart MRI show that the MDM can fully recover the myocardium motion in three dimensions.

  6. Meshless deformable models for 3D cardiac motion and strain analysis from tagged MRI.

    PubMed

    Wang, Xiaoxu; Chen, Ting; Zhang, Shaoting; Schaerer, Joël; Qian, Zhen; Huh, Suejung; Metaxas, Dimitris; Axel, Leon

    2015-01-01

    Tagged magnetic resonance imaging (TMRI) provides a direct and noninvasive way to visualize the in-wall deformation of the myocardium. Due to the through-plane motion, the tracking of 3D trajectories of the material points and the computation of 3D strain field call for the necessity of building 3D cardiac deformable models. The intersections of three stacks of orthogonal tagging planes are material points in the myocardium. With these intersections as control points, 3D motion can be reconstructed with a novel meshless deformable model (MDM). Volumetric MDMs describe an object as point cloud inside the object boundary and the coordinate of each point can be written in parametric functions. A generic heart mesh is registered on the TMRI with polar decomposition. A 3D MDM is generated and deformed with MR image tagging lines. Volumetric MDMs are deformed by calculating the dynamics function and minimizing the local Laplacian coordinates. The similarity transformation of each point is computed by assuming its neighboring points are making the same transformation. The deformation is computed iteratively until the control points match the target positions in the consecutive image frame. The 3D strain field is computed from the 3D displacement field with moving least squares. We demonstrate that MDMs outperformed the finite element method and the spline method with a numerical phantom. Meshless deformable models can track the trajectory of any material point in the myocardium and compute the 3D strain field of any particular area. The experimental results on in vivo healthy and patient heart MRI show that the MDM can fully recover the myocardium motion in three dimensions. PMID:25157446

  7. Meshless deformable models for 3D cardiac motion and strain analysis from tagged MRI

    PubMed Central

    Wang, Xiaoxu; Chen, Ting; Zhang, Shaoting; Schaerer, Joël; Qian, Zhen; Huh, Suejung; Metaxas, Dimitris; Axel, Leon

    2016-01-01

    Tagged magnetic resonance imaging (TMRI) provides a direct and noninvasive way to visualize the in-wall deformation of the myocardium. Due to the through-plane motion, the tracking of 3D trajectories of the material points and the computation of 3D strain field call for the necessity of building 3D cardiac deformable models. The intersections of three stacks of orthogonal tagging planes are material points in the myocardium. With these intersections as control points, 3D motion can be reconstructed with a novel meshless deformable model (MDM). Volumetric MDMs describe an object as point cloud inside the object boundary and the coordinate of each point can be written in parametric functions. A generic heart mesh is registered on the TMRI with polar decomposition. A 3D MDM is generated and deformed with MR image tagging lines. Volumetric MDMs are deformed by calculating the dynamics function and minimizing the local Laplacian coordinates. The similarity transformation of each point is computed by assuming its neighboring points are making the same transformation. The deformation is computed iteratively until the control points match the target positions in the consecutive image frame. The 3D strain field is computed from the 3D displacement field with moving least squares. We demonstrate that MDMs outperformed the finite element method and the spline method with a numerical phantom. Meshless deformable models can track the trajectory of any material point in the myocardium and compute the 3D strain field of any particular area. The experimental results on in vivo healthy and patient heart MRI show that the MDM can fully recover the myocardium motion in three dimensions. PMID:25157446

  8. 3D interactive tractography-informed resting-state fMRI connectivity

    PubMed Central

    Chamberland, Maxime; Bernier, Michaël; Fortin, David; Whittingstall, Kevin; Descoteaux, Maxime

    2015-01-01

    In the past decade, the fusion between diffusion magnetic resonance imaging (dMRI) and functional magnetic resonance imaging (fMRI) has opened the way for exploring structure-function relationships in vivo. As it stands, the common approach usually consists of analysing fMRI and dMRI datasets separately or using one to inform the other, such as using fMRI activation sites to reconstruct dMRI streamlines that interconnect them. Moreover, given the large inter-individual variability of the healthy human brain, it is possible that valuable information is lost when a fixed set of dMRI/fMRI analysis parameters such as threshold values are assumed constant across subjects. By allowing one to modify such parameters while viewing the results in real-time, one can begin to fully explore the sensitivity of structure-function relations and how they differ across brain areas and individuals. This is especially important when interpreting how structure-function relationships are altered in patients with neurological disorders, such as the presence of a tumor. In this study, we present and validate a novel approach to achieve this: First, we present an interactive method to generate and visualize tractography-driven resting-state functional connectivity, which reduces the bias introduced by seed size, shape and position. Next, we demonstrate that structural and functional reconstruction parameters explain a significant portion of intra- and inter-subject variability. Finally, we demonstrate how our proposed approach can be used in a neurosurgical planning context. We believe this approach will promote the exploration of structure-function relationships in a subject-specific aspect and will open new opportunities for connectomics. PMID:26321901

  9. 3D MRI-based multicomponent FSI models for atherosclerotic plaques.

    PubMed

    Tang, Dalin; Yang, Chun; Zheng, Jie; Woodard, Pamela K; Sicard, Gregorio A; Saffitz, Jeffrey E; Yuan, Chun

    2004-07-01

    A three-dimensional (3D) MRI-based computational model with multicomponent plaque structure and fluid-structure interactions (FSI) is introduced to perform mechanical analysis for human atherosclerotic plaques and identify critical flow and stress/strain conditions which may be related to plaque rupture. Three-dimensional geometry of a human carotid plaque was reconstructed from 3D MR images and computational mesh was generated using Visualization Toolkit. Both the artery wall and the plaque components were assumed to be hyperelastic, isotropic, incompressible, and homogeneous. The flow was assumed to be laminar, Newtonian, viscous, and incompressible. The fully coupled fluid and structure models were solved by ADINA, a well-tested finite element package. Results from two-dimensional (2D) and 3D models, based on ex vivo MRI and histological images (HI), with different component sizes and plaque cap thickness, under different pressure and axial stretch conditions, were obtained and compared. Our results indicate that large lipid pools and thin plaque caps are associated with both extreme maximum (stretch) and minimum (compression when negative) stress/strain levels. Large cyclic stress/strain variations in the plaque under pulsating pressure were observed which may lead to artery fatigue and possible plaque rupture. Large-scale patient studies are needed to validate the computational findings for possible plaque vulnerability assessment and rupture predictions. PMID:15298432

  10. Ultrafast 3D spin-echo acquisition improves Gadolinium-enhanced MRI signal contrast enhancement

    PubMed Central

    Han, S. H.; Cho, F. H.; Song, Y. K.; Paulsen, J.; Song, Y. Q.; Kim, Y. R.; Kim, J. K.; Cho, G.; Cho, H.

    2014-01-01

    Long scan times of 3D volumetric MR acquisitions usually necessitate ultrafast in vivo gradient-echo acquisitions, which are intrinsically susceptible to magnetic field inhomogeneities. This is especially problematic for contrast-enhanced (CE)-MRI applications, where non-negligible T2* effect of contrast agent deteriorates the positive signal contrast and limits the available range of MR acquisition parameters and injection doses. To overcome these shortcomings without degrading temporal resolution, ultrafast spin-echo acquisitions were implemented. Specifically, a multiplicative acceleration factor from multiple spin echoes (×32) and compressed sensing (CS) sampling (×8) allowed highly-accelerated 3D Multiple-Modulation-Multiple-Echo (MMME) acquisition. At the same time, the CE-MRI of kidney with Gd-DOTA showed significantly improved signal enhancement for CS-MMME acquisitions (×7) over that of corresponding FLASH acquisitions (×2). Increased positive contrast enhancement and highly accelerated acquisition of extended volume with reduced RF irradiations will be beneficial for oncological and nephrological applications, in which the accurate in vivo 3D quantification of contrast agent concentration is necessary with high temporal resolution. PMID:24863102

  11. Study of the Usefulness of the 3D-distortion Correction in MRI.

    PubMed

    Yasuda, Shino; Yamakoshi, Kazunori

    2016-09-01

    Static magnetic field non-uniformity and gradient magnetic field non-linearity can be considered as the causes of geometric distortion in MRI images. The impact of a distortion in imaging such as whole body imaging or whole spine imaging can be serious. A standard 2D-distortion correction method does not correct the distortion in the slice encoding direction. This study examined the effect of 3D-distortion correction with a correction effect in both the imaging plane and the slice-encoding plane using three MRI devices with differing static magnetic field intensities and boa diameters. Imaging of a nickel sulfate bottle phantom attached to the MRI device was conducted using a CT scan to measure the distortion rate based on the CT image. The result of the distortion rate at -39.1% in the Z-axis direction was reduced to -1.3%, and the distortion rate at about -9.8% in the magnetic X-axis was reduced to -1.7%. In addition, the reduction effect was greater on the 70 cm boa device compared to the 60 cm boa device, and it was also greater at 1.5 T compared to 3 T. 3D-distortion correction is believed to be useful for wide scope imaging using large FOV. PMID:27647597

  12. Computer-aided assessment of anomalies in the scoliotic spine in 3-D MRI images.

    PubMed

    Jäger, Florian; Hornegger, Joachim; Schwab, Siegfried; Janka, Rolf

    2009-01-01

    The assessment of anomalies in the scoliotic spine using Magnetic Resonance Imaging (MRI) is an essential task during the planning phase of a patient's treatment and operations. Due to the pathologic bending of the spine, this is an extremely time consuming process as an orthogonal view onto every vertebra is required. In this article we present a system for computer-aided assessment (CAA) of anomalies in 3-D MRI images of the spine relying on curved planar reformations (CPR). We introduce all necessary steps, from the pre-processing of the data to the visualization component. As the core part of the framework is based on a segmentation of the spinal cord we focus on this. The proposed segmentation method is an iterative process. In every iteration the segmentation is updated by an energy based scheme derived from Markov random field (MRF) theory. We evaluate the segmentation results on public available clinical relevant 3-D MRI data sets of scoliosis patients. In order to assess the quality of the segmentation we use the angle between automatically computed planes through the vertebra and planes estimated by medical experts. This results in a mean angle difference of less than six degrees.

  13. Study of the Usefulness of the 3D-distortion Correction in MRI.

    PubMed

    Yasuda, Shino; Yamakoshi, Kazunori

    2016-09-01

    Static magnetic field non-uniformity and gradient magnetic field non-linearity can be considered as the causes of geometric distortion in MRI images. The impact of a distortion in imaging such as whole body imaging or whole spine imaging can be serious. A standard 2D-distortion correction method does not correct the distortion in the slice encoding direction. This study examined the effect of 3D-distortion correction with a correction effect in both the imaging plane and the slice-encoding plane using three MRI devices with differing static magnetic field intensities and boa diameters. Imaging of a nickel sulfate bottle phantom attached to the MRI device was conducted using a CT scan to measure the distortion rate based on the CT image. The result of the distortion rate at -39.1% in the Z-axis direction was reduced to -1.3%, and the distortion rate at about -9.8% in the magnetic X-axis was reduced to -1.7%. In addition, the reduction effect was greater on the 70 cm boa device compared to the 60 cm boa device, and it was also greater at 1.5 T compared to 3 T. 3D-distortion correction is believed to be useful for wide scope imaging using large FOV.

  14. A Comprehensive System for Intraoperative 3D Brain Deformation Recovery

    PubMed Central

    DeLorenzo, Christine; Papademetris, Xenophon; Vives, Kenneth P.; Spencer, Dennis D.; Duncan, James S.

    2010-01-01

    During neurosurgery, brain deformation renders preoperative images unreliable for localizing pathologic structures. In order to visualize the current brain anatomy, it is necessary to nonrigidly warp these preoperative images to reflect the intraoperative brain. This can be accomplished using a biomechanical model driven by sparse intraoperative information. In this paper, a linear elastic model of the brain is developed which can infer volumetric brain deformation given the cortical surface displacement. This model was tested on both a realistic brain phantom and in vivo, proving its ability to account for large brain deformations. Also, an efficient semiautomatic strategy for preoperative cortical feature detection is outlined, since accurate segmentation of cortical features can aid intraoperative cortical surface tracking. PMID:18044612

  15. 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

  16. 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.

  17. 3D hyperpolarized He-3 MRI of ventilation using a multi-echo projection acquisition

    PubMed Central

    Holmes, James H.; O’Halloran, Rafael L.; Brodsky, Ethan K.; Jung, Youngkyoo; Block, Walter F.; Fain, Sean B.

    2010-01-01

    A method is presented for high resolution 3D imaging of the whole lung using inhaled hyperpolarized (HP) He-3 MR with multiple half-echo radial trajectories that can accelerate imaging through undersampling. A multiple half-echo radial trajectory can be used to reduce the level of artifact for undersampled 3D projection reconstruction (PR) imaging by increasing the amount of data acquired per unit time for HP He-3 lung imaging. The point spread functions (PSFs) for breath-held He-3 MRI using multiple half-echo trajectories were evaluated using simulations to predict the effects of T2* and gas diffusion on image quality. Results from PSF simulations were consistent with imaging results in volunteer studies showing improved image quality with increasing number of echoes using up to 8 half-echoes. The 8 half-echo acquisition is shown to accommodate lost breath-holds as short as 6 s using a retrospective reconstruction at reduced resolution as well as to allow reduced breath-hold time compared to an equivalent Cartesian trajectory. Furthermore, preliminary results from a 3D dynamic inhalation-exhalation maneuver are demonstrated using the 8 half-echo trajectory. Results demonstrate the first high resolution 3D PR imaging of ventilation and respiratory dynamics in humans using HP He-3 MR. PMID:18429034

  18. 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.

  19. 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.

  20. 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.

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

    PubMed

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

    2015-08-21

    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 (2.5 mm)3 voxel size, deformation fields could be recovered well up to a downsampling factor of 2, i.e. (5 mm)3. In a therapy guidance scenario MRI, imaging speed could accordingly increase approximately fourfold, with acceptable loss of estimated motion quality.

  2. 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.

  3. 3D segmentation of masses in DCE-MRI images using FCM and adaptive MRF

    NASA Astrophysics Data System (ADS)

    Zhang, Chengjie; Li, Lihua

    2014-03-01

    Dynamic contrast enhanced magnetic resonance imaging (DCE-MRI) is a sensitive imaging modality for the detection of breast cancer. Automated segmentation of breast lesions in DCE-MRI images is challenging due to inherent signal-to-noise ratios and high inter-patient variability. A novel 3D segmentation method based on FCM and MRF is proposed in this study. In this method, a MRI image is segmented by spatial FCM, firstly. And then MRF segmentation is conducted to refine the result. We combined with the 3D information of lesion in the MRF segmentation process by using segmentation result of contiguous slices to constraint the slice segmentation. At the same time, a membership matrix of FCM segmentation result is used for adaptive adjustment of Markov parameters in MRF segmentation process. The proposed method was applied for lesion segmentation on 145 breast DCE-MRI examinations (86 malignant and 59 benign cases). An evaluation of segmentation was taken using the traditional overlap rate method between the segmented region and hand-drawing ground truth. The average overlap rates for benign and malignant lesions are 0.764 and 0.755 respectively. Then we extracted five features based on the segmentation region, and used an artificial neural network (ANN) to classify between malignant and benign cases. The ANN had a classification performance measured by the area under the ROC curve of AUC=0.73. The positive and negative predictive values were 0.86 and 0.58, respectively. The results demonstrate the proposed method not only achieves a better segmentation performance in accuracy also has a reasonable classification performance.

  4. RF Pulse Designs for 3D MRI Providing Uniform Tipping in Inhomogeneous B1 Fields

    PubMed Central

    Liu, Hui; Matson, Gerald B.

    2011-01-01

    Although high-field MRI offers increased signal-to-noise (S/N), the non-uniform tipping produced by conventional RF pulses leads to spatially dependent contrast and sub-optimal S/N, thus complicating the interpretation of the MR images. For structural imaging, 3D sequences which do not make use of frequency-selective RF pulses have become popular. Therefore, the aim of this research was to develop non-slice-selective (NSS) RF pulses with immunity to both B1 inhomogeneity and resonance offset. To accomplish this, an optimization routine based on optimal control theory was used to design new NSS pulses with desired ranges of immunity to B1 inhomogeneity and resonance offset. The design allows the phase of transverse magnetization produced by the pulses to vary. While the emphasis is on shallow tip designs, new designs for 30°, 60°, 90° and 180° degree NSS RF pulses are also provided. These larger tip angle pulses are compared with recently published NSS pulses. Evidence is presented that the pulses presented in this article have equivalent performance but are shorter than the recently published pulses. Although the NSS pulses generate higher specific absorption rates (SAR) and larger magnetization transfer (MT) effects than the rectangular pulses they replace, they nevertheless show promise for 3D MRI experiments at high field. PMID:21523819

  5. 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. PMID:25155697

  6. 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.

  7. Locating the Acupoint Baihui (GV20) Beneath the Cerebral Cortex with MRI Reconstructed 3D Neuroimages

    PubMed Central

    Shen, Ein-Yiao; Chen, Fun-Jou; Chen, Yun-Yin; Lin, Ming-Fan

    2011-01-01

    Baihui (GV20) is one of the most important acupoints of the Du meridian (the government vessel) and is commonly used in neurology and psychiatry and as a distal point of anorectal disorders by general practitioners. The anatomical relationship between the scalp region of the acupoint and the underlying corresponding cortex remains obscure. In this study, we first prepared the indicator for MRI scanning on a GE 1.5 T excite machine in a mode suitable for 3D reconstruction. The 3D Avizo software system (version 6.0, Mercury Computer Systems, Inc., Germany) was then used for image processing and the resulting data subsequently analyzed using descriptive statistics and analysis of variance (ANOVA). The mean distance from the Baihui anterior to the central sulcus in the adult group was greater than that in the child group (22.7 ± 2.2 and 19.7 ± 2.2 mm, resp., P = .042), whereas in the child group the distance between the Baihui anterior and the precentral sulcus was greater than in the adult group (6.8 ± 0.8 and 3.8 ± 0.8 mm, resp., P < .001). This MRI presentation demonstrates that the location of Baihui (GV20) can be identified using the distance from the central or precentral sulcus. PMID:21785620

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

    PubMed Central

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

    2014-01-01

    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. PMID:25155697

  9. Statistical shape model-based segmentation of brain MRI images.

    PubMed

    Bailleul, Jonathan; Ruan, Su; Constans, Jean-Marc

    2007-01-01

    We propose a segmentation method that automatically delineates structures contours from 3D brain MRI images using a statistical shape model. We automatically build this 3D Point Distribution Model (PDM) in applying a Minimum Description Length (MDL) annotation to a training set of shapes, obtained by registration of a 3D anatomical atlas over a set of patients brain MRIs. Delineation of any structure from a new MRI image is first initialized by such registration. Then, delineation is achieved in iterating two consecutive steps until the 3D contour reaches idempotence. The first step consists in applying an intensity model to the latest shape position so as to formulate a closer guess: our model requires far less priors than standard model in aiming at direct interpretation rather than compliance to learned contexts. The second step consists in enforcing shape constraints onto previous guess so as to remove all bias induced by artifacts or low contrast on current MRI. For this, we infer the closest shape instance from the PDM shape space using a new estimation method which accuracy is significantly improved by a huge increase in the model resolution and by a depth-search in the parameter space. The delineation results we obtained are very encouraging and show the interest of the proposed framework. PMID:18003193

  10. 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

  11. Combining supine MRI and 3D optical scanning for improved surgical planning of breast conserving surgeries

    NASA Astrophysics Data System (ADS)

    Pallone, Matthew J.; Poplack, Steven P.; Barth, Richard J., Jr.; Paulsen, Keith D.

    2012-02-01

    Image-guided wire localization is the current standard of care for the excision of non-palpable carcinomas during breast conserving surgeries (BCS). The efficacy of this technique depends upon the accuracy of wire placement, maintenance of the fixed wire position (despite patient movement), and the surgeon's understanding of the spatial relationship between the wire and tumor. Notably, breast shape can vary significantly between the imaging and surgical positions. Despite this method of localization, re-excision is needed in approximately 30% of patients due to the proximity of cancer to the specimen margins. These limitations make wire localization an inefficient and imprecise procedure. Alternatively, we investigate a method of image registration and finite element (FE) deformation which correlates preoperative supine MRIs with 3D optical scans of the breast surface. MRI of the breast can accurately define the extents of very small cancers. Furthermore, supine breast MR reduces the amount of tissue deformation between the imaging and surgical positions. At the time of surgery, the surface contour of the breast may be imaged using a handheld 3D laser scanner. With the MR images segmented by tissue type, the two scans are approximately registered using fiducial markers present in both acquisitions. The segmented MRI breast volume is then deformed to match the optical surface using a FE mechanical model of breast tissue. The resulting images provide the surgeon with 3D views and measurements of the tumor shape, volume, and position within the breast as it appears during surgery which may improve surgical guidance and obviate the need for wire localization.

  12. Simulation of MRI-Guided Transurethral Conformal 3-D Ultrasound Therapy of the Prostate

    NASA Astrophysics Data System (ADS)

    Burtnyk, Mathieu; Chopra, Rajiv; Bronskill, Michael

    2007-05-01

    The capability of MRI to measure spatial heating patterns during therapy delivery with ultrasound makes adaptive thermal therapy possible. Active feedback provided by MR thermometry enables on-line adjustment of the treatment to compensate for tissue/perfusion changes during heating. The feasibility of performing 3-D conformal thermal therapy of the entire prostate gland with a multi-element transurethral ultrasound heating applicator was considered in this study. The major challenge was using MR temperature feedback to adjust simultaneously the device's rate of rotation and the power and frequency of multiple independent ultrasound transducers, to shape the region of thermal damage to the prostate gland in all spatial dimensions while sparing surrounding tissues from damage. The 3-D Bioheat Transfer Equation was used to model the ultrasound therapy using manually segmented MRI prostate geometries from 20 prostate cancer patients. Average prostate dimensions (±SD) were: length: 37.8±7.2 mm, width: 47.1±5.5 mm, height: 28.9±5.7 mm. Typical treatments of the entire prostate volume take less than 30 min. Results from various treatment strategies were compared by calculating the percentage volume of under- and over-treated tissue and the potential thermal damage incurred by important adjacent anatomical structures using "dose-effect" curves. Visualization tools were developed to investigate patient-specific prostate and periprostatic anatomy, as well as the simulated coagulated volumes in 3-D, enabling evaluation of individual patient outcomes. These simulations also enabled the investigation of the number and size of transducer segments required for accurate treatment delivery. In general, the under-treated fraction can be maintained below 1% of the prostate volume, but the over-treated fraction can range up to 15%, emphasizing the importance of accurate location of sensitive adjacent structures.

  13. 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. PMID:23366825

  14. 3D Cardiac Motion Reconstruction from CT Data and Tagged MRI

    PubMed Central

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

    2016-01-01

    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. PMID:23366825

  15. 3D perfused brain phantom for interstitial ultrasound thermal therapy and imaging: design, construction and characterization.

    PubMed

    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.

  16. 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.

  17. Bayesian estimation of optical properties of the human head via 3D structural MRI

    NASA Astrophysics Data System (ADS)

    Barnett, Alexander H.; Culver, Joseph P.; Sorensen, A. Gregory; Dale, Anders M.; Boas, David A.

    2003-10-01

    Knowledge of the baseline optical properties of the tissues of the human head is essential for absolute cerebral oximetry, and for quantitative studies of brain activation. In this work we numerically model the utility of signals from a small 6-optode time-resolved diffuse optical tomographic apparatus for inferring baseline scattering and absorption coefficients of the scalp, skull and brain, when complete geometric information is available from magnetic resonance imaging (MRI). We use an optical model where MRI-segmented tissues are assumed homogeneous. We introduce a noise model capturing both photon shot noise and forward model numerical accuracy, and use Bayesian inference to predict errorbars and correlations on the measurments. We also sample from the full posterior distribution using Markov chain Monte Carlo. We conclude that ~ 106 detected photons are sufficient to measure the brain"s scattering and absorption to a few percent. We present preliminary results using a fast multi-layer slab model, comparing the case when layer thicknesses are known versus unknown.

  18. Multi-Shot 3D Slice-Select Tailored RF Pulses for MRI

    PubMed Central

    Stenger, V. Andrew; Boada, Fernando E.; Noll, Douglas C.

    2011-01-01

    A multi-shot three-dimensional slice-select tailored RF pulse method is presented for the excitation of slice profiles with arbitrary resolution. This method is derived from the linearity of the small tip angle approximation, allowing for the decomposition of small tip angle tailored RF pulses into separate excitations. The final image is created by complex summation of the images acquired from the individual excitations. This technique overcomes the limitation of requiring long pulse to excite thin slices with adequate resolution. This has implications in applications including T2*-weighted functional MRI in brain regions corrupted by intravoxel dephasing artifacts due to susceptibility variations. Simulations, phantom experiments, and human brain images are presented. It is demonstrated that at most four shots of 40 ms pulse length are needed to excite a 5 mm thick slice in the brain with reduced susceptibility artifacts at 3T. PMID:12111943

  19. 3-D volumetric MRI evaluation of the placenta in fetuses with complex congenital heart disease

    PubMed Central

    Andescavage, Nickie; Yarish, Alexa; Donofrio, Mary; Bulas, Dorothy; Evangelou, Iordanis; Vezina, Gilbert; McCarter, Robert; DuPlessis, Adre; Limperopoulos, Catherine

    2015-01-01

    Introduction Placental insufficiency remains a common cause of perinatal mortality and neurodevelopmental morbidity. Congenital heart disease (CHD) in the fetus and its relationship to placental function is unknown. This study explores placental health and its relationship to neonatal outcomes by comparing placental volumes in healthy pregnancies and pregnancies complicated by CHD using in vivo three-dimensional MRI studies. Methods In a prospective observational study, pregnant women greater than 18 weeks gestation with normal pregnancies or pregnancies complicated by CHD were recruited and underwent fetal MR imaging. The placenta was manually outlined and the volume was calculated in cm3. Brain volume was also calculated and clinical data were also collected. Relationships, including interactive effects, between placental and fetal growth, including brain growth, were evaluated using longitudinal multiple linear regression analysis. Results 135 women underwent fetal MRI between 18 and 39 weeks gestation (mean 31.6 ± 4.4). Placental volume increased exponentially with gestational age (p=0.041). Placental volume was positively associated with birth weight (p <0.001) and increased more steeply with birth weight in CHD-affected fetuses (p=0.046). Total brain and cerebral volumes were smaller in the CHD group (p<0.001), but brainstem volume (p<0.001) was larger. Placental volumes were not associated with brain volumes. Discussion Impaired placental growth in CHD is associated with gestational age and birth weight at delivery. Abnormalities in placental development may contribute to the significant morbidity in this high-risk population. Assessment of placental volume by MRI allows for in vivo assessments of placental development. PMID:26190037

  20. Histological Evaluation of 3D MRI-Guided Transurethral Ultrasound Therapy in the Prostate

    NASA Astrophysics Data System (ADS)

    Vedula, Siddharth; Boyes, Aaron; Chopra, Rajiv; Bronskill, Michael

    2010-03-01

    Previous work from our group has shown that transurethral ultrasound therapy, with a single ultrasound transducer guided by temperature feedback from a single MRI plane (slice), can be used to treat a targeted region accurately in the prostate gland. We have extended this approach to a larger, 3D, targeted volume within the prostate, using a multi-element transducer controlled concurrently by temperature feedback from multiple imaging planes. Animals were placed supine in a 1.5 T clinical MRI, and the transurethral heating device was positioned with image guidance. A four-element transducer (each element was 5 mm long, operating at ˜8 MHz) was rotated to treat a targeted volume around the device. Temperature maps transverse to each element were acquired during heating and used to control the acoustic power of each element and the rate of rotation of the device. T2-weighted and contrast-enhanced (CE) MR images were obtained pre- and post-heating. Following the treatment, prostates were removed and fixed, axially sliced, stained with H&E, and digitally imaged at high-resolution to outline boundaries of cell death. Slice alignment and image registration techniques were developed to enable quantitative comparison of the axial MRI images and matching histological sections. Prostate sections showed clear regions of coagulative necrosis, extending ˜20 mm along the urethra, which correlated well with CE MRI data and transducer length. After registration, the outer border of coagulative necrosis on H&E conformed well to the target isotherm, similar to results from our previous (single element) acute studies. These results confirm that our previous analysis techniques for a single transducer can be extended to multiple elements, and that a large volumetric ablation of the prostate gland is feasible with a high degree of accuracy.

  1. 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.

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

    PubMed Central

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

    2010-01-01

    We present a novel integrated wavelet-domain based framework (w-ICA) for 3-D de-noising 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 de-noising 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 de-noised wavelet coefficients corresponding to the three viewing geometries for each sub-band. This results in a robust set of de-noised wavelet coefficients for each voxel. Given the decorrelated nature of these de-noised 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, the analysis module where we combine a new 3-D wavelet denoising approach with better signal separation properties of ICA in the wavelet domain, to yield an activation component that corresponds closely to the true underlying signal and 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 (ROC) 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

  3. Evaluation of segmented 3D acquisition schemes for whole-brain high-resolution arterial spin labeling at 3 T.

    PubMed

    Vidorreta, Marta; Balteau, Evelyne; Wang, Ze; De Vita, Enrico; Pastor, María A; Thomas, David L; Detre, John A; Fernández-Seara, María A

    2014-11-01

    Recent technical developments have significantly increased the signal-to-noise ratio (SNR) of arterial spin labeled (ASL) perfusion MRI. Despite this, typical ASL acquisitions still employ large voxel sizes. The purpose of this work was to implement and evaluate two ASL sequences optimized for whole-brain high-resolution perfusion imaging, combining pseudo-continuous ASL (pCASL), background suppression (BS) and 3D segmented readouts, with different in-plane k-space trajectories. Identical labeling and BS pulses were implemented for both sequences. Two segmented 3D readout schemes with different in-plane trajectories were compared: Cartesian (3D GRASE) and spiral (3D RARE Stack-Of-Spirals). High-resolution perfusion images (2 × 2 × 4 mm(3) ) were acquired in 15 young healthy volunteers with the two ASL sequences at 3 T. The quality of the perfusion maps was evaluated in terms of SNR and gray-to-white matter contrast. Point-spread-function simulations were carried out to assess the impact of readout differences on the effective resolution. The combination of pCASL, in-plane segmented 3D readouts and BS provided high-SNR high-resolution ASL perfusion images of the whole brain. Although both sequences produced excellent image quality, the 3D RARE Stack-Of-Spirals readout yielded higher temporal and spatial SNR than 3D GRASE (spatial SNR = 8.5 ± 2.8 and 3.7 ± 1.4; temporal SNR = 27.4 ± 12.5 and 15.6 ± 7.6, respectively) and decreased through-plane blurring due to its inherent oversampling of the central k-space region, its reduced effective TE and shorter total readout time, at the expense of a slight increase in the effective in-plane voxel size. PMID:25263944

  4. 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. PMID:26737946

  5. 3D-neuronavigation in vivo through a patient's brain during a spontaneous migraine headache.

    PubMed

    DaSilva, Alexandre F; Nascimento, Thiago D; Love, Tiffany; DosSantos, Marcos F; Martikainen, Ilkka K; Cummiford, Chelsea M; DeBoer, Misty; Lucas, Sarah R; Bender, MaryCatherine A; Koeppe, Robert A; Hall, Theodore; Petty, Sean; Maslowski, Eric; Smith, Yolanda R; Zubieta, Jon-Kar

    2014-01-01

    A growing body of research, generated primarily from MRI-based studies, shows that migraine appears to occur, and possibly endure, due to the alteration of specific neural processes in the central nervous system. However, information is lacking on the molecular impact of these changes, especially on the endogenous opioid system during migraine headaches, and neuronavigation through these changes has never been done. This study aimed to investigate, using a novel 3D immersive and interactive neuronavigation (3D-IIN) approach, the endogenous µ-opioid transmission in the brain during a migraine headache attack in vivo. This is arguably one of the most central neuromechanisms associated with pain regulation, affecting multiple elements of the pain experience and analgesia. A 36 year-old female, who has been suffering with migraine for 10 years, was scanned in the typical headache (ictal) and nonheadache (interictal) migraine phases using Positron Emission Tomography (PET) with the selective radiotracer [(11)C]carfentanil, which allowed us to measure µ-opioid receptor availability in the brain (non-displaceable binding potential - µOR BPND). The short-life radiotracer was produced by a cyclotron and chemical synthesis apparatus on campus located in close proximity to the imaging facility. Both PET scans, interictal and ictal, were scheduled during separate mid-late follicular phases of the patient's menstrual cycle. During the ictal PET session her spontaneous headache attack reached severe intensity levels; progressing to nausea and vomiting at the end of the scan session. There were reductions in µOR BPND in the pain-modulatory regions of the endogenous µ-opioid system during the ictal phase, including the cingulate cortex, nucleus accumbens (NAcc), thalamus (Thal), and periaqueductal gray matter (PAG); indicating that µORs were already occupied by endogenous opioids released in response to the ongoing pain. To our knowledge, this is the first time that changes

  6. 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.

  7. 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.

  8. Multi-feature-based plaque characterization in ex vivo MRI trained by registration to 3D histology

    NASA Astrophysics Data System (ADS)

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

    2012-01-01

    We present a new method for automated characterization of atherosclerotic plaque composition in ex vivo MRI. It uses MRI intensities as well as four other types of features: smoothed, gradient magnitude and Laplacian images at several scales, and the distances to the lumen and outer vessel wall. The ground truth for fibrous, necrotic and calcified tissue was provided by histology and μCT in 12 carotid plaque specimens. Semi-automatic registration of a 3D stack of histological slices and μCT images to MRI allowed for 3D rotations and in-plane deformations of histology. By basing voxelwise classification on different combinations of features, we evaluated their relative importance. To establish whether training by 3D registration yields different results than training by 2D registration, we determined plaque composition using (1) a 2D slice-based registration approach for three manually selected MRI and histology slices per specimen, and (2) an approach that uses only the three corresponding MRI slices from the 3D-registered volumes. Voxelwise classification accuracy was best when all features were used (73.3 ± 6.3%) and was significantly better than when only original intensities and distance features were used (Friedman, p < 0.05). Although 2D registration or selection of three slices from the 3D set slightly decreased accuracy, these differences were non-significant.

  9. Fast imaging of laboratory core floods using 3D compressed sensing RARE MRI.

    PubMed

    Ramskill, N P; Bush, I; Sederman, A J; Mantle, M D; Benning, M; Anger, B C; Appel, M; Gladden, L F

    2016-09-01

    Three-dimensional (3D) imaging of the fluid distributions within the rock is essential to enable the unambiguous interpretation of core flooding data. Magnetic resonance imaging (MRI) has been widely used to image fluid saturation in rock cores; however, conventional acquisition strategies are typically too slow to capture the dynamic nature of the displacement processes that are of interest. Using Compressed Sensing (CS), it is possible to reconstruct a near-perfect image from significantly fewer measurements than was previously thought necessary, and this can result in a significant reduction in the image acquisition times. In the present study, a method using the Rapid Acquisition with Relaxation Enhancement (RARE) pulse sequence with CS to provide 3D images of the fluid saturation in rock core samples during laboratory core floods is demonstrated. An objective method using image quality metrics for the determination of the most suitable regularisation functional to be used in the CS reconstructions is reported. It is shown that for the present application, Total Variation outperforms the Haar and Daubechies3 wavelet families in terms of the agreement of their respective CS reconstructions with a fully-sampled reference image. Using the CS-RARE approach, 3D images of the fluid saturation in the rock core have been acquired in 16min. The CS-RARE technique has been applied to image the residual water saturation in the rock during a water-water displacement core flood. With a flow rate corresponding to an interstitial velocity of vi=1.89±0.03ftday(-1), 0.1 pore volumes were injected over the course of each image acquisition, a four-fold reduction when compared to a fully-sampled RARE acquisition. Finally, the 3D CS-RARE technique has been used to image the drainage of dodecane into the water-saturated rock in which the dynamics of the coalescence of discrete clusters of the non-wetting phase are clearly observed. The enhancement in the temporal resolution that has

  10. Fast imaging of laboratory core floods using 3D compressed sensing RARE MRI

    NASA Astrophysics Data System (ADS)

    Ramskill, N. P.; Bush, I.; Sederman, A. J.; Mantle, M. D.; Benning, M.; Anger, B. C.; Appel, M.; Gladden, L. F.

    2016-09-01

    Three-dimensional (3D) imaging of the fluid distributions within the rock is essential to enable the unambiguous interpretation of core flooding data. Magnetic resonance imaging (MRI) has been widely used to image fluid saturation in rock cores; however, conventional acquisition strategies are typically too slow to capture the dynamic nature of the displacement processes that are of interest. Using Compressed Sensing (CS), it is possible to reconstruct a near-perfect image from significantly fewer measurements than was previously thought necessary, and this can result in a significant reduction in the image acquisition times. In the present study, a method using the Rapid Acquisition with Relaxation Enhancement (RARE) pulse sequence with CS to provide 3D images of the fluid saturation in rock core samples during laboratory core floods is demonstrated. An objective method using image quality metrics for the determination of the most suitable regularisation functional to be used in the CS reconstructions is reported. It is shown that for the present application, Total Variation outperforms the Haar and Daubechies3 wavelet families in terms of the agreement of their respective CS reconstructions with a fully-sampled reference image. Using the CS-RARE approach, 3D images of the fluid saturation in the rock core have been acquired in 16 min. The CS-RARE technique has been applied to image the residual water saturation in the rock during a water-water displacement core flood. With a flow rate corresponding to an interstitial velocity of vi = 1.89 ± 0.03 ft day-1, 0.1 pore volumes were injected over the course of each image acquisition, a four-fold reduction when compared to a fully-sampled RARE acquisition. Finally, the 3D CS-RARE technique has been used to image the drainage of dodecane into the water-saturated rock in which the dynamics of the coalescence of discrete clusters of the non-wetting phase are clearly observed. The enhancement in the temporal resolution

  11. Fast imaging of laboratory core floods using 3D compressed sensing RARE MRI.

    PubMed

    Ramskill, N P; Bush, I; Sederman, A J; Mantle, M D; Benning, M; Anger, B C; Appel, M; Gladden, L F

    2016-09-01

    Three-dimensional (3D) imaging of the fluid distributions within the rock is essential to enable the unambiguous interpretation of core flooding data. Magnetic resonance imaging (MRI) has been widely used to image fluid saturation in rock cores; however, conventional acquisition strategies are typically too slow to capture the dynamic nature of the displacement processes that are of interest. Using Compressed Sensing (CS), it is possible to reconstruct a near-perfect image from significantly fewer measurements than was previously thought necessary, and this can result in a significant reduction in the image acquisition times. In the present study, a method using the Rapid Acquisition with Relaxation Enhancement (RARE) pulse sequence with CS to provide 3D images of the fluid saturation in rock core samples during laboratory core floods is demonstrated. An objective method using image quality metrics for the determination of the most suitable regularisation functional to be used in the CS reconstructions is reported. It is shown that for the present application, Total Variation outperforms the Haar and Daubechies3 wavelet families in terms of the agreement of their respective CS reconstructions with a fully-sampled reference image. Using the CS-RARE approach, 3D images of the fluid saturation in the rock core have been acquired in 16min. The CS-RARE technique has been applied to image the residual water saturation in the rock during a water-water displacement core flood. With a flow rate corresponding to an interstitial velocity of vi=1.89±0.03ftday(-1), 0.1 pore volumes were injected over the course of each image acquisition, a four-fold reduction when compared to a fully-sampled RARE acquisition. Finally, the 3D CS-RARE technique has been used to image the drainage of dodecane into the water-saturated rock in which the dynamics of the coalescence of discrete clusters of the non-wetting phase are clearly observed. The enhancement in the temporal resolution that has

  12. Analysis of passive cardiac constitutive laws for parameter estimation using 3D tagged MRI.

    PubMed

    Hadjicharalambous, Myrianthi; Chabiniok, Radomir; Asner, Liya; Sammut, Eva; Wong, James; Carr-White, Gerald; Lee, Jack; Razavi, Reza; Smith, Nicolas; Nordsletten, David

    2015-08-01

    An unresolved issue in patient-specific models of cardiac mechanics is the choice of an appropriate constitutive law, able to accurately capture the passive behavior of the myocardium, while still having uniquely identifiable parameters tunable from available clinical data. In this paper, we aim to facilitate this choice by examining the practical identifiability and model fidelity of constitutive laws often used in cardiac mechanics. Our analysis focuses on the use of novel 3D tagged MRI, providing detailed displacement information in three dimensions. The practical identifiability of each law is examined by generating synthetic 3D tags from in silico simulations, allowing mapping of the objective function landscape over parameter space and comparison of minimizing parameter values with original ground truth values. Model fidelity was tested by comparing these laws with the more complex transversely isotropic Guccione law, by characterizing their passive end-diastolic pressure-volume relation behavior, as well as by considering the in vivo case of a healthy volunteer. These results show that a reduced form of the Holzapfel-Ogden law provides the best balance between identifiability and model fidelity across the tests considered. PMID:25510227

  13. Atlas-registration based image segmentation of MRI human thigh muscles in 3D space

    NASA Astrophysics Data System (ADS)

    Ahmad, Ezak; Yap, Moi Hoon; Degens, Hans; McPhee, Jamie S.

    2014-03-01

    Automatic segmentation of anatomic structures of magnetic resonance thigh scans can be a challenging task due to the potential lack of precisely defined muscle boundaries and issues related to intensity inhomogeneity or bias field across an image. In this paper, we demonstrate a combination framework of atlas construction and image registration methods to propagate the desired region of interest (ROI) between atlas image and the targeted MRI thigh scans for quadriceps muscles, femur cortical layer and bone marrow segmentations. The proposed system employs a semi-automatic segmentation method on an initial image in one dataset (from a series of images). The segmented initial image is then used as an atlas image to automate the segmentation of other images in the MRI scans (3-D space). The processes include: ROI labeling, atlas construction and registration, and morphological transform correspondence pixels (in terms of feature and intensity value) between the atlas (template) image and the targeted image based on the prior atlas information and non-rigid image registration methods.

  14. On the validity of 3D polymer gel dosimetry: III. MRI-related error sources

    NASA Astrophysics Data System (ADS)

    Vandecasteele, Jan; De Deene, Yves

    2013-01-01

    In MRI (PAGAT) polymer gel dosimetry, there exists some controversy on the validity of 3D dose verifications of clinical treatments. The relative contribution of important sources of uncertainty in MR scanning to the overall accuracy and precision of 3D MRI polymer gel dosimetry is quantified in this study. The performance in terms of signal-to-noise and imaging artefacts was evaluated on three different MR scanners (two 1.5 T and a 3 T scanner). These include: (1) B0-field inhomogeneity, (2) B1-field inhomogeneity, (3) dielectric effects (losses and standing waves) and (4) temperature inhomogeneity during scanning. B0-field inhomogeneities that amount to maximum 5 ppm result in dose deviations of up to 4.3% and deformations of up to 5 pixels. Compensation methods are proposed. B1-field inhomogeneities were found to induce R2 variations in large anthropomorphic phantoms both at 1.5 and 3 T. At 1.5 T these effects are mainly caused by the coil geometry resulting in dose deviations of up to 25%. After the correction of the R2 maps using a heuristic flip angle-R2 relation, these dose deviations are reduced to 2.4%. At 3 T, the dielectric properties of the gel phantoms are shown to strongly influence B1-field homogeneity, hence R2 homogeneity, especially of large anthropomorphic phantoms. The low electrical conductivity of polymer gel dosimeters induces standing wave patterns resulting in dose deviations up to 50%. Increasing the conductivity of the gel by adding NaCl reduces the dose deviation to 25% after which the post-processing is successful in reducing the remaining inhomogeneities caused by the coil geometry to within 2.4%. The measurements are supported by computational modelling of the B1-field. Finally, temperature fluctuations of 1 °C frequently encountered in clinical MRI scanners result in dose deviations up to 15%. It is illustrated that with adequate temperature stabilization, the dose uncertainty is reduced to within 2.58%. Both authors contributed

  15. 3D culture of murine neural stem cells on decellularized mouse brain sections.

    PubMed

    De Waele, Jorrit; Reekmans, Kristien; Daans, Jasmijn; Goossens, Herman; Berneman, Zwi; Ponsaerts, Peter

    2015-02-01

    Transplantation of neural stem cells (NSC) in diseased or injured brain tissue is widely studied as a potential treatment for various neurological pathologies. However, effective cell replacement therapy relies on the intrinsic capacity of cellular grafts to overcome hypoxic and/or immunological barriers after transplantation. In this context, it is hypothesized that structural support for grafted NSC will be of utmost importance. With this study, we present a novel decellularization protocol for 1.5 mm thick mouse brain sections, resulting in the generation of acellular three-dimensional (3D) brain sections. Next, the obtained 3D brain sections were seeded with murine NSC expressing both the eGFP and luciferase reporter proteins (NSC-eGFP/Luc). Using real-time bioluminescence imaging, the survival and growth of seeded NSC-eGFP/Luc cells was longitudinally monitored for 1-7 weeks in culture, indicating the ability of the acellular brain sections to support sustained ex vivo growth of NSC. Next, the organization of a 3D maze-like cellular structure was examined using confocal microscopy. Moreover, under mitogenic stimuli (EGF and hFGF-2), most cells in this 3D culture retained their NSC phenotype. Concluding, we here present a novel protocol for decellularization of mouse brain sections, which subsequently support long-term 3D culture of undifferentiated NSC.

  16. 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.

  17. A super-resolution framework for 3-D high-resolution and high-contrast imaging using 2-D multislice MRI.

    PubMed

    Shilling, Richard Z; Robbie, Trevor Q; Bailloeul, Timothée; Mewes, Klaus; Mersereau, Russell M; Brummer, Marijn E

    2009-05-01

    A novel super-resolution reconstruction (SRR) framework in magnetic resonance imaging (MRI) is proposed. Its purpose is to produce images of both high resolution and high contrast desirable for image-guided minimally invasive brain surgery. The input data are multiple 2-D multislice inversion recovery MRI scans acquired at orientations with regular angular spacing rotated around a common frequency encoding axis. The output is a 3-D volume of isotropic high resolution. The inversion process resembles a localized projection reconstruction problem. Iterative algorithms for reconstruction are based on the projection onto convex sets (POCS) formalism. Results demonstrate resolution enhancement in simulated phantom studies, and ex vivo and in vivo human brain scans, carried out on clinical scanners. A comparison with previously published SRR methods shows favorable characteristics in the proposed approach.

  18. 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

  19. The correlation of 3D DT-MRI fiber disruption with structural and mechanical degeneration in porcine myocardium.

    PubMed

    Zhang, Song; Crow, J Allen; Yang, Xiaoyong; Chen, Joseph; Borazjani, Ali; Mullins, Katie B; Chen, Wei; Cooper, Robert C; McLaughlin, Ronald M; Liao, Jun

    2010-10-01

    Evaluation of structural parameters following a myocardial infarction (MI) is important to assess left ventricular function and remodeling. In this study, we assessed the capability of 3D diffusion tensor magnetic resonance imaging (DT-MRI) to assess tissue degeneration shortly after an MI using a porcine model of infarction. Two days after an induced infarction, hearts were explanted and immediately scanned by a 3T MRI scanner with a diffusion tensor imaging protocol. 3D fiber tracks and clustering models were generated from the diffusion-weighted imaging data. We found in a normal explanted heart that DT-MRI fibers showed a multilayered helical structure, with fiber architecture and fiber density reflecting the integrity of muscle fibers. For infarcted heart explants, we observed either a lack of fibers or disruption of fibers in the infarcted regions. Contours of the disrupted DT-MRI fibers were found to be consistent with the infarcted regions. Both histological and mechanical analysis of the infarcted hearts suggested DT-MRI fiber disruption correlated with altered microstructure and tissue mechanics. The ability of 3D DT-MRI to accurately distinguish viable myocardium from dead myocardium only 2 days post infarct without the use of radioisotopes or ionotropic agents makes it a promising approach to evaluate cardiac damage early post-MI. PMID:20499182

  20. 3D conformal MRI-guided transurethral ultrasound therapy: results of gel phantom experiments

    NASA Astrophysics Data System (ADS)

    N'Djin, W. A.; Burtnyk, M.; McCormick, S.; Bronskill, M.; Chopra, R.

    2011-09-01

    MRI-guided transurethral ultrasound therapy shows promise for minimally invasive treatment of localized prostate cancer. Previous in-vivo studies demonstrated the feasibility of performing conservative treatments using real-time temperature feedback to control accurately the establishment of coagulative lesions within circumscribed prostate regions. This in-vitro study tested device configuration and control options for achieving full prostate treatments. A multi-channel MRI compatible ultrasound therapy system was evaluated in gel phantoms using 3 canine prostate models. Prostate profiles were 5 mm-step-segmented from T2-weighted MR images performed during previous in-vivo experiments. During ultrasound exposures, each ultrasound element was controlled independently by the 3D controller. Decisions on acoustic power, frequency, and device rotation rate were made in real time based on MR thermometry feedback and prostate radii. Low and high power treatment approaches using maximum acoustic powers of 10 or 20 W.cm-2 were tested as well as single and dual-frequency strategies (4.05/13.10 MHz). The dual-frequency strategy used either the fundamental frequency or the 3rd harmonic component, depending on the prostate radius. The 20 W.cm-2 dual frequency approach was the most efficient configuration in achieving full prostate treatments. Treatment times were about half the duration of those performed with 10 W.cm-2 configurations. Full prostate coagulations were performed in 16.3±6.1 min at a rate of 1.8±0.2 cm3.min-1, and resulted in very little undertreated tissue (<3%). Surrounding organs positioned beyond a safety distance of 1.4±1.0 mm from prostate boundaries were not damaged, particularly rectal wall tissues. In this study, a 3D, MR-thermometry-guided transurethral ultrasound therapy was validated in vitro in a tissue-mimicking phantom for performing full prostate treatment. A dual-frequency configuration with 20 W.cm-2 ultrasound intensity exposure showed good

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

    PubMed

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

    2015-03-11

    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

  2. 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.

  3. 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

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

    PubMed

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

    2015-03-11

    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.

  5. A novel 3D partitioned active shape model for segmentation of brain MR images.

    PubMed

    Zhao, Zheen; Aylward, Stephen R; Teoh, Earn Khwang

    2005-01-01

    A 3D Partitioned Active Shape Model (PASM) is proposed in this paper to address the problems of the 3D Active Shape Models (ASM). When training sets are small. It is usually the case in 3D segmentation, 3D ASMs tend to be restrictive. This is because the allowable region spanned by relatively few eigenvectors cannot capture the full range of shape variability. The 3D PASM overcomes this limitation by using a partitioned representation of the ASM. Given a Point Distribution Model (PDM), the mean mesh is partitioned into a group of small tiles. In order to constrain deformation of tiles, the statistical priors of tiles are estimated by applying Principal Component Analysis to each tile. To avoid the inconsistency of shapes between tiles, training samples are projected as curves in one hyperspace instead of point clouds in several hyperspaces. The deformed points are then fitted into the allowable region of the model by using a curve alignment scheme. The experiments on 3D human brain MRIs show that when the numbers of the training samples are limited, the 3D PASMs significantly improve the segmentation results as compared to 3D ASMs and 3D Hierarchical ASMs.

  6. [MRI compatibility of deep brain stimulator].

    PubMed

    Zhang, Yujing

    2013-07-01

    Deep brain stimulation (DBS) therapy develops rapidly in clinical application. The structures of deep brain stimulator and magnetic resonance imaging (MRI) equipment are introduced, the interactions are analyzed, and the two compatible problems of radio frequency (RF) heating and imaging artifact are summarized in this paper.

  7. 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.

  8. Spatiotemporal Encoding As A Robust Basis for Fast 3D In Vivo MRI

    PubMed Central

    Ben-Eliezer, Noam; Frydman, Lucio

    2016-01-01

    Recent studies have described some of the new opportunities opened within the context of ultrafast 2D imaging, by the advent of spatiotemporal encoding methods. This paper explores the potential of integrating these non-Fourier, single scan 2D MRI principles, with multi-slice and with phase encoding schemes acting along a third dimension. In unison, these combinations enable the acquisition of complete three-dimensional images from volumes-of-interest within a one-second timescale. A number of alternatives are hereby explored for carrying out these very rapid 3D acquisitions, including: (i) the use of two-dimensional slice-selective, spatiotemporal encoding excitation radiofrequency pulses, (ii) driven-equilibrium slice selective schemes, and (iii) phase encoded volumetric approaches. Whenever tested under in vivo conditions, the ‘hybrid’ schemes combining spatiotemporal encoding with k-encoding imaging principles, proved superior to traditional schemes based on EPI. The resulting images were found less affected by field inhomogeneities and by other potential offset-derived distortions, owing to a combination of factors whose origin is discussed. Further features, extensions and applications of these principles are also addressed. PMID:21360603

  9. 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/.

  10. JULIDE: a software tool for 3D reconstruction and statistical analysis of autoradiographic mouse brain sections.

    PubMed

    Ribes, Delphine; Parafita, Julia; Charrier, Rémi; Magara, Fulvio; Magistretti, Pierre J; Thiran, Jean-Philippe

    2010-11-23

    In this article we introduce JULIDE, a software toolkit developed to perform the 3D reconstruction, intensity normalization, volume standardization by 3D image registration and voxel-wise statistical analysis of autoradiographs of mouse brain sections. This software tool has been developed in the open-source ITK software framework and is freely available under a GPL license. The article presents the complete image processing chain from raw data acquisition to 3D statistical group analysis. Results of the group comparison in the context of a study on spatial learning are shown as an illustration of the data that can be obtained with this tool.

  11. 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

  12. MRI and MRS of human brain tumors.

    PubMed

    Hou, Bob L; Hu, Jiani

    2009-01-01

    The purpose of this chapter is to provide an introduction to magnetic resonance imaging (MRI) and magnetic resonance spectroscopy (MRS) of human brain tumors, including the primary applications and basic terminology involved. Readers who wish to know more about this broad subject should seek out the referenced books (1. Tofts (2003) Quantitative MRI of the brain. Measuring changes caused by disease. Wiley; Bradley and Stark (1999) 2. Magnetic resonance imaging, 3rd Edition. Mosby Inc; Brown and Semelka (2003) 3. MRI basic principles and applications, 3rd Edition. Wiley-Liss) or reviews (4. Top Magn Reson Imaging 17:127-36, 2006; 5. JMRI 24:709-724, 2006; 6. Am J Neuroradiol 27:1404-1411, 2006).MRI is the most popular means of diagnosing human brain tumors. The inherent difference in the magnetic resonance (MR) properties of water between normal tissues and tumors results in contrast differences on the image that provide the basis for distinguishing tumors from normal tissues. In contrast to MRI, which provides spatial maps or images using water signals of the tissues, proton MRS detects signals of tissue metabolites. MRS can complement MRI because the observed MRS peaks can be linked to inherent differences in biochemical profiles between normal tissues and tumors.The goal of MRI and MRS is to characterize brain tumors, including tumor core, edge, edema, volume, types, and grade. The commonly used brain tumor MRI protocol includes T2-weighted images and T1-weighted images taken both before and after the injection of a contrast agent (typically gadolinium: Gd). The commonly used MRS technique is either point-resolved spectroscopy (PRESS) or stimulated echo acquisition mode (STEAM).

  13. 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

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

    PubMed

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

    2016-09-01

    Ultra-high-field MRI provides large increases in signal-to-noise ratio (SNR) 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, there 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 multichannel 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. Copyright © 2016 John Wiley & Sons, Ltd.

  15. 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. PMID:26231917

  16. 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.

  17. High-throughput 3D whole-brain quantitative histopathology in rodents

    PubMed Central

    Vandenberghe, Michel E.; Hérard, Anne-Sophie; Souedet, Nicolas; Sadouni, Elmahdi; Santin, Mathieu D.; Briet, Dominique; Carré, Denis; Schulz, Jocelyne; Hantraye, Philippe; Chabrier, Pierre-Etienne; Rooney, Thomas; Debeir, Thomas; Blanchard, Véronique; Pradier, Laurent; Dhenain, Marc; Delzescaux, Thierry

    2016-01-01

    Histology is the gold standard to unveil microscopic brain structures and pathological alterations in humans and animal models of disease. However, due to tedious manual interventions, quantification of histopathological markers is classically performed on a few tissue sections, thus restricting measurements to limited portions of the brain. Recently developed 3D microscopic imaging techniques have allowed in-depth study of neuroanatomy. However, quantitative methods are still lacking for whole-brain analysis of cellular and pathological markers. Here, we propose a ready-to-use, automated, and scalable method to thoroughly quantify histopathological markers in 3D in rodent whole brains. It relies on block-face photography, serial histology and 3D-HAPi (Three Dimensional Histology Analysis Pipeline), an open source image analysis software. We illustrate our method in studies involving mouse models of Alzheimer’s disease and show that it can be broadly applied to characterize animal models of brain diseases, to evaluate therapeutic interventions, to anatomically correlate cellular and pathological markers throughout the entire brain and to validate in vivo imaging techniques. PMID:26876372

  18. 3D Data Mapping and Real-Time Experiment Control and Visualization in Brain Slices.

    PubMed

    Navarro, Marco A; Hibbard, Jaime V K; Miller, Michael E; Nivin, Tyler W; Milescu, Lorin S

    2015-10-20

    Here, we propose two basic concepts that can streamline electrophysiology and imaging experiments in brain slices and enhance data collection and analysis. The first idea is to interface the experiment with a software environment that provides a 3D scene viewer in which the experimental rig, the brain slice, and the recorded data are represented to scale. Within the 3D scene viewer, the user can visualize a live image of the sample and 3D renderings of the recording electrodes with real-time position feedback. Furthermore, the user can control the instruments and visualize their status in real time. The second idea is to integrate multiple types of experimental data into a spatial and temporal map of the brain slice. These data may include low-magnification maps of the entire brain slice, for spatial context, or any other type of high-resolution structural and functional image, together with time-resolved electrical and optical signals. The entire data collection can be visualized within the 3D scene viewer. These concepts can be applied to any other type of experiment in which high-resolution data are recorded within a larger sample at different spatial and temporal coordinates.

  19. 3D Data Mapping and Real-Time Experiment Control and Visualization in Brain Slices.

    PubMed

    Navarro, Marco A; Hibbard, Jaime V K; Miller, Michael E; Nivin, Tyler W; Milescu, Lorin S

    2015-10-20

    Here, we propose two basic concepts that can streamline electrophysiology and imaging experiments in brain slices and enhance data collection and analysis. The first idea is to interface the experiment with a software environment that provides a 3D scene viewer in which the experimental rig, the brain slice, and the recorded data are represented to scale. Within the 3D scene viewer, the user can visualize a live image of the sample and 3D renderings of the recording electrodes with real-time position feedback. Furthermore, the user can control the instruments and visualize their status in real time. The second idea is to integrate multiple types of experimental data into a spatial and temporal map of the brain slice. These data may include low-magnification maps of the entire brain slice, for spatial context, or any other type of high-resolution structural and functional image, together with time-resolved electrical and optical signals. The entire data collection can be visualized within the 3D scene viewer. These concepts can be applied to any other type of experiment in which high-resolution data are recorded within a larger sample at different spatial and temporal coordinates. PMID:26488641

  20. 3D Slicer as a Tool for Interactive Brain Tumor Segmentation

    PubMed Central

    Kikinis, Ron; Pieper, Steve

    2014-01-01

    User interaction is required for reliable segmentation of brain tumors in clinical practice and in clinical research. By incorporating current research tools, 3D Slicer provides a set of easy to use interactive tools that can be efficiently used for this purpose. PMID:22255945

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

    PubMed Central

    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. PMID:25999810

  2. 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.

  3. 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

  4. Active-contour-model-based edge restriction and attraction field regularization for brain MRI segmentation

    NASA Astrophysics Data System (ADS)

    Luan, H.; Qi, Feihu

    2004-11-01

    Constructing 3D models of the object of interest from brain MRI is useful in numerous biomedical imaging application. In general, the construction of the 3D models is generally carried out according to the contours obtained from a 2D segmentation of each MR slice, so the equality of the 3D model strongly depends on the precision of the segmentation process. Active contour model is an effective edge-based method in segmenting an object of interest. However, its application, which segment boundary of anatomical structure of brain MRI, encounters many difficulties due to undesirable properties of brain MRI, for example complex background, intensity inhomogeneity and discontinuous edges. This paper proposes an active contour model to solve the problems of automatically segmenting the object of interest from a brain MRI. In this proposed algorithm, a new method of calculating attraction field has been developed. This method is based on edge restriction and attraction field regularization. Edge restriction introduces prior knowledge about the object of interest to free contours of being affected by edges of other anatomical structures or spurious edges, while attraction field regularization enables our algorithm to extract boundary correctly even at the place, where the edge of object of interest is discontinuous, by diffusing the edge information gotten after edge restriction. When we apply this proposed algorithm to brain MRI, the result shows this proposed algorithm could overcome those difficulties we mentioned above and convergence to object boundary quickly and accurately.

  5. 4T 7Li 3D MRSI in the brains of bipolar disorder subjects

    PubMed Central

    Lee, Jing-Huei; Adler, Caleb; Norris, Matthew; Chu, Wen-Jang; Fugate, Elizabeth M; Strakowski, Stephen M.; Komoroski, Richard A.

    2012-01-01

    This work demonstrates the first whole brain “high spatial resolution” 7Li MRSI in bipolar disorder subjects. The in vivo quantification is validated by a phantom containing 5 mM lithium salt using the identical RF sequence and imaging protocol. This study is the first demonstration of the 7Li distribution in the brain of bipolar disorder patients on lithium therapy using a 3D MRSI approach. The results show that brain lithium level is strongly correlated with serum lithium concentration. The brain-to-serum lithium ratio for the average brain and the local maximum were 0.39 ± 0.08 (r = 0.93) and 0.92 ± 0.16 (r= 0.90), respectively. The lithium distribution is found to be non-uniform throughout the brain for all patients, which is somewhat unexpected and highly intriguing. This uneven distribution is more evident in subjects at a higher therapeutic serum lithium level. This finding may suggest that lithium targets specific brain tissues and/or certain enzymatic and macromolecular sites that are associated with therapeutic effect. Further investigations of bipolar disorder patients on lithium therapy using 3D 7Li MRSI are warranted. PMID:22692991

  6. 3D brain atlas reconstructor service--online repository of three-dimensional models of brain structures.

    PubMed

    Majka, Piotr; Kowalski, Jakub M; Chlodzinska, Natalia; Wójcik, Daniel K

    2013-10-01

    Brain atlases are important tools of neuroscience. Traditionally prepared in paper book format, more and more commonly they take digital form which extends their utility. To simplify work with different atlases, to lay the ground for developing universal tools which could abstract from the origin of the atlas, efforts are being made to provide common interfaces to these atlases. 3D Brain Atlas Reconstructor service (3dBARs) described here is a repository of digital representations of different brain atlases in CAF format which we recently proposed and a repository of 3D models of brain structures. A graphical front-end is provided for creating and viewing the reconstructed models as well as the underlying 2D atlas data. An application programming interface (API) facilitates programmatic access to the service contents from other websites. From a typical user's point of view, 3dBARs offers an accessible way to mine publicly available atlasing data with a convenient browser based interface, without the need to install extra software. For a developer of services related to brain atlases, 3dBARs supplies mechanisms for enhancing functionality of other software. The policy of the service is to accept new datasets as delivered by interested parties and we work with the researchers who obtain original data to make them available to the neuroscience community at large. The functionality offered by the 3dBARs situates it at the core of present and future general atlasing services tying it strongly to the global atlasing neuroinformatics infrastructure. PMID:23943281

  7. 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.

  8. 3D of Brain Shape and Volume After Cranial Vault Remodeling Surgery for Craniosynostosis Correction in Infants

    PubMed Central

    Paniagua, Beatriz; Emodi, Omri; Hill, Jonathan; Fishbaugh, James; Pimenta, Luiz A; Aylward, Stephen R.; Andinet, Enquobahrie; Gerig, Guido; Gilmore, John; van Aalst, John A; Styner, Martin

    2013-01-01

    The skull of young children is made up of bony plates that enable growth. Craniosynostosis is a birth defect that causes one or more sutures on an infant’s skull to close prematurely. Corrective surgery focuses on cranial and orbital rim shaping to return the skull to a more normal shape. Functional problems caused by craniosynostosis such as speech and motor delay can improve after surgical correction, but a post-surgical analysis of brain development in comparison with age-matched healthy controls is necessary to assess surgical outcome. Full brain segmentations obtained from pre- and post-operative computed tomography (CT) scans of 8 patients with single suture sagittal (n=5) and metopic (n=3), non-syndromic craniosynostosis from 41 to 452 days-of-age were included in this study. Age-matched controls obtained via 4D acceleration-based regression of a cohort of 402 full brain segmentations from healthy controls magnetic resonance images (MRI) were also used for comparison (ages 38 to 825 days). 3D point-based models of patient and control cohorts were obtained using SPHARM-PDM shape analysis tool. From a full dataset of regressed shapes, 240 healthy regressed shapes between 30 and 588 days-of-age (time step = 2.34 days) were selected. Volumes and shape metrics were obtained for craniosynostosis and healthy age-matched subjects. Volumes and shape metrics in single suture craniosynostosis patients were larger than age-matched controls for pre- and post-surgery. The use of 3D shape and volumetric measurements show that brain growth is not normal in patients with single suture craniosynostosis. PMID:24465118

  9. 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.

  10. 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.

  11. 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

  12. Demonstration of Normal and Abnormal Fetal Brains Using 3D Printing from In Utero MR Imaging Data.

    PubMed

    Jarvis, D; Griffiths, P D; Majewski, C

    2016-09-01

    3D printing is a new manufacturing technology that produces high-fidelity models of complex structures from 3D computer-aided design data. Radiology has been particularly quick to embrace the new technology because of the wide access to 3D datasets. Models have been used extensively to assist orthopedic, neurosurgical, and maxillofacial surgical planning. In this report, we describe methods used for 3D printing of the fetal brain by using data from in utero MR imaging.

  13. Demonstration of Normal and Abnormal Fetal Brains Using 3D Printing from In Utero MR Imaging Data.

    PubMed

    Jarvis, D; Griffiths, P D; Majewski, C

    2016-09-01

    3D printing is a new manufacturing technology that produces high-fidelity models of complex structures from 3D computer-aided design data. Radiology has been particularly quick to embrace the new technology because of the wide access to 3D datasets. Models have been used extensively to assist orthopedic, neurosurgical, and maxillofacial surgical planning. In this report, we describe methods used for 3D printing of the fetal brain by using data from in utero MR imaging. PMID:27079366

  14. Prostate MRI and 3D MR Spectroscopy: How We Do It

    PubMed Central

    Verma, Sadhna; Rajesh, Arumugam; Fütterer, Jurgen J.; Turkbey, Baris; Scheenen, Tom W. J.; Pang, Yuxi; Choyke, Peter L.; Kurhanewicz, John

    2010-01-01

    OBJECTIVE This review is a primer on the technical aspects of performing a high-quality MRI and MR spectroscopic imaging examination of the prostate. CONCLUSION MRI and MR spectroscopic imaging are useful tools in the localization, staging, and functional assessment of prostate cancer. Performing a high-quality MR spectroscopic examination requires understanding of the technical aspects and limitations of spectral acquisition, postprocessing techniques, and spectral evaluation. PMID:20489079

  15. 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.

  16. Motion correction in MRI of the brain.

    PubMed

    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.

  17. 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.

  18. 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.

  19. Tissue Tracking: Applications for Brain MRI Classification

    PubMed Central

    Melonakos, John; Gao, Yi; Tannenbaum, Allen

    2013-01-01

    Bayesian classification methods have been extensively used in a variety of image processing applications, including medical image analysis. The basic procedure is to combine data-driven knowledge in the likelihood terms with clinical knowledge in the prior terms to classify an image into a pre-determined number of classes. In many applications, it is difficult to construct meaningful priors and, hence, homogeneous priors are assumed. In this paper, we show how expectation-maximization weights and neighboring posterior probabilities may be combined to make intuitive use of the Bayesian priors. Drawing upon insights from computer vision tracking algorithms, we cast the problem in a tissue tracking framework. We show results of our algorithm on the classification of gray and white matter along with surrounding cerebral spinal fluid in brain MRI scans. We show results of our algorithm on 20 brain MRI datasets along with validation against expert manual segmentations. PMID:24392193

  20. Tissue tracking: applications for brain MRI classification

    NASA Astrophysics Data System (ADS)

    Melonakos, John; Gao, Yi; Tannenbaum, Allen

    2007-03-01

    Bayesian classification methods have been extensively used in a variety of image processing applications, including medical image analysis. The basic procedure is to combine data-driven knowledge in the likelihood terms with clinical knowledge in the prior terms to classify an image into a pre-determined number of classes. In many applications, it is difficult to construct meaningful priors and, hence, homogeneous priors are assumed. In this paper, we show how expectation-maximization weights and neighboring posterior probabilities may be combined to make intuitive use of the Bayesian priors. Drawing upon insights from computer vision tracking algorithms, we cast the problem in a tissue tracking framework. We show results of our algorithm on the classification of gray and white matter along with surrounding cerebral spinal fluid in brain MRI scans. We show results of our algorithm on 20 brain MRI datasets along with validation against expert manual segmentations.

  1. 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

  2. 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.

  3. Neuroinformatics for genome-wide 3D gene expression mapping in the mouse brain.

    PubMed

    Ng, Lydia; Pathak, Sayan D; Kuan, Chihchau; Lau, Chris; Dong, Hongwei; Sodt, Andrew; Dang, Chinh; Avants, Brian; Yushkevich, Paul; Gee, James C; Haynor, David; Lein, Ed; Jones, Allan; Hawrylycz, Mike

    2007-01-01

    Large scale gene expression studies in the mammalian brain offer the promise of understanding the topology, networks and ultimately the function of its complex anatomy, opening previously unexplored avenues in neuroscience. High-throughput methods permit genome-wide searches to discover genes that are uniquely expressed in brain circuits and regions that control behavior. Previous gene expression mapping studies in model organisms have employed situ hybridization (ISH), a technique that uses labeled nucleic acid probes to bind to specific mRNA transcripts in tissue sections. A key requirement for this effort is the development of fast and robust algorithms for anatomically mapping and quantifying gene expression for ISH. We describe a neuroinformatics pipeline for automatically mapping expression profiles of ISH data and its use to produce the first genomic scale 3-D mapping of gene expression in a mammalian brain. The pipeline is fully automated and adaptable to other organisms and tissues. Our automated study of over 20,000 genes indicates that at least 78.8 percent are expressed at some level in the adult C56BL/6J mouse brain. In addition to providing a platform for genomic scale search, high-resolution images and visualization tools for expression analysis are available at the Allen Brain Atlas web site (http://www.brain-map.org).

  4. 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

    2013-01-01

    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

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

    PubMed

    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. 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

  7. 3D Quantification of Wall Shear Stress and Oscillatory Shear Index Using a Finite-Element Method in 3D CINE PC-MRI Data of the Thoracic Aorta.

    PubMed

    Sotelo, Julio; Urbina, Jesus; Valverde, Israel; Tejos, Cristian; Irarrazaval, Pablo; Andia, Marcelo E; Uribe, Sergio; Hurtado, Daniel E

    2016-06-01

    Several 2D methods have been proposed to estimate WSS and OSI from PC-MRI, neglecting the longitudinal velocity gradients that typically arise in cardiovascular flow, particularly on vessel geometries whose cross section and centerline orientation strongly vary in the axial direction. Thus, the contribution of longitudinal velocity gradients remains understudied. In this work, we propose a 3D finite-element method for the quantification of WSS and OSI from 3D-CINE PC-MRI that accounts for both in-plane and longitudinal velocity gradients. We demonstrate the convergence and robustness of the method on cylindrical geometries using a synthetic phantom based on the Poiseuille flow equation. We also show that, in the presence of noise, the method is both stable and accurate. Using computational fluid dynamics simulations, we show that the proposed 3D method results in more accurate WSS estimates than those obtained from a 2D analysis not considering out-of-plane velocity gradients. Further, we conclude that for irregular geometries the accurate prediction of WSS requires the consideration of longitudinal gradients in the velocity field. Additionally, we compute 3D maps of WSS and OSI for 3D-CINE PC-MRI data sets from an aortic phantom and sixteen healthy volunteers and two patients. The OSI values show a greater dispersion than WSS, which is strongly dependent on the PC-MRI resolution. We envision that the proposed 3D method will improve the estimation of WSS and OSI from 3D-CINE PC-MRI images, allowing for more accurate estimates in vessels with pathologies that induce high longitudinal velocity gradients, such as coarctations and aneurisms.

  8. 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. PMID:26930054

  9. NOTE: A 3D MRI sequence for computer assisted surgery of the lumbar spine

    NASA Astrophysics Data System (ADS)

    Hoad, C. L.; Martel, A. L.; Kerslake, R.; Grevitt, M.

    2001-08-01

    The aim of this research was to develop a magnetic resonance (MR) sequence capable of producing images suitable for use with computer assisted surgery (CAS) of the lumbar spine. These images needed good tissue contrast between bone and soft tissue to allow for image segmentation and generation of a 3D-surface model of the bone for surface registration. A 3D double echo fast gradient echo sequence was designed. Images were filtered for noise and non-uniformity and combined into a single data set. Registration experiments were carried out to directly compare segmentation of MR and computed tomography (CT) images using a physical model of a spine. These experiments showed the MR data produced adequate surface registration in 90% of the experiments compared to 100% with CT data. The MR images acquired using the sequence and processing described in this article are suitable to be used with CAS of the spine.

  10. Functional neurology of a brain system: a 3D olfactory bulb model to process natural odorants.

    PubMed

    Migliore, Michele; Cavarretta, Francesco; Hines, Michael L; Shepherd, Gordon M

    2013-01-01

    The network of interactions between mitral and granule cells in the olfactory bulb is a critical step in the processing of odor information underlying the neural basis of smell perception. We are building the first computational model in 3 dimensions of this network in order to analyze the rules for connectivity and function within it. The initial results indicate that this network can be modeled to simulate experimental results on the activation of the olfactory bulb by natural odorants, providing a much more powerful approach for 3D simulation of brain neurons and microcircuits.

  11. Free-breathing 3D cardiac MRI using iterative image-based respiratory motion correction.

    PubMed

    Moghari, Mehdi H; Roujol, Sébastien; Chan, Raymond H; Hong, Susie N; Bello, Natalie; Henningsson, Markus; Ngo, Long H; Goddu, Beth; Goepfert, Lois; Kissinger, Kraig V; Manning, Warren J; Nezafat, Reza

    2013-10-01

    Respiratory motion compensation using diaphragmatic navigator gating with a 5 mm gating window is conventionally used for free-breathing cardiac MRI. Because of the narrow gating window, scan efficiency is low resulting in long scan times, especially for patients with irregular breathing patterns. In this work, a new retrospective motion compensation algorithm is presented to reduce the scan time for free-breathing cardiac MRI that increasing the gating window to 15 mm without compromising image quality. The proposed algorithm iteratively corrects for respiratory-induced cardiac motion by optimizing the sharpness of the heart. To evaluate this technique, two coronary MRI datasets with 1.3 mm(3) resolution were acquired from 11 healthy subjects (seven females, 25 ± 9 years); one using a navigator with a 5 mm gating window acquired in 12.0 ± 2.0 min and one with a 15 mm gating window acquired in 7.1 ± 1.0 min. The images acquired with a 15 mm gating window were corrected using the proposed algorithm and compared to the uncorrected images acquired with the 5 and 15 mm gating windows. The image quality score, sharpness, and length of the three major coronary arteries were equivalent between the corrected images and the images acquired with a 5 mm gating window (P-value > 0.05), while the scan time was reduced by a factor of 1.7. PMID:23132549

  12. 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.

  13. Model-based 3-D segmentation of multiple sclerosis lesions in dual-echo MRI data

    NASA Astrophysics Data System (ADS)

    Kamber, Micheline; Collins, D. Louis; Shinghal, Rajjan; Francis, G. S.; Evans, Alan C.

    1992-09-01

    This paper describes the development and use of a brain tissue probability model for the segmentation of multiple sclerosis lesions in magnetic resonance (MR) images of the human brain. Based on MR data obtained from a group of healthy volunteers, the model was constructed to provide prior probabilities of grey matter, white matter, ventricular cerebrospinal fluid (CSF), and external CSF distribution per unit voxel in a standardized 3- dimensional `brain space.' In comparison to purely data-driven segmentation, the use of the model to guide the segmentation of multiple sclerosis lesions reduced the volume of false positive lesions by 50%.

  14. Proton HR-MAS spectroscopy and quantitative pathologic analysis of MRI/3D-MRSI-targeted postsurgical prostate tissues.

    PubMed

    Swanson, Mark G; Vigneron, Daniel B; Tabatabai, Z Laura; Males, Ryan G; Schmitt, Lars; Carroll, Peter R; James, Joyce K; Hurd, Ralph E; Kurhanewicz, John

    2003-11-01

    Proton high-resolution magic angle spinning ((1)H HR-MAS) NMR spectroscopy and quantitative histopathology were performed on the same 54 MRI/3D-MRSI-targeted postsurgical prostate tissue samples. Presurgical MRI/3D-MRSI targeted healthy and malignant prostate tissues with an accuracy of 81%. Even in the presence of substantial tissue heterogeneity, distinct (1)H HR-MAS spectral patterns were observed for different benign tissue types and prostate cancer. Specifically, healthy glandular tissue was discriminated from prostate cancer based on significantly higher levels of citrate (P = 0.04) and polyamines (P = 0.01), and lower (P = 0.02) levels of the choline-containing compounds choline, phosphocholine (PC), and glycerophosphocholine (GPC). Predominantly stromal tissue lacked both citrate and polyamines, but demonstrated significantly (P = 0.01) lower levels of choline compounds than cancer. In addition, taurine, myo-inositol, and scyllo-inositol were all higher in prostate cancer vs. healthy glandular and stromal tissues. Among cancer samples, larger increases in choline, and decreases in citrate and polyamines (P = 0.05) were observed with more aggressive cancers, and a MIB-1 labeling index correlated (r = 0.62, P = 0.01) with elevated choline. The elucidation of spectral patterns associated with mixtures of different prostate tissue types and cancer grades, and the inclusion of new metabolic markers for prostate cancer may significantly improve the clinical interpretation of in vivo prostate MRSI data.

  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. The Digital Bee Brain: Integrating and Managing Neurons in a Common 3D Reference System

    PubMed Central

    Rybak, Jürgen; Kuß, Anja; Lamecker, Hans; Zachow, Stefan; Hege, Hans-Christian; Lienhard, Matthias; Singer, Jochen; Neubert, Kerstin; Menzel, Randolf

    2010-01-01

    The honeybee standard brain (HSB) serves as an interactive tool for relating morphologies of bee brain neurons and provides a reference system for functional and bibliographical properties (http://www.neurobiologie.fu-berlin.de/beebrain/). The ultimate goal is to document not only the morphological network properties of neurons collected from separate brains, but also to establish a graphical user interface for a neuron-related data base. Here, we review the current methods and protocols used to incorporate neuronal reconstructions into the HSB. Our registration protocol consists of two separate steps applied to imaging data from two-channel confocal microscopy scans: (1) The reconstruction of the neuron, facilitated by an automatic extraction of the neuron's skeleton based on threshold segmentation, and (2) the semi-automatic 3D segmentation of the neuropils and their registration with the HSB. The integration of neurons in the HSB is performed by applying the transformation computed in step (2) to the reconstructed neurons of step (1). The most critical issue of this protocol in terms of user interaction time – the segmentation process – is drastically improved by the use of a model-based segmentation process. Furthermore, the underlying statistical shape models (SSM) allow the visualization and analysis of characteristic variations in large sets of bee brain data. The anatomy of neural networks composed of multiple neurons that are registered into the HSB are visualized by depicting the 3D reconstructions together with semantic information with the objective to integrate data from multiple sources (electrophysiology, imaging, immunocytochemistry, molecular biology). Ultimately, this will allow the user to specify cell types and retrieve their morphologies along with physiological characterizations. PMID:20827403

  17. 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.

  18. 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. PMID:26424492

  19. 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.

  20. 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.

  1. Prospective motion correction of 3D echo-planar imaging data for functional MRI using optical tracking.

    PubMed

    Todd, Nick; Josephs, Oliver; Callaghan, Martina F; Lutti, Antoine; Weiskopf, Nikolaus

    2015-06-01

    We evaluated the performance of an optical camera based prospective motion correction (PMC) system in improving the quality of 3D echo-planar imaging functional MRI data. An optical camera and external marker were used to dynamically track the head movement of subjects during fMRI scanning. PMC was performed by using the motion information to dynamically update the sequence's RF excitation and gradient waveforms such that the field-of-view was realigned to match the subject's head movement. Task-free fMRI experiments on five healthy volunteers followed a 2 × 2 × 3 factorial design with the following factors: PMC on or off; 3.0mm or 1.5mm isotropic resolution; and no, slow, or fast head movements. Visual and motor fMRI experiments were additionally performed on one of the volunteers at 1.5mm resolution comparing PMC on vs PMC off for no and slow head movements. Metrics were developed to quantify the amount of motion as it occurred relative to k-space data acquisition. The motion quantification metric collapsed the very rich camera tracking data into one scalar value for each image volume that was strongly predictive of motion-induced artifacts. The PMC system did not introduce extraneous artifacts for the no motion conditions and improved the time series temporal signal-to-noise by 30% to 40% for all combinations of low/high resolution and slow/fast head movement relative to the standard acquisition with no prospective correction. The numbers of activated voxels (p<0.001, uncorrected) in both task-based experiments were comparable for the no motion cases and increased by 78% and 330%, respectively, for PMC on versus PMC off in the slow motion cases. The PMC system is a robust solution to decrease the motion sensitivity of multi-shot 3D EPI sequences and thereby overcome one of the main roadblocks to their widespread use in fMRI studies.

  2. Prospective motion correction of 3D echo-planar imaging data for functional MRI using optical tracking

    PubMed Central

    Todd, Nick; Josephs, Oliver; Callaghan, Martina F.; Lutti, Antoine; Weiskopf, Nikolaus

    2015-01-01

    We evaluated the performance of an optical camera based prospective motion correction (PMC) system in improving the quality of 3D echo-planar imaging functional MRI data. An optical camera and external marker were used to dynamically track the head movement of subjects during fMRI scanning. PMC was performed by using the motion information to dynamically update the sequence's RF excitation and gradient waveforms such that the field-of-view was realigned to match the subject's head movement. Task-free fMRI experiments on five healthy volunteers followed a 2 × 2 × 3 factorial design with the following factors: PMC on or off; 3.0 mm or 1.5 mm isotropic resolution; and no, slow, or fast head movements. Visual and motor fMRI experiments were additionally performed on one of the volunteers at 1.5 mm resolution comparing PMC on vs PMC off for no and slow head movements. Metrics were developed to quantify the amount of motion as it occurred relative to k-space data acquisition. The motion quantification metric collapsed the very rich camera tracking data into one scalar value for each image volume that was strongly predictive of motion-induced artifacts. The PMC system did not introduce extraneous artifacts for the no motion conditions and improved the time series temporal signal-to-noise by 30% to 40% for all combinations of low/high resolution and slow/fast head movement relative to the standard acquisition with no prospective correction. The numbers of activated voxels (p < 0.001, uncorrected) in both task-based experiments were comparable for the no motion cases and increased by 78% and 330%, respectively, for PMC on versus PMC off in the slow motion cases. The PMC system is a robust solution to decrease the motion sensitivity of multi-shot 3D EPI sequences and thereby overcome one of the main roadblocks to their widespread use in fMRI studies. PMID:25783205

  3. 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.

  4. Whole-brain quantitative mapping of metabolites using short echo 3D-proton- MRSI

    PubMed Central

    Lecocq, Angèle; Le Fur, Yann; Maudsley, Andrew A; Le Troter, Arnaud; Sheriff, Sulaiman; Sabati, Mohamad; Donnadieu, Maxime; Confort-Gouny, Sylviane; Cozzone, Patrick J.; Guye, Maxime; Ranjeva, Jean-Philippe

    2014-01-01

    Purpose To improve the extent over which whole brain quantitative 3D-MRSI maps can be obtained and be used to explore brain metabolism in a population of healthy volunteers. Materials and Methods Two short TE (20 ms) acquisitions of 3D Echo Planar Spectroscopic Imaging at two orientations, one in the anterior commissure – posterior commissure (AC-PC) plane and the second tilted in the AC-PC +15° plane were obtained at 3T in a group of ten healthy volunteers. B1+, B1−, and B0 correction procedures and normalization of metabolite signals with quantitative water proton density measurements were performed. A combination of the two spatially normalized 3D-MRSI, using a weighted mean based on the pixel wise standard deviation metabolic maps of each orientation obtained from the whole group, provided metabolite maps for each subject allowing regional metabolic profiles of all parcels of the automated anatomical labeling (AAL) atlas to be obtained. Results The combined metabolite maps derived from the two acquisitions reduced the regional inter-subject variance. The numbers of AAL regions showing NAA SD/Mean ratios lower than 30% increased from 17 in the AC-PC orientation and 41 in the AC-PC+15° orientation, to a value of 76 regions out of 116 for the combined NAA maps. Quantitatively, regional differences in absolute metabolite concentrations (mM) over the whole brain were depicted such as in the GM of frontal lobes (cNAA=10.03+1.71, cCho=1.78±0.55, cCr=7.29±1.69; cmIns=5.30±2.67) and in cerebellum (cNAA=5.28±1.77, cCho=1.60±0.41, cCr=6.95±2.15; cmIns=3.60±0.74). Conclusion A double-angulation acquisition enables improved metabolic characterization over a wide volume of the brain. PMID:25431032

  5. 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

  6. Computer-based automatic identification of neurons in gigavoxel-sized 3D human brain images.

    PubMed

    Soda, Paolo; Acciai, Ludovica; Cordelli, Ermanno; Costantini, Irene; Sacconi, Leonardo; Pavone, Francesco Saverio; Conti, Valerio; Guerrini, Renzo; Frasconi, Paolo; Iannello, Giulio

    2015-01-01

    Achieving a comprehensive knowledge of the human brain cytoarchitecture is a fundamental step to understand how the nervous system works, i.e., one of the greatest challenge of 21(st) century science. The recent development of biological tissue labeling and automated microscopic imaging systems has permitted to acquire images at the micro-resolution, which produce a huge quantity of data that cannot be manually analyzed. In case of mammals brain, automatic methods to extract objective information at the microscale have been applied until now to mice, macaque and cat 3D volume images. Here we report a method to automatically localize neurons in a sample of human brain removed during a surgical procedure for the treatments of drug resistant epilepsy in a child with hemimegalencephaly, whose neurons and neurites were fluorescence labelled and finally imaged using the two-photon fluorescence microscope. The method provides the map of both parvalbuminergic neurons and all other cells nuclei with a satisfactory f-score measured using more than two thousand human labelled soma. PMID:26738082

  7. Estimation of 3D myocardial motion from tagged MRI using LDDMM

    NASA Astrophysics Data System (ADS)

    Kotamraju, Vinay; McVeigh, Elliot; Beg, Mirza Faisal

    2007-03-01

    Non-invasive estimation of regional cardiac function is important for assessment of myocardial contractility. The use of MR tagging technique enables acquisition of intra-myocardial tissue motion by placing a spatially modulated pattern of magnetization whose deformation with the myocardium over the cardiac cycle can be imaged. Quantitative computation of parameters such as wall thickening, shearing, rotation, torsion and strain within the myocardium is traditionally achieved by processing the tag-marked MR image frames to 1) segment the tag lines and 2) detect the correspondence between points across the time-indexed frames. In this paper, we describe our approach to solving this problem using the Large Deformation Diffeomorphic Metric Mapping (LDDMM) algorithm in which tag-line segmentation and motion reconstruction occur simultaneously. Our method differs from earlier proposed non rigid registration based cardiac motion estimation methods in that our matching cost incorporates image intensity overlap via the L2 norm and the estimated tranformations are diffeomorphic. We also present a novel method of generating synthetic tag line images with known ground truth and motion characteristics that closely follow those in the original data; these can be used for validation of motion estimation algorithms. Initial validation shows that our method is able to accurately segment tag-lines and estimate a dense 3D motion field describing the motion of the myocardium in both the left and the right ventricle.

  8. Comparison of parallel and spiral tagged MRI geometries in estimation of 3-D myocardial strains

    NASA Astrophysics Data System (ADS)

    Tustison, Nicholas J.; Amini, Amir A.

    2005-04-01

    Research involving the quantification of left ventricular myocardial strain from cardiac tagged magnetic resonance imaging (MRI) is extensive. Two different imaging geometries are commonly employed by these methodologies to extract longitudinal deformation. We refer to these imaging geometries as either parallel or spiral. In the spiral configuration, four long-axis tagged image slices which intersect along the long-axis of the left ventricle are collected and in the parallel configuration, contiguous tagged long-axis images spanning the width of the left ventricle between the lateral wall and the septum are collected. Despite the number of methodologies using either or both imaging configurations, to date, no comparison has been made to determine which geometry results in more accurate estimation of strains. Using previously published work in which left ventricular myocardial strain is calculated from 4-D anatomical NURBS models, we compare the strain calculated from these two imaging geometries in both simulated tagged MR images for which ground truth strain is available as well as in in vivo data. It is shown that strains calculated using the parallel imaging protocol are more accurate than that calculated using spiral protocol.

  9. 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.

  10. 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

  11. 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.

  12. 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

  13. 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

  14. Qualitative Evaluation of a High-Resolution 3D Multi-Sequence Intracranial Vessel Wall Protocol at 3 Tesla MRI

    PubMed Central

    Yang, Wenjie; van der Kolk, Anja G.; Abrigo, Jill; Lee, Ka Lok; Chu, Winnie Chiu Wing; Zwanenburg, Jaco J. M.; Siero, Jeroen C. W.; Wong, Ka Sing; Hendrikse, Jeroen; Chen, Fiona Xiang Yan

    2016-01-01

    Background and Purpose Intracranial vessel wall imaging using MRI has great potential as a clinical method for assessing intracranial atherosclerosis. The purpose of the current study was to compare three 3T MRI vessel wall sequences with different contrast weightings (T1w, PD, T2w) and dedicated sagittal orientation perpendicular to the middle cerebral artery, to the reconstructed sagittal image from a transverse 3D T1w volumetric isotropically reconstructed turbo spin-echo acquisition (VIRTA), and provide a clinical recommendation. Materials and Methods The above-mentioned sequences were acquired in 10 consecutive Chinese ischemic stroke or TIA patients (age: 68 years, sex: 4 females) with angiographic-confirmed MCA stenosis at 3T. Institutional review board approval was obtained. Two raters qualitatively scored all images on overall image quality, presence of artifacts, and visibility of plaques. Data were compared using Repeated measures ANOVA and Sidak’s adjusted post hoc tests. Results All sequences except the T2w sequence were able to depict the walls of the large vessels of the Circle of Willis (p<0.05). T1w sagittal oblique VIRTA showed significantly more artifacts (p<0.01). Peripherally located plaques were sometimes missed on the sagittal sequences, but could be appreciated on the transverse T1w VIRTA. Conclusion With the 3T multi-sequence vessel wall protocol we were able to assess the intracranial plaque with two different image contrast weightings. The sequence of preference to include in a clinical protocol would be the transverse 3D T1w VIRTA based on absence of artifacts, larger coverage including the whole Circle of Willis, and excellent lesion depiction. PMID:27532106

  15. MRI of brain disease in veterinary patients part 1: Basic principles and congenital brain disorders.

    PubMed

    Hecht, Silke; Adams, William H

    2010-01-01

    Magnetic resonance imaging (MRI) is increasingly being used in the diagnosis of central nervous system disorders in veterinary patients and is quickly becoming the imaging modality of choice in evaluation of brain and intracranial disease. This article provides an overview of the basic principles of MRI, a description of sequences and their applications in brain imaging, and an approach to interpretation of brain MRI. A detailed discussion of imaging findings in general intracranial disorders including hydrocephalus, vasogenic edema, brain herniation, and seizure-associated changes, and the MR diagnosis of congenital brain disorders is provided. MRI evaluation of acquired brain disorders is described in a second companion article.

  16. 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.

  17. Skin Dose in Longitudinal and Transverse Linac-MRIs using Monte-Carlo and realistic 3D MRI field models

    NASA Astrophysics Data System (ADS)

    Keyvanloo Shahrestanaky, Amirmohamad

    The integration of a clinical linear accelerator (linac) with a magnetic resonance imaging (MRI) system would provide real-time tumor tracking. The magnetic fields of linac-MR systems modify the path of contaminant electrons in photon beams, which alters patient skin dose. In this work, we used Monte Carlo calculations that incorporate realistic 3D magnetic field models of longitudinal and transverse linac-MR systems to accurately quantify the changes in skin dose. The results show that fringe fields of realistic 3D B-fields decay rapidly and have a very small magnitude at the linac’s head. As a result, for longitudinal linac-MR systems only a small increase in the entrance skin dose is predicted. For transverse linac-MR systems, changes to the entrance skin dose are small for most scenarios. On the exit side, however, a fairly large increase is observed for perpendicular beams due to the electron return effect, but significantly drops for large oblique angles of incidence.

  18. Studying brain organization via spontaneous fMRI signal.

    PubMed

    Power, Jonathan D; Schlaggar, Bradley L; Petersen, Steven E

    2014-11-19

    In recent years, some substantial advances in understanding human (and nonhuman) brain organization have emerged from a relatively unusual approach: the observation of spontaneous activity, and correlated patterns in spontaneous activity, in the "resting" brain. Most commonly, spontaneous neural activity is measured indirectly via fMRI signal in subjects who are lying quietly in the scanner, the so-called "resting state." This Primer introduces the fMRI-based study of spontaneous brain activity, some of the methodological issues active in the field, and some ways in which resting-state fMRI has been used to delineate aspects of area-level and supra-areal brain organization.

  19. 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

  20. Pseudo-progression after stereotactic radiotherapy of brain metastases: lesion analysis using MRI cine-loops.

    PubMed

    Wiggenraad, Ruud; Bos, Petra; Verbeek-de Kanter, Antoinette; Lycklama À Nijeholt, Geert; van Santvoort, Jan; Taphoorn, Martin; Struikmans, Henk

    2014-09-01

    Stereotactic radiotherapy (SRT) of brain metastasis can lead to lesion growth caused by radiation toxicity. The pathophysiology of this so-called pseudo-progression is poorly understood. The purpose of this study was to evaluate the use of MRI cine-loops for describing the consecutive events in this radiation induced lesion growth. Ten patients were selected from our department's database that had received SRT of brain metastases and had lesion growth caused by pseudo-progression as well as at least five follow-up MRI scans. Pre- and post SRT MRI scans were co-registered and cine-loops were made using post-gadolinium 3D T1 axial slices. The ten cine loops were discussed in a joint meeting of the authors. The use of cine-loops was superior to evaluation of separate MRI scans for interpretation of events after SRT. There was a typical lesion evolution pattern in all patients with varying time course. Initially regression of the metastases was observed, followed by an enlarging area of new contrast enhancement in the surrounding brain tissue. Analysis of consecutive MRI's using cine-loops may improve understanding of pseudo-progression. It probably represents a radiation effect in brain tissue surrounding the irradiated metastasis and not enlargement of the metastasis itself.

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

    PubMed Central

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

    2015-01-01

    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. PMID:25914510

  2. 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.

  3. 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.

  4. Framework for 3D histologic reconstruction and fusion with in vivo MRI: Preliminary results of characterizing pulmonary inflammation in a mouse model

    PubMed Central

    Rusu, Mirabela; Golden, Thea; Wang, Haibo; Gow, Andrew; Madabhushi, Anant

    2015-01-01

    Purpose: Pulmonary inflammation is associated with a variety of diseases. Assessing pulmonary inflammation on in vivo imaging may facilitate the early detection and treatment of lung diseases. Although routinely used in thoracic imaging, computed tomography has thus far not been compellingly shown to characterize inflammation in vivo. Alternatively, magnetic resonance imaging (MRI) is a nonionizing radiation technique to better visualize and characterize pulmonary tissue. Prior to routine adoption of MRI for early characterization of inflammation in humans, a rigorous and quantitative characterization of the utility of MRI to identify inflammation is required. Such characterization may be achieved by considering ex vivo histology as the ground truth, since it enables the definitive spatial assessment of inflammation. In this study, the authors introduce a novel framework to integrate 2D histology, ex vivo and in vivo imaging to enable the mapping of the extent of disease from ex vivo histology onto in vivo imaging, with the goal of facilitating computerized feature analysis and interrogation of disease appearance on in vivo imaging. The authors’ framework was evaluated in a preclinical preliminary study aimed to identify computer extracted features on in vivo MRI associated with chronic pulmonary inflammation. Methods: The authors’ image analytics framework first involves reconstructing the histologic volume in 3D from individual histology slices. Second, the authors map the disease ground truth onto in vivo MRI via coregistration with 3D histology using the ex vivo lung MRI as a conduit. Finally, computerized feature analysis of the disease extent is performed to identify candidate in vivo imaging signatures of disease presence and extent. Results: The authors evaluated the framework by assessing the quality of the 3D histology reconstruction and the histology—MRI fusion, in the context of an initial use case involving characterization of chronic

  5. MRI of Blood–Brain Barrier Permeability in Cerebral Ischemia

    PubMed Central

    Ewing, James R.; Chopp, Michael

    2013-01-01

    Quantitative measurement of blood–brain barrier (BBB) permeability using MRI and its application to cerebral ischemia are reviewed. Measurement of BBB permeability using MRI has been employed to evaluate ischemic damage during acute and subacute phases of stroke and to predict hemorrhagic transformation. There is also an emerging interest on the development and use of MRI to monitor vascular structural changes and angiogenesis during stroke recovery. In this review, we describe MRI BBB permeability and susceptibility-weighted MRI measurements and its applications to evaluate ischemic damage during the acute and subacute phases of stroke and vascular remodeling during stroke recovery. PMID:23997835

  6. Postmortem diffusion MRI of the human brainstem and thalamus for deep brain stimulator electrode localization.

    PubMed

    Calabrese, Evan; Hickey, Patrick; Hulette, Christine; Zhang, Jingxian; Parente, Beth; Lad, Shivanand P; Johnson, G Allan

    2015-08-01

    Deep brain stimulation (DBS) is an established surgical therapy for medically refractory tremor disorders including essential tremor (ET) and is currently under investigation for use in a variety of other neurologic and psychiatric disorders. There is growing evidence that the anti-tremor effects of DBS for ET are directly related to modulation of the dentatorubrothalamic tract (DRT), a white matter pathway that connects the cerebellum, red nucleus, and ventral intermediate nucleus of the thalamus. Emerging white matter targets for DBS, like the DRT, will require improved three-dimensional (3D) reference maps of deep brain anatomy and structural connectivity for accurate electrode targeting. High-resolution diffusion MRI of postmortem brain specimens can provide detailed volumetric images of important deep brain nuclei and 3D reconstructions of white matter pathways with probabilistic tractography techniques. We present a high spatial and angular resolution diffusion MRI template of the postmortem human brainstem and thalamus with 3D reconstructions of the nuclei and white matter tracts involved in ET circuitry. We demonstrate registration of these data to in vivo, clinical images from patients receiving DBS therapy, and correlate electrode proximity to tractography of the DRT with improvement of ET symptoms. PMID:26043869

  7. Assessment of left and right atrial 3D hemodynamics in patients with atrial fibrillation: a 4D flow MRI study.

    PubMed

    Markl, Michael; Carr, Maria; Ng, Jason; Lee, Daniel C; Jarvis, Kelly; Carr, James; Goldberger, Jeffrey J

    2016-05-01

    Atrial fibrillation (AF) is associated with embolic stroke due to thrombus formation in the left atrium (LA). Based on the relationship of atrial stasis to thromboembolism and the marked disparity in pulmonary versus systemic thromboembolism in AF, we tested the hypothesis that flow velocity distributions in the left (LA) versus right atrium (RA) in patients with would demonstrate increased stasis. Whole heart 4D flow MRI was performed in 62 AF patients (n = 33 in sinus rhythm during imaging, n = 29 with persistent AF) and 8 controls for the assessment of in vivo atrial 3D blood flow. 3D segmentation of the LA and RA geometry and normalized velocity histograms assessed atrial velocity distribution and stasis (% of atrial velocities <0.2 m/s). Atrial hemodynamics were similar for RA and LA and significantly correlated (mean velocity: r = 0.64; stasis: r = 0.55, p < 0.001). RA and LA mean and median velocities were lower in AF patients by 15-33 % and stasis was elevated by 11-19 % compared to controls. There was high inter-individual variability in LA/RA mean velocity ratio (range 0.5-1.8) and LA/RA stasis ratio (range 0.7-1.7). Patients with a history of AF and in sinus rhythm showed most pronounced differences in atrial flow (reduced mean velocities, higher stasis in the LA). While there is no systematic difference in LA versus RA flow velocity profiles, high variability was noted. Further delineation of patient specific factors and/or regional atrial effects on the LA and RA flow velocity profiles, as well as other factors such as differences in procoagulant factors, may explain the more prevalent systemic versus pulmonary thromboembolism in patients with AF. PMID:26820740

  8. On the Significance of Motion Degradation in High-Resolution 3D μMRI of Trabecular Bone

    PubMed Central

    Bhagat, Yusuf A.; Rajapakse, Chamith S.; Magland, Jeremy F.; Wald, Michael J.; Song, Hee Kwon; Leonard, Mary B.; Wehrli, Felix W.

    2011-01-01

    Rationale and Objectives Subtle subject movement during high-resolution 3D μMR imaging of trabecular bone (TB) causes blurring, thereby rendering the data unreliable for quantitative analysis. In this work, the effects of translational and rotational motion displacements have been evaluated qualitatively and quantitatively. Materials and Methods In Experiment I, motion was induced by applying various simulated and previously observed in vivo trajectories as phase shifts to k-space or rotation angles to k-space segments of a virtually motion-free data set. In Experiment II, images that were visually free of motion artifacts from two groups of 10 healthy individuals, differing in age, were selected for probing the effects of motion on TB parameters. In both experiments, images were rated for motion severity and the scores were compared to a focus criterion, the normalized gradient squared (NGS). Results Strong correlations were observed between the motion quality scores and the corresponding NGS values (R2= 0.52–0.64; p<0.01). The results from Experiment I demonstrated consistently lower image quality and alterations in structural parameters of 9–45% with increased amplitude of displacements. In Experiment II, the significant differences in structural parameter group means of the motion-free images were lost upon motion degradation. Autofocusing, a post-processing correction method, partially recovered the sharpness of the original motion-free images in 13/20 subjects. Conclusion Quantitative TB structural measures are highly sensitive to subtle motion-induced degradation which adversely affects precision and statistical power. The results underscore the influence of subject movement in high-resolution 3D μMRI and its correction for TB structure analysis. PMID:21816638

  9. 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.

  10. 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.

  11. 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. PMID:26496803

  12. 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

  13. MRI segmentation of the human brain: challenges, methods, and applications.

    PubMed

    Despotović, Ivana; Goossens, Bart; Philips, Wilfried

    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.

  14. 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.

  15. 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

  16. 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.

  17. Quantitative MRI Measures in SIV-Infected Macaque Brains.

    PubMed

    Zhang, Xiaodong; Li, Chunxia

    2013-01-01

    Multiple MRI modalities including Diffusion Tensor Imaging (DTI), perfusion MRI, in vivo MR Spectroscopy (MRS), volumetric MRI, contrast-enhanced MRI, and functional MRI have demonstrated abnormalities of the structural and functional integrity as well as neurochemical alterations of the HIV-infected central nervous system (CNS). MRI has been proposed as a robust imaging approach for the characterization of the stage of progression in HIV infection. However, the interpretation of the MRI findings of HIV patients is complicated by the fact that these clinical studies cannot readily be controlled. Simian immunodeficiency virus (SIV) infected macaques exhibit neuropathological symptoms similar to those of HIV patients, and are an important model for studying the course of CNS infection, cognitive impairment, and neuropathology of HIV disease as well as treatment efficacy. MRI of non-human primates (NHPs) is of limited benefit on most clinical scanners operating at or below 1.5 Tesla because this low field strength does not produce high-quality images of the relatively small NHP brain. Contemporary high field MRI (3T or more) for clinical use provides impressive sensitivity for magnetic resonance signal detection and is now accessible in many imaging centers and hospitals, facilitating the use of various MRI techniques in NHP studies. In this article, several high field MRI techniques and applications in macaque models of neuroAIDS are reviewed and the relation between quantitative MRI measures and blood T-cell alterations is discussed. PMID:24244892

  18. Extracting the inclination angle of nerve fibers within the human brain with 3D-PLI independent of system properties

    NASA Astrophysics Data System (ADS)

    Reckfort, Julia; Wiese, Hendrik; Dohmen, Melanie; Grässel, David; Pietrzyk, Uwe; Zilles, Karl; Amunts, Katrin; Axer, Markus

    2013-09-01

    The neuroimaging technique 3D-polarized light imaging (3D-PLI) has opened up new avenues to study the complex nerve fiber architecture of the human brain at sub-millimeter spatial resolution. This polarimetry technique is applicable to histological sections of postmortem brains utilizing the birefringence of nerve fibers caused by the regular arrangement of lipids and proteins in the myelin sheaths surrounding axons. 3D-PLI provides a three-dimensional description of the anatomical wiring scheme defined by the in-section direction angle and the out-of-section inclination angle. To date, 3D-PLI is the only available method that allows bridging the microscopic and the macroscopic description of the fiber architecture of the human brain. Here we introduce a new approach to retrieve the inclination angle of the fibers independently of the properties of the used polarimeters. This is relevant because the image resolution and the signal transmission inuence the measured birefringent signal (retardation) significantly. The image resolution was determined using the USAF- 1951 testchart applying the Rayleigh criterion. The signal transmission was measured by elliptical polarizers applying the Michelson contrast and histological slices of the optic tract of a postmortem brain. Based on these results, a modified retardation-inclination transfer function was proposed to extract the fiber inclination. The comparison of the actual and the inclination angles calculated with the theoretically proposed and the modified transfer function revealed a significant improvement in the extraction of the fiber inclinations.

  19. Multidimensional MRI-CT atlas of the naked mole-rat brain (Heterocephalus glaber).

    PubMed

    Seki, Fumiko; Hikishima, Keigo; Nambu, Sanae; Okanoya, Kazuo; Okano, Hirotaka J; Sasaki, Erika; Miura, Kyoko; Okano, Hideyuki

    2013-01-01

    Naked mole-rats have a variety of distinctive features such as the organization of a hierarchical society (known as eusociality), extraordinary longevity, and cancer resistance; thus, it would be worthwhile investigating these animals in detail. One important task is the preparation of a brain atlas database that provide comprehensive information containing multidimensional data with various image contrasts, which can be achievable using a magnetic resonance imaging (MRI). Advanced MRI techniques such as diffusion tensor imaging (DTI), which generates high contrast images of fiber structures, can characterize unique morphological properties in addition to conventional MRI. To obtain high spatial resolution images, MR histology, DTI, and X-ray computed tomography were performed on the fixed adult brain. Skull and brain structures were segmented as well as reconstructed in stereotaxic coordinates. Data were also acquired for the neonatal brain to allow developmental changes to be observed. Moreover, in vivo imaging of naked mole-rats was established as an evaluation tool of live animals. The data obtained comprised three-dimensional (3D) images with high tissue contrast as well as stereotaxic coordinates. Developmental differences in the visual system were highlighted in particular by DTI. Although it was difficult to delineate optic nerves in the mature adult brain, parts of them could be distinguished in the immature neonatal brain. From observation of cortical thickness, possibility of high somatosensory system development replaced to the visual system was indicated. 3D visualization of brain structures in the atlas as well as the establishment of in vivo imaging would promote neuroimaging researches towards detection of novel characteristics of eusocial naked mole-rats. PMID:24391551

  20. 3D maps from multiple MRI illustrate changing atrophy patterns as subjects progress from mild cognitive impairment to Alzheimer's disease.

    PubMed

    Whitwell, Jennifer L; Przybelski, Scott A; Weigand, Stephen D; Knopman, David S; Boeve, Bradley F; Petersen, Ronald C; Jack, Clifford R

    2007-07-01

    temporoparietal association cortices and, for the first time, substantial involvement of the frontal lobes. This pattern of progression fits well with the Braak and Braak neurofibrillary pathological staging scheme in AD. It suggests that the earliest changes occur in the anterior medial temporal lobe and fusiform gyrus, and that these changes occur at least 3 years before progression to the diagnosis of AD. These results also suggest that 3D patterns of grey matter atrophy may help to predict the time to the first diagnosis of AD in subjects with aMCI.

  1. 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.

  2. Applications of arterial spin labeled MRI in the brain.

    PubMed

    Detre, John A; Rao, Hengyi; Wang, Danny J J; Chen, Yu Fen; Wang, Ze

    2012-05-01

    Perfusion provides oxygen and nutrients to tissues and is closely tied to tissue function while disorders of perfusion are major sources of medical morbidity and mortality. It has been almost two decades since the use of arterial spin labeling (ASL) for noninvasive perfusion imaging was first reported. While initial ASL magnetic resonance imaging (MRI) studies focused primarily on technological development and validation, a number of robust ASL implementations have emerged, and ASL MRI is now also available commercially on several platforms. As a result, basic science and clinical applications of ASL MRI have begun to proliferate. Although ASL MRI can be carried out in any organ, most studies to date have focused on the brain. This review covers selected research and clinical applications of ASL MRI in the brain to illustrate its potential in both neuroscience research and clinical care.

  3. 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

  4. The extraction of 3D shape from texture and shading in the human brain.

    PubMed

    Georgieva, Svetlana S; Todd, James T; Peeters, Ronald; Orban, Guy A

    2008-10-01

    We used functional magnetic resonance imaging to investigate the human cortical areas involved in processing 3-dimensional (3D) shape from texture (SfT) and shading. The stimuli included monocular images of randomly shaped 3D surfaces and a wide variety of 2-dimensional (2D) controls. The results of both passive and active experiments reveal that the extraction of 3D SfT involves the bilateral caudal inferior temporal gyrus (caudal ITG), lateral occipital sulcus (LOS) and several bilateral sites along the intraparietal sulcus. These areas are largely consistent with those involved in the processing of 3D shape from motion and stereo. The experiments also demonstrate, however, that the analysis of 3D shape from shading is primarily restricted to the caudal ITG areas. Additional results from psychophysical experiments reveal that this difference in neuronal substrate cannot be explained by a difference in strength between the 2 cues. These results underscore the importance of the posterior part of the lateral occipital complex for the extraction of visual 3D shape information from all depth cues, and they suggest strongly that the importance of shading is diminished relative to other cues for the analysis of 3D shape in parietal regions.

  5. Building a virtual archive using brain architecture and Web 3D to deliver neuropsychopharmacology content over the Internet.

    PubMed

    Mongeau, R; Casu, M A; Pani, L; Pillolla, G; Lianas, L; Giachetti, A

    2008-05-01

    The vast amount of heterogeneous data generated in various fields of neurosciences such as neuropsychopharmacology can hardly be classified using traditional databases. We present here the concept of a virtual archive, spatially referenced over a simplified 3D brain map and accessible over the Internet. A simple prototype (available at http://aquatics.crs4.it/neuropsydat3d) has been realized using current Web-based virtual reality standards and technologies. It illustrates how primary literature or summary information can easily be retrieved through hyperlinks mapped onto a 3D schema while navigating through neuroanatomy. Furthermore, 3D navigation and visualization techniques are used to enhance the representation of brain's neurotransmitters, pathways and the involvement of specific brain areas in any particular physiological or behavioral functions. The system proposed shows how the use of a schematic spatial organization of data, widely exploited in other fields (e.g. Geographical Information Systems) can be extremely useful to develop efficient tools for research and teaching in neurosciences. PMID:18262677

  6. 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

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

    PubMed

    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

  8. Building a virtual archive using brain architecture and Web 3D to deliver neuropsychopharmacology content over the Internet.

    PubMed

    Mongeau, R; Casu, M A; Pani, L; Pillolla, G; Lianas, L; Giachetti, A

    2008-05-01

    The vast amount of heterogeneous data generated in various fields of neurosciences such as neuropsychopharmacology can hardly be classified using traditional databases. We present here the concept of a virtual archive, spatially referenced over a simplified 3D brain map and accessible over the Internet. A simple prototype (available at http://aquatics.crs4.it/neuropsydat3d) has been realized using current Web-based virtual reality standards and technologies. It illustrates how primary literature or summary information can easily be retrieved through hyperlinks mapped onto a 3D schema while navigating through neuroanatomy. Furthermore, 3D navigation and visualization techniques are used to enhance the representation of brain's neurotransmitters, pathways and the involvement of specific brain areas in any particular physiological or behavioral functions. The system proposed shows how the use of a schematic spatial organization of data, widely exploited in other fields (e.g. Geographical Information Systems) can be extremely useful to develop efficient tools for research and teaching in neurosciences.

  9. 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.

  10. Structural MRI connectome in development: challenges of the changing brain

    PubMed Central

    Hess, C P; Xu, D; Barkovich, A J

    2014-01-01

    MRI connectomics is an emerging approach to study the brain as a network of interconnected brain regions. Understanding and mapping the development of the MRI connectome may offer new insights into the development of brain connectivity and plasticity, ultimately leading to improved understanding of normal development and to more effective diagnosis and treatment of developmental disorders. In this review, we describe the attempts made to date to map the whole-brain structural MRI connectome in the developing brain and pay a special attention to the challenges associated with the rapid changes that the brain is undergoing during maturation. The two main steps in constructing a structural brain network are (i) choosing connectivity measures that will serve as the network “edges” and (ii) finding an appropriate way to divide the brain into regions that will serve as the network “nodes”. We will discuss how these two steps are usually performed in developmental studies and the rationale behind different strategies. Changes in local and global network properties that have been described during maturation in neonates and children will be reviewed, along with differences in network topology between typically and atypically developing subjects, for example, owing to pre-mature birth or hypoxic ischaemic encephalopathy. Finally, future directions of connectomics will be discussed, addressing important steps necessary to advance the study of the structural MRI connectome in development. PMID:24827379

  11. Human brain functional MRI and DTI visualization with virtual reality.

    PubMed

    Chen, Bin; Moreland, John; Zhang, Jingyu

    2011-12-01

    Magnetic resonance diffusion tensor imaging (DTI) and functional MRI (fMRI) are two active research areas in neuroimaging. DTI is sensitive to the anisotropic diffusion of water exerted by its macromolecular environment and has been shown useful in characterizing structures of ordered tissues such as the brain white matter, myocardium, and cartilage. The diffusion tensor provides two new types of information of water diffusion: the magnitude and the spatial orientation of water diffusivity inside the tissue. This information has been used for white matter fiber tracking to review physical neuronal pathways inside the brain. Functional MRI measures brain activations using the hemodynamic response. The statistically derived activation map corresponds to human brain functional activities caused by neuronal activities. The combination of these two methods provides a new way to understand human brain from the anatomical neuronal fiber connectivity to functional activities between different brain regions. In this study, virtual reality (VR) based MR DTI and fMRI visualization with high resolution anatomical image segmentation and registration, ROI definition and neuronal white matter fiber tractography visualization and fMRI activation map integration is proposed. Rationale and methods for producing and distributing stereoscopic videos are also discussed. PMID:23256049

  12. MRI brain tumor segmentation and necrosis detection using adaptive Sobolev snakes

    NASA Astrophysics Data System (ADS)

    Nakhmani, Arie; Kikinis, Ron; Tannenbaum, Allen

    2014-03-01

    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 di erent 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 di usion 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.

  13. Hypernatraemic dehydration in a neonate: brain MRI findings.

    PubMed

    Musapasaoglu, H; Agildere, A Muhtesem; Teksam, M; Tarcan, A; Gurakan, B

    2008-02-01

    Severe hypernatremic dehydration can cause serious neurological complications in neonates. The most significant problems include brain oedema, intracranial haemorrhage, sinus thrombosis, haemorrhagic infarcts and permanent brain damage. The symptoms of many of these complications are similar. With respect to brain MRI findings in hypernatremic neonates, this is a report that describes linear lesions that represent intracranial haemorrhage at the grey-white matter junction. These MRI findings may be helpful for diagnosing hypernatremic dehydration, and for ruling out differential diagnoses for complications of this disorder.

  14. 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.

  15. 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.

  16. 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

  17. 3D conformal MRI-controlled transurethral ultrasound prostate therapy: validation of numerical simulations and demonstration in tissue-mimicking gel phantoms.

    PubMed

    Burtnyk, Mathieu; N'Djin, William Apoutou; Kobelevskiy, Ilya; Bronskill, Michael; Chopra, Rajiv

    2010-11-21

    MRI-controlled transurethral ultrasound therapy uses a linear array of transducer elements and active temperature feedback to create volumes of thermal coagulation shaped to predefined prostate geometries in 3D. The specific aims of this work were to demonstrate the accuracy and repeatability of producing large volumes of thermal coagulation (>10 cc) that conform to 3D human prostate shapes in a tissue-mimicking gel phantom, and to evaluate quantitatively the accuracy with which numerical simulations predict these 3D heating volumes under carefully controlled conditions. Eleven conformal 3D experiments were performed in a tissue-mimicking phantom within a 1.5T MR imager to obtain non-invasive temperature measurements during heating. Temperature feedback was used to control the rotation rate and ultrasound power of transurethral devices with up to five 3.5 × 5 mm active transducer elements. Heating patterns shaped to human prostate geometries were generated using devices operating at 4.7 or 8.0 MHz with surface acoustic intensities of up to 10 W cm(-2). Simulations were informed by transducer surface velocity measurements acquired with a scanning laser vibrometer enabling improved calculations of the acoustic pressure distribution in a gel phantom. Temperature dynamics were determined according to a FDTD solution to Pennes' BHTE. The 3D heating patterns produced in vitro were shaped very accurately to the prostate target volumes, within the spatial resolution of the MRI thermometry images. The volume of the treatment difference falling outside ± 1 mm of the target boundary was, on average, 0.21 cc or 1.5% of the prostate volume. The numerical simulations predicted the extent and shape of the coagulation boundary produced in gel to within (mean ± stdev [min, max]): 0.5 ± 0.4 [-1.0, 2.1] and -0.05 ± 0.4 [-1.2, 1.4] mm for the treatments at 4.7 and 8.0 MHz, respectively. The temperatures across all MRI thermometry images were predicted within -0.3 ± 1.6 °C and 0

  18. 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.

  19. Structural brain MRI trait polygenic score prediction of cognitive abilities

    PubMed Central

    Luciano, Michelle; Marioni, Riccardo E; Hernández, Maria Valdés; Maniega, Susana Munoz; Hamilton, Iona F; Royle, Natalie A.; Scotland, Generation; Chauhan, Ganesh; Bis, Joshua C.; Debette, Stephanie; DeCarli, Charles; Fornage, Myriam; Schmidt, Reinhold; Ikram, M. Arfan; Launer, Lenore J.; Seshadri, Sudha; Bastin, Mark E.; Porteous, David J.; Wardlaw, Joanna; Deary, Ian J

    2016-01-01

    Structural brain magnetic resonance imaging (MRI) traits share part of their genetic variance with cognitive traits. Here, we use genetic association results from large meta-analytic studies of genome-wide association for brain infarcts, white matter hyperintensities, intracranial, hippocampal and total brain volumes to estimate polygenic scores for these traits in three Scottish samples: Generation Scotland: Scottish Family Health Study (GS:SFHS), and the Lothian Birth Cohorts of 1936 (LBC1936) and 1921 (LBC1921). These five brain MRI trait polygenic scores were then used to 1) predict corresponding MRI traits in the LBC1936 (numbers ranged 573 to 630 across traits) and 2) predict cognitive traits in all three cohorts (in 8,115 to 8,250 persons). In the LBC1936, all MRI phenotypic traits were correlated with at least one cognitive measure; and polygenic prediction of MRI traits was observed for intracranial volume. Meta-analysis of the correlations between MRI polygenic scores and cognitive traits revealed a significant negative correlation (maximal r=0.08) between the hippocampal volume polygenic score and measures of global cognitive ability collected in childhood and in old age in the Lothian Birth Cohorts. The lack of association to a related general cognitive measure when including the GS:SFHS points to either type 1 error or the importance of using prediction samples that closely match the demographics of the genome-wide association samples from which prediction is based. Ideally, these analyses should be repeated in larger samples with data on both MRI and cognition, and using MRI GWA results from even larger meta-analysis studies. PMID:26427786

  20. Effects of incremental beta-blocker dosing on myocardial mechanics of the human left ventricle: MRI 3D-tagging insight into pharmacodynamics supports theory of inner antagonism.

    PubMed

    Schmitt, Boris; Li, Tieyan; Kutty, Shelby; Khasheei, Alireza; Schmitt, Katharina R L; Anderson, Robert H; Lunkenheimer, Paul P; Berger, Felix; Kühne, Titus; Peters, Björn

    2015-07-01

    Beta-blockers contribute to treatment of heart failure. Their mechanism of action, however, is incompletely understood. Gradients in beta-blocker sensitivity of helically aligned cardiomyocytes compared with counteracting transversely intruding cardiomyocytes seem crucial. We hypothesize that selective blockade of transversely intruding cardiomyocytes by low-dose beta-blockade unloads ventricular performance. Cardiac magnetic resonance imaging (MRI) 3D tagging delivers parameters of myocardial performance. We studied 13 healthy volunteers by MRI 3D tagging during escalated intravenous administration of esmolol. The circumferential, longitudinal, and radial myocardial shortening was determined for each dose. The curves were analyzed for peak value, time-to-peak, upslope, and area-under-the-curve. At low doses, from 5 to 25 μg·kg(-1)·min(-1), peak contraction increased while time-to-peak decreased yielding a steeper upslope. Combining the values revealed a left shift of the curves at low doses compared with baseline without esmolol. At doses of 50 to 150 μg·kg(-1)·min(-1), a right shift with flattening occurred. In healthy volunteers we found more pronounced myocardial shortening at low compared with clinical dosage of beta-blockers. In patients with ventricular hypertrophy and higher prevalence of transversely intruding cardiomyocytes selective low-dose beta-blockade could be even more effective. MRI 3D tagging could help to determine optimal individual beta-blocker dosing avoiding undesirable side effects. PMID:25888512

  1. 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. PMID:23757180

  2. MRI evaluation and safety in the developing brain.

    PubMed

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

    2015-03-01

    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 1.5-T and 3-T 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, and 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

  3. 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

  4. New opportunities for quantitative and time efficient 3D MRI of liquid and solid electrochemical cell components: Sectoral Fast Spin Echo and SPRITE.

    PubMed

    Romanenko, Konstantin; Forsyth, Maria; O'Dell, Luke A

    2014-11-01

    The ability to image electrochemical processes in situ using nuclear magnetic resonance imaging (MRI) offers exciting possibilities for understanding and optimizing materials in batteries, fuel cells and supercapacitors. In these applications, however, the quality of the MRI measurement is inherently limited by the presence of conductive elements in the cell or device. To overcome related difficulties, optimal methodologies have to be employed. We show that time-efficient three dimensional (3D) imaging of liquid and solid lithium battery components can be performed by Sectoral Fast Spin Echo and Single Point Imaging with T1 Enhancement (SPRITE), respectively. The former method is based on the generalized phase encoding concept employed in clinical MRI, which we have adapted and optimized for materials science and electrochemistry applications. Hard radio frequency pulses, short echo spacing and centrically ordered sectoral phase encoding ensure accurate and time-efficient full volume imaging. Mapping of density, diffusivity and relaxation time constants in metal-containing liquid electrolytes is demonstrated. 1, 2 and 3D SPRITE approaches show strong potential for rapid high resolution (7)Li MRI of lithium electrode components.

  5. New opportunities for quantitative and time efficient 3D MRI of liquid and solid electrochemical cell components: Sectoral Fast Spin Echo and SPRITE

    NASA Astrophysics Data System (ADS)

    Romanenko, Konstantin; Forsyth, Maria; O'Dell, Luke A.

    2014-11-01

    The ability to image electrochemical processes in situ using nuclear magnetic resonance imaging (MRI) offers exciting possibilities for understanding and optimizing materials in batteries, fuel cells and supercapacitors. In these applications, however, the quality of the MRI measurement is inherently limited by the presence of conductive elements in the cell or device. To overcome related difficulties, optimal methodologies have to be employed. We show that time-efficient three dimensional (3D) imaging of liquid and solid lithium battery components can be performed by Sectoral Fast Spin Echo and Single Point Imaging with T1 Enhancement (SPRITE), respectively. The former method is based on the generalized phase encoding concept employed in clinical MRI, which we have adapted and optimized for materials science and electrochemistry applications. Hard radio frequency pulses, short echo spacing and centrically ordered sectoral phase encoding ensure accurate and time-efficient full volume imaging. Mapping of density, diffusivity and relaxation time constants in metal-containing liquid electrolytes is demonstrated. 1, 2 and 3D SPRITE approaches show strong potential for rapid high resolution 7Li MRI of lithium electrode components.

  6. New opportunities for quantitative and time efficient 3D MRI of liquid and solid electrochemical cell components: Sectoral Fast Spin Echo and SPRITE.

    PubMed

    Romanenko, Konstantin; Forsyth, Maria; O'Dell, Luke A

    2014-11-01

    The ability to image electrochemical processes in situ using nuclear magnetic resonance imaging (MRI) offers exciting possibilities for understanding and optimizing materials in batteries, fuel cells and supercapacitors. In these applications, however, the quality of the MRI measurement is inherently limited by the presence of conductive elements in the cell or device. To overcome related difficulties, optimal methodologies have to be employed. We show that time-efficient three dimensional (3D) imaging of liquid and solid lithium battery components can be performed by Sectoral Fast Spin Echo and Single Point Imaging with T1 Enhancement (SPRITE), respectively. The former method is based on the generalized phase encoding concept employed in clinical MRI, which we have adapted and optimized for materials science and electrochemistry applications. Hard radio frequency pulses, short echo spacing and centrically ordered sectoral phase encoding ensure accurate and time-efficient full volume imaging. Mapping of density, diffusivity and relaxation time constants in metal-containing liquid electrolytes is demonstrated. 1, 2 and 3D SPRITE approaches show strong potential for rapid high resolution (7)Li MRI of lithium electrode components. PMID:25442778

  7. 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

  8. 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. PMID:23682203

  9. A 3D multi-modal and multi-dimensional digital brain model as a framework for data sharing.

    PubMed

    Mailly, Philippe; Haber, Suzanne N; Groenewegen, Henk J; Deniau, Jean-Michel

    2010-12-15

    Computer based three-dimensional reconstruction and co-registration of experimental data provide powerful tools for integration of observation derived from various technical approaches leading to better understanding of brain functions. Here we describe a method to build a 3D multi-modal and multi-dimensional model of brain structures providing framework for data sharing. All image processing, registration and 3D reconstruction were performed using open source software IMOD package software and ImageJ. The reconstruction procedure is based on series of AChE and Nissl stained sections aligned to blockface pictures. Integration of experimental data into the reference model is achieved by co-registration of Nissl sections of experimental brain cases by positioning landmarks on corresponding anatomical structures. To overcome the challenge of comparing for experimental sections with those of the reference model, adjustment of experimental model to the brain model was done section by section and limited to the structures of interest. For this adjustment we stress the use of cytoarchitectural criteria for accurate registration of anatomical structures and co-registration procedures.

  10. 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.

  11. [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.

  12. 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.

  13. Effect of Task-Correlated Physiological Fluctuations and Motion in 2D and 3D Echo-Planar Imaging in a Higher Cognitive Level fMRI Paradigm

    PubMed Central

    Ladstein, Jarle; Evensmoen, Hallvard R.; Håberg, Asta K.; Kristoffersen, Anders; Goa, Pål E.

    2016-01-01

    Purpose: To compare 2D and 3D echo-planar imaging (EPI) in a higher cognitive level fMRI paradigm. In particular, to study the link between the presence of task-correlated physiological fluctuations and motion and the fMRI contrast estimates from either 2D EPI or 3D EPI datasets, with and without adding nuisance regressors to the model. A signal model in the presence of partly task-correlated fluctuations is derived, and predictions for contrast estimates with and without nuisance regressors are made. Materials and Methods: Thirty-one healthy volunteers were scanned using 2D EPI and 3D EPI during a virtual environmental learning paradigm. In a subgroup of 7 subjects, heart rate and respiration were logged, and the correlation with the paradigm was evaluated. FMRI analysis was performed using models with and without nuisance regressors. Differences in the mean contrast estimates were investigated by analysis-of-variance using Subject, Sequence, Day, and Run as factors. The distributions of group level contrast estimates were compared. Results: Partially task-correlated fluctuations in respiration, heart rate and motion were observed. Statistically significant differences were found in the mean contrast estimates between the 2D EPI and 3D EPI when using a model without nuisance regressors. The inclusion of nuisance regressors for cardiorespiratory effects and motion reduced the difference to a statistically non-significant level. Furthermore, the contrast estimate values shifted more when including nuisance regressors for 3D EPI compared to 2D EPI. Conclusion: The results are consistent with 3D EPI having a higher sensitivity to fluctuations compared to 2D EPI. In the presence partially task-correlated physiological fluctuations or motion, proper correction is necessary to get expectation correct contrast estimates when using 3D EPI. As such task-correlated physiological fluctuations or motion is difficult to avoid in paradigms exploring higher cognitive functions, 2

  14. 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

  15. 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

  16. In-vivo human brain molecular imaging with a brain-dedicated PET/MRI system.

    PubMed

    Cho, Zang Hee; Son, Young Don; Choi, Eun Jung; Kim, Hang Keun; Kim, Jeong Hee; Lee, Sang Yoon; Ogawa, Seiji; Kim, Young Bo

    2013-02-01

    Advances in the new-generation of ultra-high-resolution, brain-dedicated positron emission tomography-magnetic resonance imaging (PET/MRI) systems have begun to provide many interesting insights into the molecular dynamics of the brain. First, the finely delineated structural information from ultra-high-field MRI can help us to identify accurate landmark structures, thereby making it easier to locate PET activation sites that are anatomically well-correlated with metabolic or ligand-specific organs in the neural structures in the brain. This synergistic potential of PET/MRI imaging is discussed in terms of neuroscience and neurological research from both translational and basic research perspectives. Experimental results from the hippocampus, thalamus, and brainstem obtained with (18)F-fluorodeoxyglucose and (11)C-3-amino-4-(2-dimethylaminomethylphenylsulfanyl)benzonitrile are used to demonstrate the potential of this new brain PET/MRI system.

  17. 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.

  18. 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.

  19. 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 ...

  20. Knowledge-based 3D segmentation of the brain in MR images for quantitative multiple sclerosis lesion tracking

    NASA Astrophysics Data System (ADS)

    Fisher, Elizabeth; Cothren, Robert M., Jr.; Tkach, Jean A.; Masaryk, Thomas J.; Cornhill, J. Fredrick

    1997-04-01

    Brain segmentation in magnetic resonance (MR) images is an important step in quantitative analysis applications, including the characterization of multiple sclerosis (MS) lesions over time. Our approach is based on a priori knowledge of the intensity and three-dimensional (3D) spatial relationships of structures in MR images of the head. Optimal thresholding and connected-components analysis are used to generate a starting point for segmentation. A 3D radial search is then performed to locate probable locations of the intra-cranial cavity (ICC). Missing portions of the ICC surface are interpolated in order to exclude connected structures. Partial volume effects and inter-slice intensity variations in the image are accounted for automatically. Several studies were conducted to validate the segmentation. Accuracy was tested by calculating the segmented volume and comparing to known volumes of a standard MR phantom. Reliability was tested by comparing calculated volumes of individual segmentation results from multiple images of the same subject. The segmentation results were also compared to manual tracings. The average error in volume measurements for the phantom was 1.5% and the average coefficient of variation of brain volume measurements of the same subject was 1.2%. Since the new algorithm requires minimal user interaction, variability introduced by manual tracing and interactive threshold or region selection was eliminated. Overall, the new algorithm was shown to produce a more accurate and reliable brain segmentation than existing manual and semi-automated techniques.

  1. 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

  2. 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

  3. 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. PMID:26438877

  4. 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.

  5. 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

  6. In vivo MRI-Based 3D FSI RV/LV Models for Human Right Ventricle and Patch Design for Potential Computer-Aided Surgery Optimization.

    PubMed

    Yang, Chun; Tang, Dalin; Haber, Idith; Geva, Tal; Del Nido, Pedro J

    2007-01-01

    Right ventricular dysfunction is one of the more common causes of heart failure in patients with congenital heart defects. Use of computer-assisted procedures is becoming more popular in clinical decision making process and computer-aided surgeries. A 3D in vivo MRI-based RV/LV combination model with fluid-structure interaction (FSI), RV-LV interaction, and RV-patch interaction was introduced to perform mechanical analysis for human right ventricle with potential clinical applications. Patient-specific RV/LV morphologies were acquired by using planar tagged MRI. The 3D RV/LV FSI model was solved using a commercial finite element package ADINA. Our results indicated that flow and stress/strain distributions in the right ventricle are closely related to RV morphology, material properties and blood pressure conditions. Patches with material properties better matching RV tissue properties and smaller size lead to better RV function recoveries. Computational RV volumes showed very good agreement with MRI data (error < 3%). More patient studies are needed to establish baseline database so that computational simulations can be used to replace empirical and often risky clinical experimentation to examine the efficiency and suitability of various reconstructive procedures in diseased hearts and optimal design can be found.

  7. 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.

  8. 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.

  9. 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.

  10. 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

  11. THE GENOME IN 3D: A NEW FRONTIER IN HUMAN BRAIN RESEARCH

    PubMed Central

    Mitchell, Amanda C.; Bharadwaj, Rahul; Whittle, Catheryne; Krueger, Winfried; Mirnics, Karoly; Hurd, Yasmin; Rasmussen, Theodore; Akbarian, Schahram

    2013-01-01

    Less than 1.5% of the human genome encodes protein. However, vast portions of the human genome are subject to transcriptional and epigenetic regulation and many non-coding regulatory DNA elements are thought to regulate the spatial organization of interphase chromosomes. For example, chromosomal ‘loopings’ are pivotal for the orderly process of gene expression, by enabling distal regulatory enhancer or silencer elements to directly interact with proximal promoter and transcription start sites, potentially bypassing hundreds of kilobases of interspersed sequence on the linear genome. To date, however, epigenetic studies in the human brain are mostly limited to the exploration of DNA methylation and posttranslational modifications of the nucleosome core histones. In contrast, very little is known about the regulation of supranucleosomal structures in brain nuclei. Here, we show that chromosome conformation capture (3C), a widely used approach to study higher order chromatin, is applicable to tissue collected postmortem, thereby informing about genome organization in the human brain. We introduce 3C protocols for brain, and compare higher order chromatin structures at the chromosome 6p22.2–22.1 schizophrenia and bipolar susceptibility locus and neurodevelopmental risk genes (DPP10, MCPH1) in adult prefrontal cortex and various cell culture systems, including neurons derived from reprogrammed skin cells. We predict that the exploration of three-dimensional genome architectures and function will open up new frontiers in human brain research and psychiatric genetics, and provide novel insights into the epigenetic risk architectures of regulatory non-coding DNA. PMID:23958183

  12. 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. PMID:25865822

  13. 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.

  14. Landmark-based morphometrics of the normal adult brain using MRI.

    PubMed

    Free, S L; O'Higgins, P; Maudgil, D D; Dryden, I L; Lemieux, L; Fish, D R; Shorvon, S D

    2001-05-01

    We describe the application of statistical shape analysis to homologous landmarks on the cortical surface of the adult human brain. Statistical shape analysis has a sound theoretical basis. Landmarks are identified on the surface of a 3-D reconstruction of the segmented cortical surface from magnetic resonance image (MRI) data. Using publicly available software (morphologika) the location and size dependence of the landmarks are removed and the differences in landmark distribution across subjects are analysed using principal component analysis. These differences, representing shape differences between subjects, can be visually assessed using wireframe models and transformation grids. The MRI data of 58 adult brains (27 female and 15 left handed) were examined. Shape differences in the whole brain are described which concern the relative orientation of frontal lobe sulci. Analysis of all 116 hemispheres revealed a statistically significant difference (P < 0.001) between left and right hemispheres. This finding was significant for right- but not left-handed subjects alone. No other significant age, gender, handedness, or brain-size correlations with shape differences were found.

  15. Creation of 3D digital anthropomorphic phantoms which model actual patient non-rigid body motion as determined from MRI and position tracking studies of volunteers

    NASA Astrophysics Data System (ADS)

    Connolly, C. M.; Konik, A.; Dasari, P. K. R.; Segars, P.; Zheng, S.; Johnson, K. L.; Dey, J.; King, M. A.

    2011-03-01

    Patient motion can cause artifacts, which can lead to difficulty in interpretation. The purpose of this study is to create 3D digital anthropomorphic phantoms which model the location of the structures of the chest and upper abdomen of human volunteers undergoing a series of clinically relevant motions. The 3D anatomy is modeled using the XCAT phantom and based on MRI studies. The NURBS surfaces of the XCAT are interactively adapted to fit the MRI studies. A detailed XCAT phantom is first developed from an EKG triggered Navigator acquisition composed of sagittal slices with a 3 x 3 x 3 mm voxel dimension. Rigid body motion states are then acquired at breath-hold as sagittal slices partially covering the thorax, centered on the heart, with 9 mm gaps between them. For non-rigid body motion requiring greater sampling, modified Navigator sequences covering the entire thorax with 3 mm gaps between slices are obtained. The structures of the initial XCAT are then adapted to fit these different motion states. Simultaneous to MRI imaging the positions of multiple reflective markers on stretchy bands about the volunteer's chest and abdomen are optically tracked in 3D via stereo imaging. These phantoms with combined position tracking will be used to investigate both imaging-data-driven and motion-tracking strategies to estimate and correct for patient motion. Our initial application will be to cardiacperfusion SPECT imaging where the XCAT phantoms will be used to create patient activity and attenuation distributions for each volunteer with corresponding motion tracking data from the markers on the body-surface. Monte Carlo methods will then be used to simulate SPECT acquisitions, which will be used to evaluate various motion estimation and correction strategies.

  16. 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.

  17. 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

  18. 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%.

  19. 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.

  20. Free-Breathing 3D Imaging of Right Ventricular Structure and Function Using Respiratory and Cardiac Self-Gated Cine MRI

    PubMed Central

    Zhu, Yanchun; Liu, Jing; Weinsaft, Jonathan; Spincemaille, Pascal; Nguyen, Thanh D.; Prince, Martin R.; Bao, Shanglian; Xie, Yaoqin; Wang, Yi

    2015-01-01

    Providing a movie of the beating heart in a single prescribed plane, cine MRI has been widely used in clinical cardiac diagnosis, especially in the left ventricle (LV). Right ventricular (RV) morphology and function are also important for the diagnosis of cardiopulmonary diseases and serve as predictors for the long term outcome. The purpose of this study is to develop a self-gated free-breathing 3D imaging method for RV quantification and to evaluate its performance by comparing it with breath-hold 2D cine imaging in 7 healthy volunteers. Compared with 2D, the 3D RV functional measurements show a reduction of RV end-diastole volume (RVEDV) by 10%, increase of RV end-systole volume (RVESV) by 1.8%, reduction of RV systole volume (RVSV) by 21%, and reduction of RV ejection fraction (RVEF) by 12%. High correlations between the two techniques were found (RVEDV: 0.94; RVESV: 0.85; RVSV: 0.95; and RVEF: 0.89). Compared with 2D, the 3D image quality measurements show a small reduction in blood SNR, myocardium-blood CNR, myocardium contrast, and image sharpness. In conclusion, the proposed self-gated free-breathing 3D cardiac cine imaging technique provides comparable image quality and correlated functional measurements to those acquired with the multiple breath-hold 2D technique in RV. PMID:26185764

  1. [Identification of offending vessels in trigeminal neuralgia and hemifacial spasm using SPGR-MRI and 3D-TOF-MRA].

    PubMed

    Niwa, Y; Shiotani, M; Karasawa, H; Ohseto, K; Naganuma, Y

    1996-04-01

    We investigated 100 consecutive patients with trigeminal neuralgia (TN) and 53 patients with hemifacial spasm (HFS) concerning the anatomical relationship between the root entry (exit) zone (REZ) of cranial nerve and the offending artery, using spoiled GRASS MRI (SPGR-MRI) and three dimensional-time of fly-MRA (MRA). In 67 of 100 (67%) patiets with TN, this new radiological method, SPGR-MRI and MRA demonstrated the relationship between the fifth cranial nerve root and offending artery causing neurovascular compression (NVC), and in 46 of 53 (87%) with HFS, demonstrated the similar relationship between seventh and eighth nerve complex and offending artery. Microvascular decompression (MVD) was performed in 10 with HFS, and NVC of the REZ of the facial nerve caused by the offending artery was exactly predicted by SPGR-MRI and MRA in 9 (90%). The combination of SPGR-MRI and MRA is very useful for demonstrating NVC as the cause of TN and HFS. On the other hand, we investigated asymptomatic 206 trigeminal and 253 facial nerves about the relationship between their REZ and the surrounding structures using the similar method. The contact of REZ of cranial nerve with surrounding artery is demonstrated in 31.6% of trigeminal nerves and in 22.5% of facial nerves. These results indicate that the contact of REZ of cranial nerve with surrounding artery is not rare in healthy subjects, though causing TN and HFS in particular patients. In this context, we discussed the difference between the contact which is asymptomatic and the compression which is symptomatic.

  2. Studying the freely-behaving brain with fMRI.

    PubMed

    Maguire, Eleanor A

    2012-08-15

    Given that the brain evolved to function in the real world then it seems reasonable to want to examine how it operates in that context. But of course the world is complex, as are the brain's responses to it, and MRI scanners are inherently restrictive environments. This combination of challenges makes the prospect of studying the freely-behaving brain with fMRI disconcerting to anyone sensible. When designing naturalistic fMRI experiments it is necessary to ensure that the thoughts or behaviours under scrutiny are not unduly perturbed or constrained by the imaging process, while still being amenable to experimental manipulation and control, and result in meaningful and interpretable data. This is difficult to achieve. Here, briefly, and in a highly subjective and selective manner, I consider: why we might want to deploy free-behaviour designs in an fMRI context, how to go about it, review some examples of it in action, and decide finally whether it is worth it (it is).

  3. 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

  4. 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

  5. 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. PMID

  6. 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.

  7. 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).

  8. 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.

  9. 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

    2015-01-01

    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 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. PMID:26437432

  10. 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.

  11. A hybrid framework of multiple active appearance models and global registration for 3D prostate segmentation in MRI

    NASA Astrophysics Data System (ADS)

    Ghose, Soumya; Oliver, Arnau; Martí, Robert; Lladó, Xavier; Freixenet, Jordi; Mitra, Jhimli; Vilanova, Joan C.; Meriaudeau, Fabrice

    2012-02-01

    Real-time fusion of Magnetic Resonance (MR) and Trans Rectal Ultra Sound (TRUS) images aid in the localization of malignant tissues in TRUS guided prostate biopsy. Registration performed on segmented contours of the prostate reduces computational complexity and improves the multimodal registration accuracy. However, accurate and computationally efficient 3D segmentation of the prostate in MR images could be a challenging task due to inter-patient shape and intensity variability of the prostate gland. In this work, we propose to use multiple statistical shape and appearance models to segment the prostate in 2D and a global registration framework to impose shape restriction in 3D. Multiple mean parametric models of the shape and appearance corresponding to the apex, central and base regions of the prostate gland are derived from principal component analysis (PCA) of prior shape and intensity information of the prostate from the training data. The estimated parameters are then modified with the prior knowledge of the optimization space to achieve segmentation in 2D. The 2D segmented slices are then rigidly registered with the average 3D model produced by affine registration of the ground truth of the training datasets to minimize pose variations and impose 3D shape restriction. The proposed method achieves a mean Dice similarity coefficient (DSC) value of 0.88+/-0.11, and mean Hausdorff distance (HD) of 3.38+/-2.81 mm when validated with 15 prostate volumes of a public dataset in leave-one-out validation framework. The results achieved are better compared to some of the works in the literature.

  12. Accurate High-Resolution Measurements of 3-D Tissue Dynamics With Registration-Enhanced Displacement Encoded MRI

    PubMed Central

    Merchant, Samer S.; Hsu, Edward W.

    2014-01-01

    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. PMID:24771572

  13. Highly accelerated 3D dynamic contrast enhanced MRI from sparse spiral sampling using integrated partial separability model and JSENSE

    NASA Astrophysics Data System (ADS)

    Lyu, Jingyuan; Spincemaille, Pascal; Wang, Yi; Zhou, Yihang; Ren, Fuquan; Ying, Leslie

    2014-05-01

    Dynamic contrast enhanced MRI requires high spatial resolution for morphological information and high temporal resolution for contrast pharmacokinetics. The current techniques usually have to compromise the spatial information for the required temporal resolution. This paper presents a novel method that effectively integrates sparse sampling, parallel imaging, partial separable (PS) model, and sparsity constraints for highly accelerated DCE-MRI. Phased array coils were used to continuously acquire data from a stack of variable-density spiral trajectory with a golden angle. In reconstruction, the sparsity constraints, the coil sensitivities, spatial and temporal bases of the PS model are jointly estimated through alternating optimization. Experimental results from in vivo DCE liver imaging data show that the proposed method is able to achieve high spatial and temporal resolutions at the same time.

  14. 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%.

  15. 3D Segmentation of Rodent Brain Structures Using Hierarchical Shape Priors and Deformable Models

    PubMed Central

    Zhang, Shaoting; Huang, Junzhou; Uzunbas, Mustafa; Shen, Tian; Delis, Foteini; Huang, Xiaolei; Volkow, Nora; Thanos, Panayotis; Metaxas, Dimitris N.

    2016-01-01

    In this paper, we propose a method to segment multiple rodent brain structures simultaneously. This method combines deformable models and hierarchical shape priors within one framework. The deformation module employs both gradient and appearance information to generate image forces to deform the shape. The shape prior module uses Principal Component Analysis to hierarchically model the multiple structures at both global and local levels. At the global level, the statistics of relative positions among different structures are modeled. At the local level, the shape statistics within each structure is learned from training samples. Our segmentation method adaptively employs both priors to constrain the intermediate deformation result. This prior constraint improves the robustness of the model and benefits the segmentation accuracy. Another merit of our prior module is that the size of the training data can be small, because the shape prior module models each structure individually and combines them using global statistics. This scheme can preserve shape details better than directly applying PCA on all structures. We use this method to segment rodent brain structures, such as the cerebellum, the left and right striatum, and the left and right hippocampus. The experiments show that our method works effectively and this hierarchical prior improves the segmentation performance. PMID:22003750

  16. 3D segmentation of rodent brain structures using hierarchical shape priors and deformable models.

    PubMed

    Zhang, Shaoting; Huang, Junzhou; Uzunbas, Mustafa; Shen, Tian; Delis, Foteini; Huang, Xiaolei; Volkow, Nora; Thanos, Panayotis; Metaxas, Dimitris N

    2011-01-01

    In this paper, we propose a method to segment multiple rodent brain structures simultaneously. This method combines deformable models and hierarchical shape priors within one framework. The deformation module employs both gradient and appearance information to generate image forces to deform the shape. The shape prior module uses Principal Component Analysis to hierarchically model the multiple structures at both global and local levels. At the global level, the statistics of relative positions among different structures are modeled. At the local level, the shape statistics within each structure is learned from training samples. Our segmentation method adaptively employs both priors to constrain the intermediate deformation result. This prior constraint improves the robustness of the model and benefits the segmentation accuracy. Another merit of our prior module is that the size of the training data can be small, because the shape prior module models each structure individually and combines them using global statistics. This scheme can preserve shape details better than directly applying PCA on all structures. We use this method to segment rodent brain structures, such as the cerebellum, the left and right striatum, and the left and right hippocampus. The experiments show that our method works effectively and this hierarchical prior improves the segmentation performance. PMID:22003750

  17. Information fusion approach for detection of brain structures in MRI

    NASA Astrophysics Data System (ADS)

    Shademan, Azad; Soltanian-Zadeh, Hamid

    2002-05-01

    This paper presents an information fusion approach for automatic detection of mid-brain nuclei (caudate, putamen, globus pallidus, and thalamus) from MRI. The method is based on fusion of anatomical information, obtained from brain atlases and expert physicians, into MRI numerical information within a fuzzy framework, employed to model intrinsic uncertainty of problem. First step of this method is segmentation of brain tissues (gray matter, white matter, and cerebrospinal fluid). Physical landmarks such as inter-hemispheric plane alongside numerical information from segmentation step are then used to describe the nuclei. Each nucleus is defined according to a unique description according to physical landmarks and anatomical landmarks, most of which are the previously detected nuclei. Also, a detected nucleus in slice n serves as key landmark to detect same nucleus in slice n+1. These steps construct fuzzy decision maps. Overall decision is made after fusing all of decisions according to a fusion operator. This approach has been implemented to detect caudate, putamen, and thalamus from a sequence of axial T1-weighted brain MRI's. Our experience shows that final nuclei detection results are highly dependent upon primary tissue segmentation. The method is validated by comparing resultant nuclei volumes with those obtained using manual segmentation performed by expert physicians.

  18. 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.

  19. 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.

  20. 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.

  1. 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

  2. Integration of ultra-high field MRI and histology for connectome based research of brain disorders

    PubMed Central

    Yang, Shan; Yang, Zhengyi; Fischer, Karin; Zhong, Kai; Stadler, Jörg; Godenschweger, Frank; Steiner, Johann; Heinze, Hans-Jochen; Bernstein, Hans-Gert; Bogerts, Bernhard; Mawrin, Christian; Reutens, David C.; Speck, Oliver; Walter, Martin

    2013-01-01

    Ultra-high field magnetic resonance imaging (MRI) became increasingly relevant for in vivo neuroscientific research because of improved spatial resolutions. However, this is still the unchallenged domain of histological studies, which long played an important role in the investigation of neuropsychiatric disorders. While the field of biological psychiatry strongly advanced on macroscopic levels, current developments are rediscovering the richness of immunohistological information when attempting a multi-level systematic approach to brain function and dysfunction. For most studies, histology sections lost information on three-dimensional reconstructions. Translating histological sections to 3D-volumes would thus not only allow for multi-stain and multi-subject alignment in post mortem data, but also provide a crucial step in big data initiatives involving the network analyses currently performed with in vivo MRI. We therefore investigated potential pitfalls during integration of MR and histological information where no additional blockface information is available. We demonstrated that strengths and requirements from both methods can be effectively combined at a spatial resolution of 200 μm. However, the success of this approach is heavily dependent on choices of hardware, sequence and reconstruction. We provide a fully automated pipeline that optimizes histological 3D reconstructions, providing a potentially powerful solution not only for primary human post mortem research institutions in neuropsychiatric research, but also to help alleviate the massive workloads in neuroanatomical atlas initiatives. We further demonstrate (for the first time) the feasibility and quality of ultra-high spatial resolution (150 μm isotopic) imaging of the entire human brain MRI at 7T, offering new opportunities for analyses on MR-derived information. PMID:24098272

  3. Robust nonrigid registration to capture brain shift from intraoperative MRI.

    PubMed

    Clatz, Olivier; Delingette, Hervé; Talos, Ion-Florin; Golby, Alexandra J; Kikinis, Ron; Jolesz, Ferenc A; Ayache, Nicholas; Warfield, Simon K

    2005-11-01

    We present a new algorithm to register 3-D preoperative magnetic resonance (MR) images to intraoperative MR images of the brain which have undergone brain shift. This algorithm relies on a robust estimation of the deformation from a sparse noisy set of measured displacements. We propose a new framework to compute the displacement field in an iterative process, allowing the solution to gradually move from an approximation formulation (minimizing the sum of a regularization term and a data error term) to an interpolation formulation (least square minimization of the data error term). An outlier rejection step is introduced in this gradual registration process using a weighted least trimmed squares approach, aiming at improving the robustness of the algorithm. We use a patient-specific model discretized with the finite element method in order to ensure a realistic mechanical behavior of the brain tissue. To meet the clinical time constraint, we parallelized the slowest step of the algorithm so that we can perform a full 3-D image registration in 35 s (including the image update time) on a heterogeneous cluster of 15 personal computers. The algorithm has been tested on six cases of brain tumor resection, presenting a brain shift of up to 14 mm. The results show a good ability to recover large displacements, and a limited decrease of accuracy near the tumor resection cavity.

  4. Quantification of regional fractional ventilation in human subjects by measurement of hyperpolarized 3He washout with 2D and 3D MRI.

    PubMed

    Horn, Felix C; Deppe, Martin H; Marshall, Helen; Parra-Robles, Juan; Wild, Jim M

    2014-01-15

    Multiple-breath washout hyperpolarized (3)He MRI was used to calculate regional parametric images of fractional ventilation (r) as the ratio of fresh gas entering a volume unit to the total end inspiratory volume of the unit. Using a single dose of inhaled hyperpolarized gas and a total acquisition time of under 1 min, gas washout was measured by dynamic acquisitions during successive breaths with a fixed delay. A two-dimensional (2D) imaging protocol was investigated in four healthy subjects in the supine position, and in a second protocol the capability of extending the washout imaging to a three-dimensional (3D) acquisition covering the whole lungs was tested. During both protocols, subjects were breathing comfortably, only restricted by synchronization of breathing to the sequence timings. The 3D protocol was also successfully tested on one patient with cystic fibrosis. Mean r values from each volunteer were compared with global gas volume turnover, as calculated from flow measurement at the mouth divided by total lung volume (from MRI images), and a significant correlation (r = 0.74, P < 0.05) was found. The effects of gravity on R were investigated, and an average decrease in r of 5.5%/cm (Δr = 0.016 ± 0.006 cm(-1)) from posterior to anterior was found in the right lung. Intersubject reproducibility of r imaging with the 2D and 3D protocol was tested, and a significant correlation between repeated experiments was found in a pixel-by-pixel comparison. The proposed methods can be used to measure r on a regional basis. PMID:24311749

  5. MRI of brain tissue oxygen tension under hyperbaric conditions.

    PubMed

    Muir, Eric R; Cardenas, Damon P; Duong, Timothy Q

    2016-06-01

    The brain depends on a continuous supply of oxygen to maintain its structural and functional integrity. This study measured T1 from MRI under normobaric air, normobaric oxygen, hyperbaric air, and hyperbaric oxygen (HBO) conditions as a marker of tissue pO2 since dissolved molecular oxygen acts as an endogenous contrast agent. Brain tissue T1 decreased corresponding to increased pO2 with increasing inhaled oxygen concentrations, and tissue oxygenation was estimated from the T1 changes between different inhaled oxygen levels. Tissue pO2 difference maps between different oxygen conditions showed heterogeneous pO2 changes in the brain. MRI-derived tissue pO2 was markedly lower than the arterial pO2 but was slightly higher than venous pO2. Additionally, for comparison with published extracellular tissue pO2 data obtained using oxygen electrodes and other invasive techniques, a model was used to estimate extracellular and intracellular pO2 from the MRI-derived mean tissue pO2. This required multiple assumptions, and so the effects of the assumptions and parameters used in modeling brain pO2 were evaluated. MRI-derived pO2 values were strongly dependent on assumptions about the extra- and intracellular compartments but were relatively less sensitive to variations in the relaxivity constant of oxygen and contribution from oxygen in the cerebral blood compartment. This approach may prove useful in evaluating tissue oxygenation in disease states such as stroke.

  6. 3D characterization of brain atrophy in Alzheimer's disease and mild cognitive impairment using tensor-based morphometry.

    PubMed

    Hua, Xue; Leow, Alex D; Lee, Suh; Klunder, Andrea D; Toga, Arthur W; Lepore, Natasha; Chou, Yi-Yu; Brun, Caroline; Chiang, Ming-Chang; Barysheva, Marina; Jack, Clifford R; Bernstein, Matt A; Britson, Paula J; Ward, Chadwick P; Whitwell, Jennifer L; Borowski, Bret; Fleisher, Adam S; Fox, Nick C; Boyes, Richard G; Barnes, Josephine; Harvey, Danielle; Kornak, John; Schuff, Norbert; Boreta, Lauren; Alexander, Gene E; Weiner, Michael W; Thompson, Paul M

    2008-05-15

    Tensor-based morphometry (TBM) creates three-dimensional maps of disease-related differences in brain structure, based on nonlinearly registering brain MRI scans to a common image template. Using two different TBM designs (averaging individual differences versus aligning group average templates), we compared the anatomical distribution of brain atrophy in 40 patients with Alzheimer's disease (AD), 40 healthy elderly controls, and 40 individuals with amnestic mild cognitive impairment (aMCI), a condition conferring increased risk for AD. We created an unbiased geometrical average image template for each of the three groups, which were matched for sex and age (mean age: 76.1 years+/-7.7 SD). We warped each individual brain image (N=120) to the control group average template to create Jacobian maps, which show the local expansion or compression factor at each point in the image, reflecting individual volumetric differences. Statistical maps of group differences revealed widespread medial temporal and limbic atrophy in AD, with a lesser, more restricted distribution in MCI. Atrophy and CSF space expansion both correlated strongly with Mini-Mental State Exam (MMSE) scores and Clinical Dementia Rating (CDR). Using cumulative p-value plots, we investigated how detection sensitivity was influenced by the sample size, the choice of search region (whole brain, temporal lobe, hippocampus), the initial linear registration method (9- versus 12-parameter), and the type of TBM design. In the future, TBM may help to (1) identify factors that resist or accelerate the disease process, and (2) measure disease burden in treatment trials.

  7. 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

  8. The brain MRI classification problem from wavelets perspective

    NASA Astrophysics Data System (ADS)

    Bendib, Mohamed M.; Merouani, Hayet F.; Diaba, Fatma

    2015-02-01

    Haar and Daubechies 4 (DB4) are the most used wavelets for brain MRI (Magnetic Resonance Imaging) classification. The former is simple and fast to compute while the latter is more complex and offers a better resolution. This paper explores the potential of both of them in performing Normal versus Pathological discrimination on the one hand, and Multiclassification on the other hand. The Whole Brain Atlas is used as a validation database, and the Random Forest (RF) algorithm is employed as a learning approach. The achieved results are discussed and statistically compared.

  9. Complex and magnitude-only preprocessing of 2D and 3D BOLD fMRI data at 7 T.

    PubMed

    Barry, Robert L; Strother, Stephen C; Gore, John C

    2012-03-01

    A challenge to ultra high field functional magnetic resonance imaging is the predominance of noise associated with physiological processes unrelated to tasks of interest. This degradation in data quality may be partially reversed using a series of preprocessing algorithms designed to retrospectively estimate and remove the effects of these noise sources. However, such algorithms are routinely validated only in isolation, and thus consideration of their efficacies within realistic preprocessing pipelines and on different data sets is often overlooked. We investigate the application of eight possible combinations of three pseudo-complementary preprocessing algorithms - phase regression, Stockwell transform filtering, and retrospective image correction - to suppress physiological noise in 2D and 3D functional data at 7 T. The performance of each preprocessing pipeline was evaluated using data-driven metrics of reproducibility and prediction. The optimal preprocessing pipeline for both 2D and 3D functional data included phase regression, Stockwell transform filtering, and retrospective image correction. This result supports the hypothesis that a complex preprocessing pipeline is preferable to a magnitude-only pipeline, and suggests that functional magnetic resonance imaging studies should retain complex images and externally monitor subjects' respiratory and cardiac cycles so that these supplementary data may be used to retrospectively reduce noise and enhance overall data quality.

  10. 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

  11. A novel brain stimulation technology provides compatibility with MRI.

    PubMed

    Serano, Peter; Angelone, Leonardo M; Katnani, Husam; Eskandar, Emad; Bonmassar, Giorgio

    2015-04-29

    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.

  12. 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'.

  13. 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’.

  14. 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. PMID:27512372

  15. 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.

  16. 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

  17. 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)).

  18. Human brain diffusion tensor imaging at submillimeter isotropic resolution on a 3 Tesla clinical MRI scanner

    PubMed Central

    Chang, Hing-Chiu; Sundman, Mark; Petit, Laurent; Guhaniyogi, Shayan; Chu, Mei-Lan; Petty, Christopher; Song, Allen W.; Chen, Nan-kuei

    2015-01-01

    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 submillimeter isotropic resolution. To our knowledge, in vivo human brain DTI at 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 × 0.85 mm3) in vivo human brain DTI on a 3 Tesla 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 × 2 mm3). PMID:26072250

  19. 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.

  20. 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

    2016-11-01

    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.

  1. 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.

  2. 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

  3. 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.

  4. 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

  5. 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

  6. [Application of CT and MRI in the Diagnosis of Paragonimiasis in Brain and Spinal Cord].

    PubMed

    Li, Qiang; Qin, Da-ming

    2015-02-01

    Clinical data of 22 cases with paragonimiasis in brain and spinal cord in the Central Hospital of Enshi Tujia and Miao Autonomous Prefecture during 2003 -2012 were retrospectively analyzed. Twenty-two cases aged from 6 to 17 years old, including 15 males and 7 females, were from the countryside, and had a history of eating raw crabs. CT and MRI showed that all the cases had cerebral lesion, 16 cases had unilateral lesion of cerebral hemisphere, and 6 cases had bilateral hemisphere lesions. There were mainly two kinds of imaging changes: (1) the infarct and low- density edema of large area with focal hemorrhage; (2) annular lesions. Among the 6 cases with intracerebral hematoma, 2 patients received surgical removal, and all the patients were treated with praziquantel, 25 mg/kg each time, 3 times per day, 3 d for a course. This regimen was repeated at a 7-day interval. All the patients were cured and discharged from hospital.

  7. 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

  8. 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.

  9. Brain activity during stepping: a novel MRI-compatible device.

    PubMed

    Hollnagel, Christoph; Brügger, Mike; Vallery, Heike; Wolf, Peter; Dietz, Volker; Kollias, Spyros; Riener, Robert

    2011-09-30

    Little is known about the impact of supraspinal centers on the control of human locomotion. Analyzing brain activity can help to clarify their impact and to improve the effects of locomotor training. A fMRI-compatible pneumatic robotic device is presented that can generate freely programmable, highly repetitive periodic active and passive leg movements comprised by hip, knee, and ankle joint displacements. Forces of up to 400N can be applied to each foot while the subject is lying in a supine position. Magnetic interference of the device with the magnetic field of the scanner is measurable, but does not affect the image quality as obtained by a usual image analysis procedure. In a first experiment, brain activity of one healthy subject was acquired during nine different gait-like movement conditions. Brain activity in the somatosensory and motor function related areas increased more when the subject actively moved the legs than when the legs were passively moved by the device. In almost all conditions, mean head motion could be limited to 2mm within the duration of one fMRI scan by a specifically developed head and trunk fixation system. Based on these results, it is concluded that our device will significantly contribute to a better understanding of human locomotor control and related therapeutic effects in spinal cord injured and stroke patients, and thereby, to improve training approaches. PMID:21827788

  10. Multi-material 3-D viscoelastic model of a transtibial residuum from in-vivo indentation and MRI data.

    PubMed

    Sengeh, David M; Moerman, Kevin M; Petron, Arthur; Herr, Hugh

    2016-06-01

    Although the socket is critical in a prosthetic system for a person with limb amputation, the methods of its design are largely artisanal. A roadblock for a repeatable and quantitative socket design process is the lack of predictive and patient specific biomechanical models of the residuum. This study presents the evaluation of such a model using a combined experimental-numerical approach. The model geometry and tissue boundaries are derived from magnetic resonance imaging (MRI). The soft tissue non-linear elastic and viscoelastic mechanical behavior was evaluated using inverse finite element analysis (FEA) of in-vivo indentation experiments. A custom designed robotic in-vivo indentation system was used to provide a rich experimental data set of force versus time at 18 sites across a limb. During FEA, the tissues were represented by two layers, namely the skin-adipose layer and an underlying muscle-soft tissue complex. The non-linear elastic behavior was modeled using 2nd order Ogden hyperelastic formulations, and viscoelasticity was modeled using the quasi-linear theory of viscoelasticity. To determine the material parameters for each tissue, an inverse FEA based optimization routine was used that minimizes the combined mean of the squared force differences between the numerical and experimental force-time curves for indentations at 4 distinct anatomical regions on the residuum. The optimization provided the following material parameters for the skin-adipose layer: [c=5.22kPam=4.79γ=3.57MPaτ=0.32s] and for the muscle-soft tissue complex [c=5.20kPam=4.78γ=3.47MPaτ=0.34s]. These parameters were evaluated to predict the force-time curves for the remaining 14 anatomical locations. The mean percentage error (mean absolute error/ maximum experimental force) for these predictions was 7±3%. The mean percentage error at the 4 sites used for the optimization was 4%. PMID:26946095

  11. 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.

  12. 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

  13. Impossible expectations: fMRI adaptation in the lateral occipital complex (LOC) is modulated by the statistical regularities of 3D structural information.

    PubMed

    Freud, Erez; Ganel, Tzvi; Avidan, Galia

    2015-11-15

    fMRI adaptation (fMRIa), the attenuation of fMRI signal which follows repeated presentation of a stimulus, is a well-documented phenomenon. Yet, the underlying neural mechanisms supporting this effect are not fully understood. Recently, short-term perceptual expectations, induced by specific experimental settings, were shown to play an important modulating role in fMRIa. Here we examined the role of long-term expectations, based on 3D structural statistical regularities, in the modulation of fMRIa. To this end, human participants underwent fMRI scanning while performing a same-different task on pairs of possible (regular, expected) objects and spatially impossible (irregular, unexpected) objects. We hypothesized that given the spatial irregularity of impossible objects in relation to real-world visual experience, the visual system would always generate a prediction which is biased to the possible version of the objects. Consistently, fMRIa effects in the lateral occipital cortex (LOC) were found for possible, but not for impossible objects. Additionally, in alternating trials the order of stimulus presentation modulated LOC activity. That is, reduced activation was observed in trials in which the impossible version of the object served as the prime object (i.e. first object) and was followed by the possible version compared to the reverse order. These results were also supported by the behavioral advantage observed for trials that were primed by possible objects. Together, these findings strongly emphasize the importance of perceptual expectations in object representation and provide novel evidence for the role of real-world statistical regularities in eliciting fMRIa.

  14. Spatial heterogeneity analysis of brain activation in fMRI

    PubMed Central

    Gupta, Lalit; Besseling, René M.H.; Overvliet, Geke M.; Hofman, Paul A.M.; de Louw, Anton; Vaessen, Maarten J.; Aldenkamp, Albert P.; Ulman, Shrutin; Jansen, Jacobus F.A.; Backes, Walter H.

    2014-01-01

    In many brain diseases it can be qualitatively observed that spatial patterns in blood oxygenation level dependent (BOLD) activation maps appear more (diffusively) distributed than in healthy controls. However, measures that can quantitatively characterize this spatial distributiveness in individual subjects are lacking. In this study, we propose a number of spatial heterogeneity measures to characterize brain activation maps. The proposed methods focus on different aspects of heterogeneity, including the shape (compactness), complexity in the distribution of activated regions (fractal dimension and co-occurrence matrix), and gappiness between activated regions (lacunarity). To this end, functional MRI derived activation maps of a language and a motor task were obtained in language impaired children with (Rolandic) epilepsy and compared to age-matched healthy controls. Group analysis of the activation maps revealed no significant differences between patients and controls for both tasks. However, for the language task the activation maps in patients appeared more heterogeneous than in controls. Lacunarity was the best measure to discriminate activation patterns of patients from controls (sensitivity 74%, specificity 70%) and illustrates the increased irregularity of gaps between activated regions in patients. The combination of heterogeneity measures and a support vector machine approach yielded further increase in sensitivity and specificity to 78% and 80%, respectively. This illustrates that activation distributions in impaired brains can be complex and more heterogeneous than in normal brains and cannot be captured fully by a single quantity. In conclusion, heterogeneity analysis has potential to robustly characterize the increased distributiveness of brain activation in individual patients. PMID:25161893

  15. Phase II trial of temozolomide and reirradiation using conformal 3D-radiotherapy in recurrent brain gliomas

    PubMed Central

    2014-01-01

    Purpose This phase II trial was designed to assess the response rate, survival benefits and toxicity profile of temozolomide, and brain reirradiation using conformal radiotherapy (RT) for treatment of recurrent high grade glioma. Design Open-label phase II trial. Patients Twenty-nine patients had been enrolled in the study between February 2006 and June 2009. Patients had to show unequivocal evidence of tumour recurrence on gadolinium-enhanced magnetic resonance imaging (MRI) after failing conventional RT with or without temozolomide and surgery for initial disease. Histology included recurrent anaplastic astrocytoma, glioblastoma multiforme. Interventions Patients were treated by temozolomide at a dose of 200 mg/m2/day for chemonaïve patients, and at a dose of 150 mg/m2/day to previously treated patients, for 4-5 cycles. Then, patients underwent reirradiation by conformal RT at a dose of 30-40 Gy by conventional fractionation. Main outcome measures The primary end point of the study was response. The secondary end points included survival benefit. Results All the 29 patients were treated with temozolomide and reirradiation. Two patients achieved complete remission (CR), 4 achieved partial remission (PR), with an overall objective response rate of 20.6%, and further 10 patients had stable disease (SD), with a SD rate of 34.4%. The mean progression free survival (PFS) was 10.1 months, and the mean overall survival (OS) was 11.4 months. Additionally, treatment significantly improved quality of life (QOL). Treatment was tolerated well with mild grade 1, 2 nausea/vomiting in 40% of cycles, and mild grade 1, 2 haematological toxicities (neutropenia/thrombocytoprnia) in 8.6% of cycles. Conclusions Temozolomide and conformal RT had an anti-tumor activity in recurrent high grade glioma, and represented a good treatment hope for patients with recurrent brain glioma. PMID:25333019

  16. 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

  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

    2016-01-01

    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

  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. 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.

  20. Brain tumor segmentation in MRI based on fuzzy aggregators

    NASA Astrophysics Data System (ADS)

    Zhu, Yan; Liao, Qingmin; Dou, Weibei; Ruan, Su

    2005-07-01

    Magnetic Resonance Image (MRI) is widely used in radiology diagnosis, especially in pathology detection in human brain. Most of the methods now applied to automatically segment brain tumors rely on T1-weighted sequences exclusively despite the fact that the imaging agent is multi-spectral. The work focuses on the integration or fusion of information provided by each sequence, i.e. T1, T2 and PD. Based on the fuzzy aggregators proposed in fuzzy theory, a system integrating all these information is established. The paper discusses some famous operators, their properties and application in tumor segmentation. In particular, Davies-Bouldin index is used to determine the parameters of the parametric operations. The result shows the importance of data fusion in segmentation process, discovers that T-norms are less robust to noise compared with mean operators. Meanwhile, weights allocated illustrate the order of importance of each spectrum in pathology detection, and are in agreement with their characteristic.

  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. PMID:26465238

  2. 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

  3. 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.

  4. Brain perfusion SPECT and MRI in foetal alcohol syndrome.

    PubMed

    Riikonen, R; Salonen, I; Partanen, K; Verho, S

    1999-10-01

    Six boys and five girls with a mean age of 8.6 (range 3 to 13) years with foetal alcohol syndrome (FAS) were studied by MRI and single photon emission computed tomography (SPECT) to find specific areas of vulnerability. Morphological anomalies shown in six of 11 patients by MRI were situated both cortically and subcortically: cortical atrophy (N = 2), dilated ventricle (N = 1), corpus callosum hypoplasia (N = 1), cerebellar atrophy (N = 2), one of the latter with Arnold-Chiari malformation (N = 1). Delayed myelination of the white matter was seen in two patients. Volumetric studies of the hippocampus showed morphological left-right asymmetry in five of eight patients. However, SPECT showed mild hypoperfusion of the left hemisphere in all 10 subjects. The negative left-right index was located especially in the left parietooccipital region, i.e. in the brain areas implicated in arithmetical and logical-grammatical functions, which are known to be affected in FAS. Normal left-right dominance was also lacking in the frontal area, i.e. the brain area affected in attention-deficit-hyperactivity disorder (ADHD). Detection of these abnormalities, although they are not unique to FAS, may be helpful in the diagnosis and any attempts at rehabilitation. Diverse morphological and functional abnormalities are more frequent than has usually been believed even in less impaired children with FAS.

  5. Investigating the physiology of brain activation with MRI

    NASA Astrophysics Data System (ADS)

    Buxton, Richard B.; Uludag, Kamil; Dubowitz, David J.

    2004-04-01

    Functional magnetic resonance imaging (fMRI) has become a powerful tool for investigating the working human brain based on the blood oxygenation level dependent (BOLD) effect on the MR signal. However, despite the widespread use of fMRI techniques for mapping brain activation, the basic physiological mechanisms underlying the observed signal changes are still poorly understood. Arterial spin labeling (ASL) techniques, which measure cerebral blood flow (CBF) and the BOLD effect simultaneously, provide a useful tool for investigating these physiological questions. In this paper, recent results of studies manipulating the baseline CBF both pharmacologically and physiologically will be discussed. These data are consistent with a feed-forward mechanism of neurovascular coupling, and suggest that the CBF change itself may be a more robust reflection of neural activity changes than the BOLD effect. Consistent with these data, a new thermodynamic hypothesis is proposed for the physiological function of CBF regulation: maintenance of the [O2]/[CO2] concentration ratio at the mitochondria in order to preserve the free energy available from oxidative metabolism. A kinetic model based on this hypothesis provides a reasonable quantitative description of the CBF changes associated with neural activity and altered blood gases (CO2 and O2).

  6. Brain CT and MRI: differential diagnosis of imaging findings.

    PubMed

    Masdeu, Joseph C; Gadhia, Rajan; Faridar, Alireza

    2016-01-01

    Following a traditional approach, in Chapters 5 and 14-29 in the previous volume, diverse brain diseases are listed and their imaging findings described in detail. In this chapter the approach is from the imaging finding to the disease: for instance, what list of diseases can give rise to a contrast-enhancing mass in the cerebellopontine angle? Imaging findings that are reviewed in succession include the location of the lesion, its multiplicity and symmetry, its volume, ranging from atrophy to mass effect, its homogeneity, its density, measurable by computed tomography (CT), its appearance on T1, T2, and diffusion magnetic resonance imaging (MRI), and, finally, its characteristics after the infusion of intravenous contrast. A differential diagnosis for each finding is provided. While the approach adopted in this chapter is unconventional, we hope that it will be most helpful to anyone reading images. Furthermore, it could serve as the basis to create or complete image databases to guide in the interpretation of brain CT and MRI. PMID:27430457

  7. 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…

  8. 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.

  9. Multi-modal MRI of mild traumatic brain injury

    PubMed Central

    Narayana, Ponnada A.; Yu, Xintian; Hasan, Khader M.; Wilde, Elisabeth A.; Levin, Harvey S.; Hunter, Jill V.; Miller, Emmy R.; Patel, Vipul Kumar S.; Robertson, Claudia S.; McCarthy, James J.

    2014-01-01

    Multi-modal magnetic resonance imaging (MRI) that included high resolution structural imaging, diffusion tensor imaging (DTI), magnetization transfer ratio (MTR) imaging, and magnetic resonance spectroscopic imaging (MRSI) were performed in mild traumatic brain injury (mTBI) patients with negative computed tomographic scans and in an orthopedic-injured (OI) group without concomitant injury to the brain. The OI group served as a comparison group for mTBI. MRI scans were performed both in the acute phase of injury (~24 h) and at follow-up (~90 days). DTI data was analyzed using tract based spatial statistics (TBSS). Global and regional atrophies were calculated using tensor-based morphometry (TBM). MTR values were calculated using the standard method. MRSI was analyzed using LC Model. At the initial scan, the mean diffusivity (MD) was significantly higher in the mTBI cohort relative to the comparison group in several white matter (WM) regions that included internal capsule, external capsule, superior corona radiata, anterior corona radiata, posterior corona radiata, inferior fronto-occipital fasciculus, inferior longitudinal fasciculus, forceps major and forceps minor of the corpus callosum, superior longitudinal fasciculus, and corticospinal tract in the right hemisphere. TBSS analysis failed to detect significant differences in any DTI measures between the initial and follow-up scans either in the mTBI or OI group. No significant differences were found in MRSI, MTR or morphometry between the mTBI and OI cohorts either at the initial or follow-up scans with or without family wise error (FWE) correction. Our study suggests that a number of WM tracts are affected in mTBI in the acute phase of injury and that these changes disappear by 90 days. This study also suggests that none of the MRI-modalities used in this study, with the exception of DTI, is sensitive in detecting changes in the acute phase of mTBI. PMID:25610770

  10. Multi-modal MRI of mild traumatic brain injury.

    PubMed

    Narayana, Ponnada A; Yu, Xintian; Hasan, Khader M; Wilde, Elisabeth A; Levin, Harvey S; Hunter, Jill V; Miller, Emmy R; Patel, Vipul Kumar S; Robertson, Claudia S; McCarthy, James J

    2015-01-01

    Multi-modal magnetic resonance imaging (MRI) that included high resolution structural imaging, diffusion tensor imaging (DTI), magnetization transfer ratio (MTR) imaging, and magnetic resonance spectroscopic imaging (MRSI) were performed in mild traumatic brain injury (mTBI) patients with negative computed tomographic scans and in an orthopedic-injured (OI) group without concomitant injury to the brain. The OI group served as a comparison group for mTBI. MRI scans were performed both in the acute phase of injury (~24 h) and at follow-up (~90 days). DTI data was analyzed using tract based spatial statistics (TBSS). Global and regional atrophies were calculated using tensor-based morphometry (TBM). MTR values were calculated using the standard method. MRSI was analyzed using LC Model. At the initial scan, the mean diffusivity (MD) was significantly higher in the mTBI cohort relative to the comparison group in several white matter (WM) regions that included internal capsule, external capsule, superior corona radiata, anterior corona radiata, posterior corona radiata, inferior fronto-occipital fasciculus, inferior longitudinal fasciculus, forceps major and forceps minor of the corpus callosum, superior longitudinal fasciculus, and corticospinal tract in the right hemisphere. TBSS analysis failed to detect significant differences in any DTI measures between the initial and follow-up scans either in the mTBI or OI group. No significant differences were found in MRSI, MTR or morphometry between the mTBI and OI cohorts either at the initial or follow-up scans with or without family wise error (FWE) correction. Our study suggests that a number of WM tracts are affected in mTBI in the acute phase of injury and that these changes disappear by 90 days. This study also suggests that none of the MRI-modalities used in this study, with the exception of DTI, is sensitive in detecting changes in the acute phase of mTBI.

  11. Patient-Specific Carotid Plaque Progression Simulation Using 3D Meshless Generalized Finite Difference Models with Fluid-Structure Interactions Based on Serial In Vivo MRI Data.

    PubMed

    Yang, Chun; Tang, Dalin; Atluri, Satya

    2011-01-01

    Previously, we introduced a computational procedure based on three-dimensional meshless generalized finite difference (MGFD) method and serial magnetic resonance imaging (MRI) data to quantify patient-specific carotid atherosclerotic plaque growth functions and simulate plaque progression. Structure-only models were used in our previous report. In this paper, fluid-stricture interaction (FSI) was added to improve on prediction accuracy. One participating patient was scanned three times (T1, T2, and T3, at intervals of about 18 months) to obtain plaque progression data. Blood flow was assumed to laminar, Newtonian, viscous and incompressible. The Navier-Stokes equations with arbitrary Lagrangian-Eulerian (ALE) formulation were used as the governing equations. Plaque material was assumed to be uniform, homogeneous, isotropic, linear, and nearly incompressible. The linear elastic model was used. The 3D FSI plaque model was discretized and solved using a meshless generalized finite difference (GFD) method. Growth functions with a) morphology alone; b) morphology and plaque wall stress (PWS); morphology and flow shear stress (FSS), and d) morphology, PWS and FSS were introduced to predict future plaque growth based on previous time point data. Starting from the T2 plaque geometry, plaque progression was simulated by solving the FSI model and adjusting plaque geometry using plaque growth functions iteratively until T3 is reached. Numerically simulated plaque progression agreed very well with the target T3 plaque geometry with errors ranging from 8.62%, 7.22%, 5.77% and 4.39%, with the growth function including morphology, plaque wall stress and flow shear stress terms giving the best predictions. Adding flow shear stress term to the growth function improved the prediction error from 7.22% to 4.39%, a 40% improvement. We believe this is the first time 3D plaque progression FSI simulation based on multi-year patient-tracking data was reported. Serial MRI-based progression

  12. 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

    2012-04-01

    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.

  13. A methodology to accurately quantify patellofemoral cartilage contact kinematics by combining 3D image shape registration and cine-PC MRI velocity data

    PubMed Central

    Borotikar, Bhushan S.; Sipprell, William H.; Wible, Emily E.; Sheehan, Frances T.

    2012-01-01

    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 0.47mm–0.77mm for the patella and femur and 0.68mm–0.86 mm for the patellofemoral joint. For purely quantifying joint kinematics, CPC remains an analytically simpler and more accurate (accuracy < 0.33mm) 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. PMID:22284428

  14. 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

  15. 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.

  16. MRI measurement of angiogenesis and the therapeutic effect of acute marrow stromal cell administration on traumatic brain injury.

    PubMed

    Li, Lian; Chopp, Michael; Ding, Guang Liang; Qu, Chang Sheng; Li, Qing Jiang; Lu, Mei; Wang, Shiyang; Nejad-Davarani, Siamak P; Mahmood, Asim; Jiang, Quan

    2012-11-01

    Using magnetic resonance imaging (MRI), the present study was undertaken to investigate the therapeutic effect of acute administration of human bone marrow stromal cells (hMSCs) on traumatic brain injury (TBI) and to measure the temporal profile of angiogenesis after the injury with or without cell intervention. Male Wistar rats (300 to 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, 3 × 10(6) hMSCs) 6 hours after TBI. In-vivo MRI acquisitions of T2-weighted imaging, cerebral blood flow (CBF), three-dimensional (3D) gradient echo imaging, and blood-to-brain transfer constant (Ki) of contrast agent were performed on all animals 2 days after injury and weekly for 6 weeks. Sensorimotor function and spatial learning were evaluated. Volumetric changes in the trauma-induced brain lesion and the lateral ventricles were tracked and quantified using T2 maps, and hemodynamic alteration and blood-brain barrier permeability were monitored by CBF and Ki, respectively. Our data show that transplantation of hMSCs 6 hours after TBI leads to reduced cerebral atrophy, early and enhanced cerebral tissue perfusion and improved functional outcome compared with controls. The hMSC treatment increases angiogenesis in the injured brain, which may promote neurologic recovery after TBI.

  17. Brain potential and functional MRI evidence for how to handle two languages with one brain.

    PubMed

    Rodriguez-Fornells, Antoni; Rotte, Michael; Heinze, Hans-Jochen; Nösselt, Tömme; Münte, Thomas F

    2002-02-28

    Bilingual individuals need effective mechanisms to prevent interference from one language while processing material in the other. Here we show, using event-related brain potentials and functional magnetic resonance imaging (fMRI), that words from the non-target language are rejected at an early stage before semantic analysis in bilinguals. Bilingual Spanish/Catalan and monolingual Spanish subjects were instructed to press a button when presented with words in one language, while ignoring words in the other language and pseudowords. The brain potentials of bilingual subjects in response to words of the non-target language were not sensitive to word frequency, indicating that the meaning of non-target words was not accessed in bilinguals. The fMRI activation patterns of bilinguals included a number of areas previously implicated in phonological and pseudoword processing, suggesting that bilinguals use an indirect phonological access route to the lexicon of the target language to avoid interference.

  18. 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.

  19. Brain MRI Segmentation with Multiphase Minimal Partitioning: A Comparative Study

    PubMed Central

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

    2007-01-01

    This paper presents the implementation and quantitative evaluation of a multiphase three-dimensional deformable model in 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 minimize the sensitivity of the method to initial conditions while avoiding the need for a priori information. This random initialization ensures robustness of the method with respect to the initialization and the minimization set up. Postprocessing corrections with morphological operators were applied to refine the details of the global segmentation method. A clinical study was performed on a database of 10 adult brain MRI volumes to compare the level set segmentation to three other methods: “idealized” intensity thresholding, fuzzy connectedness, and an expectation maximization classification using hidden Markov random fields. Quantitative evaluation of segmentation accuracy was performed with comparison to manual segmentation computing true positive and false positive volume fractions. A statistical comparison of the segmentation methods was performed through a Wilcoxon analysis of these error rates and results showed very high quality and stability of the multiphase three-dimensional level set method. PMID:18253474

  20. Fetal Brain during a Binge Drinking Episode: A dynamic susceptibility contrast MRI fetal brain perfusion study

    PubMed Central

    Kochunov, Peter; Castro, Carlos; Davis, Duff M; Dudley, Donald; Wey, Hsiao-Ying; Purdy, David; Fox, Peter T; Simerly, Calvin; Schatten, Gerald

    2010-01-01

    We assessed the effects of a single episode of maternal alcohol intoxication on fetal brain blood perfusion in three pregnant dam (baboons) at the 24th week of pregnancy, using dynamic susceptibility contrast MRI. Following the oral administration of alcohol there was a four-fold increase in the peak contrast concentrations in the fetal brain. Additionally, we observed a two-to-three fold increase in the contrast uptake and washout rates in fetal brain. The underlying mechanisms of these changes are unknown but we hypothesized these could include the alcohol-mediated changes in placental permeability and fetal cerebral blood flow. Our findings indicate that alcohol intoxication produced profound changes, which may detrimentally influence neurodevelopmental processes in the brain. PMID:20505549

  1. A Quantitative MRI Method for Imaging Blood-Brain Barrier Leakage in Experimental Traumatic Brain Injury

    PubMed Central

    Watts, Lora Talley; Jiang, Zhao; Shen, Qiang; Li, Yunxia; Duong, Timothy Q.

    2014-01-01

    Blood-brain barrier (BBB) disruption is common following traumatic brain injury (TBI). Dynamic contrast enhanced (DCE) MRI can longitudinally measure the transport coefficient Ktrans which reflects BBB permeability. Ktrans measurements however are not widely used in TBI research because it is generally considered to be noisy and possesses low spatial resolution. We improved spatiotemporal resolution and signal sensitivity of Ktrans MRI in rats by using a high-sensitivity surface transceiver coil. To overcome the signal drop off profile of the surface coil, a pre-scan module was used to map the flip angle (B1 field) and magnetization (M0) distributions. A series of T1-weighted gradient echo images were acquired and fitted to the extended Kety model with reversible or irreversible leakage, and the best model was selected using F-statistics. We applied this method to study the rat brain one hour following controlled cortical impact (mild to moderate TBI), and observed clear depiction of the BBB damage around the impact regions, which matched that outlined by Evans Blue extravasation. Unlike the relatively uniform T2 contrast showing cerebral edema, Ktrans shows a pronounced heterogeneous spatial profile in and around the impact regions, displaying a nonlinear relationship with T2. This improved Ktrans MRI method is also compatible with the use of high-sensitivity surface coil and the high-contrast two-coil arterial spin-labeling method for cerebral blood flow measurement, enabling more comprehensive investigation of the pathophysiology in TBI. PMID:25478693

  2. 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

  3. 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

    2014-07-01

    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

  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. 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.

  6. 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

  7. Application of State-Space Smoothing to fMRI Data for Calculation of Lagged Transinformation between Human Brain Activations

    NASA Astrophysics Data System (ADS)

    Watanabe, Jobu

    2009-09-01

    Mutual information can be given a directional sense by introducing a time lag in one of the variables. In an author's previous study, to investigate the network dynamics of human brain regions, lagged transinformation (LTI) was introduced using time delayed mutual information. The LTI makes it possible to quantify the time course of dynamic information transfer between regions in the temporal domain. The LTI was applied to functional magnetic resonance imaging (fMRI) data involved in neural processing of the transformation and comparison from three-dimensional (3D) visual information to a two-dimensional (2D) location to calculate directed information flows between the activated brain regions. In the present study, for more precise estimation of LTI, Kalman filter smoothing was applied to the same fMRI data. Because the smoothing method exploits the full length of the time series data for the estimation, its application increases the precision. Large information flows were found from the bilateral prefrontal cortices to the parietal cortices. The results suggest that information of the 3D images stored as working memory was retrieved and transferred from the prefrontal cortices to the parietal cortices for comparison with information of the 2D images.

  8. Myelin and iron concentration in the human brain: a quantitative study of MRI contrast.

    PubMed

    Stüber, Carsten; Morawski, Markus; Schäfer, Andreas; Labadie, Christian; Wähnert, Miriam; Leuze, Christoph; Streicher, Markus; Barapatre, Nirav; Reimann, Katja; Geyer, Stefan; Spemann, Daniel; Turner, Robert

    2014-06-01

    During the last five years ultra-high-field magnetic resonance imaging (MRI) has enabled an unprecedented view of living human brain. Brain tissue contrast in most MRI sequences is known to reflect mainly the spatial distributions of myelin and iron. These distributions have been shown to overlap significantly in many brain regions, especially in the cortex. It is of increasing interest to distinguish and identify cortical areas by their appearance in MRI, which has been shown to be feasible in vivo. Parcellation can benefit greatly from quantification of the independent contributions of iron and myelin to MRI contrast. Recent studies using susceptibility mapping claim to allow such a separation of the effects of myelin and iron in MRI. We show, using post-mortem human brain tissue, that this goal can be achieved. After MRI scanning of the block with appropriate T1 mapping and T2* weighted sequences, we section the block and apply a novel technique, proton induced X-ray emission (PIXE), to spatially map iron, phosphorus and sulfur elemental concentrations, simultaneously with 1μm spatial resolution. Because most brain phosphorus is located in myelin phospholipids, a calibration step utilizing element maps of sulfur enables semi-quantitative ex vivo mapping of myelin concentration. Combining results for iron and myelin concentration in a linear model, we have accurately modeled MRI tissue contrasts. Conversely, iron and myelin concentrations can now be estimated from appropriate MRI measurements in post-mortem brain samples. PMID:24607447

  9. 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.

  10. 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

  11. 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

  12. 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

    2015-01-01

    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

  13. 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

  14. Vascular Factors and Multiple Measures of Early Brain Health: CARDIA Brain MRI Study

    PubMed Central

    Launer, Lenore J.; Lewis, Cora E.; Schreiner, Pamela J.; Sidney, Steve; Battapady, Harsha; Jacobs, David R.; Lim, Kelvin O.; D’Esposito, Mark; Zhang, Qian; Reis, Jared; Davatzikos, Christos; Bryan, R. Nick

    2015-01-01

    Objective To identify early changes in brain structure and function that are associated with cardiovascular risk factors (CVRF). Design Cross-sectional brain Magnetic Resonance I (MRI) study. Setting Community based cohort in three U.S. sites. Participants A Caucasian and African-American sub-sample (n= 680; mean age 50.3 yrs) attending the 25 year follow-up exam of the Coronary Artery Risk Development in Young Adults Study. Primary and Secondary Outcomes 3T brain MR images processed for quantitative estimates of: total brain (TBV) and abnormal white matter (AWM) volume; white matter fractional anisotropy (WM-FA); and gray matter cerebral blood flow (GM-CBF). Total intracranial volume is TBV plus cerebral spinal fluid (TICV). A Global Cognitive Function (GCF) score was derived from tests of speed, memory and executive function. Results Adjusting for TICV and demographic factors, current smoking was significantly associated with lower GM-CBF and TBV, and more AWM (all <0.05); SA with lower GM-CBF, WM-FA and TBV (p=0.01); increasing BMI with decreasing GM-CBF (p<0003); hypertension with lower GM-CBF, WM-FA, and TBV and higher AWM (all <0.05); and diabetes with lower TBV (p=0.007). The GCS was lower as TBV decreased, AWM increased, and WM-FA (all p<0.01). Conclusion In middle age adults, CVRF are associated with brain health, reflected in MRI measures of structure and perfusion, and cognitive functioning. These findings suggest markers of mid-life cardiovascular and brain health should be considered as indication for early intervention and future risk of late-life cerebrovascular disease and dementia. PMID:25812012

  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. The influence of resolution recovery by using collimator detector response during 3D OSEM image reconstruction on (99m)Tc-ECD brain SPET images.

    PubMed

    Kalantari, Faraz; Rajabi, Hossein; Ay, Mohammad Reza; Razavi-Ratki, Sied Kazem; Fard-Esfahani, Armaghan; Beiki, Davood; Eftekhari, Mohammad; Fallahi, Babak; Sadeghian, Leila; Emami-Ardekani, Alireza

    2012-01-01

    Partial volume effect, due to the poor spatial resolution of single photon emission tomography (SPET), significantly restricts the absolute quantification of the regional brain uptake and limits the accuracy of the absolute measurement of blood flow. In this study the importance of compensation for the collimator-detector response (CDR) in the technetium-99m ethyl cysteinate dimer ((99m)Tc-ECD) brain SPET was assessed, by incorporating system response in the ordered-subsets expectation maximization (OSEM) reconstruction algorithm. By placing a point source of (99m)Tc at different distances from the face of the collimator, CDR were found and modeled using Gaussian functions. A fillable slice of the brain phantom was designed and filled by (99m)Tc. Projections acquired from the phantom and also 4 patients who underwent the (99m)Tc-ECD brain SPET were used in this study. To reconstruct the images, 3D OSEM algorithm was used. System blurring functions were modeled, during the reconstruction in both projection and backprojection steps. Our results were compared with the conventional resolution recovery using Metz filter in filtered backprojection (FBP). Visual inspection of the images was performed by six nuclear medicine specialists. Quantitative analysis was also studied by calculating the contrast and the count density of the reconstructed images. For the phantom images, background counts and noise were decreased by 3D OSEM compared to the FBP-Metz method. Quantitatively, the ratio of the counts of the occupied hot region to that of the cold region of the reconstructed by FBP-Metz images was 1.14. This value was decreased from 1.12 to 0.86 for 3D OSEM of 2 and 30 iterations respectively. The reference value was 0.85 for the planar image. For clinical images, hot to cold regions (grey to white matter), the count ratio was increased from 1.44 in FBP-Metz to 3.2 and 4 in 3D OSEM with 10 and 20 iterations respectively. Based on the interpretability of images, the best

  17. 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.

  18. 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

  19. Quantitative Histological Validation of Diffusion MRI Fiber Orientation Distributions in the Rat Brain

    PubMed Central

    de Crespigny, Alex; Bolstad, Ingeborg; D'Arceuil, Helen; Bjaalie, Jan G.; Dale, Anders M.

    2010-01-01

    Diffusion MRI (dMRI) is widely used to measure microstructural features of brain white matter, but commonly used dMRI measures have limited capacity to resolve the orientation structure of complex fiber architectures. While several promising new approaches have been proposed, direct quantitative validation of these methods against relevant histological architectures remains missing. In this study, we quantitatively compare neuronal fiber orientation distributions (FODs) derived from ex vivo dMRI data against histological measurements of rat brain myeloarchitecture using manual recordings of individual myelin stained fiber orientations. We show that accurate FOD estimates can be obtained from dMRI data, even in regions with complex architectures of crossing fibers with an intrinsic orientation error of approximately 5–6 degrees in these regions. The reported findings have implications for both clinical and research studies based on dMRI FOD measures, and provide an important biological benchmark for improved FOD reconstruction and fiber tracking methods. PMID:20062822

  20. fMRI Brain-Computer Interface: A Tool for Neuroscientific Research and Treatment

    PubMed Central

    Sitaram, Ranganatha; Caria, Andrea; Veit, Ralf; Gaber, Tilman; Rota, Giuseppina; Kuebler, Andrea; Birbaumer, Niels

    2007-01-01

    Brain-computer interfaces based on functional magnetic resonance imaging (fMRI-BCI) allow volitional control of anatomically specific regions of the brain. Technological advancement in higher field MRI scanners, fast data acquisition sequences, preprocessing algorithms, and robust statistical analysis are anticipated to make fMRI-BCI more widely available and applicable. This noninvasive technique could potentially complement the traditional neuroscientific experimental methods by varying the activity of the neural substrates of a region of interest as an independent variable to study its effects on behavior. If the neurobiological basis of a disorder (e.g., chronic pain, motor diseases, psychopathy, social phobia, depression) is known in terms of abnormal activity in certain regions of the brain, fMRI-BCI can be targeted to modify activity in those regions with high specificity for treatment. In this paper, we review recent results of the application of fMRI-BCI to neuroscientific research and psychophysiological treatment. PMID:18274615

  1. [Research progress of techniques of 7 T MRI system in brain imaging].

    PubMed

    Lin, Lan; Hao, Dongmei; Bai, Yanping; Gao, Hongjian; Wu, Shuicai

    2013-10-01

    7 T high field magnetic resonance imaging (MRI) provides a useful tool for microscopic spatial resolution visualizing anatomy. In addition, it enables the observation and analysis of tissue metabolism and function. 7 T MRI is now developing fast both in its technology and in its potential prospective medical applications. This review introduces current applications and possible future developments of the 7 T MRI in the field of human brain imaging for clinical studies and practices.

  2. Visualization of brain surface features using registered partially segmented MRI scans

    NASA Astrophysics Data System (ADS)

    Myers, Loyd M.; Brinkley, James F.

    1995-04-01

    Intraoperative brain mapping of cortical language sites has generated a need for accurate visualization of the cortical surface with its associated arteries and veins. We describe a technique for registering multiple magnetic resonance imaging studies, segmenting those studies, and visualizing the combined vessels and cortical surface. The patient receives three pre-operative MRI scans corresponding to the three tissue types to be visualized. The studies are read into three volumes in the visualization software and voxel size information is then used to interpolate each of the volumes producing cubic voxels. The volumes are then cropped and translated interactively to be the exact same dimension and orientation. A region growing algorithm is applied to the most homogeneous volume (usually the vein data) to produce a mask which approximates the cortical region. A morphological dilation is performed on the mask expanding it to include features on or near the cortical surface. The mask is applied to the cortical surface, artery, and vein volumes, and they then become the green, red, and blue channels of a composite RGB volume. The resulting volume is selectively weighted and input to a ray-tracing algorithm which produces the final image. This technique provides neurosurgeons with an image containing the landmarks necessary to record intraoperative brain mapping data. Example results are presented which show that the generated cortical surface, including surface veins and arteries, corresponds closely to intraoperative photographs of the exposed cortical surface taken at the time of surgery. When combined with an image database and integrated into an interactive program this technique allows neurosurgeons to obtain accurate 3-D stimulation maps of functional areas on the brain surface.

  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. Chédiak-Higashi syndrome: brain MRI and MR spectroscopy manifestations.

    PubMed

    Lolli, Valentina; Soto Ares, Gustavo; Pruvo, Jean-Pierre; Abou Chahla, Wadih; Jissendi-Tchofo, Patrice

    2015-07-01

    Chédiak-Higashi syndrome is a rare inherited metabolic disorder characterized by partial oculocutaneous albinism, immunodeficiency, and neurological dysfunction. We present the brain magnetic resonance imaging (MRI) and MR spectroscopy (MRS) findings obtained during the accelerated phase of the disorder in an 8-year-old. The brain MRI manifestations at recurrences 15 months and 24 months later are reported as well. PMID:25875633

  5. Independent component analysis for brain fMRI does not select for independence

    PubMed Central

    Daubechies, I.; Roussos, E.; Takerkart, S.; Benharrosh, M.; Golden, C.; D'Ardenne, K.; Richter, W.; Cohen, J. D.; Haxby, J.

    2009-01-01

    InfoMax and FastICA are the independent component analysis algorithms most used and apparently most effective for brain fMRI. We show that this is linked to their ability to handle effectively sparse components rather than independent components as such. The mathematical design of better analysis tools for brain fMRI should thus emphasize other mathematical characteristics than independence. PMID:19556548

  6. A diffusion tensor MRI atlas of the postmortem rhesus macaque brain.

    PubMed

    Calabrese, Evan; Badea, Alexandra; Coe, Christopher L; Lubach, Gabriele R; Shi, Yundi; Styner, Martin A; Johnson, G Allan

    2015-08-15

    The rhesus macaque (Macaca mulatta) is the most widely used nonhuman primate for modeling the structure and function of the brain. Brain atlases, and particularly those based on magnetic resonance imaging (MRI), have become important tools for understanding normal brain structure, and for identifying structural abnormalities resulting from disease states, exposures, and/or aging. Diffusion tensor imaging (DTI)-based MRI brain atlases are widely used in both human and macaque brain imaging studies because of the unique contrasts, quantitative diffusion metrics, and diffusion tractography that they can provide. Previous MRI and DTI atlases of the rhesus brain have been limited by low contrast and/or low spatial resolution imaging. Here we present a microscopic resolution MRI/DTI atlas of the rhesus brain based on 10 postmortem brain specimens. The atlas includes both structural MRI and DTI image data, a detailed three-dimensional segmentation of 241 anatomic structures, diffusion tractography, cortical thickness estimates, and maps of anatomic variability among atlas specimens. This atlas incorporates many useful features from previous work, including anatomic label nomenclature and ontology, data orientation, and stereotaxic reference frame, and further extends prior analyses with the inclusion of high-resolution multi-contrast image data.

  7. Sensitivity and reproducibility of a new fast 3D segmentation technique for clinical MR-based brain volumetry in multiple sclerosis.

    PubMed

    Lukas, Carsten; Hahn, Horst K; Bellenberg, Barbara; Rexilius, Jan; Schmid, Gebhard; Schimrigk, Sebastian K; Przuntek, Horst; Köster, Odo; Peitgen, Heinz-Otto

    2004-11-01

    Fast, reliable and easy-to-use methods to quantify brain atrophy are of increasing importance in clinical studies on neuro-degenerative diseases. Here, ILAB 4, a new volumetry software that uses a fast semi-automated 3D segmentation of thin-slice T1-weighted 3D MR images based on a modified watershed transform and an automatic histogram analysis was evaluated. It provides the cerebral volumes: whole brain, white matter, gray matter and intracranial cavity. Inter- and intra-rater reliability and scan-rescan reproducibility were excellent in measuring whole brain volumes (coefficients of variation below 0.5%) of volunteers and patients. However, gray and white matter volumes were more susceptible to image quality. High accuracy of the absolute volume results (+/-5 ml) were shown by phantom and preparation measurements. Analysis times were 6 min for processing of 128 slices. The proposed technique is reliable and highly suitable for quantitative studies of brain atrophy, e.g., in multiple sclerosis. PMID:15536555

  8. 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.

  9. 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.

  10. 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

  11. 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

  12. 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.

  13. Parallel workflow tools to facilitate human brain MRI post-processing

    PubMed Central

    Cui, Zaixu; Zhao, Chenxi; Gong, Gaolang

    2015-01-01

    Multi-modal magnetic resonance imaging (MRI) techniques are widely applied in human brain studies. To obtain specific brain measures of interest from MRI datasets, a number of complex image post-processing steps are typically required. Parallel workflow tools have recently been developed, concatenating individual processing steps and enabling fully automated processing of raw MRI data to obtain the final results. These workflow tools are also designed to make optimal use of available computational resources and to support the parallel processing of different subjects or of independent processing steps for a single subject. Automated, parallel MRI post-processing tools can greatly facilitate relevant brain investigations and are being increasingly applied. In this review, we briefly summarize these parallel workflow tools and discuss relevant issues. PMID:26029043

  14. A robust framework for soft tissue simulations with application to modeling brain tumor mass effect in 3D MR images.

    PubMed

    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. PMID:18029982

  15. Enzyme-Immobilized 3D-Printed Reactors for Online Monitoring of Rat Brain Extracellular Glucose and Lactate.

    PubMed

    Su, Cheng-Kuan; Yen, Shuo-Chih; Li, Tzu-Wen; Sun, Yuh-Chang

    2016-06-21

    In this study we constructed a highly sensitive system for in vivo monitoring of the concentrations of rat brain extracellular glucose and lactate. This system involved microdialysis (MD) sampling and fluorescence determination in conjunction with a novel sample derivatization scheme in which glucose oxidase and lactate oxidase were immobilized in ABS flow bioreactors (manufactured through low-cost three-dimensional printing (3DP)), via fused deposition modeling, for online oxidization of sampled glucose and lactate, respectively, in rat brain microdialysate. After optimizing the experimental conditions for MD sampling, the manufacture of the designed flow reactors, the enzyme immobilization procedure, and the online derivatization scheme, the available sampling frequency was 15 h(-1) and the system's detection limits reached as low as 0.060 mM for glucose and 0.059 mM for lactate, based on a 20-μL conditioned microdialysate; these characteristics were sufficient to reliably determine the concentrations of extracellular glucose and lactate in the brains of living rats. To demonstrate the system's applicability, we performed (i) spike analyses of offline-collected rat brain microdialysate and (ii) in vivo dynamic monitoring of the extracellular glucose and lactate in living rat brains, in addition to triggering neuronal depolarization by perfusing a high-K(+) medium from the implanted MD probe. Our analytical results and demonstrations confirm that postprinting functionalization of analytical devices manufactured using 3DP technology can be a powerful strategy for extending the diversity and adaptability of currently existing analytical configurations. PMID:27232384

  16. Enzyme-Immobilized 3D-Printed Reactors for Online Monitoring of Rat Brain Extracellular Glucose and Lactate.

    PubMed

    Su, Cheng-Kuan; Yen, Shuo-Chih; Li, Tzu-Wen; Sun, Yuh-Chang

    2016-06-21

    In this study we constructed a highly sensitive system for in vivo monitoring of the concentrations of rat brain extracellular glucose and lactate. This system involved microdialysis (MD) sampling and fluorescence determination in conjunction with a novel sample derivatization scheme in which glucose oxidase and lactate oxidase were immobilized in ABS flow bioreactors (manufactured through low-cost three-dimensional printing (3DP)), via fused deposition modeling, for online oxidization of sampled glucose and lactate, respectively, in rat brain microdialysate. After optimizing the experimental conditions for MD sampling, the manufacture of the designed flow reactors, the enzyme immobilization procedure, and the online derivatization scheme, the available sampling frequency was 15 h(-1) and the system's detection limits reached as low as 0.060 mM for glucose and 0.059 mM for lactate, based on a 20-μL conditioned microdialysate; these characteristics were sufficient to reliably determine the concentrations of extracellular glucose and lactate in the brains of living rats. To demonstrate the system's applicability, we performed (i) spike analyses of offline-collected rat brain microdialysate and (ii) in vivo dynamic monitoring of the extracellular glucose and lactate in living rat brains, in addition to triggering neuronal depolarization by perfusing a high-K(+) medium from the implanted MD probe. Our analytical results and demonstrations confirm that postprinting functionalization of analytical devices manufactured using 3DP technology can be a powerful strategy for extending the diversity and adaptability of currently existing analytical configurations.

  17. 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

  18. The Ultrasound Brain Helmet: New Transducers and Volume Registration for In Vivo Simultaneous Multi-Transducer 3-D Transcranial Imaging

    PubMed Central

    Lindsey, Brooks D.; Light, Edward D.; Nicoletto, Heather A.; Bennett, Ellen R.; Laskowitz, Daniel T.; Smith, Stephen W.

    2012-01-01

    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. PMID:21693401

  19. Construction of brain atlases based on a multi-center MRI dataset of 2020 Chinese adults.

    PubMed

    Liang, Peipeng; Shi, Lin; Chen, Nan; Luo, Yishan; Wang, Xing; Liu, Kai; Mok, Vincent C T; Chu, Winnie C W; Wang, Defeng; Li, Kuncheng

    2015-01-01

    Despite the known morphological differences (e.g., brain shape and size) in the brains of populations of different origins (e.g., age and race), the Chinese brain atlas is less studied. In the current study, we developed a statistical brain atlas based on a multi-center high quality magnetic resonance imaging (MRI) dataset of 2020 Chinese adults (18-76 years old). We constructed 12 Chinese brain atlas from the age 20 year to the age 75 at a 5 years interval. New Chinese brain standard space, coordinates, and brain area labels were further defined. The new Chinese brain atlas was validated in brain registration and segmentation. It was found that, as contrast to the MNI152 template, the proposed Chinese atlas showed higher accuracy in hippocampus segmentation and relatively smaller shape deformations during registration. These results indicate that a population-specific time varying brain atlas may be more appropriate for studies involving Chinese populations. PMID:26678304

  20. 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.

  1. Repeated BOLD-fMRI imaging of deep brain stimulation responses in rats.

    PubMed

    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

  2. Language comprehension in the bilingual brain: fMRI and ERP support for psycholinguistic models.

    PubMed

    van Heuven, Walter J B; Dijkstra, Ton

    2010-09-01

    In this paper, we review issues in bilingual language comprehension in the light of functional magnetic resonance imaging (fMRI) and event-related brain potential (ERP) data. Next, we consider to what extent neuroimaging data are compatible with assumptions and characteristics of available psycholinguistic models of bilingual word processing, in particular the BIA+ model. We argue that this model provides a theoretical framework that is useful for interpreting both the spatial brain activation patterns observed with fMRI and the temporal brain wave patterns of ERP studies. Finally, we demonstrate that neuroimaging data stimulate the specification of hitherto only globally described components of functional psycholinguistic models.

  3. In vivo FID-based 3D Multivoxel Longitudinal Hadamard Spectroscopic Imaging In the Human Brain at 3 T

    PubMed Central

    Tal, Assaf; Goelman, Gadi; Gonen, Oded

    2012-01-01

    We propose and demonstrate a full 3D longitudinal Hadamard Spectroscopic Imaging (L-HSI) scheme for obtaining chemical shift maps, by employing adiabatic inversion pulses to encode the spins’ positions. The approach offers several advantages over conventional Fourier-based encoding methods, including a localized point spread function; no aliasing, allowing for VOIs smaller than the object being imaged; an option for acquiring non-contiguous voxels; and inherent outer volume rejection. The latter allows for doing away with conventional outer volume suppression schemes, such as PRESS or STEAM, and acquiring non spin-echo spectra with short acquisition delay times, limited only by the excitation pulse’s duration. This, in turn, minimizes T2 decay, maximizes the signal to noise ratio, and reduces J-coupling induced signal decay. Results are presented for both a phantom and an in-vivo healthy volunteer at 3T. PMID:22576419

  4. 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.

  5. Linking a neural mass model with a 3D model of the human brain to reproduce EEG signals.

    PubMed

    Petersen, Sabine; Zimmermann, Ulf; Schmidt, Christian; Schwabe, Lars; Warkentin, Mareike; Teipel, Stefan J

    2014-06-01

    Electroencephalography (EEG) is often employed to measure electrical activity in the living human brain. Simulation studies can help unravel how the brain electrical activity pattern generates the EEG signal, still a widely unresolved question. This article describes a method to simulate brain electrical activity by using neuronal populations of a neural mass model. Implementing these populations in a finite element model of the head offers the opportunity to investigate the influence of each group of neurons to the scalp potential. This model is based on structural magnetic resonance imaging data to specify tissue composition, and diffusion tensor imaging data to model local anisotropy. We simulated the EEG signals of five neuronal populations generating α waves in the visual cortex. Our results indicate that radially oriented sources dominate over tangential sources in the generation of the scalp signal. Investigating the influence of anisotropic conductivity, we found small differences in topography and phase and larger ones for the potential amplitude compared with an isotropic conductivity distribution. The outcome of this article is a fast method based on superposition of sources for simulating time-dependent EEG signals, which can be used for further studies of neurodegenerative diseases. PMID:24515994

  6. Challenges in Identifying the Foot Motor Region in Patients with Brain Tumor on Routine MRI: Advantages of fMRI

    PubMed Central

    Fisicaro, R.A.; Jiao, R.X.; Stathopoulos, C.; Brennan, N.M. Petrovich; Peck, K.K.; Holodny, A.I.

    2016-01-01

    BACKGROUND AND PURPOSE Accurate localization of the foot/leg motor homunculus is essential because iatrogenic damage can render a patient wheelchair- or bed-bound. We hypothesized the following: 1) Readers would identify the foot motor homunculus <100% of the time on routine MR imaging, 2) neuroradiologists would perform better than nonradiologists, and 3) those with fMRI experience would perform better than those without it. MATERIALSANDMETHODS Thirty-five attending-level raters (24 neuroradiologists, 11 nonradiologists) evaluated 14 brain tumors involving the frontoparietal convexity. Raters were asked to identify the location of the foot motor homunculus and determine whether the tumor involved the foot motor area and/or motor cortex by using anatomic MR imaging. Results were compared on the basis of prior fMRI experience and medical specialty by using Mann-Whitney U test statistics. RESULTS No rater was 100% correct. Raters correctly identified whether the tumor was in the foot motor cortex 77% of the time. Raters with fMRI experience were significantly better than raters without experience at foot motor fMRI centroid predictions (13 ± 6 mm versus 20 ± 13 mm from the foot motor cortex center, P = 2 × 10−6) and arrow placement in the motor gyrus (67% versus 47%, P = 7 × 10−5). Neuroradiologists were significantly better than nonradiologists at foot motor fMRI centroid predictions (15 ± 8 mm versus 20 ± 14 mm, P = .005) and arrow placement in the motor gyrus (61% versus 46%, P = .008). CONCLUSIONS The inability of experienced readers to consistently identify the location of the foot motor homunculus on routine MR imaging argues for using fMRI in the preoperative setting. Experience with fMRI leads to improved accuracy in identifying anatomic structures, even on routine MR imaging. PMID:25882288

  7. Extracting brain regions from rest fMRI with total-variation constrained dictionary learning.

    PubMed

    Abraham, Alexandre; Dohmatob, Elvis; Thirion, Bertrand; Samaras, Dimitris; Varoquaux, Gael

    2013-01-01

    Spontaneous brain activity reveals mechanisms of brain function and dysfunction. Its population-level statistical analysis based on functional images often relies on the definition of brain regions that must summarize efficiently the covariance structure between the multiple brain networks. In this paper, we extend a network-discovery approach, namely dictionary learning, to readily extract brain regions. To do so, we introduce a new tool drawing from clustering and linear decomposition methods by carefully crafting a penalty. Our approach automatically extracts regions from rest fMRI that better explain the data and are more stable across subjects than reference decomposition or clustering methods.

  8. 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.

  9. 3D brain tumor segmentation in multimodal MR images based on learning population- and patient-specific feature sets.

    PubMed

    Jiang, Jun; Wu, Yao; Huang, Meiyan; Yang, Wei; Chen, Wufan; Feng, Qianjin

    2013-01-01

    Brain tumor segmentation is a clinical requirement for brain tumor diagnosis and radiotherapy planning. Automating this process is a challenging task due to the high diversity in appearance of tumor tissue among different patients and the ambiguous boundaries of lesions. In this paper, we propose a method to construct a graph by learning the population- and patient-specific feature sets of multimodal magnetic resonance (MR) images and by utilizing the graph-cut to achieve a final segmentation. The probabilities of each pixel that belongs to the foreground (tumor) and the background are estimated by global and custom classifiers that are trained through learning population- and patient-specific feature sets, respectively. The proposed method is evaluated using 23 glioma image sequences, and the segmentation results are compared with other approaches. The encouraging evaluation results obtained, i.e., DSC (84.5%), Jaccard (74.1%), sensitivity (87.2%), and specificity (83.1%), show that the proposed method can effectively make use of both population- and patient-specific information. PMID:23816459

  10. Functional MRI-based identification of brain areas involved in motor imagery for implantable brain-computer interfaces.

    PubMed

    Hermes, D; Vansteensel, M J; Albers, A M; Bleichner, M G; Benedictus, M R; Mendez Orellana, C; Aarnoutse, E J; Ramsey, N F

    2011-04-01

    For the development of minimally invasive brain-computer interfaces (BCIs), it is important to accurately localize the area of implantation. Using fMRI, we investigated which brain areas are involved in motor imagery. Twelve healthy subjects performed a motor execution and imagery task during separate fMRI and EEG measurements. fMRI results showed that during imagery, premotor and parietal areas were most robustly activated in individual subjects, but surprisingly, no activation was found in the primary motor cortex. EEG results showed that spectral power decreases in contralateral sensorimotor rhythms (8-24 Hz) during both movement and imagery. To further verify the involvement of the motor imagery areas found with fMRI, one epilepsy patient performed the same task during both fMRI and ECoG recordings. Significant ECoG low (8-24 Hz) and high (65-95 Hz) frequency power changes were observed selectively on premotor cortex and these co-localized with fMRI. During a subsequent BCI task, excellent performance (91%) was obtained based on ECoG power changes from the localized premotor area. These results indicate that other areas than the primary motor area may be more reliably activated during motor imagery. Specifically, the premotor cortex may be a better area to implant an invasive BCI.

  11. Functional MRI-based identification of brain areas involved in motor imagery for implantable brain-computer interfaces

    NASA Astrophysics Data System (ADS)

    Hermes, D.; Vansteensel, M. J.; Albers, A. M.; Bleichner, M. G.; Benedictus, M. R.; Mendez Orellana, C.; Aarnoutse, E. J.; Ramsey, N. F.

    2011-04-01

    For the development of minimally invasive brain-computer interfaces (BCIs), it is important to accurately localize the area of implantation. Using fMRI, we investigated which brain areas are involved in motor imagery. Twelve healthy subjects performed a motor execution and imagery task during separate fMRI and EEG measurements. fMRI results showed that during imagery, premotor and parietal areas were most robustly activated in individual subjects, but surprisingly, no activation was found in the primary motor cortex. EEG results showed that spectral power decreases in contralateral sensorimotor rhythms (8-24 Hz) during both movement and imagery. To further verify the involvement of the motor imagery areas found with fMRI, one epilepsy patient performed the same task during both fMRI and ECoG recordings. Significant ECoG low (8-24 Hz) and high (65-95 Hz) frequency power changes were observed selectively on premotor cortex and these co-localized with fMRI. During a subsequent BCI task, excellent performance (91%) was obtained based on ECoG power changes from the localized premotor area. These results indicate that other areas than the primary motor area may be more reliably activated during motor imagery. Specifically, the premotor cortex may be a better area to implant an invasive BCI.

  12. Contribution of MRI to the diagnosis and post-therapeutic monitoring of brain stem tumours.

    PubMed

    Carsin, M; Rolland, Y; Gandon, Y; Gagey, N; Brassier, G; Simon, J

    1990-01-01

    MRI has become indispensable to the positive diagnosis of brain stem tumours which develop preferentially in young people. The prognosis of these tumours, especially infiltrating gliomas, being relatively sombre, it is important to make a precise morphological diagnosis of the lesions (increase in size, signal abnormalities) which will help both neurosurgeons and radiotherapists. As regards post-therapeutic monitoring, MRI with gadolinium contrast injection is harmless and will make it possible to follow these patients regularly and to detect recurrences.

  13. [RSF model optimization and its application to brain tumor segmentation in MRI].

    PubMed

    Cheng, Zhaoning; Song, Zhijian

    2013-04-01

    Magnetic resonance imaging (MRI) is usually obscure and non-uniform in gray, and the tumors inside are poorly circumscribed, hence the automatic tumor segmentation in MRI is very difficult. Region-scalable fitting (RSF) energy model is a new segmentation approach for some uneven grayscale images. However, the level set formulation (LSF) of RSF model is not suitable for the environment with different grey level distribution inside and outside the intial contour, and the complex intensity environment of MRI always makes it hard to get ideal segmentation results. Therefore, we improved the model by a new LSF and combined it with the mean shift method, which can be helpful for tumor segmentation and has better convergence and target direction. The proposed method has been utilized in a series of studies for real MRI images, and the results showed that it could realize fast, accurate and robust segmentations for brain tumors in MRI, which has great clinical significance. PMID:23858745

  14. Review of methods for functional brain connectivity detection using fMRI

    PubMed Central

    Li, Kaiming; Guo, Lei; Nie, Jingxin; Li, Gang; Liu, Tianming

    2009-01-01

    Since the mid of 1990s, functional connectivity study using fMRI (fcMRI) has drawn increasing attention of neuroscientists and computer scientists, since it opens a new window to explore functional network of human brain with relatively high resolution. A variety of methods for fcMRI study have been proposed. This paper intends to provide a technical review on computational methodologies developed for fcMRI analysis. From our perspective, these computational methods are classified into two general categories: model-driven methods and data-driven methods. Data-driven methods are a large family, and thus are further sub-classified into decomposition-based methods and clustering analysis methods. For each type of methods, principles, main contributors, and their advantages and drawbacks are discussed. Finally, potential applications of fcMRI are overviewed. PMID:19111443

  15. Comparison of transcranial ultrasound and cranial MRI in evaluations of brain injuries from neonatal asphyxia.

    PubMed

    Shen, Wei; Pan, Jia-Hua; Chen, Wei-Dong

    2015-01-01

    Full-term infants with early-stage brain injuries from asphyxia were examined with two-dimensional ultrasound and color Doppler to assess the use of ultrasound in evaluating early brain injuries after neonatal asphyxia. The sonographic features of ultrasound and color Doppler were compared to those of magnetic resonance imaging (MRI). Ultrasound was used to monitor the brain parenchyma, lateral ventricles, and cerebral hemodynamics in the asphyxia group and full-term control group 24, 48, and 72 h after birth. MRI and diffusion-weight imaging (DWI) were performed within 72 h. Cerebral edema changes were most obvious with ultrasound within 48 h of asphyxia, while the cerebral hemodynamic changes were most obvious within 24 h. These results suggested that ultrasound detected early cerebral edema better than MRI did. PMID:26770434

  16. Patch-based generation of a pseudo CT from conventional MRI sequences for MRI-only radiotherapy of the brain

    SciTech Connect

    Andreasen, Daniel; Van Leemput, Koen; Hansen, Rasmus H.; Andersen, Jon A. L.; Edmund, Jens M.

    2015-04-15

    atlas-based methods and showed a promising potential for RT of the brain based only on MRI.

  17. Fusion of rat brain histology and MRI using weighted multi-image mutual information

    NASA Astrophysics Data System (ADS)

    Palm, Christoph; Penney, Graeme P.; Crum, William R.; Schnabel, Julia A.; Pietrzyk, Uwe; Hawkes, David J.

    2008-03-01

    Introduction - Fusion of histology and MRI is frequently demanded in biomedical research to study in vitro tissue properties in an in vivo reference space. Distortions and artifacts caused by cutting and staining of histological slices as well as differences in spatial resolution make even the rigid fusion a difficult task. State-of- the-art methods start with a mono-modal restacking yielding a histological pseudo-3D volume. The 3D information of the MRI reference is considered subsequently. However, consistency of the histology volume and consistency due to the corresponding MRI seem to be diametral goals. Therefore, we propose a novel fusion framework optimizing histology/histology and histology/MRI consistency at the same time finding a balance between both goals. Method - Direct slice-to-slice correspondence even in irregularly-spaced cutting sequences is achieved by registration-based interpolation of the MRI. Introducing a weighted multi-image mutual information metric (WI), adjacent histology and corresponding MRI are taken into account at the same time. Therefore, the reconstruction of the histological volume as well as the fusion with the MRI is done in a single step. Results - Based on two data sets with more than 110 single registrations in all, the results are evaluated quantitatively based on Tanimoto overlap measures and qualitatively showing the fused volumes. In comparison to other multi-image metrics, the reconstruction based on WI is significantly improved. We evaluated different parameter settings with emphasis on the weighting term steering the balance between intra- and inter-modality consistency.

  18. Simultaneous measurement of human joint force, surface electromyograms, and functional MRI-measured brain activation.

    PubMed

    Liu, J Z; Dai, T H; Elster, T H; Sahgal, V; Brown, R W; Yue, G H

    2000-08-15

    Functional magnetic resonance imaging (fMRI) has been increasingly used in studying human brain function given its non-invasive feature and good spatial resolution. However, difficulties in acquiring data from peripheral (e.g. information from muscle) during fMRI studies of motor function hinder interpretation of fMRI data and designing more sophisticated investigations. Here we describe a system that was designed to concurrently measure handgrip force, surface electromyograms (EMG) of finger flexor and extensor muscles, and fMRI of human brain. The system included a pressure transducer built in a hydraulic environment, a heavily shielded EMG recording element, and a visual feedback structure for online monitoring of force and/or EMG signal, by the subject positioned in the scanner during an fMRI experiment. System evaluation and subsequent fMRI motor function studies have indicated that by using this system, high quality force and EMG signals can be recorded without sacrificing the quality of the fMRI data. PMID:10967361

  19. The power of using functional fMRI on small rodents to study brain pharmacology and disease

    PubMed Central

    Jonckers, Elisabeth; Shah, Disha; Hamaide, Julie; Verhoye, Marleen; Van der Linden, Annemie

    2015-01-01

    Functional magnetic resonance imaging (fMRI) is an excellent tool to study the effect of pharmacological modulations on brain function in a non-invasive and longitudinal manner. We introduce several blood oxygenation level dependent (BOLD) fMRI techniques, including resting state (rsfMRI), stimulus-evoked (st-fMRI), and pharmacological MRI (phMRI). Respectively, these techniques permit the assessment of functional connectivity during rest as well as brain activation triggered by sensory stimulation and/or a pharmacological challenge. The first part of this review describes the physiological basis of BOLD fMRI and the hemodynamic response on which the MRI contrast is based. Specific emphasis goes to possible effects of anesthesia and the animal’s physiological conditions on neural activity and the hemodynamic response. The second part of this review describes applications of the aforementioned techniques in pharmacologically induced, as well as in traumatic and transgenic disease models and illustrates how multiple fMRI methods can be applied successfully to evaluate different aspects of a specific disorder. For example, fMRI techniques can be used to pinpoint the neural substrate of a disease beyond previously defined hypothesis-driven regions-of-interest. In addition, fMRI techniques allow one to dissect how specific modifications (e.g., treatment, lesion etc.) modulate the functioning of specific brain areas (st-fMRI, phMRI) and how functional connectivity (rsfMRI) between several brain regions is affected, both in acute and extended time frames. Furthermore, fMRI techniques can be used to assess/explore the efficacy of novel treatments in depth, both in fundamental research as well as in preclinical settings. In conclusion, by describing several exemplary studies, we aim to highlight the advantages of functional MRI in exploring the acute and long-term effects of pharmacological substances and/or pathology on brain functioning along with several methodological

  20. Sources of Variation Influencing Concordance between Functional MRI and Direct Cortical Stimulation in Brain Tumor Surgery

    PubMed Central

    Morrison, Melanie A.; Tam, Fred; Garavaglia, Marco M.; Hare, Gregory M. T.; Cusimano, Michael D.; Schweizer, Tom A.; Das, Sunit; Graham, Simon J.

    2016-01-01

    Object: Preoperative functional magnetic resonance imaging (fMRI) remains a promising method to aid in the surgical management of patients diagnosed with brain tumors. For patients that are candidates for awake craniotomies, surgical decisions can potentially be improved by fMRI but this depends on the level of concordance between preoperative brain maps and the maps provided by the gold standard intraoperative method, direct cortical stimulation (DCS). There have been numerous studies of the concordance between fMRI and DCS using sensitivity and specificity measures, however the results are variable across studies and the key factors influencing variability are not well understood. Thus, the present work addresses the influence of technical factors on fMRI and DCS concordance. Methods: Motor and language mapping data were collected for a group of glioma patients (n = 14) who underwent both preoperative fMRI and intraoperative DCS in an awake craniotomy procedure for tumor removal. Normative fMRI data were also acquired in a healthy control group (n = 12). The fMRI and DCS mapping data were co-registered; true positive (TP), true negative (TN), false positive (FP), and false negative (FN) occurrences were tabulated over the exposed brain surface. Sensitivity and specificity were measured for the total group, and for the motor and language sub-groups. The influence of grid placement, fMRI statistical thresholding, and task standardization were assessed. Correlations between proportions of agreement and error were also carefully scrutinized to evaluate concordance in more detail. Results: Concordance was significantly better for motor vs. language mapping. There was an inverse relationship between TP and TN with increasing statistical threshold, and FP dominated the total error. Sensitivity and specificity were reduced when tasks were not standardized across fMRI and DCS. Conclusions: Although the agreement between fMRI and DCS is good, variability is introduced by

  1. Comparison of prostate MRI-3D transrectal ultrasound fusion biopsy for first-time and repeat biopsy patients with previous atypical small acinar proliferation

    PubMed Central

    Cool, Derek W.; Romagnoli, Cesare; Izawa, Jonathan I.; Chin, Joseph; Gardi, Lori; Tessier, David; Mercado, Ashley; Mandel, Jonathan; Ward, Aaron D.; Fenster, Aaron

    2016-01-01

    Introduction: This study evaluates the clinical benefit of magnetic resonance-transrectal ultrasound (MR-TRUS) fusion biopsy over systematic biopsy between first-time and repeat prostate biopsy patients with prior atypical small acinar proliferation (ASAP). Materials: 100 patients were enrolled in a single-centre prospective cohort study: 50 for first biopsy, 50 for repeat biopsy with prior ASAP. Multiparameteric magnetic resonance imaging (MP-MRI) and standard 12-core ultrasound biopsy (Std-Bx) were performed on all patients. Targeted biopsy using MRI-TRUS fusion (Fn-Bx) was performed f suspicious lesions were identified on the pre-biopsy MP-MRI. Classification of clinically significant disease was assessed independently for the Std-Bx vs. Fn-Bx cores to compare the two approaches. Results: Adenocarcinoma was detected in 49/100 patients (26 first biopsy, 23 ASAP biopsy), with 25 having significant disease (17 first, 8 ASAP). Fn-Bx demonstrated significantly higher per-core cancer detection rates, cancer involvement, and Gleason scores for first-time and ASAP patients. However, Fn-Bx was significantly more likely to detect significant cancer missed on Std-Bx for ASAP patients than first-time biopsy patients. The addition of Fn-Bx to Std-Bx for ASAP patients had a 166.7% relative risk reduction for missing Gleason ≥ 3 + 4 disease (number needed to image with MP-MRI=10 patients) compared to 6.3% for first biopsy (number to image=50 patients). Negative predictive value of MP-MRI for negative biopsy was 79% for first-time and 100% for ASAP patients, with median followup of 32.1 ± 15.5 months. Conclusions: MR-TRUS Fn-Bx has a greater clinical impact for repeat biopsy patients with prior ASAP than biopsy-naïve patients by detecting more significant cancers that are missed on Std-Bx. PMID:27800057

  2. Magnetic resonance imaging (MRI) detection of the murine brain response to light: Temporal differentiation and negative functional MRI changes

    SciTech Connect

    Huang, Wei ||; Palyka, I. |; Li, HaiFang

    1996-06-11

    Using a 9.4 T MRI instrument, we have obtained images of the mouse brain response to photic stimulation during a period between deep anesthesia and the early stages of arousal. The large image enhancements we observe (often >30%) are consistent with literature results extrapolated to 9.4 T. However, there are also two unusual aspects to our findings. (i) The visual area of the brain responds only to changes in stimulus intensity, suggesting that we directly detect operations of the M visual system pathway. Such a channel has been observed in mice by invasive electrophysiology, and described in detail for primates. (ii) Along with the typical positive response in the area of the occipital portion of the brain containing the visual cortex; another area displays decreased signal intensity upon stimulation. 41 refs., 4 figs.

  3. Early functional brain development in autism and the promise of sleep fMRI.

    PubMed

    Pierce, Karen

    2011-03-22

    Functional magnetic resonance imaging (fMRI) is a powerful tool for examining brain function but has yet to be systematically applied to the study of brain development in autism. Recently, however, scientists have begun to apply fMRI during natural sleep as a mechanism to study function in the developing brain. When considering the study of autism, this method opens considerable doors because it eliminates biases of past studies which only sampled from high-functioning, older populations. This paper describes the application of sleep fMRI as a way to study both extrinsic and intrinsic brain functions in autism between 12 and 36 months. Preliminary studies that use sleep fMRI method show that defects in the superior temporal gyrus (STG) in response to language are early emerging in autism and can be found in as young as 14 months in age. As such indices of abnormal early development of the STG may prove useful in the search for a biomarker of autism detectable during the infancy period. From a theoretical standpoint, examining sleep fMRI studies in autism gains some clarity when placed in context of the more established literature on structural brain development of autism which suggests that autism involves early brain overgrowth. Studies of plasticity in autism have yet to be done, but it is likely that the window of opportunity for altering the course of brain development in autism begins within the first year of life. The ability to do so relies on improving and streamlining early identification and thus early treatment efforts.

  4. Morphological asymmetries of mouse brain assessed by geometric morphometric analysis of MRI data.

    PubMed

    Barbeito-Andrés, Jimena; Bernal, Valeria; Gonzalez, Paula N

    2016-09-01

    Mammalian brain has repeated structures at both sides of the median plane, although some asymmetries have been described even under normal conditions. Characterizing normal patterns of asymmetry in mouse brain is important to recognize features that depart from expected ranges in the most widely used mammalian model. Analyses on brain morphology based on magnetic resonance image (MRI) have largely focused on volumes while less is known about shape asymmetry. We introduce a flexible protocol based on geometric morphometrics to assess patterns of asymmetry in shape and size of mouse brain from microMRI scans. After systematic digitization of landmarks and semilandmarks, we combine multivariate methods for statistical analyses with visualization tools to display the results. No preliminary treatment of the images (e.g. space normalization) is needed to collect data on MRI slices and visual representations improve the interpretation of the results. Results indicated that the protocol is highly repeatable. Asymmetry was more evident for shape than for size. Particularly, fluctuating asymmetry accounted for more variation than directional asymmetry in all brain regions. Since this approach can detect subtle shape variation between sides, it is a promising methodology to explore morphological changes in the brain of model organisms and can be applied in future studies addressing the effect of genetic and environmental factors on brain morphology. PMID:27108357

  5. Morphological asymmetries of mouse brain assessed by geometric morphometric analysis of MRI data.

    PubMed

    Barbeito-Andrés, Jimena; Bernal, Valeria; Gonzalez, Paula N

    2016-09-01

    Mammalian brain has repeated structures at both sides of the median plane, although some asymmetries have been described even under normal conditions. Characterizing normal patterns of asymmetry in mouse brain is important to recognize features that depart from expected ranges in the most widely used mammalian model. Analyses on brain morphology based on magnetic resonance image (MRI) have largely focused on volumes while less is known about shape asymmetry. We introduce a flexible protocol based on geometric morphometrics to assess patterns of asymmetry in shape and size of mouse brain from microMRI scans. After systematic digitization of landmarks and semilandmarks, we combine multivariate methods for statistical analyses with visualization tools to display the results. No preliminary treatment of the images (e.g. space normalization) is needed to collect data on MRI slices and visual representations improve the interpretation of the results. Results indicated that the protocol is highly repeatable. Asymmetry was more evident for shape than for size. Particularly, fluctuating asymmetry accounted for more variation than directional asymmetry in all brain regions. Since this approach can detect subtle shape variation between sides, it is a promising methodology to explore morphological changes in the brain of model organisms and can be applied in future studies addressing the effect of genetic and environmental factors on brain morphology.

  6. Graph theoretical analysis of structural and functional connectivity MRI in normal and pathological brain networks.

    PubMed

    Guye, Maxime; Bettus, Gaelle; Bartolomei, Fabrice; Cozzone, Patrick J

    2010-12-01

    Graph theoretical analysis of structural and functional connectivity MRI data (ie. diffusion tractography or cortical volume correlation and resting-state or task-related (effective) fMRI, respectively) has provided new measures of human brain organization in vivo. The most striking discovery is that the whole-brain network exhibits "small-world" properties shared with many other complex systems (social, technological, information, biological). This topology allows a high efficiency at different spatial and temporal scale with a very low wiring and energy cost. Its modular organization also allows for a high level of adaptation. In addition, degree distribution of brain networks demonstrates highly connected hubs that are crucial for the whole-network functioning. Many of these hubs have been identified in regions previously defined as belonging to the default-mode network (potentially explaining the high basal metabolism of this network) and the attentional networks. This could explain the crucial role of these hub regions in physiology (task-related fMRI data) as well as in pathophysiology. Indeed, such topological definition provides a reliable framework for predicting behavioral consequences of focal or multifocal lesions such as stroke, tumors or multiple sclerosis. It also brings new insights into a better understanding of pathophysiology of many neurological or psychiatric diseases affecting specific local or global brain networks such as epilepsy, Alzheimer's disease or schizophrenia. Graph theoretical analysis of connectivity MRI data provides an outstanding framework to merge anatomical and functional data in order to better understand brain pathologies. PMID:20349109

  7. MARGA: multispectral adaptive region growing algorithm for brain extraction on axial MRI.

    PubMed

    Roura, Eloy; Oliver, Arnau; Cabezas, Mariano; Vilanova, Joan C; Rovira, Alex; Ramió-Torrentà, Lluís; Lladó, Xavier

    2014-02-01

    Brain extraction, also known as skull stripping, is one of the most important preprocessing steps for many automatic brain image analysis. In this paper we present a new approach called Multispectral Adaptive Region Growing Algorithm (MARGA) to perform the skull stripping process. MARGA is based on a region growing (RG) algorithm which uses the complementary information provided by conventional magnetic resonance images (MRI) such as T1-weighted and T2-weighted to perform the brain segmentation. MARGA can be seen as an extension of the skull stripping method proposed by Park and Lee (2009) [1], enabling their use in both axial views and low quality images. Following the same idea, we first obtain seed regions that are then spread using a 2D RG algorithm which behaves differently in specific zones of the brain. This adaptation allows to deal with the fact that middle MRI slices have better image contrast between the brain and non-brain regions than superior and inferior brain slices where the contrast is smaller. MARGA is validated using three different databases: 10 simulated brains from the BrainWeb database; 2 data sets from the National Alliance for Medical Image Computing (NAMIC) database, the first one consisting in 10 normal brains and 10 brains of schizophrenic patients acquired with a 3T GE scanner, and the second one consisting in 5 brains from lupus patients acquired with a 3T Siemens scanner; and 10 brains of multiple sclerosis patients acquired with a 1.5T scanner. We have qualitatively and quantitatively compared MARGA with the well-known Brain Extraction Tool (BET), Brain Surface Extractor (BSE) and Statistical Parametric Mapping (SPM) approaches. The obtained results demonstrate the validity of MARGA, outperforming the results of those standard techniques. PMID:24380649

  8. MRI Guided Brain Stimulation without the Use of a Neuronavigation System

    PubMed Central

    Vaghefi, Ehsan; Cai, Peng; Fang, Fang; Byblow, Winston D.; Stinear, Cathy M.; Thompson, Benjamin

    2015-01-01

    A key issue in the field of noninvasive brain stimulation (NIBS) is the accurate localization of scalp positions that correspond to targeted cortical areas. The current gold standard is to combine structural and functional brain imaging with a commercially available “neuronavigation” system. However, neuronavigation systems are not commonplace outside of specialized research environments. Here we describe a technique that allows for the use of participant-specific functional and structural MRI data to guide NIBS without a neuronavigation system. Surface mesh representations of the head were generated using Brain Voyager and vectors linking key anatomical landmarks were drawn on the mesh. Our technique was then used to calculate the precise distances on the scalp corresponding to these vectors. These calculations were verified using actual measurements of the head and the technique was used to identify a scalp position corresponding to a brain area localized using functional MRI. PMID:26413537

  9. Imaging whole-brain cytoarchitecture of mouse with MRI-based quantitative susceptibility mapping.

    PubMed

    Wei, Hongjiang; Xie, Luke; Dibb, Russell; Li, Wei; Decker, Kyle; Zhang, Yuyao; Johnson, G Allan; Liu, Chunlei

    2016-08-15

    The proper microstructural arrangement of complex neural structures is essential for establishing the functional circuitry of the brain. We present an MRI method to resolve tissue microstructure and infer brain cytoarchitecture by mapping the magnetic susceptibility in the brain at high resolution. This is possible because of the heterogeneous magnetic susceptibility created by varying concentrations of lipids, proteins and irons from the cell membrane to cytoplasm. We demonstrate magnetic susceptibility maps at a nominal resolution of 10-μm isotropic, approaching the average cell size of a mouse brain. The maps reveal many detailed structures including the retina cell layers, olfactory sensory neurons, barrel cortex, cortical layers, axonal fibers in white and gray matter. Olfactory glomerulus density is calculated and structural connectivity is traced in the optic nerve, striatal neurons, and brainstem nerves. The method is robust and can be readily applied on MRI scanners at or above 7T. PMID:27181764

  10. Learning and predicting brain dynamics from fMRI: a spectral approach

    NASA Astrophysics Data System (ADS)

    Meyer, François

    2007-09-01

    Traditional neuroimaging experiments, dictated by the dogma of functional specialization, aim at identifying regions of the brain that are maximally correlated with a simple cognitive or sensory stimulus. Very recently, functional MRI (fMRI) has been used to infer subjective experience and brain states of subjects immersed in natural environments. These environments are rich with uncontrolled stimuli and resemble real life experiences. Conventional methods of analysis of neuroimaging data fail to unravel the complex activity that natural environments elicit. The contribution of this work is a novel method to predict action and sensory experiences of a subject from fMRI. This method relies on an embedding that provides an optimal coordinate system to reduce the dimensionality of the fMRI dataset while preserving its intrinsic dynamics. We learn a set of time series that are implicit functions of the fMRI data, and predict the values of these times series in the future from the knowledge of the fMRI data only. We conducted several experiments with the datasets of the 2007 Pittsburgh Experience Based Cognition competition.

  11. Diffusion MRI of the neonate brain: acquisition, processing and analysis techniques.

    PubMed

    Pannek, Kerstin; Guzzetta, Andrea; Colditz, Paul B; Rose, Stephen E

    2012-10-01

    Diffusion MRI (dMRI) is a popular noninvasive imaging modality for the investigation of the neonate brain. It enables the assessment of white matter integrity, and is particularly suited for studying white matter maturation in the preterm and term neonate brain. Diffusion tractography allows the delineation of white matter pathways and assessment of connectivity in vivo. In this review, we address the challenges of performing and analysing neonate dMRI. Of particular importance in dMRI analysis is adequate data preprocessing to reduce image distortions inherent to the acquisition technique, as well as artefacts caused by head movement. We present a summary of techniques that should be used in the preprocessing of neonate dMRI data, and demonstrate the effect of these important correction steps. Furthermore, we give an overview of available analysis techniques, ranging from voxel-based analysis of anisotropy metrics including tract-based spatial statistics (TBSS) to recently developed methods of statistical analysis addressing issues of resolving complex white matter architecture. We highlight the importance of resolving crossing fibres for tractography and outline several tractography-based techniques, including connectivity-based segmentation, the connectome and tractography mapping. These techniques provide powerful tools for the investigation of brain development and maturation. PMID:22903761

  12. Optimal Gaussian Mixture Models of Tissue Intensities in Brain MRI of Patients with Multiple-Sclerosis

    NASA Astrophysics Data System (ADS)

    Xiao, Yiming; Shah, Mohak; Francis, Simon; Arnold, Douglas L.; Arbel, Tal; Collins, D. Louis

    Brain tissue segmentation is important in studying markers in human brain Magnetic Resonance Images (MRI) of patients with diseases such as Multiple Sclerosis (MS). Parametric segmentation approaches typically assume unimodal Gaussian distributions on MRI intensities of individual tissue classes, even in applications on multi-spectral images. However, this assumption has not been rigorously verified especially in the context of MS. In this work, we evaluate the local MRI intensities of both healthy and diseased brain tissues of 21 multi-spectral MRIs (63 volumes in total) of MS patients for adherence to this assumption. We show that the tissue intensities are not uniform across the brain and vary across (anatomical) regions of the brain. Consequently, we show that Gaussian mixtures can better model the multi-spectral intensities. We utilize an Expectation Maximization (EM) based approach to learn the models along with a symmetric Jeffreys divergence criterion to study differences in intensity distributions. The effects of these findings are also empirically verified on automatic segmentation of brains with MS.

  13. Registration of fast cine cardiac MR slices to 3D preprocedural images: toward real-time registration for MRI-guided procedures

    NASA Astrophysics Data System (ADS)

    Smolikova, Renata; Wachowiak, Mark P.; Drangova, Maria

    2004-05-01

    Interventional cardiac magnetic resonance (MR) procedures are the subject of an increasing number of research studies. Typically, during the procedure only two-dimensional images of oblique slices can be presented to the interventionalist in real time. There is a clear benefit to being able to register the real-time 2D slices to a previously acquired 3D computed tomography (CT) or MR image of the heart. Results from a study of the accuracy of registration of 2D cardiac images of an anesthetized pig to a 3D volume obtained in diastole are presented. Fast cine MR images representing twenty phases of the cardiac cycle were obtained of a 2D slice in a known oblique orientation. The 2D images were initially mis-oriented at distances ranging from 2 to 20 mm, and rotations of +/-10 degrees about all three axes. Images from all 20 cardiac phases were registered to examine the effect of timing between the 2D image and the 3D pre-procedural image. Linear registration using mutual information computed with 64 histogram bins yielded the highest accuracy. For the diastolic phases, mean translation and rotation errors ranged between 0.91 and 1.32 mm and between 1.73 and 2.10 degrees. Scans acquired at other phases also had high accuracy. These results are promising for the use of real time MR in image-guided cardiac interventions, and demonstrate the feasibility of registering 2D oblique MR slices to previously acquired single-phase volumes without preprocessing.

  14. A study on the flip angle for an optimal T1-weighted image based on the 3D-THRIVE MRI technique: Focusing on the detection of a hepatocellular carcinoma (HCC)

    NASA Astrophysics Data System (ADS)

    Dong, Kyung-Rae; Goo, Eun-Hoe; Lee, Jae-Seung; Chung, Woon-Kwan; Kim, Young-Jae

    2014-04-01

    This study examined the optimal flip angle (FA) for a T1-weighted image in the detection of a hepatocellular carcinoma (HCC). A 3D-T1-weighted high-resolution isotropic volume examination (THRIVE) technique was used to determine the dependence of the signal to noise ratio (SNR) and the contrast-to-noise ratio (CNR) on the change in FA. This study targeted 40 liver cancer patients (25 men and 15 women aged 50 to 70 years with a mean age of 60.32 ± 6.2 years) who visited this hospital to undergo an abdominal MRI examination from January to June 2013. A 3.0 Tesla MRI machine (Philips, Medical System, Achieva) and a MRI receiver coil for data reception with a 16-channel multicoil were used in this study. The THRIVE (repetition time (TR): 8.1 ms, echo time (TE): 3.7 ms, matrix: 172 × 172, slice thickness: 4 mm, gap: 2 mm, field of view (FOV): 350 mm, and band width (BW): 380.1 Hz) technique was applied as a pulse sequence. The time required for the examination was 19 seconds, and the breath-hold technique was used. Axial images were obtained at five FAs: 5, 10, 15, 20 and 25°. The signal intensities of the liver, the lesion and the background noise were measured based on the acquired images before the SNR and the CNR were calculated. To evaluate the image at the FA, we used SPSS for Windows ver. 17.0 to conduct a one-way ANOVA test. A Bonferroni test was conducted as a post-hoc test. The SNRs of the hemorrhagic HCC in the 3D-THRIVE technique were 35.50 ± 4.12, 97.00 ± 10.24, 66.09 ± 7.29, 53.84 ± 5.43, and 42.92 ± 5.11 for FAs of 5, 10, 15, 20, and 25°, respectively (p = 0.0430), whereas the corresponding CNRs were 30.50 ± 3.84, 43.00 ± 5.42, 36.54 ± 4.09, 32.30 ± 2.79, and 31.69 ± 3.21 (p = 0.0003). At a small FA of 10, the SNR and the CNR showed the highest values. As the FA was increased, the SNR and the CNR values showed a decreasing tendency. In conclusion, the optimal T1-weighted image FA should be set to 10° to detect a HCC by using the 3D

  15. A brain MRI atlas of the common squirrel monkey, Saimiri sciureus

    NASA Astrophysics Data System (ADS)

    Gao, Yurui; Schilling, Kurt G.; Khare, Shweta P.; Panda, Swetasudha; Choe, Ann S.; Stepniewska, Iwona; Li, Xia; Ding, Zhoahua; Anderson, Adam; Landman, Bennett A.

    2014-03-01

    The common squirrel monkey, Saimiri sciureus, is a New World monkey with functional and microstructural organization of central nervous system similar to that of humans. It is one of the most commonly used South American primates in biomedical research. Unlike its Old World macaque cousins, no digital atlases have described the organization of the squirrel monkey brain. Here, we present a multi-modal magnetic resonance imaging (MRI) atlas constructed from the brain of an adult female squirrel monkey. In vivo MRI acquisitions include high resolution T2 structural imaging and low resolution diffusion tensor imaging. Ex vivo MRI acquisitions include high resolution T2 structural imaging and high resolution diffusion tensor imaging. Cortical regions were manually annotated on the co-registered volumes based on published histological sections.

  16. Findings at brain MRI in children with dengue fever and neurological symptoms.

    PubMed

    Rastogi, Ruchi; Garg, Bhavya

    2016-01-01

    Dengue is a flavivirus of the genus arbovirus with four serotypes, from DEN 1 to DEN 4. There has been an increase in incidence of dengue infection in children in the tropics and subtropics. Dengue has a variable clinical presentation, with many patients being asymptomatic. Its clinical manifestations in children vary from fever and arthralgia to life-threatening dengue hemorrhagic fever and dengue shock syndrome. We describe MRI findings in children with neurological involvement including dengue encephalopathy, acute hypoxic injury and dengue encephalitis. Dengue encephalopathy is usually secondary to multisystem derangement such as shock, hepatitis, coagulopathy and concurrent bacterial infection and is relatively common. Dengue encephalitis from direct neuronal invasion is rare. Nonspecific changes are seen on brain MRI in dengue infection. Clinical and laboratory findings as well as outcome do not necessarily correspond with brain MRI findings.

  17. Use of resting state functional MRI to study brain development and injury in neonates

    PubMed Central

    Smyser, Christopher D.; Neil, Jeffrey J.

    2015-01-01

    Advances in methodology have led to expanded application of resting state functional MRI (rs-fMRI) to the study of term and prematurely-born infants during the first years of life, providing fresh insight into the earliest forms of functional cerebral development. In this review, we detail our evolving understanding of the use of rs-fMRI for studying neonates. We initially focus on the biological processes of cortical development related to resting state network development. We then review technical issues principally affecting neonatal investigations, including the effects of subject motion during acquisition and image distortions related to magnetic susceptibility effects. We next summarize the literature in which rs-fMRI is used to study normal brain development during the early postnatal period, the effects of prematurity and the effects of cerebral injury. Finally, we review potential future directions for the field, such as the use of complementary imaging modalities and advanced analysis techniques. PMID:25813667

  18. MRI-related heating near deep brain stimulation electrodes: more data are needed.

    PubMed

    Gupte, Akshay A; Shrivastava, Devashish; Spaniol, Maggie A; Abosch, Aviva

    2011-01-01

    Magnetic resonance imaging (MRI) of patients with implanted deep brain stimulation (DBS) devices poses a challenge for healthcare providers. As a consequence of safety concerns about magnetic field interactions with the device, induced electrical currents and thermal damage due to radiofrequency heating, a number of stringent guidelines have been proposed by the device manufacturer. Very few detailed investigations of these safety issues have been published to date, and the stringent manufacturer guidelines have gone unchallenged, leading some hospitals and imaging centers around the world to ban or restrict the use of MRI in DBS patients. The purpose of this review is to stimulate research towards defining appropriate guidelines for the use of MRI in patients with DBS. Additionally, this review is intended to help healthcare providers and researchers make sound clinical judgments about the use of MRI in the setting of implanted DBS devices.

  19. Comparative studies of brain activation with MEG and functional MRI

    SciTech Connect

    George, J.S.; Aine, C.J.; Sanders, J.A.; Lewine, J.D.; Caprihan, A.

    1993-12-31

    The past two years have witnessed the emergence of MRI as a functional imaging methodology. Initial demonstrations involved the injection of a paramagnetic contrast agent and required ultrafast echo planar imaging capability to adequately resolve the passage of the injected bolus. By measuring the local reduction in image intensity due to magnetic susceptibility, it was possible to calculate blood volume, which changes as a function of neural activation. Later developments have exploited endogenous contrast mechanisms to monitor changes in blood volume or in venous blood oxygen content. Recently, we and others have demonstrated that it is possible to make such measurements in a clinical imager, suggesting that the large installed base of such machines might be utilized for functional imaging. Although it is likely that functional MRI (fMRI) will subsume some of the clinical and basic neuroscience applications now touted for MEG, it is also clear that these techniques offer different largely complementary, capabilities. At the very least, it is useful to compare and cross-validate the activation maps produced by these techniques. Such studies will be valuable as a check on results of neuromagnetic distributed current reconstructions and will allow better characterization of the relationship between neurophysiological activation and associated hemodynamic changes. A more exciting prospect is the development of analyses that combine information from the two modalities to produce a better description of underlying neural activity than is possible with either technique in isolation. In this paper we describe some results from initial comparative studies and outline several techniques that can be used to treat MEG and fMRI data within a unified computational framework.

  20. Distribution of Hyperpolarized Xenon in the Brain Following Sensory Stimulation: Preliminary MRI Findings

    PubMed Central

    Mazzanti, Mary L.; Walvick, Ronn P.; Zhou, Xin; Sun, Yanping; Shah, Niral; Mansour, Joey; Gereige, Jessica; Albert, Mitchell S.

    2011-01-01

    In hyperpolarized xenon magnetic resonance imaging (HP 129Xe MRI), the inhaled spin-1/2 isotope of xenon gas is used to generate the MR signal. Because hyperpolarized xenon is an MR signal source with properties very different from those generated from water-protons, HP 129Xe MRI may yield structural and functional information not detectable by conventional proton-based MRI methods. Here we demonstrate the differential distribution of HP 129Xe in the cerebral cortex of the rat following a pain stimulus evoked in the animal's forepaw. Areas of higher HP 129Xe signal corresponded to those areas previously demonstrated by conventional functional MRI (fMRI) methods as being activated by a forepaw pain stimulus. The percent increase in HP 129Xe signal over baseline was 13–28%, and was detectable with a single set of pre and post stimulus images. Recent innovations in the production of highly polarized 129Xe should make feasible the emergence of HP 129Xe MRI as a viable adjunct method to conventional MRI for the study of brain function and disease. PMID:21789173

  1. [Progress of clinical application of functional MRI in the localization of brain language area].

    PubMed

    Zhang, Nan; Lu, Junfeng; Wu, Jinsong

    2016-02-01

    For surgical operation in the functional area in the brain, it's commonly demanded to resect the lesion to the maximal extent on the basis of preserve the normal neural function, thus the precise localization of functional area is extremely important. As for the advantages of being widely available, easy to grasp and non-invasive, the functional MRI (fMRI) has come into wide use, while the application of language fMRI is still in the initial stage. It's important to choose appropriate fMRI task according to the individual condition of the subject, the commonly-adopted tasks include verb generation, picture naming, word recognition, word generation, etc. However, the effectiveness of using fMRI to localize language area is not totally satisfactory, adopting multiple task is an effective approach to improve the sensitivity of this technique. The application of resting state fMRI in the localization of language area and the further research of the role of fMRI in localizing the Chinese language area are the important future directions.

  2. Simultaneous EEG-fMRI for working memory of the human brain.

    PubMed

    Ahmad, Rana Fayyaz; Malik, Aamir Saeed; Kamel, Nidal; Reza, Faruque; Abdullah, Jafri Malin

    2016-06-01

    Memory plays an important role in human life. Memory can be divided into two categories, i.e., long term memory and short term memory (STM). STM or working memory (WM) stores information for a short span of time and it is used for information manipulations and fast response activities. WM is generally involved in the higher cognitive functions of the brain. Different studies have been carried out by researchers to understand the WM process. Most of these studies were based on neuroimaging modalities like fMRI, EEG, MEG etc., which use standalone processes. Each neuroimaging modality has some pros and cons. For example, EEG gives high temporal resolution but poor spatial resolution. On the other hand, the fMRI results have a high spatial resolution but poor temporal resolution. For a more in depth understanding and insight of what is happening inside the human brain during the WM process or during cognitive tasks, high spatial as well as high temporal resolution is desirable. Over the past decade, researchers have been working to combine different modalities to achieve a high spatial and temporal resolution at the same time. Developments of MRI compatible EEG equipment in recent times have enabled researchers to combine EEG-fMRI successfully. The research publications in simultaneous EEG-fMRI have been increasing tremendously. This review is focused on the WM research involving simultaneous EEG-fMRI data acquisition and analysis. We have covered the simultaneous EEG-fMRI application in WM and data processing. Also, it adds to potential fusion methods which can be used for simultaneous EEG-fMRI for WM and cognitive tasks.

  3. Modification of a Colliculo-thalamocortical Mouse Brain Slice, Incorporating 3-D printing of Chamber Components and Multi-scale Optical Imaging.

    PubMed

    Slater, Bernard J; Fan, Anthony Y; Stebbings, Kevin A; Saif, M Taher A; Llano, Daniel A

    2015-01-01

    The ability of the brain to process sensory information relies on both ascending and descending sets of projections. Until recently, the only way to study these two systems and how they interact has been with the use of in vivo preparations. Major advances have been made with acute brain slices containing the thalamocortical and cortico-thalamic pathways in the somatosensory, visual, and auditory systems. With key refinements to our recent modification of the auditory thalamocortical slice(1), we are able to more reliably capture the projections between most of the major auditory midbrain and forebrain structures: the inferior colliculus (IC), medial geniculate body (MGB), thalamic reticular nucleus (TRN), and the auditory cortex (AC). With portions of all these connections retained, we are able to answer detailed questions that complement the questions that can be answered with in vivo preparations. The use of flavoprotein autofluorescence imaging enables us to rapidly assess connectivity in any given slice and guide the ensuing experiment. Using this slice in conjunction with recording and imaging techniques, we are now better equipped to understand how information processing occurs at each point in the auditory forebrain as information ascends to the cortex, and the impact of descending cortical modulation. 3-D printing to build slice chamber components permits double-sided perfusion and broad access to networks within the slice and maintains the widespread connections key to fully utilizing this preparation. PMID:26437382

  4. Structural Image Analysis of the Brain in Neuropsychology Using Magnetic Resonance Imaging (MRI) Techniques.

    PubMed

    Bigler, Erin D

    2015-09-01

    Magnetic resonance imaging (MRI) of the brain provides exceptional image quality for visualization and neuroanatomical classification of brain structure. A variety of image analysis techniques provide both qualitative as well as quantitative methods to relate brain structure with neuropsychological outcome and are reviewed herein. Of particular importance are more automated methods that permit analysis of a broad spectrum of anatomical measures including volume, thickness and shape. The challenge for neuropsychology is which metric to use, for which disorder and the timing of when image analysis methods are applied to assess brain structure and pathology. A basic overview is provided as to the anatomical and pathoanatomical relations of different MRI sequences in assessing normal and abnormal findings. Some interpretive guidelines are offered including factors related to similarity and symmetry of typical brain development along with size-normalcy features of brain anatomy related to function. The review concludes with a detailed example of various quantitative techniques applied to analyzing brain structure for neuropsychological outcome studies in traumatic brain injury.

  5. MRI confirms loss of blood-brain barrier integrity in a mouse model of disseminated candidiasis.

    PubMed

    Navarathna, Dhammika H M L P; Munasinghe, Jeeva; Lizak, Martin J; Nayak, Debasis; McGavern, Dorian B; Roberts, David D

    2013-09-01

    Disseminated candidiasis primarily targets the kidneys and brain in mice and humans. Damage to these critical organs leads to the high mortality associated with such infections, and invasion across the blood-brain barrier can result in fungal meningoencephalitis. Candida albicans can penetrate a brain endothelial cell barrier in vitro through transcellular migration, but this mechanism has not been confirmed in vivo. MRI using the extracellular vascular contrast agent gadolinium diethylenetriaminepentaacetic acid demonstrated that integrity of the blood-brain barrier is lost during C. albicans invasion. Intravital two-photon laser scanning microscopy was used to provide the first real-time demonstration of C. albicans colonizing the living brain, where both yeast and filamentous forms of the pathogen were found. Furthermore, we adapted a previously described method utilizing MRI to monitor inflammatory cell recruitment into infected tissues in mice. Macrophages and other phagocytes were visualized in kidney and brain by the administration of ultrasmall iron oxide particles. In addition to obtaining new insights into the passage of C. albicans across the brain microvasculature, these imaging methods provide useful tools to study further the pathogenesis of C. albicans infections, to define the roles of Candida virulence genes in kidney versus brain infection and to assess new therapeutic measures for drug development.

  6. Appraising the Role of Iron in Brain Aging and Cognition: Promises and Limitations of MRI Methods

    PubMed Central

    Daugherty, Ana M; Raz, Naftali

    2015-01-01

    Age-related increase in frailty is accompanied by a fundamental shift in cellular iron homeostasis. By promoting oxidative stress, the intracellular accumulation of non-heme iron outside of binding complexes contributes to chronic inflammation and interferes with normal brain metabolism. In the absence of direct non-invasive biomarkers of brain oxidative stress, iron accumulation estimated in vivo may serve as its proxy indicator. Hence, developing reliable in vivo measurements of brain iron content via magnetic resonance imaging (MRI) is of significant interest in human neuroscience. To date, by estimating brain iron content through various MRI methods, significant age differences and age-related increases in iron content of the basal ganglia have been revealed across multiple samples. Less consistent are the findings that pertain to the relationship between elevated brain iron content and systemic indices of vascular and metabolic dysfunction. Only a handful of cross-sectional investigations have linked high iron content in various brain regions and poor performance on assorted cognitive tests. The even fewer longitudinal studies indicate that iron accumulation may precede shrinkage of the basal ganglia and thus predict poor maintenance of cognitive functions. This rapidly developing field will benefit from introduction of higher-field MRI scanners, improvement in iron-sensitive and -specific acquisition sequences and post-processing analytic and computational methods, as well as accumulation of data from long-term longitudinal investigations. This review describes the potential advantages and promises of MRI-based assessment of brain iron, summarizes recent findings and highlights the limitations of the current methodology. PMID:26248580

  7. Appraising the Role of Iron in Brain Aging and Cognition: Promises and Limitations of MRI Methods.

    PubMed

    Daugherty, Ana M; Raz, Naftali

    2015-09-01

    Age-related increase in frailty is accompanied by a fundamental shift in cellular iron homeostasis. By promoting oxidative stress, the intracellular accumulation of no