Science.gov

Sample records for 3d brain mri

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

    NASA Astrophysics Data System (ADS)

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

    2012-05-01

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

  2. 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. PMID:23836390

  3. Whole brain 3D T2-weighted BOLD fMRI at 7T

    PubMed Central

    Hua, Jun; Qin, Qin; van Zijl, Peter C. M.; Pekar, James J.; Jones, Craig K.

    2014-01-01

    Purpose A new acquisition scheme for T2-weighted spin-echo BOLD fMRI is introduced. Methods It employs a T2-preparation module to induce BOLD contrast, followed by a single-shot 3D fast gradient-echo readout with short TE. It differs from most spin-echo BOLD sequences in that BOLD contrast is generated before the readout, which eliminates the “dead time” due to long TE required for T2 contrast, and substantially improves acquisition efficiency. This approach, termed “3D T2prep-GRE”, was implemented at 7T with a typical spatial (2.5×2.5×2.5mm3) and temporal (TR=2.3s) resolution for fMRI and whole-brain coverage (55 slices), and compared with the widely used 2D spin-echo EPI sequence. Results In fMRI experiments of simultaneous visual/motor activities, 3D T2prep-GRE showed minimal distortion and little signal dropout across the whole brain. Its lower power deposition allowed greater spatial coverage (55 versus 17 slices with identical TR, resolution and power level), temporal SNR (60% higher) and CNR (35% higher) efficiency than 2D spin-echo EPI. It also showed smaller T2* contamination. Conclusion This approach is expected to be useful for ultra-high field fMRI, especially for regions near air cavities. The concept of using T2-preparation to generate BOLD contrast can be combined with many other sequences at any field strength. PMID:24338901

  4. Construction of an MRI 3D high resolution sheep brain template.

    PubMed

    Ella, Arsène; Keller, Matthieu

    2015-12-01

    Sheep is a developing animal model used in the field of neurosciences for the study of many behavioral, physiological or pathophysiological mechanisms, including for example, the central control of social behavior, brain injury or neurodegenerative diseases. However, sheep remains an orphan species in the field of magnetic resonance imaging (MRI). Therefore, a mean image (template), resulting of registrations of multiple subject images is needed and currently does not exist. In this study, we: i) computed multimodal high resolution 3D in-vivo sheep brain templates of T1 weighted (T1W) and T2W images, ii) computed gray matter (GM), white matter (WM) and cerebrospinal fluid (CSF) prior probability maps using linear and optimized non-linear registrations iii) used prior probability maps to perform the segmentation of a single brain tissues. Computed multimodal sheep brain templates showed to preserve and underline all brain patterns of a single T1W or T2W image, and prior probability maps allowed to improve the segmentation of brain tissues. Finally, we demonstrated that these templates and prior probability maps were able to be portable in other publicly available imaging software and could be used as standardized spaces for multi-institution neuroimaging studies or other neuroscience methods. PMID:26363468

  5. 3D MRI brain image segmentation based on region restricted EM algorithm

    NASA Astrophysics Data System (ADS)

    Li, Zhong; Fan, Jianping

    2008-03-01

    This paper presents a novel algorithm of 3D human brain tissue segmentation and classification in magnetic resonance image (MRI) based on region restricted EM algorithm (RREM). The RREM is a level set segmentation method while the evolution of the contours was driven by the force field composed by the probability density functions of the Gaussian models. Each tissue is modeled by one or more Gaussian models restricted by free shaped contour so that the Gaussian models are adaptive to the local intensities. The RREM is guaranteed to be convergency and achieving the local minimum. The segmentation avoids to be trapped in the local minimum by the split and merge operation. A fuzzy rule based classifier finally groups the regions belonging to the same tissue and forms the segmented 3D image of white matter (WM) and gray matter (GM) which are of major interest in numerous applications. The presented method can be extended to segment brain images with tumor or the images having part of the brain removed with the adjusted classifier.

  6. Simulation of 3D MRI brain images for quantitative evaluation of image segmentation algorithms

    NASA Astrophysics Data System (ADS)

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

    2000-06-01

    To model the true shape of MRI brain images, automatically classified T1-weighted 3D MRI images (gray matter, white matter, cerebrospinal fluid, scalp/bone and background) are utilized for simulation of grayscale data and imaging artifacts. For each class, Gaussian distribution of grayscale values is assumed, and mean and variance are computed from grayscale images. A random generator fills up the class images with Gauss-distributed grayscale values. Since grayscale values of neighboring voxels are not correlated, a Gaussian low-pass filtering is done, preserving class region borders. To simulate anatomical variability, a Gaussian distribution in space with user-defined mean and variance can be added at any user-defined position. Several imaging artifacts can be added: (1) to simulate partial volume effects, every voxel is averaged with neighboring voxels if they have a different class label; (2) a linear or quadratic bias field can be added with user-defined strength and orientation; (3) additional background noise can be added; and (4) artifacts left over after spoiling can be simulated by adding a band with increasing/decreasing grayscale values. With this method, realistic-looking simulated MRI images can be produced to test classification and segmentation algorithms regarding accuracy and robustness even in the presence of artifacts.

  7. 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

  8. 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

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

    PubMed Central

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

    2013-01-01

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

  10. 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.

  11. 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.

  12. 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

  13. 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

  14. 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. PMID:24728041

  15. Construction of a neuroanatomical shape complex atlas from 3D MRI brain structures.

    PubMed

    Chen, Ting; Rangarajan, Anand; Eisenschenk, Stephan J; Vemuri, Baba C

    2012-04-15

    Brain atlas construction has attracted significant attention lately in the neuroimaging community due to its application to the characterization of neuroanatomical shape abnormalities associated with various neurodegenerative diseases or neuropsychiatric disorders. Existing shape atlas construction techniques usually focus on the analysis of a single anatomical structure in which the important inter-structural information is lost. This paper proposes a novel technique for constructing a neuroanatomical shape complex atlas based on an information geometry framework. A shape complex is a collection of neighboring shapes - for example, the thalamus, amygdala and the hippocampus circuit - which may exhibit changes in shape across multiple structures during the progression of a disease. In this paper, we represent the boundaries of the entire shape complex using the zero level set of a distance transform function S(x). We then re-derive the relationship between the stationary state wave function ψ(x) of the Schrödinger equation [formula in text] and the eikonal equation [formula in text] satisfied by any distance function. This leads to a one-to-one map (up to scale) between ψ(x) and S(x) via an explicit relationship. We further exploit this relationship by mapping ψ(x) to a unit hypersphere whose Riemannian structure is fully known, thus effectively turn ψ(x) into the square-root of a probability density function. This allows us to make comparisons - using elegant, closed-form analytic expressions - between shape complexes represented as square-root densities. A shape complex atlas is constructed by computing the Karcher mean ψ¯(x) in the space of square-root densities and then inversely mapping it back to the space of distance transforms in order to realize the atlas shape. We demonstrate the shape complex atlas computation technique via a set of experiments on a population of brain MRI scans including controls and epilepsy patients with either right anterior

  16. Construction of Neuroanatomical Shape Complex Atlas from 3D Brain MRI

    PubMed Central

    Chen, Ting; Rangarajan, Anand; Eisenschenk, Stephan J.; Vemuri, Baba C.

    2010-01-01

    This paper proposes a novel technique for constructing a neuroanatomical shape complex atlas using an information geometry framework. A shape complex is a collection of shapes in a local neighborhood. We represent the boundary of the entire shape complex using the zero level set of a distance function S(x). The spatial relations between the different anatomical structures constituting the shape complex are captured via the distance transform. We then leverage the well known relationship between the stationary state wave function ψ(x) of the Schrödinger equation −ħ2∇2ψ + ψ = 0 and the eikonal equation ‖∇S‖ = 1 satisfied by any distance function S(x). This leads to a one-to-one map between ψ(x) and S(x) and allows for recovery of S(x) from ψ(x) through an explicit mathematical relationship. Since the wave function can be regarded as a square-root density function, we are able to exploit this connection and convert shape complex distance transforms into probability density functions. Furthermore, square-root density functions can be seen as points on a unit hypersphere whose Riemannian structure is fully known. A shape complex atlas is constructed by first computing the Karcher mean ψ̄(x) of the wave functions, followed by an inverse mapping of the estimated mean back to the space of distance transforms in order to realize the atlas. We demonstrate the shape complex atlas computation via a set of experiments on a population of brain MRI scans. We also present modes of variation from the computed atlas for the control population to demonstrate the shape complex variability. PMID:20879384

  17. Construction of neuroanatomical shape complex atlas from 3D brain MRI.

    PubMed

    Chen, Ting; Rangarajan, Anand; Eisenschenk, Stephan J; Vemuri, Baba C

    2010-01-01

    This paper proposes a novel technique for constructing a neuroanatomical shape complex atlas using an information geometry framework. A shape complex is a collection of shapes in a local neighborhood. We represent the boundary of the entire shape complex using the zero level set of a distance function S(x). The spatial relations between the different anatomical structures constituting the shape complex are captured via the distance transform. We then leverage the well known relationship between the stationary state wave function psi(x) of the Schrödinger equation -h2nabla2 psi + psi = 0 and the eikonal equation //nablaS// = 1 satisfied by any distance function S(x). This leads to a one-to-one map between psi(x) and S(x) and allows for recovery of S(x) from psi(x) through an explicit mathematical relationship. Since the wave function can be regarded as a square-root density function, we are able to exploit this connection and convert shape complex distance transforms into probability density functions. Furthermore, square-root density functions can be seen as points on a unit hypersphere whose Riemannian structure is fully known. A shape complex atlas is constructed by first computing the Karcher mean psi(x) of the wave functions, followed by an inverse mapping of the estimated mean back to the space of distance transforms in order to realize the atlas. We demonstrate the shape complex atlas computation via a set of experiments on a population of brain MRI scans. We also present modes of variation from the computed atlas for the control population to demonstrate the shape complex variability. PMID:20879384

  18. 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

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

    PubMed Central

    Helgason, Thordur; Ramon, Ceon; jr, Halldór Jónsson; Carraro, Ugo

    2014-01-01

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

  20. 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.

  1. Compatibility of glass-guided recording microelectrodes in the brain stem of squirrel monkeys with high-resolution 3D MRI.

    PubMed

    Tammer, R; Ehrenreich, L; Boretius, S; Watanabe, T; Frahm, J; Michaelis, T

    2006-06-15

    Knowledge of the precise position of recording microelectrodes within the brain of a non-human primate is essential for a reliable exploration of very small anatomic structures. This work demonstrates the compatibility of a newly developed glass-guided microelectrode design and microfeed equipment with high-resolution 3D magnetic resonance imaging (MRI). T1- and T2-weighted images allow for the non-invasive visualization of chronically implanted microelectrodes within the brain stem of squirrel monkeys in vivo. Neural extracellular multi-unit recordings proved the functionality of the microelectrode before and after the use of 3D MRI suggesting the preservation of normal brain tissue at the tip of the electrode. Because histology confirmed the absence of lesions attributable to MRI, the approach offers an interactive monitoring during the course of neuroethological experiments. Consequently, MRI may become an in vivo alternative to common histological post mortem verifications of electrode tracks and hence may avoid the early sacrificing of primates after only a small number of experiments. PMID:16343640

  2. MRI Volume Fusion Based on 3D Shearlet Decompositions.

    PubMed

    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

  3. 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

  4. 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

  5. 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

  6. 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/.

  7. 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

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

    PubMed Central

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

    2014-01-01

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

  9. 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…

  10. 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

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

    PubMed Central

    Cash, Sydney S.

    2015-01-01

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

  12. 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.

  13. 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

  14. 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. PMID:25573020

  15. Comparison of 3D orientation distribution functions measured with confocal microscopy and diffusion MRI.

    PubMed

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

    2016-04-01

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

  16. 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

  17. 3D mapping of somatotopic reorganization with small animal functional MRI

    PubMed Central

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

    2009-01-01

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

  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. MR image denoising method for brain surface 3D modeling

    NASA Astrophysics Data System (ADS)

    Zhao, De-xin; Liu, Peng-jie; Zhang, De-gan

    2014-11-01

    Three-dimensional (3D) modeling of medical images is a critical part of surgical simulation. In this paper, we focus on the magnetic resonance (MR) images denoising for brain modeling reconstruction, and exploit a practical solution. We attempt to remove the noise existing in the MR imaging signal and preserve the image characteristics. A wavelet-based adaptive curve shrinkage function is presented in spherical coordinates system. The comparative experiments show that the denoising method can preserve better image details and enhance the coefficients of contours. Using these denoised images, the brain 3D visualization is given through surface triangle mesh model, which demonstrates the effectiveness of the proposed method.

  20. Creating Physical 3D Stereolithograph Models of Brain and Skull

    PubMed Central

    Kelley, Daniel J.; Farhoud, Mohammed; Meyerand, M. Elizabeth; Nelson, David L.; Ramirez, Lincoln F.; Dempsey, Robert J.; Wolf, Alan J.; Alexander, Andrew L.; Davidson, Richard J.

    2007-01-01

    The human brain and skull are three dimensional (3D) anatomical structures with complex surfaces. However, medical images are often two dimensional (2D) and provide incomplete visualization of structural morphology. To overcome this loss in dimension, we developed and validated a freely available, semi-automated pathway to build 3D virtual reality (VR) and hand-held, stereolithograph models. To evaluate whether surface visualization in 3D was more informative than in 2D, undergraduate students (n = 50) used the Gillespie scale to rate 3D VR and physical models of both a living patient-volunteer's brain and the skull of Phineas Gage, a historically famous railroad worker whose misfortune with a projectile tamping iron provided the first evidence of a structure-function relationship in brain. Using our processing pathway, we successfully fabricated human brain and skull replicas and validated that the stereolithograph model preserved the scale of the VR model. Based on the Gillespie ratings, students indicated that the biological utility and quality of visual information at the surface of VR and stereolithograph models were greater than the 2D images from which they were derived. The method we developed is useful to create VR and stereolithograph 3D models from medical images and can be used to model hard or soft tissue in living or preserved specimens. Compared to 2D images, VR and stereolithograph models provide an extra dimension that enhances both the quality of visual information and utility of surface visualization in neuroscience and medicine. PMID:17971879

  1. Breast Tissue 3D Segmentation and Visualization on MRI

    PubMed Central

    Cui, Xiangfei; Sun, Feifei

    2013-01-01

    Tissue segmentation and visualization are useful for breast lesion detection and quantitative analysis. In this paper, a 3D segmentation algorithm based on Kernel-based Fuzzy C-Means (KFCM) is proposed to separate the breast MR images into different tissues. Then, an improved volume rendering algorithm based on a new transfer function model is applied to implement 3D breast visualization. Experimental results have been shown visually and have achieved reasonable consistency. PMID:23983676

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 3D MRI-based tumor delineation of ocular melanoma and its comparison with conventional techniques

    SciTech Connect

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

    2005-11-15

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

  8. 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

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-01-01

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

  11. 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

  12. Comparison of Parallel MRI Reconstruction Methods for Accelerated 3D Fast Spin-Echo Imaging

    PubMed Central

    Xiao, Zhikui; Hoge, W. Scott; Mulkern, R.V.; Zhao, Lei; Hu, Guangshu; Kyriakos, Walid E.

    2014-01-01

    Parallel MRI (pMRI) achieves imaging acceleration by partially substituting gradient-encoding steps with spatial information contained in the component coils of the acquisition array. Variable-density subsampling in pMRI was previously shown to yield improved two-dimensional (2D) imaging in comparison to uniform subsampling, but has yet to be used routinely in clinical practice. In an effort to reduce acquisition time for 3D fast spin-echo (3D-FSE) sequences, this work explores a specific nonuniform sampling scheme for 3D imaging, subsampling along two phase-encoding (PE) directions on a rectilinear grid. We use two reconstruction methods—2D-GRAPPA-Operator and 2D-SPACE RIP—and present a comparison between them. We show that high-quality images can be reconstructed using both techniques. To evaluate the proposed sampling method and reconstruction schemes, results via simulation, phantom study, and in vivo 3D human data are shown. We find that fewer artifacts can be seen in the 2D-SPACE RIP reconstructions than in 2D-GRAPPA-Operator reconstructions, with comparable reconstruction times. PMID:18727083

  13. 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

  14. 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

  15. 3D MRI Analysis of the Lower Legs of Treated Idiopathic Congenital Talipes Equinovarus (Clubfoot)

    PubMed Central

    Duce, Suzanne L.; D’Alessandro, Mariella; Du, Yimeng; Jagpal, Baljit; Gilbert, Fiona J.; Crichton, Lena; Barker, Simon; Collinson, J. Martin; Miedzybrodzka, Zosia

    2013-01-01

    Background Idiopathic congenital talipes equinovarus (CTEV) is the commonest form of clubfoot. Its exact cause is unknown, although it is related to limb development. The aim of this study was to quantify the anatomy of the muscle, subcutaneous fat, tibia, fibula and arteries in the lower legs of teenagers and young adults with CTEV using 3D magnetic resonance imaging (MRI), and thus to investigate the anatomical differences between CTEV participants and controls. Methodology/Principal Findings The lower legs of six CTEV (2 bilateral, 4 unilateral) and five control young adults (age 12–28) were imaged using a 3T MRI Philips scanner. 5 of the CTEV participants had undergone soft-tissue and capsular release surgery. 3D T1-weighted and 3D magnetic resonance angiography (MRA) images were acquired. Segmentation software was used for volumetric, anatomical and image analysis. Kolmogorov-Smirnov tests were performed. The volumes of the lower affected leg, muscle, tibia and fibula in unilateral CTEV participants were consistently smaller compared to their contralateral unaffected leg, this was most pronounced in muscle. The proportion of muscle in affected CTEV legs was significantly reduced compared with control and unaffected CTEV legs, whilst proportion of muscular fat increased. No spatial abnormalities in the location or branching of arteries were detected, but hypoplastic anomalies were observed. Conclusions/Significance Combining 3D MRI and MRA is effective for quantitatively characterizing CTEV anatomy. Reduction in leg muscle volume appears to be a sensitive marker. Since 5/6 CTEV cases had soft-tissue surgery, further work is required to confirm that the treatment did not affect the MRI features observed. We propose that the proportion of muscle and intra-muscular fat within the lower leg could provide a valuable addition to current clinical CTEV classification. These measures could be useful for clinical care and guiding treatment pathways, as well as

  16. 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.

  17. Assessing tumor response after loco-regional liver cancer therapies: the role of 3D MRI

    PubMed Central

    Chapiro, Julius; Lin, MingDe; Duran, Rafael; Schernthaner, Rüdiger E; Geschwind, Jean-François

    2015-01-01

    Assessing the tumor response of liver cancer lesions after intraarterial therapies is of major clinical interest. Over the last two decades, tumor response criteria have come a long way from purely size-based, anatomic methods such as the Response Evaluation Criteria in Solid Tumors towards more functional, enhancement- and diffusion-based parameters with a strong emphasis on MRI as the ultimate imaging modality. However, the relatively low reproducibility of those one- and 2D techniques (modified Response Evaluation Criteria in Solid Tumors and the European Association for the Study of the Liver criteria) provided the rationale for the development of new, 3D quantitative assessment techniques. This review will summarize and compare the existing methodologies used for 3D quantitative tumor analysis and provide an overview of the published clinical evidence for the benefits of 3D quantitative tumor response assessment techniques. PMID:25371052

  18. 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.

  19. Reduction of Breast Density Following Tamoxifen Treatment Evaluated by 3-D MRI: Preliminary Study

    PubMed Central

    Chen, Jeon-Hor; Chang, Yeun-Chung; Chang, Daniel; Wang, Yi-Ting; Nie, Ke; Chang, Ruey-Feng; Nalcioglu, Orhan; Huang, Chiun-Sheng; Su, Min-Ying

    2010-01-01

    This study analyzed the change of breast density in women receiving tamoxifen treatment using 3-D MRI. Sixteen women were studied. Each woman received breast MRI before and after tamoxifen. The breast and the fibroglandular tissue were segmented using a computer-assisted algorithm, based on T1-weighted images. The fibroglandular tissue volume (FV) and breast volume (BV) were measured and the ratio was calculated as the percent breast density (%BD). The changes in breast volume (ΔBV), fibroglandular tissue volume (ΔFV), and percent density (Δ%BD) between two MRI studies were analyzed and correlated with treatment duration and baseline breast density. The ΔFV showed a reduction in all 16 women. The Δ%BD showed a mean reduction of 5.8%. The reduction of FV was significantly correlated with baseline FV (P<0.001) and treatment duration (P=0.03). The percentage change in FV was correlated with duration (P=0.049). The reduction in %BD was positively correlated with baseline %BD (p=0.02). Women with higher baseline %BD showed more reduction of %BD. 3D MRI may be useful for the measurement of the small changes of ΔFV and Δ%BD after tamoxifen. These changes can potentially be used to correlate with the future reduction of cancer risk. PMID:20832226

  20. 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

  1. Role of 3D MRI with proset technique in the evaluation of lumbar radiculopathy.

    PubMed

    Grasso, D; Borreggine, C; Melchionda, D; Bristogiannis, C; Stoppino, L P; Macarini, L

    2013-01-01

    The aim of this study is to demonstrate the effectiveness of 3-Dimensional Magnetic Resonance Imaging (3D MRI) using the ProSet technique in the diagnosis of lumbar radiculopathy and to compare morphological findings with clinical and neurophysiological data. 40 patients suffering from L5 or S1 mono-radiculopathy caused by a disc herniation were evaluated through preliminary clinical assessment and electromyography (EMG) technique. Both conventional spin-echo sequences and 3D coronal FFE with selective water excitation (ProSet imaging) were acquired. Indentation, swelling and tilt angle of the nerve root were assessed by means of a 3D MR radiculography. 3D ProSet multiplanar reconstructions (MPR) were used for quantitative measurements of L5 and S1 nerve root widths. Widths of the symptomatic nerve root were compared with those of the contralateral nerve. Data were processed using Epi Info 3.3 software (CDC, Atlanta, GA, USA) and were compared through a paired t-Student test. We observed an abnormal tilt angle in 22 patients (57,2 percent, P less than 0.05). Morphologic alterations such as monolateral swelling or indentation of the involved roots were found in 36 patients (90 percent, P less than0.01) using 3D MR radiculography. In 10 patients, EMG revealed more nerve roots involved, while 3D FFE with ProSet technique shows a single root involved. In 2 patients, alterations were demonstrated only through EMG technique. We suggest that 3D MR radiculography can provide more information than other techniques about symptomatic disc herniation, supporting the detection of morphological changes of all nerve segments. 3D FFE with ProSet technique demonstrates high sensibility to exactly identify the level of the root involved and can provide an extremely useful tool to lead a surgical planning. PMID:24152846

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. Imaging knee position using MRI, RSA/CT and 3D digitisation.

    PubMed

    McPherson, A; Kärrholm, J; Pinskerova, V; Sosna, A; Martelli, S

    2005-02-01

    The purpose of this study was to compare 3 methods of imaging knee position. Three fresh cadaver knees were imaged at 6 flexion angles between 0 degrees and 120 degrees by MRI, a combination of RSA and CT and 3D digitisation (in two knees). Virtual models of all 42 positions were created using suitable computer software. Each virtual model was aligned to a newly defined anatomically based Cartesian coordinate system. The angular rotations around the 3 coordinate system axes were calculated directly from the aligned virtual models using rigid body kinematics and found to be equally accurate for the 3 methods. The 3 rotations in each knee could be depicted using anatomy-based diagrams for all 3 methods. We conclude that the 3 methods of data acquisition are equally and adequately accurate in vitro. MRI may be the most useful in vivo. PMID:15598452

  8. 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

  9. MRI 3D CISS- A Novel Imaging Modality in Diagnosing Trigeminal Neuralgia - A Review.

    PubMed

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

    2016-03-01

    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

  10. 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.

  11. 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

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. Automatic "pipeline" analysis of 3-D MRI data for clinical trials: application to multiple sclerosis.

    PubMed

    Zijdenbos, Alex P; Forghani, Reza; Evans, Alan C

    2002-10-01

    The quantitative analysis of magnetic resonance imaging (MRI) data has become increasingly important in both research and clinical studies aiming at human brain development, function, and pathology. Inevitably, the role of quantitative image analysis in the evaluation of drug therapy will increase, driven in part by requirements imposed by regulatory agencies. However, the prohibitive length of time involved and the significant intraand inter-rater variability of the measurements obtained from manual analysis of large MRI databases represent major obstacles to the wider application of quantitative MRI analysis. We have developed a fully automatic "pipeline" image analysis framework and have successfully applied it to a number of large-scale, multicenter studies (more than 1,000 MRI scans). This pipeline system is based on robust image processing algorithms, executed in a parallel, distributed fashion. This paper describes the application of this system to the automatic quantification of multiple sclerosis lesion load in MRI, in the context of a phase III clinical trial. The pipeline results were evaluated through an extensive validation study, revealing that the obtained lesion measurements are statistically indistinguishable from those obtained by trained human observers. Given that intra- and inter-rater measurement variability is eliminated by automatic analysis, this system enhances the ability to detect small treatment effects not readily detectable through conventional analysis techniques. While useful for clinical trial analysis in multiple sclerosis, this system holds widespread potential for applications in other neurological disorders, as well as for the study of neurobiology in general. PMID:12585710

  17. 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.

  18. Atlas-Guided Segmentation of Vervet Monkey Brain MRI

    PubMed Central

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

    2011-01-01

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

  19. 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

  20. SPASM: a 3D-ASM for segmentation of sparse and arbitrarily oriented cardiac MRI data.

    PubMed

    van Assen, Hans C; Danilouchkine, Mikhail G; Frangi, Alejandro F; Ordás, Sebastián; Westenberg, Jos J M; Reiber, Johan H C; Lelieveldt, Boudewijn P F

    2006-04-01

    A new technique (SPASM) based on a 3D-ASM is presented for automatic segmentation of cardiac MRI image data sets consisting of multiple planes with arbitrary orientations, and with large undersampled regions. Model landmark positions are updated in a two-stage iterative process. First, landmark positions close to intersections with images are updated. Second, the update information is propagated to the regions without image information, such that new locations for the whole set of the model landmarks are obtained. Feature point detection is performed by a fuzzy inference system, based on fuzzy C-means clustering. Model parameters were optimized on a computer cluster and the computational load distributed by grid computing. SPASM was applied to image data sets with an increasing sparsity (from 2 to 11 slices) comprising images with different orientations and stemming from different MRI acquisition protocols. Segmentation outcomes and calculated volumes were compared to manual segmentation on a dense short-axis data configuration in a 3D manner. For all data configurations, (sub-)pixel accuracy was achieved. Performance differences between data configurations were significantly different (p<0.05) for SA data sets with less than 6 slices, but not clinically relevant (volume differences<4 ml). Comparison to results from other 3D model-based methods showed that SPASM performs comparable to or better than these other methods, but SPASM uses considerably less image data. Sensitivity to initial model placement proved to be limited within a range of position perturbations of approximately 20 mm in all directions. PMID:16439182

  1. 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

  2. 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.

  3. 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

  4. 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

  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. 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.

  7. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

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

  9. 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.

  10. 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

  11. 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

  12. 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.

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

    PubMed

    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%. PMID

  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. [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. PMID:24195387

  16. 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.

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

    PubMed

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

    2016-01-01

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

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

    PubMed 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. 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. PMID:19272995

  20. 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.

  1. 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). PMID:19381963

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

    PubMed

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

    2013-09-01

    The visual system's flexibility in estimating depth is remarkable: We readily perceive 3-D structure under diverse conditions from the seemingly random dots of a "magic eye" stereogram to the aesthetically beautiful, but obviously flat, canvasses of the Old Masters. Yet, 3-D perception is often enhanced when different cues specify the same depth. This perceptual process is understood as Bayesian inference that improves sensory estimates. Despite considerable behavioral support for this theory, insights into the cortical circuits involved are limited. Moreover, extant work tested quantitatively similar cues, reducing some of the challenges associated with integrating computationally and qualitatively different signals. Here we address this challenge by measuring fMRI responses to depth structures defined by shading, binocular disparity, and their combination. We quantified information about depth configurations (convex "bumps" vs. concave "dimples") in different visual cortical areas using pattern classification analysis. We found that fMRI responses in dorsal visual area V3B/KO were more discriminable when disparity and shading concurrently signaled depth, in line with the predictions of cue integration. Importantly, by relating fMRI and psychophysical tests of integration, we observed a close association between depth judgments and activity in this area. Finally, using a cross-cue transfer test, we found that fMRI responses evoked by one cue afford classification of responses evoked by the other. This reveals a generalized depth representation in dorsal visual cortex that combines qualitatively different information in line with 3-D perception. PMID:23647559

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

    PubMed

    Blinowski, Grzegorz; Kamiński, Maciej; Wawer, Dariusz

    2014-08-01

    The problem of functional connectivity in the brain is in the focus of attention nowadays, since it is crucial for understanding information processing in the brain. A large repertoire of measures of connectivity have been devised, some of them being capable of estimating time-varying directed connectivity. Hence, there is a need for a dedicated software tool for visualizing the propagation of electrical activity in the brain. To this aim, the Trans3D application was developed. It is an open access tool based on widely available libraries and supporting both Windows XP/Vista/7(™), Linux and Mac environments. Trans3D can create animations of activity propagation between electrodes/sensors, which can be placed by the user on the scalp/cortex of a 3D model of the head. Various interactive graphic functions for manipulating and visualizing components of the 3D model and input data are available. An application of the Trans3D tool has helped to elucidate the dynamics of the phenomena of information processing in motor and cognitive tasks, which otherwise would have been very difficult to observe. Trans3D is available at: http://www.eeg.pl/. PMID:24967953

  4. 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

    2010-01-01

    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. PMID:21124830

  5. 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

  6. 3D MRI of impaired hyperpolarized 129Xe uptake in a rat model of pulmonary fibrosis.

    PubMed

    Cleveland, Zackary I; Virgincar, Rohan S; Qi, Yi; Robertson, Scott H; Degan, Simone; Driehuys, Bastiaan

    2014-12-01

    A variety of pulmonary pathologies, in particular interstitial lung diseases, are characterized by thickening of the pulmonary blood-gas barrier, and this thickening results in reduced gas exchange. Such diffusive impairment is challenging to quantify spatially, because the distributions of the metabolically relevant gases (CO2 and O2) cannot be detected directly within the lungs. Hyperpolarized (HP) (129)Xe is a promising surrogate for these metabolic gases, because MR spectroscopy and imaging allow gaseous alveolar (129)Xe to be detected separately from (129)Xe dissolved in the red blood cells (RBCs) and the adjacent tissues, which comprise blood plasma and lung interstitium. Because (129)Xe reaches the RBCs by diffusing across the same barrier tissues (blood plasma and interstitium) as O2, barrier thickening will delay (129)Xe transit and, thus, reduce RBC-specific (129)Xe MR signal. Here we have exploited these properties to generate 3D, MR images of (129)Xe uptake by the RBCs in two groups of rats. In the experimental group, unilateral fibrotic injury was generated prior to imaging by instilling bleomycin into one lung. In the control group, a unilateral sham instillation of saline was performed. Uptake of (129)Xe by the RBCs, quantified as the fraction of RBC signal relative to total dissolved (129)Xe signal, was significantly reduced (P = 0.03) in the injured lungs of bleomycin-treated animals. In contrast, no significant difference (P = 0.56) was observed between the saline-treated and untreated lungs of control animals. Together, these results indicate that 3D MRI of HP (129)Xe dissolved in the pulmonary tissues can provide useful biomarkers of impaired diffusive gas exchange resulting from fibrotic thickening. PMID:24816478

  7. 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.

  8. Segmentation of human brain using structural MRI.

    PubMed

    Helms, Gunther

    2016-04-01

    Segmentation of human brain using structural MRI is a key step of processing in imaging neuroscience. The methods have undergone a rapid development in the past two decades and are now widely available. This non-technical review aims at providing an overview and basic understanding of the most common software. Starting with the basis of structural MRI contrast in brain and imaging protocols, the concepts of voxel-based and surface-based segmentation are discussed. Special emphasis is given to the typical contrast features and morphological constraints of cortical and sub-cortical grey matter. In addition to the use for voxel-based morphometry, basic applications in quantitative MRI, cortical thickness estimations, and atrophy measurements as well as assignment of cortical regions and deep brain nuclei are briefly discussed. Finally, some fields for clinical applications are given. PMID:26739264

  9. 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. PMID:26835884

  10. 3-D in vivo brain tumor geometry study by scaling analysis

    NASA Astrophysics Data System (ADS)

    Torres Hoyos, F.; Martín-Landrove, M.

    2012-02-01

    A new method, based on scaling analysis, is used to calculate fractal dimension and local roughness exponents to characterize in vivo 3-D tumor growth in the brain. Image acquisition was made according to the standard protocol used for brain radiotherapy and radiosurgery, i.e., axial, coronal and sagittal magnetic resonance T1-weighted images, and comprising the brain volume for image registration. Image segmentation was performed by the application of the k-means procedure upon contrasted images. We analyzed glioblastomas, astrocytomas, metastases and benign brain tumors. The results show significant variations of the parameters depending on the tumor stage and histological origin.

  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. 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

  13. Effects of scatter on model parameter estimates in 3D PET studies of the human brain

    SciTech Connect

    Cherry, S.R.; Huang, S.C.

    1995-08-01

    Phantom measurements and simulated data were used to characterize the effects of scatter on 3D PET projection data, reconstructed images and model parameter estimates. Scatter distributions were estimated form studies of the 3D Hoffman brain phantom by the 2D/3D difference method. The total scatter fraction in the projection data was 40%, but reduces to 27% when only those counts within the boundary of the brain are considered. After reconstruction, the whole brain scatter fraction is 20%, averaging 10% in cortical gray matter, 21% in basal ganglia and 40% in white matter. The scatter contribution varies by almost a factor of two from the edge to the center of the brain due to the shape of the scatter distribution and the effects of attenuation correction. The effect of scatter on estimates of cerebral metabolic rate for glucose (CMRGI) and cerebral blood flow (CBF) is evaluated by simulating typical gray matter time activity curves (TAC`s) and adding a scatter component based on whole-brain activity. Both CMRGI and CBF change in a linear fashion with scatter fraction. Efforts of between 10 and 30% will typically result if 3D studies are not corrected for scatter. The authors also present results from a simple and fast scatter correction which fits a gaussian function to the scattered events outside the brain. This reduced the scatter fraction to <2% in a range of phantom studies with different activity distributions. Using this correction, quantitative errors in 3D PET studies of CMRGI and CBF can be reduced to well below 10%.

  14. 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

  15. 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

  16. 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

  17. 3-D sonography for diagnosis of osteoarthrosis and disk degeneration of the temporomandibular joint, compared with MRI.

    PubMed

    Landes, Constantin A; Goral, Wojciech; Mack, Martin G; Sader, Robert

    2006-05-01

    This study determined the value of three-dimensional (3-D) sonography for the assessment of osteoarthrosis and disk degeneration of the temporomandibular joint (TMJ). Sixty-eight patients (136 TMJ) with clinical dysfunction were examined by 272 sonographic 3-D scans. An 8- to 12.5-MHz motor-angulated transducer positioned inferior-parallel to the zygomatic arch scanned the region-of-interest. 3-D condylar morphology was compared with subsequent magnetic resonance imaging (MRI). Fifty-three datasets were complete, i.e., 106 TMJ, 212 examinations. 3-D sonographic examination took 5 min and attained 70% sensitivity/76% specificity/75% accuracy; positive predictive value was 44%%; negative predictive value was 90%. Disk degeneration was diagnosed synonymously with 64%/73%/71%/42%/ 87%. 3-D sonography proved to be reliable for exclusion of osteoarthrosis as disk degeneration compared with MRI, whereas the presence of osteoarthrosis and disk dislocation cannot be reliably diagnosed. Prospective use will include routine screening, using more sophisticated equipment with higher frequency in real-time 3-D viewing. PMID:16677921

  18. 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

  19. 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

  20. 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. PMID:26053196

  1. Synthetic ground truth for validation of brain tumor MRI segmentation.

    PubMed

    Prastawa, Marcel; Bullitt, Elizabeth; Gerig, Guido

    2005-01-01

    Validation and method of comparison for segmentation of magnetic resonance images (MRI) presenting pathology is a challenging task due to the lack of reliable ground truth. We propose a new method for generating synthetic multi-modal 3D brain MRI with tumor and edema, along with the ground truth. Tumor mass effect is modeled using a biomechanical model, while tumor and edema infiltration is modeled as a reaction-diffusion process that is guided by a modified diffusion tensor MRI. We propose the use of warping and geodesic interpolation on the diffusion tensors to simulate the displacement and the destruction of the white matter fibers. We also model the process where the contrast agent tends to accumulate in cortical csf regions and active tumor regions to obtain contrast enhanced T1w MR image that appear realistic. The result is simulated multi-modal MRI with ground truth available as sets of probability maps. The system will be able to generate large sets of simulation images with tumors of varying size, shape and location, and will additionally generate infiltrated and deformed healthy tissue probabilities. PMID:16685825

  2. A Monte Carlo correction for the effect of Compton scattering in 3-D PET brain imaging

    SciTech Connect

    Levin, C.S.; Dahlbom, M.; Hoffman, E.J.

    1995-08-01

    A Monte Carlo simulation has been developed to simulate and correct for the effect of Compton scatter in 3-D acquired PET brain scans. The method utilizes the 3-D reconstructed image volume as the source intensity distribution for a photon-tracking Monte Carlo simulation. It is assumed that the number of events in each pixel of the image represents the isotope concentration at that location in the brain. The history of each annihilation photon`s interactions in the scattering medium is followed, and the sinograms for the scattered and unscattered photon pairs are generated in a simulated 3-D PET acquisition. The calculated scatter contribution is used to correct the original data set. The method is general and can be applied to any scanner configuration or geometry. In its current form the simulation requires 25 hours on a single Sparc 10 CPU when every pixel in a 15-plane, 128 x 128 pixel image volume is sampled, and less than 2 hours when 16 pixels (4 x 4) are grouped as a single pixel. Results of the correction applied to 3-D human and phantom studies are presented.

  3. 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.

  4. 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.

  5. 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.

  6. 3D Multislab, Multishot Acquisition for Fast, Whole-Brain MR Elastography with High SNR Efficiency

    PubMed Central

    Johnson, Curtis L; Holtrop, Joseph L; McGarry, Matthew DJ; Weaver, John B; Paulsen, Keith D; Georgiadis, John G; Sutton, Bradley P

    2014-01-01

    Purpose To develop an acquisition scheme for generating magnetic resonance elastography (MRE) displacement data with whole-brain coverage, high spatial resolution, and adequate signal-to-noise ratio (SNR) in a short scan time. Theory and Methods A 3D multislab, multishot acquisition for whole-brain MRE with 2.0 mm isotropic spatial resolution is proposed. The multislab approach allowed for the use of short repetition time to achieve very high SNR efficiency. High SNR efficiency allowed for a reduced acquisition time of only six minutes while the minimum SNR needed for inversion was maintained. Results The mechanical property maps estimated from whole-brain displacement data with nonlinear inversion (NLI) demonstrated excellent agreement with neuroanatomical features, including the cerebellum and brainstem. A comparison with an equivalent 2D acquisition illustrated the improvement in SNR efficiency of the 3D multislab acquisition. The flexibility afforded by the high SNR efficiency allowed for higher resolution with a 1.6 mm isotropic voxel size, which generated higher estimates of brainstem stiffness compared with the 2.0 mm isotropic acquisition. Conclusions The acquisition presented allows for the capture of whole-brain MRE displacement data in a short scan time, and may be used to generate local mechanical property estimates of neuroanatomical features throughout the brain. PMID:24347237

  7. Brain MRI findings in Wernicke encephalopathy.

    PubMed

    Wicklund, Meredith R; Knopman, David S

    2013-08-01

    A 71-year-old woman with myelofibrosis on chemotherapy experienced an acute illness with nausea, vomiting, and diarrhea. Two weeks later, she developed an acute confusional state characterized by disorientation and fluctuating alertness with normal speech and language. Her neurologic examination demonstrated an upper motor neuron pattern of right hemiparesis. She reported double vision though ophthalmoparesis was not appreciated. Her gait was normal. While hospitalized, she developed generalized tonic-clonic seizures. Brain MRI revealed a small area of restricted diffusion of the left precentral gyrus (figure). She was diagnosed with a stroke with secondary seizures; however, as the confusional state resolved, she developed profound retrograde and anterograde amnesia. Review of the brain MRI showed high T2 signal in the medial thalamus and contrast enhancement of the mamillary bodies; a diagnosis of Wernicke-Korsakoff syndrome was entertained and she was started on thiamine replacement. The encephalopathy and hemiparesis resolved though she remains severely amnestic. PMID:24195023

  8. MRI of radiation injury to the brain

    SciTech Connect

    Curnes, J.T.; Laster, D.W.; Ball, M.R.; Moody, D.M.; Witcofski, R.L.

    1986-07-01

    Nine patients with a history of radiation of 2400-6000 rad (24-60 Gy) to the brain were examined by magnetic resonance imaging (MRI) and computed tomography (CT). MRI demonstrated abnormalities in the periventricular white matter in all patients. The abnormal periventricular signal was characterized by a long T2 and was demonstrated best on coronal spin-echo (SE) 1000/80 images. A characteristic scalloped appearance at the junction of the gray-white matter was seen on MR images of seven patients, and represented extensive white-matter damage involving the more peripheral arcuate fiber systems. This differs from transependymal absorption, which is seen best on SE 3000/80 images and has a smooth peripheral margin. Cranial CT demonstrated white-matter lucencies in six cases but generally failed to display the extent of white-matter injury demonstrated by MRI. MRI is uniquely suited to detect radiation injury to the brain because of its extreme sensitivity to white-matter edema.

  9. Data-driven optimization and evaluation of 2D EPI and 3D PRESTO for BOLD fMRI at 7 Tesla: I. Focal coverage.

    PubMed

    Barry, Robert L; Strother, Stephen C; Gatenby, J Christopher; Gore, John C

    2011-04-01

    Blood oxygenation level dependent (BOLD) functional magnetic resonance imaging (fMRI) is commonly performed using 2D single-shot echo-planar imaging (EPI). However, single-shot EPI at 7 Tesla (T) often suffers from significant geometric distortions (due to low bandwidth (BW) in the phase-encode (PE) direction) and amplified physiological noise. Recent studies have suggested that 3D multi-shot sequences such as PRESTO may offer comparable BOLD contrast-to-noise ratio with increased volume coverage and decreased geometric distortions. Thus, a four-way group-level comparison was performed between 2D and 3D acquisition sequences at two in-plane resolutions. The quality of fMRI data was evaluated via metrics of prediction and reproducibility using NPAIRS (Non-parametric Prediction, Activation, Influence and Reproducibility re-Sampling). Group activation maps were optimized for each acquisition strategy by selecting the number of principal components that jointly maximized prediction and reproducibility, and showed good agreement in sensitivity and specificity for positive BOLD changes. High-resolution EPI exhibited the highest z-scores of the four acquisition sequences; however, it suffered from the lowest BW in the PE direction (resulting in the worst geometric distortions) and limited spatial coverage, and also caused some subject discomfort through peripheral nerve stimulation (PNS). In comparison, PRESTO also had high z-scores (higher than EPI for a matched in-plane resolution), the highest BW in the PE direction (producing images with superior geometric fidelity), the potential for whole-brain coverage, and no reported PNS. This study provides evidence to support the use of 3D multi-shot acquisition sequences in lieu of single-shot EPI for ultra high field BOLD fMRI at 7T. PMID:21232613

  10. MRI data driven partial volume effects correction in PET imaging using 3D local multi-resolution analysis

    NASA Astrophysics Data System (ADS)

    Le Pogam, Adrien; Lamare, Frederic; Hatt, Mathieu; Fernandez, Philippe; Le Rest, Catherine Cheze; Visvikis, Dimitris

    2013-02-01

    PET partial volume effects (PVE) resulting from the limited resolution of PET scanners is still a quantitative issue that PET/MRI scanners do not solve by themselves. A recently proposed voxel-based locally adaptive 3D multi-resolution PVE correction based on the mutual analysis of wavelet decompositions was applied on 12 clinical 18F-FLT PET/T1 MRI images of glial tumors, and compared to a PET only voxel-wise iterative deconvolution approach. Quantitative and qualitative results demonstrated the interest of exploiting PET/MRI information with higher uptake increases (19±8% vs. 11±7%, p=0.02), as well as more convincing visual restoration of details within tumors with respect to deconvolution of the PET uptake only. Further studies are now required to demonstrate the accuracy of this restoration with histopathological validation of the uptake in tumors.

  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. 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.

  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. Vascular phenotyping of brain tumors using magnetic resonance microscopy (μMRI)

    PubMed Central

    Kim, Eugene; Zhang, Jiangyang; Hong, Karen; Benoit, Nicole E; Pathak, Arvind P

    2011-01-01

    Abnormal vascular phenotypes have been implicated in neuropathologies ranging from Alzheimer's disease to brain tumors. The development of transgenic mouse models of such diseases has created a crucial need for characterizing the murine neurovasculature. Although histologic techniques are excellent for imaging the microvasculature at submicron resolutions, they offer only limited coverage. It is also challenging to reconstruct the three-dimensional (3D) vasculature and other structures, such as white matter tracts, after tissue sectioning. Here, we describe a novel method for 3D whole-brain mapping of the murine vasculature using magnetic resonance microscopy (μMRI), and its application to a preclinical brain tumor model. The 3D vascular architecture was characterized by six morphologic parameters: vessel length, vessel radius, microvessel density, length per unit volume, fractional blood volume, and tortuosity. Region-of-interest analysis showed significant differences in the vascular phenotype between the tumor and the contralateral brain, as well as between postinoculation day 12 and day 17 tumors. These results unequivocally show the feasibility of using μMRI to characterize the vascular phenotype of brain tumors. Finally, we show that combining these vascular data with coregistered images acquired with diffusion-weighted MRI provides a new tool for investigating the relationship between angiogenesis and concomitant changes in the brain tumor microenvironment. PMID:21386855

  15. 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

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

    PubMed Central

    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

  17. 3D PATTERN OF BRAIN ABNORMALITIES IN WILLIAMS SYNDROME VISUALIZED USING TENSOR-BASED MORPHOMETRY

    PubMed Central

    Chiang, Ming-Chang; Reiss, Allan L.; Lee, Agatha D.; Bellugi, Ursula; Galaburda, Albert M.; Korenberg, Julie R.; Mills, Debra L.; Toga, Arthur W.; Thompson, Paul M.

    2009-01-01

    Williams syndrome (WS) is a neurodevelopmental disorder associated with deletion of ~20 contiguous genes in chromosome band 7q11.23. Individuals with WS exhibit mild to moderate mental retardation, but are relatively more proficient in specific language and musical abilities. We used tensor-based morphometry (TBM) to visualize the complex pattern of gray/white matter reductions in WS, based on fluid registration of structural brain images. Methods 3D T1-weighted brain MRIs of 41 WS subjects (age: 29.2±9.2SD years; 23F/18M) and 39 age-matched healthy controls (age: 27.5±7.4 years; 23F/16M) were fluidly registered to a minimum deformation target. Fine-scale volumetric differences were mapped between diagnostic groups. Local regions were identified where regional structure volumes were associated with diagnosis, and with intelligence quotient (IQ) scores. Brain asymmetry was also mapped and compared between diagnostic groups. Results WS subjects exhibited widely distributed brain volume reductions (~10–15% reduction; P < 0.0002, permutation test). After adjusting for total brain volume, the frontal lobes, anterior cingulate, superior temporal gyrus, amygdala, fusiform gyrus and cerebellum were found to be relatively preserved in WS, but parietal and occipital lobes, thalamus and basal ganglia, and midbrain were disproportionally decreased in volume (P < 0.0002). These regional volumes also correlated positively with performance IQ in adult WS subjects (age ≥ 30 years, P = 0.038). Conclusion TBM facilitates 3D visualization of brain volume reductions in WS. Reduced parietal/occipital volumes may be associated with visuospatial deficits in WS. By contrast, frontal lobes, amygdala, and cingulate gyrus are relatively preserved or even enlarged, consistent with unusual affect regulation and language production in WS. PMID:17512756

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

    NASA Astrophysics Data System (ADS)

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

    2000-04-01

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

  19. 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

  20. Coculture System with an Organotypic Brain Slice and 3D Spheroid of Carcinoma Cells

    PubMed Central

    Chuang, Han-Ning; Lohaus, Raphaela; Hanisch, Uwe-Karsten; Binder, Claudia

    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 prognosis1,2. Especially the tumor associated macrophages (TAM) support migration, invasion and proliferation3. 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 cells4,5. Therefore, functions of these tissue-specific cell types seem to be very important in the process of brain metastasis6,7. 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 behavior8. 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 impossible8. 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 the brain

  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. Intraoperative MRI in pediatric brain tumors.

    PubMed

    Choudhri, Asim F; Siddiqui, Adeel; Klimo, Paul; Boop, Frederick A

    2015-09-01

    Intraoperative magnetic resonance imaging (iMRI) has emerged as an important tool in guiding the surgical management of children with brain tumors. Recent advances have allowed utilization of high field strength systems, including 3-tesla MRI, resulting in diagnostic-quality scans that can be performed while the child is on the operating table. By providing information about the possible presence of residual tumor, it allows the neurosurgeon to both identify and resect any remaining tumor that is thought to be safely accessible. By fusing the newly obtained images with the surgical guidance software, the images have the added value of aiding in navigation to any residual tumor. This is important because parenchyma often shifts during surgery. It also gives the neurosurgeon insight into whether any immediate postoperative complications have occurred. If any complications have occurred, the child is already in the operating room and precious minutes lost in transport and communications are saved. In this article we review the three main approaches to an iMRI system design. We discuss the possible roles for iMRI during intraoperative planning and provide guidance to help radiologists and neurosurgeons alike in the collaborative management of these children. PMID:26346145

  3. Segmentation of center brains and optic lobes in 3D confocal images of adult fruit fly brains.

    PubMed

    Lam, Shing Chun Benny; Ruan, Zongcai; Zhao, Ting; Long, Fuhui; Jenett, Arnim; Simpson, Julie; Myers, Eugene W; Peng, Hanchuan

    2010-02-01

    Automatic alignment (registration) of 3D images of adult fruit fly brains is often influenced by the significant displacement of the relative locations of the two optic lobes (OLs) and the center brain (CB). In one of our ongoing efforts to produce a better image alignment pipeline of adult fruit fly brains, we consider separating CB and OLs and align them independently. This paper reports our automatic method to segregate CB and OLs, in particular under conditions where the signal to noise ratio (SNR) is low, the variation of the image intensity is big, and the relative displacement of OLs and CB is substantial. We design an algorithm to find a minimum-cost 3D surface in a 3D image stack to best separate an OL (of one side, either left or right) from CB. This surface is defined as an aggregation of the respective minimum-cost curves detected in each individual 2D image slice. Each curve is defined by a list of control points that best segregate OL and CB. To obtain the locations of these control points, we derive an energy function that includes an image energy term defined by local pixel intensities and two internal energy terms that constrain the curve's smoothness and length. Gradient descent method is used to optimize this energy function. To improve both the speed and robustness of the method, for each stack, the locations of optimized control points in a slice are taken as the initialization prior for the next slice. We have tested this approach on simulated and real 3D fly brain image stacks and demonstrated that this method can reasonably segregate OLs from CBs despite the aforementioned difficulties. PMID:19698789

  4. 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

  5. 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.

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

    PubMed

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

    2016-05-01

    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

  7. 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

  8. Thermal impact of an active 3-D microelectrode array implanted in the brain.

    PubMed

    Kim, Sohee; Tathireddy, Prashant; Normann, Richard A; Solzbacher, Florian

    2007-12-01

    A chronically implantable, wireless neural interface device will require integrating electronic circuitry with the interfacing microelectrodes in order to eliminate wired connections. Since the integrated circuit (IC) dissipates a certain amount of power, it will raise the temperature in surrounding tissues where it is implanted. In this paper, the thermal influence of the integrated 3-D Utah electrode array (UEA) device implanted in the brain was investigated by numerical simulation using finite element analysis (FEA) and by experimental measurement in vitro as well as in vivo. The numerically calculated and experimentally measured temperature increases due to the UEA implantation were in good agreement. The experimentally validated numerical model predicted that the temperature increases linearly with power dissipation through the UEA, with a slope of 0.029 degree C/mW over the power dissipation levels expected to be used. The influences of blood perfusion, brain metabolism, and UEA geometry on tissue heating were also investigated using the numerical model. PMID:18198706

  9. 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. PMID:26780787

  10. 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.

  11. Microtesla MRI of the human brain combined with MEG

    PubMed Central

    Zotev, Vadim S.; Matlashov, Andrei N.; Volegov, Petr L.; Savukov, Igor M.; Espy, Michelle A.; Mosher, John C.; Gomez, John J.; Kraus, Robert H.

    2008-01-01

    One of the challenges in functional brain imaging is integration of complementary imaging modalities, such as magnetoencephalography (MEG) and functional magnetic resonance imaging (fMRI). MEG, which uses highly sensitive superconducting quantum interference devices (SQUIDs) to directly measure magnetic fields of neuronal currents, cannot be combined with conventional high-field MRI in a single instrument. Indirect matching of MEG and MRI data leads to significant co-registration errors. A recently proposed imaging method-SQUID-based microtesla MRI-can be naturally combined with MEG in the same system to directly provide structural maps for MEG-localized sources. It enables easy and accurate integration of MEG and MRI/fMRI, because microtesla MR images can be precisely matched to structural images provided by high-field MRI and other techniques. Here we report the first images of the human brain by microtesla MRI, together with auditory MEG (functional) data, recorded using the same seven-channel SQUID system during the same imaging session. The images were acquired at 46 microtesla measurement field with pre-polarization at 30 mT. We also estimated transverse relaxation times for different tissues at microtesla fields. Our results demonstrate feasibility and potential of human brain imaging by microtesla MRI. They also show that two new types of imaging equipment-low-cost systems for anatomical MRI of the human brain at microtesla fields, and more advanced instruments for combined functional (MEG) and structural (microtesla MRI) brain imaging-are practical. PMID:18619876

  12. 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

  13. 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

  14. 3D MRI of non-Gaussian 3He gas diffusion in the rat lung

    NASA Astrophysics Data System (ADS)

    Jacob, Richard E.; Laicher, Gernot; Minard, Kevin R.

    2007-10-01

    In 3He magnetic resonance images of pulmonary air spaces, the confining architecture of the parenchymal tissue results in a non-Gaussian distribution of signal phase that non-exponentially attenuates image intensity as diffusion weighting is increased. Here, two approaches previously used for the analysis of non-Gaussian effects in the lung are compared and related using diffusion-weighted 3He MR images of mechanically ventilated rats. One approach is model-based and was presented by Yablonskiy et al., while the other approach utilizes the second order decay contribution that is predicted from the cumulant expansion theorem. Total lung coverage is achieved using a hybrid 3D pulse sequence that combines conventional phase encoding with sparse radial sampling for efficient gas usage. This enables the acquisition of nine 3D images using a total of only ˜1 L of hyperpolarized 3He gas. Diffusion weighting ranges from 0 s/cm 2 to 40 s/cm 2. Results show that the non-Gaussian effects of 3He gas diffusion in healthy rat lungs are directly attributed to the anisotropic geometry of lung microstructure as predicted by the Yablonskiy model, and that quantitative analysis over the entire lung can be reliably repeated in time-course studies of the same animal.

  15. Age- and race-dependence of the fibroglandular breast density analyzed on 3D MRI

    PubMed Central

    Nie, Ke; Su, Min-Ying; Chau, Man-Kwun; Chan, Siwa; Nguyen, Hoanglong; Tseng, Tiffany; Huang, Yuhong; McLaren, Christine E.; Nalcioglu, Orhan; Chen, Jeon-Hor

    2010-01-01

    Purpose: The purpose of this study was to evaluate the age- and race-dependence of the breast fibroglandular tissue density based on three-dimensional breast MRI. Methods: The normal breasts of 321 consecutive patients including Caucasians, Asians, and Hispanics were studied. The subjects were separated into three age groups: Younger than 45, between 45 and 55, and older than 55. Computer algorithms based on body landmarks were used to segment the breast, and fuzzy c-means algorithm was used to segment the fibroglandular tissue. Linear regression analysis was applied to compare mean differences among different age groups and race∕ethnicity groups. The obtained parameters were not normally distributed, and the transformed data, natural log (ln) for the fibroglandular tissue volume, and the square root for the percent density were used for statistical analysis. Results: On the average, the transformed fibroglandular tissue volume and percent density decreased significantly with age. Racial differences in mean transformed percent density were found among women older than 45, but not among women younger than 45. Mean percent density was higher in Asians compared to Caucasians and Hispanics; the difference remained significant after adjustment for age, but not significant after adjusted for both age and breast volume. There was no significant difference in the density between the Caucasians and the Hispanics. Conclusions: The results analyzed using the MRI-based method show age- and race-dependence, which is consistent with literature using mammography-based methods. PMID:20632587

  16. 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.

  17. Microtesla MRI of the human brain combined with MEG

    NASA Astrophysics Data System (ADS)

    Zotev, Vadim S.; Matlashov, Andrei N.; Volegov, Petr L.; Savukov, Igor M.; Espy, Michelle A.; Mosher, John C.; Gomez, John J.; Kraus, Robert H.

    2008-09-01

    One of the challenges in functional brain imaging is integration of complementary imaging modalities, such as magnetoencephalography (MEG) and functional magnetic resonance imaging (fMRI). MEG, which uses highly sensitive superconducting quantum interference devices (SQUIDs) to directly measure magnetic fields of neuronal currents, cannot be combined with conventional high-field MRI in a single instrument. Indirect matching of MEG and MRI data leads to significant co-registration errors. A recently proposed imaging method—SQUID-based microtesla MRI—can be naturally combined with MEG in the same system to directly provide structural maps for MEG-localized sources. It enables easy and accurate integration of MEG and MRI/fMRI, because microtesla MR images can be precisely matched to structural images provided by high-field MRI and other techniques. Here we report the first images of the human brain by microtesla MRI, together with auditory MEG (functional) data, recorded using the same seven-channel SQUID system during the same imaging session. The images were acquired at 46 μT measurement field with pre-polarization at 30 mT. We also estimated transverse relaxation times for different tissues at microtesla fields. Our results demonstrate feasibility and potential of human brain imaging by microtesla MRI. They also show that two new types of imaging equipment—low-cost systems for anatomical MRI of the human brain at microtesla fields, and more advanced instruments for combined functional (MEG) and structural (microtesla MRI) brain imaging—are practical.

  18. 3-D Cytoarchitectonic parcellation of human orbitofrontal cortex. Correlation with postmortem MRI

    PubMed Central

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

    2010-01-01

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

  19. 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

  20. 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

  1. 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

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

    PubMed

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

    2010-07-15

    With the recent increase in the number of three-dimensional (3D) applications, the need for interfaces to these applications has increased. Although the eye tracking method has been widely used as an interaction interface for hand-disabled persons, this approach cannot be used for depth directional navigation. To solve this problem, we propose a new brain computer interface (BCI) method in which the BCI and eye tracking are combined to analyze depth navigation, including selection and two-dimensional (2D) gaze direction, respectively. The proposed method is novel in the following five ways compared to previous works. First, a device to measure both the gaze direction and an electroencephalogram (EEG) pattern is proposed with the sensors needed to measure the EEG attached to a head-mounted eye tracking device. Second, the reliability of the BCI interface is verified by demonstrating that there is no difference between the real and the imaginary movements for the same work in terms of the EEG power spectrum. Third, depth control for the 3D interaction interface is implemented by an imaginary arm reaching movement. Fourth, a selection method is implemented by an imaginary hand grabbing movement. Finally, for the independent operation of gazing and the BCI, a mode selection method is proposed that measures a user's concentration by analyzing the pupil accommodation speed, which is not affected by the operation of gazing and the BCI. According to experimental results, we confirmed the feasibility of the proposed 3D interaction method using eye tracking and a BCI. PMID:20580646

  3. 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.

  4. 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

  5. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2000-06-01

    The purpose of individual 3D region-of-interest atlas extraction is to automatically define anatomically meaningful regions in 3D MRI images for quantification of functional parameters (PET, SPECT: rMRGlu, rCBF). The first step of atlas extraction is to automatically classify brain tissue types into gray matter (GM), white matter (WM), cerebrospinal fluid (CSF), scalp/bone (SB) and background (BG). A feed-forward neural network with back-propagation training algorithm is used and compared to other numerical classifiers. It can be trained by a sample from the individual patient data set in question. Classification is done by a 'winner takes all' decision. Automatic extraction of a user-specified number of training points is done in a cross-sectional slice. Background separation is done by simple region growing. The most homogeneous voxels define the region for WM training point extraction (TPE). Non-white-matter and nonbackground regions are analyzed for GM and CSF training points. For SB TPE, the distance from the BG region is one feature. For each class, spatially uniformly distributed training points are extracted by a random generator from these regions. Simulated and real 3D MRI images are analyzed and error rates for TPE and classification calculated. The resulting class images can be analyzed for extraction of anatomical ROIs.

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

    NASA Astrophysics Data System (ADS)

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

    2005-04-01

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

  8. 3D morphology of the rear foot from MRI data: technical validation and clinical description

    NASA Astrophysics Data System (ADS)

    Stindel, Eric; Udupa, Jayaram K.; Hirsch, Bruce E.; Odhner, Dewey; Couture, Christine

    1998-06-01

    The purpose of this work is to characterize the 3D morphology of the bones of the rear foot using MR data. This work has two subaims: (1) to study the variability of the various computed architectural measures as a result of the subjectivity and variations in the various processing operations; (2) to study the morphology of the bones included in the peritalar complex. Each image data set utilized in this study consists of 60 longitudinal slices of the foot acquired on a 1.5 T commercial GE MR system. Our description of the rear foot morphology is based mainly on the principal axes, which represent the inertia axes of the bones, as well as on the bone surfaces. We use the live-wire method for segmenting and forming the surfaces of the bones. In the first part of this work, we focus on the dependence of the principal axes system on segmentation and on scan orientation. In the second part, we describe the normal morphology of the rear foot considering the four bones (calcaneus, cuboid, navicular, talus) and compare them to a population from the Upper Pleistocene. We conclude that this non-invasive method can be used in live patients to characterize the bone morphology or as a comparative method to classify population of bones. in spite of the variations involved in the various processing operations.

  9. Plane Localization in 3-D Fetal Neurosonography for Longitudinal Analysis of the Developing Brain.

    PubMed

    Yaqub, Mohammad; Rueda, Sylvia; Kopuri, Anil; Melo, Pedro; Papageorghiou, A T; Sullivan, Peter B; McCormick, Kenneth; Noble, J Alison

    2016-07-01

    The parasagittal (PS) plane is a 2-D diagnostic plane used routinely in cranial ultrasonography of the neonatal brain. This paper develops a novel approach to find the PS plane in a 3-D fetal ultrasound scan to allow image-based biomarkers to be tracked from prebirth through the first weeks of postbirth life. We propose an accurate plane-finding solution based on regression forests (RF). The method initially localizes the fetal brain and its midline automatically. The midline on several axial slices is used to detect the midsagittal plane, which is used as a constraint in the proposed RF framework to detect the PS plane. The proposed learning algorithm guides the RF learning method in a novel way by: 1) using informative voxels and voxel informative strength as a weighting within the training stage objective function, and 2) introducing regularization of the RF by proposing a geometrical feature within the training stage. Results on clinical data indicate that the new automated method is more reproducible than manual plane finding obtained by two clinicians. PMID:26011873

  10. 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

  11. Automatic training and reliability estimation for 3D ASM applied to cardiac MRI segmentation.

    PubMed

    Tobon-Gomez, Catalina; Sukno, Federico M; Butakoff, Constantine; Huguet, Marina; Frangi, Alejandro F

    2012-07-01

    Training active shape models requires collecting manual ground-truth meshes in a large image database. While shape information can be reused across multiple imaging modalities, intensity information needs to be imaging modality and protocol specific. In this context, this study has two main purposes: (1) to test the potential of using intensity models learned from MRI simulated datasets and (2) to test the potential of including a measure of reliability during the matching process to increase robustness. We used a population of 400 virtual subjects (XCAT phantom), and two clinical populations of 40 and 45 subjects. Virtual subjects were used to generate simulated datasets (MRISIM simulator). Intensity models were trained both on simulated and real datasets. The trained models were used to segment the left ventricle (LV) and right ventricle (RV) from real datasets. Segmentations were also obtained with and without reliability information. Performance was evaluated with point-to-surface and volume errors. Simulated intensity models obtained average accuracy comparable to inter-observer variability for LV segmentation. The inclusion of reliability information reduced volume errors in hypertrophic patients (EF errors from 17 ± 57% to 10 ± 18%; LV MASS errors from -27 ± 22 g to -14 ± 25 g), and in heart failure patients (EF errors from -8 ± 42% to -5 ± 14%). The RV model of the simulated images needs further improvement to better resemble image intensities around the myocardial edges. Both for real and simulated models, reliability information increased segmentation robustness without penalizing accuracy. PMID:22683992

  12. Automatic training and reliability estimation for 3D ASM applied to cardiac MRI segmentation

    NASA Astrophysics Data System (ADS)

    Tobon-Gomez, Catalina; Sukno, Federico M.; Butakoff, Constantine; Huguet, Marina; Frangi, Alejandro F.

    2012-07-01

    Training active shape models requires collecting manual ground-truth meshes in a large image database. While shape information can be reused across multiple imaging modalities, intensity information needs to be imaging modality and protocol specific. In this context, this study has two main purposes: (1) to test the potential of using intensity models learned from MRI simulated datasets and (2) to test the potential of including a measure of reliability during the matching process to increase robustness. We used a population of 400 virtual subjects (XCAT phantom), and two clinical populations of 40 and 45 subjects. Virtual subjects were used to generate simulated datasets (MRISIM simulator). Intensity models were trained both on simulated and real datasets. The trained models were used to segment the left ventricle (LV) and right ventricle (RV) from real datasets. Segmentations were also obtained with and without reliability information. Performance was evaluated with point-to-surface and volume errors. Simulated intensity models obtained average accuracy comparable to inter-observer variability for LV segmentation. The inclusion of reliability information reduced volume errors in hypertrophic patients (EF errors from 17 ± 57% to 10 ± 18% LV MASS errors from -27 ± 22 g to -14 ± 25 g), and in heart failure patients (EF errors from -8 ± 42% to -5 ± 14%). The RV model of the simulated images needs further improvement to better resemble image intensities around the myocardial edges. Both for real and simulated models, reliability information increased segmentation robustness without penalizing accuracy.

  13. 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

  14. 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.

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

    PubMed

    Thompson, Larissa; Dias, Humberto Galvão; Campos, Tarcísio Passos Ribeiro

    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

  16. 3D surface analysis of hippocampal microvasculature in the irradiated brain.

    PubMed

    Craver, Brianna M; Acharya, Munjal M; Allen, Barrett D; Benke, Sarah N; Hultgren, Nan W; Baulch, Janet E; Limoli, Charles L

    2016-06-01

    Cranial irradiation used to control CNS malignancies can also disrupt the vasculature and impair neurotransmission and cognition. Here we describe two distinct methodologies for quantifying early and late radiation injury in CNS microvasculature. Intravascular fluorescently labeled lectin was used to visualize microvessels in the brain of the irradiated mouse 2 days post exposure and RECA-1 immunostaining was similarly used to visualize microvessels in the brain of the irradiated rat 1-month post exposure. Confocal microscopy, image deconvolution and 3-dimensional rendering methods were used to define vascular structure in a ∼4 × 10(7) μm(3) defined region of the brain. Quantitative analysis of these 3D images revealed that irradiation caused significant short- and long-term reductions in capillary density, diameter and volume. In mice, irradiation reduced mean vessel volume from 2,250 to 1,470 μm(3) and mean vessel diameter from 5.0 to 4.5 μm, resulting in significant reductions of 34% and 10%, in the hippocampus respectively. The number of vessel branch points and area was also found to also drop significantly in mice 2 days after irradiation. For rats, immunostaining revealed a significant, three-fold drop in capillary density 1 month after exposure compared to controls. Such radiation-induced disruption of the CNS microvasculature may be contributory if not causal to any number of neurocognitive side effects that manifest in cancer patients following cranial radiotherapy. This study demonstrates the utility of two distinct methodologies for quantifying these important adverse effects of radiotherapy. Environ. Mol. Mutagen. 57:341-349, 2016. © 2016 Wiley Periodicals, Inc. PMID:27175611

  17. 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

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

    PubMed Central

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

    2013-01-01

    The full potential of magnetic resonance spectroscopic imaging (MRSI) is often limited by localization artifacts, motion-related artifacts, scanner instabilities, and long measurement times. Localized adiabatic selective refocusing (LASER) provides accurate B1-insensitive spatial excitation even at high magnetic fields. Spiral encoding accelerates MRSI acquisition, and thus, enables 3D-coverage without compromising spatial resolution. Real-time position-and shim/frequency-tracking using MR navigators correct motion- and scanner instability-related artifacts. Each of these three advanced MRI techniques provides superior MRSI data compared to commonly used methods. In this work, we integrated in a single pulse sequence these three promising approaches. Real-time correction of motion, shim, and frequency-drifts using volumetric dual-contrast echo planar imaging-based navigators were implemented in an MRSI sequence that uses low-power gradient modulated short-echo time LASER localization and time efficient spiral readouts, in order to provide fast and robust 3D-MRSI in the human brain at 3T. The proposed sequence was demonstrated to be insensitive to motion- and scanner drift-related degradations of MRSI data in both phantoms and volunteers. Motion and scanner drift artifacts were eliminated and excellent spectral quality was recovered in the presence of strong movement. Our results confirm the expected benefits of combining a spiral 3D-LASER-MRSI sequence with real-time correction. The new sequence provides accurate, fast, and robust 3D metabolic imaging of the human brain at 3T. This will further facilitate the use of 3D-MRSI for neuroscience and clinical applications. PMID:24201013

  19. Model-based segmentation of individual brain structures from MRI data

    NASA Astrophysics Data System (ADS)

    Collins, D. Louis; Peters, Terence M.; Dai, Weiqian; Evans, Alan C.

    1992-09-01

    This paper proposes a methodology that enables an arbitrary 3-D MRI brain image-volume to be automatically segmented and classified into neuro-anatomical components using multiresolution registration and matching with a novel volumetric brain structure model (VBSM). This model contains both raster and geometric data. The raster component comprises the mean MRI volume after a set of individual volumes of normal volunteers have been transformed to a standardized brain-based coordinate space. The geometric data consists of polyhedral objects representing anatomically important structures such as cortical gyri and deep gray matter nuclei. The method consists of iteratively registering the data set to be segmented to the VBSM using deformations based on local image correlation. This segmentation process is performed hierarchically in scale-space. Each step in decreasing levels of scale refines the fit of the previous step and provides input to the next. Results from phantom and real MR data are presented.

  20. An open-source, automated platform for visualizing subdural electrodes using 3D CT-MRI coregistration

    PubMed Central

    Pearce, Allison; Krish, Veena T.; Wagenaar, Joost; Chen, Weixuan; Zheng, Yuanjie; Wang, Hongzhi; Lucas, Timothy H.; Gee, James C.; Litt, Brian; Davis, Kathryn A.

    2014-01-01

    Objective Visualizing implanted subdural electrodes in 3D space can greatly aid planning, executing, and validating resection in epilepsy surgery. Coregistration software is available, but cost, complexity, insufficient accuracy or validation limit adoption. We present a fully automated open-source application, based upon a novel method using post-implant CT and post-implant MR images, for accurately visualizing intracranial electrodes in 3D space. Methods CT-MR rigid brain coregistration, MR non-rigid registration, and prior-based segmentation were carried out on 7 subjects. Post-implant CT, post-implant MR, and an external labeled atlas were then aligned in the same space. The coregistration algorithm was validated by manually marking identical anatomical landmarks on the post-implant CT and post-implant MR images. Following coregistration, distances between the center of the landmark masks on the post-implant MR and the coregistered CT images were calculated for all subjects. Algorithms were implemented in open-source software and translated into a “drag and drop” desktop application for Apple Mac OS X. Results Despite post-operative brain deformation, the method was able to automatically align intra-subject multi-modal images and segment cortical subregions so that all electrodes could be visualized on the parcellated brain. Manual marking of anatomical landmarks validated the coregistration algorithm with a mean misalignment distance of 2.87 ± 0.58 mm between the landmarks. Software was easily used by operators without prior image processing experience. Significance We demonstrate an easy to use, novel platform for accurately visualizing subdural electrodes in 3D space on a parcellated brain. We rigorously validated this method using quantitative measures. The method is unique because it involves no pre-processing, is fully automated, and freely available worldwide. A desktop application, as well as the source code, are both available for download on the

  1. Compartment modeling anslysis of C-11 flumazenil kinetics in human brain using dynamic 2D and 3D PET

    SciTech Connect

    Choi, Y.; Simpson, N.; Townsend, D.W.

    1994-05-01

    We examined the feasibility of compartment modeling analysis and the numerical accuracy of model parameters of radioligand delivery and binding in the brain using 2D and 3D PET. Two subjects were injected with C-11 flumazenil (FMZ) i.v., and imaged over the brain with a dynamic sequence of 6x20 s, 2x30 s, 4x90 s, 4x180 s, 2x300 s, 2x600 s, and 2x1200 s frames. Different scatter correction methods were applied to the 3D data: No scatter correction (NOC), dual-energy window subtraction (DEW) and convolution-subtraction (CON). The kinetic data for regions listed below were fitted to a 2-compartment, 2-parameter model. Both 2D and 3D results are similar and within the expected range. The 3D %SE was less than 2D despite the smaller dose. The effect of the scatter in 3D parameter estimates appears to be small. These preliminary data indicate temporally sufficient kinetic data can be acquired in 3D mode to perform compartmental analysis of C-11 FMZ. Improved sensitivity in 3D may allow more accurate receptor characterization especially in small structures or in low specific binding areas.

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

    PubMed Central

    Despotović, Ivana

    2015-01-01

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

  3. 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

  4. A fast way to visualize the brain surface with volume rendering of MRI data.

    PubMed

    Matsumoto, S; Asato, R; Konishi, J

    1999-11-01

    The preprocessing of 3-dimensional (3D) MRI data constitutes a bottleneck in the process of visualizing the brain surface with volume rendering. As a fast way to achieve this preprocessing, the authors propose a simple pipeline based on an algorithm of seed-growing type, for approximate segmentation of the intradural space in T1-weighted 3D MRI data. Except for the setting of a seed and four parameters, this pipeline proceeds in an unsupervised manner; no interactive intermediate step is involved. It was tested with 15 datasets from normal adults. The result was reproducible in that as long as the seed was located within the cerebral white matter, identical segmentation was achieved for each dataset. Although the pipeline ran with gross segmentation error along the floor of the cranial cavity, it performed well along the cranial vault so that subsequent volume rendering permitted the observation of the sulco-gyral pattern over cerebral convexities. Use of this pipeline followed by volume rendering is a handy approach to the visualization of the brain surface from 3D MRI data. PMID:10587913

  5. 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.

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

    NASA Astrophysics Data System (ADS)

    Lindsey, Brooks D.

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

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

    NASA Astrophysics Data System (ADS)

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

    2008-03-01

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

  8. 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

  9. 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

  10. 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.

  11. 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

  12. The construction of a Chinese MRI brain atlas: a morphometric comparison study between Chinese and Caucasian cohorts.

    PubMed

    Tang, Yuchun; Hojatkashani, Cornelius; Dinov, Ivo D; Sun, Bo; Fan, Lingzhong; Lin, Xiangtao; Qi, Hengtao; Hua, Xue; Liu, Shuwei; Toga, Arthur W

    2010-05-15

    We developed a novel brain atlas template to facilitate computational brain studies of Chinese subjects and populations using high quality magnetic resonance imaging (MRI) and well-validated image analysis techniques. To explore the ethnicity-based structural brain differences, we used the MRI scans of 35 Chinese male subjects (24.03+/-2.06 years) and compared them to an age-matched cohort of 35 Caucasian males (24.03+/-2.06 years). Global volumetric measures were used to identify significant group differences in the brain length, width, height and AC-PC line distance. Using the LONI BrainParser, 56 brain structures were automatically labeled and analyzed for all subjects. We identified significant ethnicity differences in brain structure volumes, suggesting that a population-specific brain atlas may be more appropriate for studies involving Chinese populations. To address this, we constructed a 3D Chinese brain atlas based on high resolution 3.0T MRI scans of 56 right-handed male Chinese volunteers (24.46+/-1.81 years). All Chinese brains were spatially normalized by using linear and nonlinear transformation via the "AIR Make Atlas" pipeline workflow within the LONI pipeline environment. This high-resolution Chinese brain atlas was compared to the ICBM152 template, which was constructed using Caucasian brains. PMID:20152910

  13. Geometrically undistorted MRI in the presence of field inhomogeneities using compressed sensing accelerated broadband 3D phase encoded turbo spin-echo imaging

    NASA Astrophysics Data System (ADS)

    van Gorp, Jetse S.; Bakker, Chris J. G.; Bouwman, Job G.; Smink, Jouke; Zijlstra, Frank; Seevinck, Peter R.

    2015-01-01

    In this study, we explore the potential of compressed sensing (CS) accelerated broadband 3D phase-encoded turbo spin-echo (3D-PE-TSE) for the purpose of geometrically undistorted imaging in the presence of field inhomogeneities. To achieve this goal 3D-PE-SE and 3D-PE-TSE sequences with broadband rf pulses and dedicated undersampling patterns were implemented on a clinical scanner. Additionally, a 3D multi-spectral spin-echo (ms3D-SE) sequence was implemented for reference purposes. First, we demonstrated the influence of susceptibility induced off-resonance effects on the spatial encoding of broadband 3D-SE, ms3D-SE, 3D-PE-SE and 3D-PE-TSE using a grid phantom containing a titanium implant (Δχ = 182 ppm) with x-ray CT as a gold standard. These experiments showed that the spatial encoding of 3D-PE-(T)SE was unaffected by susceptibility induced off-resonance effects, which caused geometrical distortions and/or signal hyper-intensities in broadband 3D-SE and, to a lesser extent, in ms3D-SE frequency encoded methods. Additionally, an SNR analysis was performed and the temporally resolved signal of 3D-PE-(T)SE sequences was exploited to retrospectively decrease the acquisition bandwidth and obtain field offset maps. The feasibility of CS acceleration was studied retrospectively and prospectively for the 3D-PE-SE sequence using an existing CS algorithm adapted for the reconstruction of 3D data with undersampling in all three phase encoded dimensions. CS was combined with turbo-acceleration by variable density undersampling and spherical stepwise T2 weighting by randomly sorting consecutive echoes in predefined spherical k-space layers. The CS-TSE combination resulted in an overall acceleration factor of 60, decreasing the original 3D-PE-SE scan time from 7 h to 7 min. Finally, CS accelerated 3D-PE-TSE in vivo images of a titanium screw were obtained within 10 min using a micro-coil demonstrating the feasibility of geometrically undistorted MRI near severe

  14. Geometrically undistorted MRI in the presence of field inhomogeneities using compressed sensing accelerated broadband 3D phase encoded turbo spin-echo imaging.

    PubMed

    van Gorp, Jetse S; Bakker, Chris J G; Bouwman, Job G; Smink, Jouke; Zijlstra, Frank; Seevinck, Peter R

    2015-01-21

    In this study, we explore the potential of compressed sensing (CS) accelerated broadband 3D phase-encoded turbo spin-echo (3D-PE-TSE) for the purpose of geometrically undistorted imaging in the presence of field inhomogeneities. To achieve this goal 3D-PE-SE and 3D-PE-TSE sequences with broadband rf pulses and dedicated undersampling patterns were implemented on a clinical scanner. Additionally, a 3D multi-spectral spin-echo (ms3D-SE) sequence was implemented for reference purposes. First, we demonstrated the influence of susceptibility induced off-resonance effects on the spatial encoding of broadband 3D-SE, ms3D-SE, 3D-PE-SE and 3D-PE-TSE using a grid phantom containing a titanium implant (Δχ = 182 ppm) with x-ray CT as a gold standard. These experiments showed that the spatial encoding of 3D-PE-(T)SE was unaffected by susceptibility induced off-resonance effects, which caused geometrical distortions and/or signal hyper-intensities in broadband 3D-SE and, to a lesser extent, in ms3D-SE frequency encoded methods. Additionally, an SNR analysis was performed and the temporally resolved signal of 3D-PE-(T)SE sequences was exploited to retrospectively decrease the acquisition bandwidth and obtain field offset maps. The feasibility of CS acceleration was studied retrospectively and prospectively for the 3D-PE-SE sequence using an existing CS algorithm adapted for the reconstruction of 3D data with undersampling in all three phase encoded dimensions. CS was combined with turbo-acceleration by variable density undersampling and spherical stepwise T2 weighting by randomly sorting consecutive echoes in predefined spherical k-space layers. The CS-TSE combination resulted in an overall acceleration factor of 60, decreasing the original 3D-PE-SE scan time from 7 h to 7 min. Finally, CS accelerated 3D-PE-TSE in vivo images of a titanium screw were obtained within 10 min using a micro-coil demonstrating the feasibility of geometrically undistorted MRI near severe

  15. 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.

  16. 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

  17. 3D Standard Brain of the Red Flour Beetle Tribolium Castaneum: A Tool to Study Metamorphic Development and Adult Plasticity

    PubMed Central

    Dreyer, David; Vitt, Holger; Dippel, Stefan; Goetz, Brigitte; el Jundi, Basil; Kollmann, Martin; Huetteroth, Wolf; Schachtner, Joachim

    2009-01-01

    The red flour beetle Tribolium castaneum is emerging as a further standard insect model beside Drosophila. Its genome is fully sequenced and it is susceptible for genetic manipulations including RNA-interference. We use this beetle to study adult brain development and plasticity primarily with respect to the olfactory system. In the current study, we provide 3D standard brain atlases of freshly eclosed adult female and male beetles (A0). The atlases include eight paired and three unpaired neuropils including antennal lobes (ALs), optic lobe neuropils, mushroom body calyces and pedunculi, and central complex. For each of the two standard brains, we averaged brain areas of 20 individual brains. Additionally, we characterized eight selected olfactory glomeruli from 10 A0 female and male beetles respectively, which we could unequivocally recognize from individual to individual owing to their size and typical position in the ALs. In summary, comparison of the averaged neuropil volumes revealed no sexual dimorphism in any of the reconstructed neuropils in A0 Tribolium brains. Both, the female and male 3D standard brain are also used for interspecies comparisons, and, importantly, will serve as future volumetric references after genetical manipulation especially regarding metamorphic development and adult plasticity. PMID:20339482

  18. 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

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

    PubMed Central

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

    2015-01-01

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

  20. 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

  1. 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

  2. The Extraction of 3D Shape from Texture and Shading in the Human Brain

    PubMed Central

    Georgieva, Svetlana S.; Todd, James T.; Peeters, Ronald

    2008-01-01

    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. PMID:18281304

  3. 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

  4. Brain damage in methylmalonic aciduria: 2-methylcitrate induces cerebral ammonium accumulation and apoptosis in 3D organotypic brain cell cultures

    PubMed Central

    2013-01-01

    Background Methylmalonic aciduria is an inborn error of metabolism characterized by accumulation of methylmalonate (MMA), propionate and 2-methylcitrate (2-MCA) in body fluids. Early diagnosis and current treatment strategies aimed at limiting the production of these metabolites are only partially effective in preventing neurological damage. Methods To explore the metabolic consequences of methylmalonic aciduria on the brain, we used 3D organotypic brain cell cultures from rat embryos. We challenged the cultures at two different developmental stages with 1 mM MMA, propionate or 2-MCA applied 6 times every 12 h. In a dose–response experiment cultures were challenged with 0.01, 0.1, 0.33 and 1 mM 2-MCA. Immunohistochemical staining for different brain cell markers were used to assess cell viability, morphology and differentiation. Significant changes were validated by western blot analysis. Biochemical markers were analyzed in culture media. Apoptosis was studied by immunofluorescence staining and western blots for activated caspase-3. Results Among the three metabolites tested, 2-MCA consistently produced the most pronounced effects. Exposure to 2-MCA caused morphological changes in neuronal and glial cells already at 0.01 mM. At the biochemical level the most striking result was a significant ammonium increase in culture media with a concomitant glutamine decrease. Dose–response studies showed significant and parallel changes of ammonium and glutamine starting from 0.1 mM 2-MCA. An increased apoptosis rate was observed by activation of caspase-3 after exposure to at least 0.1 mM 2-MCA. Conclusion Surprisingly, 2-MCA, and not MMA, seems to be the most toxic metabolite in our in vitro model leading to delayed axonal growth, apoptosis of glial cells and to unexpected ammonium increase. Morphological changes were already observed at 2-MCA concentrations as low as 0.01 mM. Increased apoptosis and ammonium accumulation started at 0.1 mM thus suggesting that ammonium

  5. Molecular MRI enables early and sensitive detection of brain metastases.

    PubMed

    Serres, Sébastien; Soto, Manuel Sarmiento; Hamilton, Alastair; McAteer, Martina A; Carbonell, W Shawn; Robson, Matthew D; Ansorge, Olaf; Khrapitchev, Alexandre; Bristow, Claire; Balathasan, Lukxmi; Weissensteiner, Thomas; Anthony, Daniel C; Choudhury, Robin P; Muschel, Ruth J; Sibson, Nicola R

    2012-04-24

    Metastasis to the brain is a leading cause of cancer mortality. The current diagnostic method of gadolinium-enhanced MRI is sensitive only to larger tumors, when therapeutic options are limited. Earlier detection of brain metastases is critical for improved treatment. We have developed a targeted MRI contrast agent based on microparticles of iron oxide that enables imaging of endothelial vascular cell adhesion molecule-1 (VCAM-1). Our objectives here were to determine whether VCAM-1 is up-regulated on vessels associated with brain metastases, and if so, whether VCAM-1-targeted MRI enables early detection of these tumors. Early up-regulation of cerebrovascular VCAM-1 expression was evident on tumor-associated vessels in two separate murine models of brain metastasis. Metastases were detectable in vivo using VCAM-1-targeted MRI 5 d after induction (<1,000 cells). At clinical imaging resolutions, this finding is likely to translate to detection at tumor volumes two to three orders of magnitude smaller (0.3-3 × 10(5) cells) than those volumes detectable clinically (10(7)-10(8) cells). VCAM-1 expression detected by MRI increased significantly (P < 0.0001) with tumor progression, and tumors showed no gadolinium enhancement. Importantly, expression of VCAM-1 was shown in human brain tissue containing both established metastases and micrometastases. Translation of this approach to the clinic could increase therapeutic options and change clinical management in a substantial number of cancer patients. PMID:22451897

  6. Molecular MRI enables early and sensitive detection of brain metastases

    PubMed Central

    Serres, Sébastien; Soto, Manuel Sarmiento; Hamilton, Alastair; McAteer, Martina A.; Carbonell, W. Shawn; Robson, Matthew D.; Ansorge, Olaf; Khrapitchev, Alexandre; Bristow, Claire; Balathasan, Lukxmi; Weissensteiner, Thomas; Anthony, Daniel C.; Choudhury, Robin P.; Muschel, Ruth J.; Sibson, Nicola R.

    2012-01-01

    Metastasis to the brain is a leading cause of cancer mortality. The current diagnostic method of gadolinium-enhanced MRI is sensitive only to larger tumors, when therapeutic options are limited. Earlier detection of brain metastases is critical for improved treatment. We have developed a targeted MRI contrast agent based on microparticles of iron oxide that enables imaging of endothelial vascular cell adhesion molecule-1 (VCAM-1). Our objectives here were to determine whether VCAM-1 is up-regulated on vessels associated with brain metastases, and if so, whether VCAM-1–targeted MRI enables early detection of these tumors. Early up-regulation of cerebrovascular VCAM-1 expression was evident on tumor-associated vessels in two separate murine models of brain metastasis. Metastases were detectable in vivo using VCAM-1–targeted MRI 5 d after induction (<1,000 cells). At clinical imaging resolutions, this finding is likely to translate to detection at tumor volumes two to three orders of magnitude smaller (0.3–3 × 105 cells) than those volumes detectable clinically (107–108 cells). VCAM-1 expression detected by MRI increased significantly (P < 0.0001) with tumor progression, and tumors showed no gadolinium enhancement. Importantly, expression of VCAM-1 was shown in human brain tissue containing both established metastases and micrometastases. Translation of this approach to the clinic could increase therapeutic options and change clinical management in a substantial number of cancer patients. PMID:22451897

  7. 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.

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

    PubMed

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

    2015-05-26

    Differential diagnosis of brain magnetic resonance imaging (MRI) enhancement(s) remains a significant problem, which may be difficult to resolve without biopsy, which can be often dangerous or even impossible. Such MRI enhancement(s) can result from metastasis of primary tumors such as lung or breast, radiation necrosis, infections, or a new primary brain tumor (glioma, meningioma). Neurological symptoms are often the same on initial presentation. To develop a more precise noninvasive MRI diagnostic method, we have engineered a new class of poly(β-l-malic acid) polymeric nanoimaging agents (NIAs). The NIAs carrying attached MRI tracer are able to pass through the blood-brain barrier (BBB) and specifically target cancer cells for efficient imaging. A qualitative/quantitative "MRI virtual biopsy" method is based on a nanoconjugate carrying MRI contrast agent gadolinium-DOTA and antibodies recognizing tumor-specific markers and extravasating through the BBB. In newly developed double tumor xenogeneic mouse models of brain metastasis this noninvasive method allowed differential diagnosis of HER2- and EGFR-expressing brain tumors. After MRI diagnosis, breast and lung cancer brain metastases were successfully treated with similar tumor-targeted nanoconjugates carrying molecular inhibitors of EGFR or HER2 instead of imaging contrast agent. The treatment resulted in a significant increase in animal survival and markedly reduced immunostaining for several cancer stem cell markers. Novel NIAs could be useful for brain diagnostic MRI in the clinic without currently performed brain biopsies. This technology shows promise for differential MRI diagnosis and treatment of brain metastases and other pathologies when biopsies are difficult to perform. PMID:25906400

  9. Three-dimensional textural features of conventional MRI improve diagnostic classification of childhood brain tumours.

    PubMed

    Fetit, Ahmed E; Novak, Jan; Peet, Andrew C; Arvanitits, Theodoros N

    2015-09-01

    The aim of this study was to assess the efficacy of three-dimensional texture analysis (3D TA) of conventional MR images for the classification of childhood brain tumours in a quantitative manner. The dataset comprised pre-contrast T1 - and T2-weighted MRI series obtained from 48 children diagnosed with brain tumours (medulloblastoma, pilocytic astrocytoma and ependymoma). 3D and 2D TA were carried out on the images using first-, second- and higher order statistical methods. Six supervised classification algorithms were trained with the most influential 3D and 2D textural features, and their performances in the classification of tumour types, using the two feature sets, were compared. Model validation was carried out using the leave-one-out cross-validation (LOOCV) approach, as well as stratified 10-fold cross-validation, in order to provide additional reassurance. McNemar's test was used to test the statistical significance of any improvements demonstrated by 3D-trained classifiers. Supervised learning models trained with 3D textural features showed improved classification performances to those trained with conventional 2D features. For instance, a neural network classifier showed 12% improvement in area under the receiver operator characteristics curve (AUC) and 19% in overall classification accuracy. These improvements were statistically significant for four of the tested classifiers, as per McNemar's tests. This study shows that 3D textural features extracted from conventional T1 - and T2-weighted images can improve the diagnostic classification of childhood brain tumours. Long-term benefits of accurate, yet non-invasive, diagnostic aids include a reduction in surgical procedures, improvement in surgical and therapy planning, and support of discussions with patients' families. It remains necessary, however, to extend the analysis to a multicentre cohort in order to assess the scalability of the techniques used. PMID:26256809

  10. 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

  11. 3D watershed-based segmentation of internal structures within MR brain images

    NASA Astrophysics Data System (ADS)

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

    2000-06-01

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

  12. A non-invasive, 3D, dynamic MRI method for measuring muscle moment arms in vivo: demonstration in the human ankle joint and Achilles tendon.

    PubMed

    Clarke, E C; Martin, J H; d'Entremont, A G; Pandy, M G; Wilson, D R; Herbert, R D

    2015-01-01

    Muscle moment arms are used widely in biomechanical analyses. Often they are measured in 2D or at a series of static joint positions. In the present study we demonstrate a simple MRI method for measuring muscle moment arms dynamically in 3D from a single range-of-motion cycle. We demonstrate this method in the Achilles tendon for comparison with other methods, and validate the method using a custom apparatus. The method involves registration of high-resolution joint geometry from MRI scans of the stationary joint with low-resolution geometries from ultrafast MRI scans of the slowly moving joint. Tibio-talar helical axes and 3D Achilles tendon moment arms were calculated throughout passive rotation for 10 adult subjects, and compared with recently published data. A simple validation was conducted by comparing MRI measurements with direct physical measurements made on a phantom. The moment arms measured using our method and those of others were similar and there was good agreement between physical measurements (mean 41.0mm) and MRI measurements (mean 39.5mm) made on the phantom. This new method can accurately measure muscle moment arms from a single range-of-motion cycle without the need to control rotation rate or gate the scanning. Supplementary data includes custom software to assist implementation. PMID:25466777

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

    PubMed

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

    2016-07-01

    OBJECT The goal of this study was to investigate the significance of contrast-enhanced T1-weighted (T1W) MRI-based 3D reconstruction of dural tail sign (DTS) in meningioma resection. METHODS Between May 2013 and August 2014, 18 cases of convexity and parasagittal meningiomas showing DTS on contrast-enhanced T1W MRI were selected. Contrast-enhanced T1W MRI-based 3D reconstruction of DTS was conducted before surgical treatment. The vertical and anteroposterior diameters of DTS on the contrast-enhanced T1W MR images and 3D reconstruction images were measured and compared. Surgical incisions were designed by referring to the 3D reconstruction and MR images, and then the efficiency of the 2 methods was evaluated with assistance of neuronavigation. RESULTS Three-dimensional reconstruction of DTS can reveal its overall picture. In most cases, the DTS around the tumor is uneven, whereas the DTS around the dural vessels presents longer extensions. There was no significant difference (p > 0.05) between the vertical and anteroposterior diameters of DTS measured on the contrast-enhanced T1W MR and 3D reconstruction images. The 3D images of DTS were more intuitive, and the overall picture of DTS could be revealed in 1 image, which made it easier to design the incision than by using the MR images. Meanwhile, assessment showed that the incisions designed using 3D images were more accurate than those designed using MR images (ridit analysis by SAS, F = 7.95; p = 0.008). Pathological examination showed that 34 dural specimens (except 2 specimens from 1 tumor) displayed tumor invasion. The distance of tumor cell invasion was 1.0-21.6 mm (5.4 ± 4.41 mm [mean ± SD]). Tumor cell invasion was not observed at the dural resection margin in all 36 specimens. CONCLUSIONS Contrast-enhanced T1W MRI-based 3D reconstruction can intuitively and accurately reveal the size and shape of DTS, and thus provides guidance for designing meningioma incisions. PMID:26654184

  14. 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.

  15. Associative image analysis: a method for automated quantification of 3D multi-parameter images of brain tissue

    PubMed Central

    Bjornsson, Christopher S; Lin, Gang; Al-Kofahi, Yousef; Narayanaswamy, Arunachalam; Smith, Karen L; Shain, William; Roysam, Badrinath

    2009-01-01

    Brain structural complexity has confounded prior efforts to extract quantitative image-based measurements. We present a systematic ‘divide and conquer’ methodology for analyzing three-dimensional (3D) multi-parameter images of brain tissue to delineate and classify key structures, and compute quantitative associations among them. To demonstrate the method, thick (~100 μm) slices of rat brain tissue were labeled using 3 – 5 fluorescent signals, and imaged using spectral confocal microscopy and unmixing algorithms. Automated 3D segmentation and tracing algorithms were used to delineate cell nuclei, vasculature, and cell processes. From these segmentations, a set of 23 intrinsic and 8 associative image-based measurements was computed for each cell. These features were used to classify astrocytes, microglia, neurons, and endothelial cells. Associations among cells and between cells and vasculature were computed and represented as graphical networks to enable further analysis. The automated results were validated using a graphical interface that permits investigator inspection and corrective editing of each cell in 3D. Nuclear counting accuracy was >89%, and cell classification accuracy ranged from 81–92% depending on cell type. We present a software system named FARSIGHT implementing our methodology. Its output is a detailed XML file containing measurements that may be used for diverse quantitative hypothesis-driven and exploratory studies of the central nervous system. PMID:18294697

  16. [MRI with dynamic contrast enhancement in brain tumors].

    PubMed

    Panfilenko, A F; Iakovlev, S A; Pozdniakov, A V; Tiumin, L A; Shcherbuk, A Iu

    2013-01-01

    Magnetic resonance imaging (MRI) is the leading method of radiation diagnosis of brain tumors. In conditions of the artificial contrast enhancement there are more clearly differentiated the boundaries of the tumor node on the back of peritumorous edema and identified structural features of the tumor. The purpose of this study was to examine indicators of the dynamics of accumulation and removal of contrast agents by brain tumors in MRI technique with dynamic contrast and identify opportunities of this method in the differential diagnosis of various types of tumors. PMID:23814831

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

    PubMed

    Shimizu, Yuko

    2010-09-01

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

  18. 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.

  19. Use of the functional imaging modalities, f MRI r CBV and PET FDG, alters radiation therapy 3-D treatment planning in patients with malignant gliomas

    SciTech Connect

    Fitzek, M.; Pardo, F.S.; Busierre, M.

    1995-12-31

    Malignant gliomas present one of the most difficult challenges to definitive radiation therapy, not only with respect to local control, but also with respect to clinical functional status. While tumor target volume definitions for malignant gliomas are often based on CT and conventional MRI, the functional imaging modalities, echo planar rCBV (regional cerebral blood volume mapping) and 18F-fluorodeoxyglucose PET, are more sensitive modalities for the detection of neovascularization, perhaps one of the earliest signs of glial tumor initiation and progression. In order to address the clinical utility of functional imaging in radiation therapy 3-D treatment planning, we compared tumor target volume definitions and overall dosimetry in patients either undergoing co-registration of conventional Gadolinium-enhanced MRI, or co-registration of functional imaging modalities, prior to radiation therapy 3-D treatment planning.

  20. 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

  1. 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

  2. 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.

  3. Early survival prediction after intra-arterial therapies: a 3D quantitative MRI assessment of tumour response after TACE or radioembolization of colorectal cancer metastases to the liver

    PubMed Central

    Chapiro, Julius; Duran, Rafael; Lin, MingDe; Schernthaner, Rüdiger; Lesage, David; Wang, Zhijun; Savic, Lynn Jeanette; Geschwind, Jean-François

    2015-01-01

    Objectives This study evaluated the predictive role of 1D, 2D and 3D quantitative, enhancement-based MRI regarding overall survival (OS) in patients with colorectal liver metastases (CLM) following intra-arterial therapies (IAT). Methods This retrospective analysis included 29 patients who underwent transarterial chemoembolization (TACE) or radioembolization and received MRI within 6 weeks after therapy. Tumour response was assessed using 1D and 2D criteria (such as European Association for the Study of the Liver guidelines [EASL] and modified Response Evaluation Criteria in Solid Tumors [mRECIST]). In addition, a segmentation-based 3D quantification of overall (volumetric [v] RECIST) and enhancing lesion volume (quantitative [q] EASL) was performed on portal venous phase MRI. Accordingly, patients were classified as responders (R) and non-responders (NR). Survival was evaluated using Kaplan–Meier analysis and compared using Cox proportional hazard ratios (HR). Results Only enhancement-based criteria identified patients as responders. EASL and mRECIST did not predict patient survival (P = 0.27 and P = 0.44, respectively). Using uni- and multivariate analysis, qEASL was identified as the sole predictor of patient survival (9.9 months for R, 6.9 months for NR; P = 0.038; HR 0.4). Conclusion The ability of qEASL to predict survival early after IAT provides evidence for potential advantages of 3D quantitative tumour analysis. PMID:25636420

  4. 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

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

    PubMed Central

    Bihan, Denis Le; Johansen-Berg, Heidi

    2013-01-01

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

  6. 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

  7. 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.

  8. Multiresolution texture models for brain tumor segmentation in MRI.

    PubMed

    Iftekharuddin, Khan M; Ahmed, Shaheen; Hossen, Jakir

    2011-01-01

    In this study we discuss different types of texture features such as Fractal Dimension (FD) and Multifractional Brownian Motion (mBm) for estimating random structures and varying appearance of brain tissues and tumors in magnetic resonance images (MRI). We use different selection techniques including KullBack - Leibler Divergence (KLD) for ranking different texture and intensity features. We then exploit graph cut, self organizing maps (SOM) and expectation maximization (EM) techniques to fuse selected features for brain tumors segmentation in multimodality T1, T2, and FLAIR MRI. We use different similarity metrics to evaluate quality and robustness of these selected features for tumor segmentation in MRI for real pediatric patients. We also demonstrate a non-patient-specific automated tumor prediction scheme by using improved AdaBoost classification based on these image features. PMID:22255946

  9. The Locust Standard Brain: A 3D Standard of the Central Complex as a Platform for Neural Network Analysis

    PubMed Central

    el Jundi, Basil; Heinze, Stanley; Lenschow, Constanze; Kurylas, Angela; Rohlfing, Torsten; Homberg, Uwe

    2009-01-01

    Many insects use the pattern of polarized light in the sky for spatial orientation and navigation. We have investigated the polarization vision system in the desert locust. To create a common platform for anatomical studies on polarization vision pathways, Kurylas et al. (2008) have generated a three-dimensional (3D) standard brain from confocal microscopy image stacks of 10 male brains, using two different standardization methods, the Iterative Shape Averaging (ISA) procedure and the Virtual Insect Brain (VIB) protocol. Comparison of both standardization methods showed that the VIB standard is ideal for comparative volume analysis of neuropils, whereas the ISA standard is the method of choice to analyze the morphology and connectivity of neurons. The central complex is a key processing stage for polarization information in the locust brain. To investigate neuronal connections between diverse central-complex neurons, we generated a higher-resolution standard atlas of the central complex and surrounding areas, using the ISA method based on brain sections from 20 individual central complexes. To explore the usefulness of this atlas, two central-complex neurons, a polarization-sensitive columnar neuron (type CPU1a) and a tangential neuron that is activated during flight, the giant fan-shaped (GFS) neuron, were reconstructed 3D from brain sections. To examine whether the GFS neuron is a candidate to contribute to synaptic input to the CPU1a neuron, we registered both neurons into the standardized central complex. Visualization of both neurons revealed a potential connection of the CPU1a and GFS neurons in layer II of the upper division of the central body. PMID:20161763

  10. Head MRI

    MedlinePlus

    ... the head; MRI - cranial; NMR - cranial; Cranial MRI; Brain MRI; MRI - brain; MRI - head ... tell your health care provider if you have: Brain aneurysm clips Certain types of artificial heart valves ...

  11. Volume estimation of brain abnormalities in MRI data

    NASA Astrophysics Data System (ADS)

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

    2014-02-01

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

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

    PubMed Central

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

    2015-01-01

    The primary motivation and application in this article come from brain imaging studies on cognitive impairment in elderly subjects with brain disorders. We propose a regularized Haar wavelet-based approach for the analysis of three-dimensional brain image data in the framework of functional data analysis, which automatically takes into account the spatial information among neighboring voxels. We conduct extensive simulation studies to evaluate the prediction performance of the proposed approach and its ability to identify related regions to the outcome of interest, with the underlying assumption that only few relatively small subregions are truly predictive of the outcome of interest. We then apply the proposed approach to searching for brain subregions that are associated with cognition using PET images of patients with Alzheimer’s disease, patients with mild cognitive impairment, and normal controls. PMID:26082826

  13. 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

  14. 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

  15. Scalable Fluidic Injector Arrays for Viral Targeting of Intact 3-D Brain Circuits

    PubMed Central

    Chan, Stephanie; Bernstein, Jacob; Boyden, Edward

    2010-01-01

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

  16. 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

  17. Future potential of MRI-guided focused ultrasound brain surgery.

    PubMed

    Colen, Rivka R; Jolesz, Ferenc A

    2010-08-01

    Magnetic resonance image-guided focused ultrasound surgery (MRgFUS) has surfaced as a viable noninvasive image-guided therapeutic method that integrates focused ultrasound (FUS), the therapeutic component, with magnetic resonance imaging (MRI), the image guidance module, into a real-time therapy delivery system with closed-loop control of energy delivery. The main applications for MRgFUS of the brain are thermal ablations for brain tumors and functional neurosurgery, and nonthermal, nonablative uses for disruption of the blood brain barrier (BBB) or blood clot and hematoma dissolution by liquification. The disruption of the BBB by FUS can be used for targeted delivery of chemotherapy and other therapeutic agents. MRI is used preoperatively for target definition and treatment planning, intraoperatively for procedure monitoring and control, and postoperatively for validating treatment success. Although challenges still remain, this integrated noninvasive therapy delivery system is anticipated to change current treatment paradigms in neurosurgery and the clinical neurosciences. PMID:20708551

  18. [Brain MRI findings in Japanese patients with clinically isolated syndrome].

    PubMed

    Tanaka, Masami; Motoyama, Rie; Tahara, Masayuki; Tanaka, Keiko

    2012-01-01

    Treatment of patients with clinically isolated syndrome (CIS) with disease modifying drugs including interferon β delays conversion to clinically definite multiple sclerosis (MS). However, CIS patients do not necessarily develop MS even after 20 years. Brain MRI lesions were required for CIS patients to include in clinical trials such as CHAMPS study and BENEFIT study. CIS patients with brain MRI lesions compatible to MS were considered as high risk to convert to MS in western countries. Previously we reported that asymptomatic enhancing brain lesions (AEBLs) were found in 9/23 (39.1%) of MS patients who had suffered at least one relapse in the preceding year or two relapses in the preceding 2 years, and the number of AEBLs per scan was 0.37, suggesting low disease activity of Japanese MS patients. We examined brain MRI findings in Japanese CIS patients and compared with those of Japanese MS patients at the first presentation. We reviewed brain MRI of 23 CIS visited our clinic from December 2007 to October 2010 who fulfilled the criteria proposed by Kappos et al. (2006) and Dalton et al (2002). Thirty two clinically definite MS (CDMS) patients fulfilled the first McDonald criteria (two or more attacks and objective clinical evidence of two or more lesions) proposed by Polman et al. (2005). Patients with neuromyelitis optica (NMO) and patients with NMO spectrum proposed by Wingerchuk et al. (2006) and Wingerchuk et al. (2007), respectively, were excluded. Patients with anti-aquaporin4 antibodies or with contiguous spinal cord lesion extending over three vertebral segments on MRI were also excluded. We could not obtain MRI of 11 patients with CDMS because of very long disease course, and 2 CIS and 13 CDMS patients had not been examined with MRI. So we examined 21 CIS and 8 CDMS patients at the first presentation using Paty criteria and Barkhof criteria. Eleven CIS patients did not meet any of the Barkhof criteria. Seven and 3 CIS patients met one and two of Barkhof

  19. Localisation of the brain in fetal MRI using bundled SIFT features.

    PubMed

    Keraudren, Kevin; Kyriakopoulou, Vanessa; Rutherford, Mary; Hajnal, Joseph V; Rueckert, Daniel

    2013-01-01

    Fetal MRI is a rapidly emerging diagnostic imaging tool. Its main focus is currently on brain imaging, but there is a huge potential for whole body studies. We propose a method for accurate and robust localisation of the fetal brain in MRI when the image data is acquired as a stack of 2D slices misaligned due to fetal motion. We first detect possible brain locations in 2D images with a Bag-of-Words model using SIFT features aggregated within Maximally Stable Extremal Regions (called bundled SIFT), followed by a robust fitting of an axis-aligned 3D box to the selected regions. We rely on prior knowledge of the fetal brain development to define size and shape constraints. In a cross-validation experiment, we obtained a median error distance of 5.7mm from the ground truth and no missed detection on a database of 59 fetuses. This 2D approach thus allows a robust detection even in the presence of substantial fetal motion. PMID:24505714

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

    PubMed Central

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

    2009-01-01

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

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

    PubMed

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

    2016-01-01

    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

  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. Studying the freely-behaving brain with fMRI

    PubMed Central

    Maguire, Eleanor A.

    2012-01-01

    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). PMID:22245643

  4. 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

  5. 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

  6. 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).

  7. 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

  8. 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.

  9. 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.

  10. 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.

  11. 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.

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

    PubMed

    Xue, Zhong; Shen, Dinggang; Davatzikos, Christos

    2004-10-01

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

  13. 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.

  14. 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%. PMID:22256218

  15. 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.

  16. O7.02RADIOSURGERY AND BRAIN METASTASES: ADEQUATE SEQUENCE OF BRAIN MRI CAN SIGNIFICANTLY CHANGE THE INTRACRANIAL DISEASE STAGING

    PubMed Central

    Scoccianti, S.; Greto, D.; Bordi, L.; Bono, P.; Pecchioli, G.; Casati, M.; Vanzi, E.; Compagnucci, A.; Gadda, D.; Livi, L.

    2014-01-01

    INTRODUCTION: Accurate assessment of the exact number of brain metastases is of utmost importance in the decision-making process for the appropriate treatment. The diagnostic efficacy in the detection of additional brain metastases of a double dose contrast three-dimensional, T1-Weighted Gradient-Echo Imaging was evaluated. METHODS: Before undergoing radiosurgical treatment, patients underwent a brain magnetic resonance imaging (MRI) scan to be used during the treatment planning in order to contour the targets and to locate the brain lesions as they relate to the stereotactic frame. All the patients underwent a post-contrast study with T1-weighted, 3D Magnetization-Prepared Rapid Acquisition Gradient Echo (MP RAGE) sequence. We used a double dose of gadobenate dimeglumine and slice thickness of 0.9 mm. RESULTS: Starting from October 2012 to February 2014, we treated with Gamma Knife radiosurgery (GKRS) 62 patients with brain metastases. On the diagnostic MRI, all the patients had a number of lesions ≤4. Median time interval between diagnostic MRI scan and the day of GKRS was 11 days (range 5-20) A total of 54 additional lesions were detected on MR imaging performed in the same day of the GKRS in twenty-two patients out of 62 (35.5%). A median number of 2 additional lesions were detected (range 1-8). Among these 22 patients only 14 patients had a number of lesions ≤4 on the day of treatment. Patients with a total number of lesions ≤10 were treated with GKRS. Two patients with a total number of lesions > 10 were treated with whole brain radiotherapy (WBRT). CONCLUSIONS: A double-contrast study with T1-weighted, volumetric MPRAGE sequence may offer better staging for patients with brain metastases. In our opinion, it should be recommended in all the patients with newly diagnosed brain metastases because the detection of the real number of lesions is crucial for an adequate treatment and it also may lead to choose different therapeutic strategies.

  17. 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.

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

    PubMed Central

    2013-01-01

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

  19. 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.

  20. 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

  1. 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.

  2. Functional MRI during Hippocampal Deep Brain Stimulation in the Healthy Rat Brain

    PubMed Central

    Van Den Berge, Nathalie; Vanhove, Christian; Descamps, Benedicte; Dauwe, Ine; van Mierlo, Pieter; Vonck, Kristl; Keereman, Vincent; Raedt, Robrecht; Boon, Paul; Van Holen, Roel

    2015-01-01

    Deep Brain Stimulation (DBS) is a promising treatment for neurological and psychiatric disorders. The mechanism of action and the effects of electrical fields administered to the brain by means of an electrode remain to be elucidated. The effects of DBS have been investigated primarily by electrophysiological and neurochemical studies, which lack the ability to investigate DBS-related responses on a whole-brain scale. Visualization of whole-brain effects of DBS requires functional imaging techniques such as functional Magnetic Resonance Imaging (fMRI), which reflects changes in blood oxygen level dependent (BOLD) responses throughout the entire brain volume. In order to visualize BOLD responses induced by DBS, we have developed an MRI-compatible electrode and an acquisition protocol to perform DBS during BOLD fMRI. In this study, we investigate whether DBS during fMRI is valuable to study local and whole-brain effects of hippocampal DBS and to investigate the changes induced by different stimulation intensities. Seven rats were stereotactically implanted with a custom-made MRI-compatible DBS-electrode in the right hippocampus. High frequency Poisson distributed stimulation was applied using a block-design paradigm. Data were processed by means of Independent Component Analysis. Clusters were considered significant when p-values were <0.05 after correction for multiple comparisons. Our data indicate that real-time hippocampal DBS evokes a bilateral BOLD response in hippocampal and other mesolimbic structures, depending on the applied stimulation intensity. We conclude that simultaneous DBS and fMRI can be used to detect local and whole-brain responses to circuit activation with different stimulation intensities, making this technique potentially powerful for exploration of cerebral changes in response to DBS for both preclinical and clinical DBS. PMID:26193653

  3. Shape analysis of hypertrophic and hypertensive heart disease using MRI-based 3D surface models of left ventricular geometry.

    PubMed

    Ardekani, Siamak; Jain, Saurabh; Sanzi, Alianna; Corona-Villalobos, Celia P; Abraham, Theodore P; Abraham, M Roselle; Zimmerman, Stefan L; Wu, Katherine C; Winslow, Raimond L; Miller, Michael I; Younes, Laurent

    2016-04-01

    The focus of this study was to develop advanced mathematical tools to construct high-resolution 3D models of left-ventricular (LV) geometry to evaluate focal geometric differences between patients with hypertrophic cardiomyopathy (HCM) and hypertensive heart disease (HHD) using cardiac magnetic resonance (MR) cross-sectional images. A limiting factor in 3D analysis of cardiac MR cross-sections is the low out-of-plane resolution of the acquired images. To overcome this problem, we have developed a mathematical framework to construct a population-based high-resolution 3D LV triangulated surface (template) in which an iterative matching algorithm maps a surface mesh of a normal heart to a set of cross-sectional contours that were extracted from short-axis cine cardiac MR images of patients who were diagnosed with either HCM or HHD. A statistical analysis was conducted on deformations that were estimated at each surface node to identify shape differences at end-diastole (ED), end-systole (ES), and motion-related shape variation from ED to ES. Some significant shape difference in radial thickness was detected at ES. Differences of LV 3D surface geometry were identified focally on the basal anterior septum wall. Further research is needed to relate these findings to the HCM morphological substrate and to design a classifier to discriminate among different etiologies of LV hypertrophy. PMID:26766206

  4. Noninvasive 3D pressure calculation from PC-MRI via non-iterative harmonics-based orthogonal projection: constant flow experiment.

    PubMed

    Negahdar, M J; Kadbi, Mo; Cha, J; Cebral, J; Amini, A

    2013-01-01

    Use of phase-contrast (PC) MRI in assessment of hemodynamics has significant clinical importance. In this paper we develop a novel approach to determination of hemodynamic pressures. 3D gradients of pressure obtained from Navier-Stokes equation are expanded into a series of orthogonal basis functions, and are subsequently projected onto an integrable subspace. Before the projection step however, a scheme is devised to eliminate the discontinuity at the vessel and image boundaries. In terms of the computation time, the proposed approach significantly improves on previous iterative methods for pressure calculations. The method has been validated using computational fluid dynamic simulations and in-vitro MRI studies of stenotic flows. PMID:24110706

  5. 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%.

  6. 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

  7. 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

  8. Knowledge-based localization of hippocampus in human brain MRI

    NASA Astrophysics Data System (ADS)

    Soltanian-Zadeh, Hamid; Siadat, Mohammad-Reza

    1999-05-01

    Hippocampus is an important structure of the human brain limbic system. The variations in the volume and architecture of this structure have been related to certain neurological diseases such as schizophrenia and epilepsy. This paper presents a two-stage method for localizing hippocampus in human brain MRI automatically. The first stage utilizes image processing techniques such as nonlinear filtering and histogram analysis to extract information from MRI. This stage generates binary images, locates lateral and third ventricles, and the inferior limit of Sylvian Fissure. The second stage uses a shell of expert system named VP-EXPERT to analyze the information extracted in the first stage. This stage utilizes absolute and relative spatial rules and spatial symmetry rules to locate the hippocampus. The system has been tested using MRI studies of six epilepsy patients. MRI data consisted of a total of 128 images. The system correctly identified all of the slices without hippocampus, and correctly localized hippocampus is about n 78% of the slices with hippocampus.

  9. FDG and (82)Rb PET/MRI features of brain metastasis of breast cancer.

    PubMed

    Lu, Yang

    2015-06-01

    A 64-year-old woman with stage IV breast cancer underwent an FDG and Rb PET brain studies. The PET brain images were fused with MRI brain T1 post-contrast images. The known enhancing left superoposterior frontal brain metastasis is positive on both FDG Rb PET/MRI images. The Rb PET/MRI showed better target-to-noise ratio, but showed nonspecific uptake in the superior sagittal sinus. PMID:25674864

  10. Using stress MRI to analyze the 3D changes in apical ligament geometry from rest to maximal Valsalva: a pilot study

    PubMed Central

    Luo, Jiajia; Betschart, Cornelia; Chen, Luyun; Ashton-Miller, James A.; DeLancey, John O. L.

    2014-01-01

    Introduction and hypothesis A method was developed using 3D stress magnetic resonance imaging (MRI) and was piloted to test hypotheses concerning changes in apical ligament lengths and lines of action from rest to maximal Valsalva. Methods Ten women with (cases) and ten without (controls) pelvic organ prolapse (POP) were selected from an ongoing case-control study. Supine, multiplanar stress MRI was performed at rest and at maximal Valsalva and was imported into 3D Slicer v. 3.4.1 and aligned. The 3D reconstructions of the uterus and vagina, cardinal ligament (CL), deep uterosacral ligament (USLd), and pelvic bones were created. Ligament length and orientation were then measured. Results Adequate ligament representations were possible in all 20 study participants. When cases were compared with controls, the curve length of the CL at rest was 71 ±16 mm vs. 59±9 mm (p =0.051), and the USLd was 38±16 mm vs. 36±11 mm (p =0.797). Similarly, the increase in CL length from rest to strain was 30±16 mm vs. 15±9 mm (p =0.033), and USLd was 15±12 mm vs. 7±4 mm (p =0.094). Likewise, the change in USLd angle was significantly different from CL (p <0.001). Conclusions This technique allows quantification of 3D geometry at rest and at strain. In our pilot sample, at maximal Valsalva, CL elongation was greater in cases than controls, whereas USLd was not; CL also exhibited greater changes in ligament length, and USLd exhibited greater changes in ligament inclination angle. PMID:24008367

  11. 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

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

    PubMed

    Ogawa, Akitoshi; Bordier, Cecile; Macaluso, Emiliano

    2013-01-01

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

  13. 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.

  14. 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. PMID:27033683

  15. DLP technology application: 3D head tracking and motion correction in medical brain imaging

    NASA Astrophysics Data System (ADS)

    Olesen, Oline V.; Wilm, Jakob; Paulsen, Rasmus R.; Højgaard, Liselotte; Larsen, Rasmus

    2014-03-01

    In this paper we present a novel sensing system, robust Near-infrared Structured Light Scanning (NIRSL) for three-dimensional human model scanning application. Human model scanning due to its nature of various hair and dress appearance and body motion has long been a challenging task. Previous structured light scanning methods typically emitted visible coded light patterns onto static and opaque objects to establish correspondence between a projector and a camera for triangulation. In the success of these methods rely on scanning objects with proper reflective surface for visible light, such as plaster, light colored cloth. Whereas for human model scanning application, conventional methods suffer from low signal to noise ratio caused by low contrast of visible light over the human body. The proposed robust NIRSL, as implemented with the near infrared light, is capable of recovering those dark surfaces, such as hair, dark jeans and black shoes under visible illumination. Moreover, successful structured light scan relies on the assumption that the subject is static during scanning. Due to the nature of body motion, it is very time sensitive to keep this assumption in the case of human model scan. The proposed sensing system, by utilizing the new near-infrared capable high speed LightCrafter DLP projector, is robust to motion, provides accurate and high resolution three-dimensional point cloud, making our system more efficient and robust for human model reconstruction. Experimental results demonstrate that our system is effective and efficient to scan real human models with various dark hair, jeans and shoes, robust to human body motion and produces accurate and high resolution 3D point cloud.

  16. 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

  17. 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

  18. 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

  19. 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.

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

    PubMed

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

    2014-06-01

    Displacement fields are important to analyze deformation, which is associated with functional and material tissue properties often used as indicators of health. Magnetic resonance imaging (MRI) techniques like DENSE and image registration methods like Hyperelastic Warping have been used to produce pixel-level deformation fields that are desirable in high-resolution analysis. However, DENSE can be complicated by challenges associated with image phase unwrapping, in particular offset determination. On the other hand, Hyperelastic Warping can be hampered by low local image contrast. The current work proposes a novel approach for measuring tissue displacement with both DENSE and Hyperelastic Warping, incorporating physically accurate displacements obtained by the latter to improve phase characterization in DENSE. The validity of the proposed technique is demonstrated using numerical and physical phantoms, and in vivo small animal cardiac MRI. PMID:24771572

  1. Automatic ultrasound-MRI registration for neurosurgery using the 2D and 3D LC(2) Metric.

    PubMed

    Fuerst, Bernhard; Wein, Wolfgang; Müller, Markus; Navab, Nassir

    2014-12-01

    To enable image guided neurosurgery, the alignment of pre-interventional magnetic resonance imaging (MRI) and intra-operative ultrasound (US) is commonly required. We present two automatic image registration algorithms using the similarity measure Linear Correlation of Linear Combination (LC(2)) to align either freehand US slices or US volumes with MRI images. Both approaches allow an automatic and robust registration, while the three dimensional method yields a significantly improved percentage of optimally aligned registrations for randomly chosen clinically relevant initializations. This study presents a detailed description of the methodology and an extensive evaluation showing an accuracy of 2.51mm, precision of 0.85mm and capture range of 15mm (>95% convergence) using 14 clinical neurosurgical cases. PMID:24842859

  2. 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

  3. 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

  4. 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

  5. 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.

  6. Quantitative analysis of brain pathology based on MRI and brain atlases--applications for cerebral palsy.

    PubMed

    Faria, Andreia V; Hoon, Alexander; Stashinko, Elaine; Li, Xin; Jiang, Hangyi; Mashayekh, Ameneh; Akhter, Kazi; Hsu, John; Oishi, Kenichi; Zhang, Jiangyang; Miller, Michael I; van Zijl, Peter C M; Mori, Susumu

    2011-02-01

    We have developed a new method to provide a comprehensive quantitative analysis of brain anatomy in cerebral palsy patients, which makes use of two techniques: diffusion tensor imaging and automated 3D whole brain segmentation based on our brain atlas and a nonlinear normalization technique (large-deformation diffeomorphic metric mapping). This method was applied to 13 patients and normal controls. The reliability of the automated segmentation revealed close agreement with the manual segmentation. We illustrate some potential applications for individual characterization and group comparison. This technique also provides a framework for determining the impact of various neuroanatomic features on brain functions. PMID:20920589

  7. Quantitative Analysis of Brain Pathology Based on MRI and Brain Atlases - Applications for Cerebral Palsy

    PubMed Central

    Faria, Andreia V.; Hoon, Alexander; Stachinko, Elaine; Li, Xin; Jiang, Hangyi; Mashayekh, Ameneh; Akhter, Kazi; Hsu, John; Oishi, Kenichi; Zhang, Jiangyang; Miller, Michael I.; van Zijl, Peter C.M.; Mori, Susumu

    2010-01-01

    We have developed a new method to provide a comprehensive quantitative analysis of brain anatomy in cerebral palsy patients, which makes use of two techniques: diffusion tensor imaging and automated 3D whole brain segmentation based on our brain atlas and a nonlinear normalization technique (large-deformation diffeomorphic metric mapping). This method was applied to 13 patients and normal controls. The reliability of the automated segmentation revealed close agreement with the manual segmentation. We illustrate some potential applications for individual characterization and group comparison. This technique also provides a framework for determining the impact of various neuroanatomic features on brain functions. PMID:20920589

  8. 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

  9. Longitudinal brain MRI analysis with uncertain registration.

    PubMed

    Simpson, Ivor J A; Woolrich, Mark W; Groves, Adrian R; Schnabel, Julia A

    2011-01-01

    In this paper we propose a novel approach for incorporating measures of spatial uncertainty, which are derived from non-rigid registration, into spatially normalised statistics. Current approaches to spatially normalised statistical analysis use point-estimates of the registration parameters. This is limiting as the registration will rarely be completely accurate, and therefore data smoothing is often used to compensate for the uncertainty of the mapping. We derive localised measurements of spatial uncertainty from a probabilistic registration framework, which provides a principled approach to image smoothing. We evaluate our method using longitudinal deformation features from a set of MR brain images acquired from the Alzheimer's Disease Neuroimaging Initiative. These images are spatially normalised using our probabilistic registration algorithm. The spatially normalised longitudinal features are adaptively smoothed according to the registration uncertainty. The proposed adaptive smoothing shows improved classification results, (84% correct Alzheimer's Disease vs. controls), over either not smoothing (79.6%), or using a Gaussian filter with sigma = 2mm (78.8%). PMID:21995084

  10. A Pilot Study of Improved Lesion Characterization in Breast MRI Using a 3D Radial Balanced SSFP Technique With Isotropic Resolution and Efficient Fat-Water Separation

    PubMed Central

    Moran, Catherine J.; Kelcz, Frederick; Jung, Youngkyoo; Brodsky, Ethan K.; Fain, Sean B.; Block, Walter F.

    2013-01-01

    Purpose To assess a 3D radial balanced steady state free precession technique that provides sub-millimeter isotropic resolution and inherently registered fat and water image volumes in comparison to conventional T2-weighted RARE imaging for lesion characterization in breast MRI. Materials and Methods 3D PRojection SSFP (3DPR-SSFP) combines a dual half-echo radial k-space trajectory with a linear combination fat/water separation technique (Linear Combination SSFP). A pilot study was performed in 20 patients to assess fat suppression and depiction of lesion morphology using 3DPR-SSFP. For all patients fat suppression was measured for the 3DPR-SSFP image volumes and depiction of lesion morphology was compared against corresponding T2-weighted Fast Spin Echo (FSE) datasets for 15 lesions in 11 patients. Results The isotropic 0.63 mm resolution of the 3DPR-SSFP sequence demonstrated improved depiction of lesion morphology in comparison to FSE. The 3DPR-SSFP fat and water datasets were available in a 5 minute scan time while average fat suppression with 3DPR-SSFP was 71% across all twenty patients. Conclusion 3DPR-SSFP has the potential to improve the lesion characterization information available in breast MRI, particularly in comparison to conventional FSE. A larger study is warranted to quantify the effect of 3DPR-SSFP on specificity. PMID:19557728

  11. Patient-Specific Artery Shrinkage and 3D Zero-Stress State in Multi-Component 3D FSI Models for Carotid Atherosclerotic Plaques Based on In Vivo MRI Data

    PubMed Central

    Huang, Xueying; Yang, Chun; Yuan, Chun; Liu, Fei; Canton, Gador; Zheng, Jie; Woodard, Pamela K.; Sicard, Gregorio A.; Tang, Dalin

    2009-01-01

    Image-based computational models for atherosclerotic plaques have been developed to perform mechanical analysis to quantify critical flow and stress/strain conditions related to plaque rupture which often leads directly to heart attack or stroke. An important modeling issue is how to determine zero stress state from in vivo plaque geometries. This paper presents a method to quantify human carotid artery axial and inner circumferential shrinkages by using patient-specific ex vivo and in vivo MRI images. A shrink-stretch process based on patient-specific in vivo plaque morphology and shrinkage data was introduced to shrink the in vivo geometry first to find the zero-stress state (opening angle was ignored to reduce the complexity), and then stretch and pressurize to recover the in vivo plaque geometry with computed initial stress, strain, flow pressure and velocity conditions. Effects of the shrink-stretch process on plaque stress/strain distributions were demonstrated based on patient-specific data using 3D models with fluid-structure interactions (FSI). The average artery axial and inner circumferential shrinkages were 25% and 7.9%, respectively, based on a data set obtained from 10 patients. Maximum values of maximum principal stress and strain increased 349.8% and 249% respectively with 33% axial stretch. Influence of inner circumferential shrinkage (7.9%) was not very noticeable under 33% axial stretch, but became more noticeable under smaller axial stretch. Our results indicated that accurate knowledge of artery shrinkages and the shrink-stretch process will considerably improve the accuracy of computational predictions made based on results from those in vivo MRI-based FSI models. PMID:19444328

  12. Patient-specific artery shrinkage and 3D zero-stress state in multi-component 3D FSI models for carotid atherosclerotic plaques based on in vivo MRI data.

    PubMed

    Huang, Xueying; Yang, Chun; Yuan, Chun; Liu, Fei; Canton, Gador; Zheng, Jie; Woodard, Pamela K; Sicard, Gregorio A; Tang, Dalin

    2009-06-01

    Image-based computational models for atherosclerotic plaques have been developed to perform mechanical analysis to quantify critical flow and stress/strain conditions related to plaque rupture which often leads directly to heart attack or stroke. An important modeling issue is how to determine zero stress state from in vivo plaque geometries. This paper presents a method to quantify human carotid artery axial and inner circumferential shrinkages by using patient-specific ex vivo and in vivo MRI images. A shrink-stretch process based on patient-specific in vivo plaque morphology and shrinkage data was introduced to shrink the in vivo geometry first to find the zero-stress state (opening angle was ignored to reduce the complexity), and then stretch and pressurize to recover the in vivo plaque geometry with computed initial stress, strain, flow pressure and velocity conditions. Effects of the shrink-stretch process on plaque stress/strain distributions were demonstrated based on patient-specific data using 3D models with fluid-structure interactions (FSI). The average artery axial and inner circumferential shrinkages were 25% and 7.9%, respectively, based on a data set obtained from 10 patients. Maximum values of maximum principal stress and strain increased 349.8% and 249% respectively with 33% axial stretch. Influence of inner circumferential shrinkage (7.9%) was not very noticeable under 33% axial stretch, but became more noticeable under smaller axial stretch. Our results indicated that accurate knowledge of artery shrinkages and the shrink-stretch process will considerably improve the accuracy of computational predictions made based on results from those in vivo MRI-based FSI models. PMID:19444328

  13. 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.

  14. The dynamic of FUS-induced BBB Opening in Mouse Brain assessed by contrast enhanced MRI

    NASA Astrophysics Data System (ADS)

    Jenne, Jürgen W.; Krafft, Axel J.; Maier, Florian; Krause, Marie N.; Kleber, Susanne; Huber, Peter E.; Martin-Villalba, Ana; Bock, Michael

    2010-03-01

    Focused ultrasound (FUS) in combination with the administration of gas-filled microbubbles, can induce a localized and reversible opening of the blood brain barrier (BBB). Contrast enhanced magnetic resonance imaging (MRI) has been demonstrated as a precise tool to monitor such a local BBB disruption. However, the opening/closing mechanisms of the BBB with FUS are still largely unknown. In this ongoing project, we study the BBB opening dynamics in mouse brain comparing an interstitial and an intravascular MR contrast agent (CA). FUS in mouse brain was performed with an MRI compatible treatment setup (1.7 MHz fix-focus US transducer, f' = 68 mm, NA = 0.44; focus: 8.1 mm length; O/ = 1.1 mm) in a 1.5 T whole body MRI system. For BBB opening, forty 10 ms-long FUS-pulses were applied at a repetition rate of 1 Hz at 1 MPa. The i.v. administration of the micro bubbles (50 μl SonoVue®) was started simultaneously with FUS exposure. To analyze the BBB opening process, short-term and long-term MRI signal dynamics of the interstitial MR contrast agent Magnevist® and the intravascular CA Vasovist® (Bayer-Schering) were studied. To assess short-term signal dynamics, T1-weighted inversion recovery turbo FLASH images (1s) were repeatedly acquired. Repeated 3D FLASH acquisitions (90 s) were used to assess long-term MRI signal dynamics. The short-term MRI signal enhancements showed comparable time constants for both types of MR contrast agents: 1.1 s (interstitial) vs. 0.8 s (intravascular). This time constant may serve as a time constant of the BBB opening process with the given FUS exposure parameters. For the long-term signal dynamics the intravascular CA (62±10 min) showed a fife times greater time constant as the interstitial contrast agent (12±10 min). This might be explained by the high molecular weight (˜60 kDa) of the intravascular Vasovist due to its reversible binding to blood serum albumin resulting in a prolonged half-life in the blood stream compared to the

  15. 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’.

  16. 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

  17. Depiction of Achilles Tendon Microstructure In-Vivo Using High-Resolution 3D Ultrashort Echo-Time MRI at 7T

    PubMed Central

    Han, Misung; Larson, Peder E. Z.; Liu, Jing; Krug, Roland

    2014-01-01

    Objectives To demonstrate the feasibility of depicting the internal structure of the Achilles tendon in vivo using high-resolution 3D ultrashort echo-time (UTE) magnetic resonance imaging (MRI) at 7T. Materials and Methods For our UTE imaging, a minimum-phase radiofrequency pulse and an anisotropic field-of-view 3D radial acquisition were used to minimize the echo time and scan time. A fat saturation pulse was applied every eight spoke acquisitions to reduce blurring and chemical shift artifacts from fat and to improve dynamic range of the tendon signal. Five healthy volunteers and one patient were scanned with an isotropic spatial resolution of up to 0.6 mm. Fat-suppressed UTE images were qualitatively evaluated and compared to non-fat-suppressed UTE images and longer echo-time images. Results High-resolution UTE imaging was able to visualize the microstructure of the Achilles tendon. Fat suppression substantially improved the depiction of the internal structure. The UTE images revealed a fascicular pattern in the Achilles tendon and fibrocartilage at the tendon insertion. In a patient who had tendon elongation surgery after birth there was clear depiction of disrupted tendon structure. Conclusions High-resolution fat-suppressed 3D UTE imaging at 7T allows for evaluation of the Achilles tendon microstructure in vivo. PMID:24500089

  18. The Role of Brain MRI in Mitochondrial Neurogastrointestinal Encephalomyopathy

    PubMed Central

    Scarpelli, Mauro; Ricciardi, Giuseppe Kenneth; Beltramello, Alberto; Zocca, Isabella; Calabria, Francesca; Russignan, Anna; Zappini, Francesca; Cotelli, Maria Sofia; Padovani, Alessandro; Tomelleri, Giuliano; Filosto, Massimiliano; Tonin, Paola

    2013-01-01

    Summary Leukoencephalopathy is a hallmark of mitochondrial neurogastrointestinal encephalomyopathy (MNGIE) a devastating disorder characterized by ptosis, ophthalmoparesis, gastrointestinal dysfunction and polyneuropathy. To characterize MNGIE-associated leukoencephalopathy and to correlate it with clinical, biochemical and molecular data, four MNGIE patients with heterogeneous clinical phenotypes (enteropathic arthritis, exercise intolerance, CIDP-like phenotype and typical presentation) were studied by magnetic resonance imaging (MRI) and magnetic resonance spectroscopy (MRS). Diffusion weighted imaging (DWI) with apparent diffusion coefficient (ADC) maps were also obtained. In two patients we also investigated the role of brain MRI in monitoring the evolution of leukoencephalopathy by performing follow-up imaging studies at an interval of one and two years. The extension and distribution of leukoencephalopathy were not clearly linked with age, phenotype or disease severity, and did not seem to be related to TYMP mutations, enzyme activity or pyrimidine levels. In the studied patients MRS revealed reduced N-acetyl-aspartate and increased choline signals. Although DWI appeared normal in all patients but one, ADC maps always showed moderate increased diffusivity. Leukoencephalopathy worsened over a two-year period in two patients, regardless of the clinical course, indicating a lack of correlation between clinical phenotype, size and progression of white matter abnormalities during this period. Brain MRI should be considered a very useful tool to diagnose both classical and atypical MNGIE. Serial MRIs in untreated and treated MNGIE patients will help to establish whether the leukoencephalopathy is a reversible condition or not. PMID:24199812

  19. Advanced Structural and Functional Brain MRI in Multiple Sclerosis.

    PubMed

    Giorgio, Antonio; De Stefano, Nicola

    2016-04-01

    Conventional magnetic resonance imaging (MRI) of the central nervous system is crucial for an early and reliable diagnosis and monitoring of patients with multiple sclerosis (MS). Focal white matter (WM) lesions, as detected by MRI, are the pathological hallmark of the disease and show some relation to clinical disability, especially in the long run. Gray matter (GM) involvement is evident from disease onset and includes focal (i.e., cortical lesions) and diffuse pathology (i.e., atrophy). Both accumulate over time and show close relation to physical disability and cognitive impairment. Using advanced quantitative MRI techniques such as magnetization transfer imaging (MTI), diffusion tensor imaging (DTI), proton MR spectroscopy ((1)H-MRS), and iron imaging, subtle MS pathology has been demonstrated from early stages outside focal WM lesions in the form of widespread abnormalities of the normal appearing WM and GM. In addition, studies using functional MRI have demonstrated that brain plasticity is driven by MS pathology, playing adaptive or maladaptive roles to neurologic and cognitive status and explaining, at least in part, the clinicoradiological paradox of MS. PMID:27116723

  20. State of the art survey on MRI brain tumor segmentation.

    PubMed

    Gordillo, Nelly; Montseny, Eduard; Sobrevilla, Pilar

    2013-10-01

    Brain tumor segmentation consists of separating the different tumor tissues (solid or active tumor, edema, and necrosis) from normal brain tissues: gray matter (GM), white matter (WM), and cerebrospinal fluid (CSF). In brain tumor studies, the existence of abnormal tissues may be easily detectable most of the time. However, accurate and reproducible segmentation and characterization of abnormalities are not straightforward. In the past, many researchers in the field of medical imaging and soft computing have made significant survey in the field of brain tumor segmentation. Both semiautomatic and fully automatic methods have been proposed. Clinical acceptance of segmentation techniques has depended on the simplicity of the segmentation, and the degree of user supervision. Interactive or semiautomatic methods are likely to remain dominant in practice for some time, especially in these applications where erroneous interpretations are unacceptable. This article presents an overview of the most relevant brain tumor segmentation methods, conducted after the acquisition of the image. Given the advantages of magnetic resonance imaging over other diagnostic imaging, this survey is focused on MRI brain tumor segmentation. Semiautomatic and fully automatic techniques are emphasized. PMID:23790354

  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. 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. PMID:25800209

  4. MRI-driven accretion on to magnetized stars: global 3D MHD simulations of magnetospheric and boundary layer regimes

    NASA Astrophysics Data System (ADS)

    Romanova, M. M.; Ustyugova, G. V.; Koldoba, A. V.; Lovelace, R. V. E.

    2012-03-01

    We discuss results of global three-dimensional magnetohydrodynamic simulations of accretion on to a rotating magnetized star with a tilted dipole magnetic field, where the accretion is driven by the magnetorotational instability (MRI). The simulations show that MRI-driven turbulence develops in the disc, and angular momentum is transported outwards primarily due to the magnetic stress. The turbulent flow is strongly inhomogeneous and the densest matter is in azimuthally stretched turbulent cells. We investigate two regimes of accretion: a magnetospheric regime and a boundary layer (BL) regime. In the magnetospheric regime, the magnetic field of the star is dynamically important: the accretion disc is truncated by the star's magnetic field within a few stellar radii from the star's surface, and matter flows to the star in funnel streams. The funnel streams flow towards the south and north magnetic poles but are not equal due to the inhomogeneity of the flow. The hotspots on the stellar surface are not symmetric as well. In the BL regime, the magnetic field of the star is dynamically unimportant, and matter accretes on to the surface of the star through the BL. The magnetic field in the inner disc is strongly amplified by the shear of the accretion flow, and the matter and magnetic stresses become comparable. Accreting matter forms a belt-shaped hot region on the surface of the star. The belt has inhomogeneous density distribution which varies in time due to variable accretion rate. The peaks in the variability curve are associated with accretion of individual turbulent cells. They show 20-50 per cent density amplifications at periods of ˜5-10 dynamical time-scales at the surface of the star. Spiral waves in the disc are excited in both magnetospheric and BL regimes of accretion. Results of simulations can be applied to classical T Tauri stars, accreting brown dwarfs, millisecond pulsars, dwarf novae cataclysmic variables and other stars with magnetospheres smaller

  5. Jet fuel toxicity: skin damage measured by 900-MHz MRI skin microscopy and visualization by 3D MR image processing.

    PubMed

    Sharma, Rakesh; Locke, Bruce R

    2010-09-01

    The toxicity of jet fuels was measured using noninvasive magnetic resonance microimaging (MRM) at 900-MHz magnetic field. The hypothesis was that MRM can visualize and measure the epidermis exfoliation and hair follicle size of rat skin tissue due to toxic skin irritation after skin exposure to jet fuels. High-resolution 900-MHz MRM was used to measure the change in size of hair follicle, epidermis thickening and dermis in the skin after jet fuel exposure. A number of imaging techniques utilized included magnetization transfer contrast (MTC), spin-lattice relaxation constant (T1-weighting), combination of T2-weighting with magnetic field inhomogeneity (T2*-weighting), magnetization transfer weighting, diffusion tensor weighting and chemical shift weighting. These techniques were used to obtain 2D slices and 3D multislice-multiecho images with high-contrast resolution and high magnetic resonance signal with better skin details. The segmented color-coded feature spaces after image processing of the epidermis and hair follicle structures were used to compare the toxic exposure to tetradecane, dodecane, hexadecane and JP-8 jet fuels. Jet fuel exposure caused skin damage (erythema) at high temperature in addition to chemical intoxication. Erythema scores of the skin were distinct for jet fuels. The multicontrast enhancement at optimized TE and TR parameters generated high MRM signal of different skin structures. The multiple contrast approach made visible details of skin structures by combining specific information achieved from each of the microimaging techniques. At short echo time, MRM images and digitized histological sections confirmed exfoliated epidermis, dermis thickening and hair follicle atrophy after exposure to jet fuels. MRM data showed correlation with the histopathology data for epidermis thickness (R(2)=0.9052, P<.0002) and hair root area (R(2)=0.88, P<.0002). The toxicity of jet fuels on skin structures was in the order of tetradecane

  6. 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

  7. Cortical Mapping of 3D Optical Topography in Infants

    PubMed Central

    Papademetriou, Maria D; Richards, John; Correia, Teresa; Blasi, Anna; Murphy, D. G.; Lloyd-Fox, Sarah; Johnson, Mark; Elwell, Clare E

    2014-01-01

    Precise localization of cortical activation in the early development of the infant brain remains unclear. It is challenging to co-register haemodynamic responses during functional activation in infants with the underlying anatomy of the brain. We used a multispectral imaging algorithm to reconstruct 3D optical topographic images of haemodynamic responses in an infant during voice processing. In this paper we present a method for co-registering 3D optical topography images reconstructed from functional activation data in infants onto anatomical brain images obtained from MRI structurals of the individual infants. PMID:23852529

  8. 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.

  9. 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. PMID:26819593

  10. 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

  11. 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

  12. A new method to explore the spectral impact of the piriform fossae on the singing voice: benchmarking using MRI-based 3D-printed vocal tracts.

    PubMed

    Delvaux, Bertrand; Howard, David

    2014-01-01

    The piriform fossae are the 2 pear-shaped cavities lateral to the laryngeal vestibule at the lower end of the vocal tract. They act acoustically as side-branches to the main tract, resulting in a spectral zero in the output of the human voice. This study investigates their spectral role by comparing numerical and experimental results of MRI-based 3D printed Vocal Tracts, for which a new experimental method (based on room acoustics) is introduced. The findings support results in the literature: the piriform fossae create a spectral trough in the region 4-5 kHz and act as formants repellents. Moreover, this study extends those results by demonstrating numerically and perceptually the impact of having large piriform fossae on the sung output. PMID:25048199

  13. 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.

  14. 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

  15. Automatic brain tumor detection in MRI: methodology and statistical validation

    NASA Astrophysics Data System (ADS)

    Iftekharuddin, Khan M.; Islam, Mohammad A.; Shaik, Jahangheer; Parra, Carlos; Ogg, Robert

    2005-04-01

    Automated brain tumor segmentation and detection are immensely important in medical diagnostics because it provides information associated to anatomical structures as well as potential abnormal tissue necessary to delineate appropriate surgical planning. In this work, we propose a novel automated brain tumor segmentation technique based on multiresolution texture information that combines fractal Brownian motion (fBm) and wavelet multiresolution analysis. Our wavelet-fractal technique combines the excellent multiresolution localization property of wavelets to texture extraction of fractal. We prove the efficacy of our technique by successfully segmenting pediatric brain MR images (MRIs) from St. Jude Children"s Research Hospital. We use self-organizing map (SOM) as our clustering tool wherein we exploit both pixel intensity and multiresolution texture features to obtain segmented tumor. Our test results show that our technique successfully segments abnormal brain tissues in a set of T1 images. In the next step, we design a classifier using Feed-Forward (FF) neural network to statistically validate the presence of tumor in MRI using both the multiresolution texture and the pixel intensity features. We estimate the corresponding receiver operating curve (ROC) based on the findings of true positive fractions and false positive fractions estimated from our classifier at different threshold values. An ROC, which can be considered as a gold standard to prove the competence of a classifier, is obtained to ascertain the sensitivity and specificity of our classifier. We observe that at threshold 0.4 we achieve true positive value of 1.0 (100%) sacrificing only 0.16 (16%) false positive value for the set of 50 T1 MRI analyzed in this experiment.

  16. 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. PMID:23473341

  17. Technological advances in MRI measurement of brain perfusion.

    PubMed

    Duyn, Jeff H; van Gelderen, Peter; Talagala, Lalith; Koretsky, Alan; de Zwart, Jacco A

    2005-12-01

    Measurement of brain perfusion using arterial spin labeling (ASL) or dynamic susceptibility contrast (DSC) based MRI has many potential important clinical applications. However, the clinical application of perfusion MRI has been limited by a number of factors, including a relatively poor spatial resolution, limited volume coverage, and low signal-to-noise ratio (SNR). It is difficult to improve any of these aspects because both ASL and DSC methods require rapid image acquisition. In this report, recent methodological developments are discussed that alleviate some of these limitations and make perfusion MRI more suitable for clinical application. In particular, the availability of high magnetic field strength systems, increased gradient performance, the use of RF coil arrays and parallel imaging, and increasing pulse sequence efficiency allow for increased image acquisition speed and improved SNR. The use of parallel imaging facilitates the trade-off of SNR for increases in spatial resolution. As a demonstration, we obtained DSC and ASL perfusion images at 3.0 T and 7.0 T with multichannel RF coils and parallel imaging, which allowed us to obtain high-quality images with in-plane voxel sizes of 1.5 x 1.5 mm(2). PMID:16267852

  18. Inverse Planning Approach for 3-D MRI-Based Pulse-Dose Rate Intracavitary Brachytherapy in Cervix Cancer

    SciTech Connect

    Chajon, Enrique; Dumas, Isabelle; Touleimat, Mahmoud B.Sc.; Magne, Nicolas; Coulot, Jeremy; Verstraet, Rodolfe; Lefkopoulos, Dimitri; Haie-Meder, Christine

    2007-11-01

    Purpose: The purpose of this study was to evaluate the inverse planning simulated annealing (IPSA) software for the optimization of dose distribution in patients with cervix carcinoma treated with MRI-based pulsed-dose rate intracavitary brachytherapy. Methods and Materials: Thirty patients treated with a technique using a customized vaginal mold were selected. Dose-volume parameters obtained using the IPSA method were compared with the classic manual optimization method (MOM). Target volumes and organs at risk were delineated according to the Gynecological Brachytherapy Group/European Society for Therapeutic Radiology and Oncology recommendations. Because the pulsed dose rate program was based on clinical experience with low dose rate, dwell time values were required to be as homogeneous as possible. To achieve this goal, different modifications of the IPSA program were applied. Results: The first dose distribution calculated by the IPSA algorithm proposed a heterogeneous distribution of dwell time positions. The mean D90, D100, and V100 calculated with both methods did not differ significantly when the constraints were applied. For the bladder, doses calculated at the ICRU reference point derived from the MOM differed significantly from the doses calculated by the IPSA method (mean, 58.4 vs. 55 Gy respectively; p = 0.0001). For the rectum, the doses calculated at the ICRU reference point were also significantly lower with the IPSA method. Conclusions: The inverse planning method provided fast and automatic solutions for the optimization of dose distribution. However, the straightforward use of IPSA generated significant heterogeneity in dwell time values. Caution is therefore recommended in the use of inverse optimization tools with clinical relevance study of new dosimetric rules.

  19. 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

  20. 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.

  1. 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).

  2. 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

  3. 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…

  4. 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

  5. MRI of the human brain at 130 microtesla

    PubMed Central

    Inglis, Ben; Buckenmaier, Kai; SanGiorgio, Paul; Pedersen, Anders F.; Nichols, Matthew A.; Clarke, John

    2013-01-01

    We present in vivo images of the human brain acquired with an ultralow field MRI (ULFMRI) system operating at a magnetic field B0 ∼ 130 μT. The system features prepolarization of the proton spins at Bp ∼ 80 mT and detection of the NMR signals with a superconducting, second-derivative gradiometer inductively coupled to a superconducting quantum interference device (SQUID). We report measurements of the longitudinal relaxation time T1 of brain tissue, blood, and scalp fat at B0 and Bp, and cerebrospinal fluid at B0. We use these T1 values to construct inversion recovery sequences that we combine with Carr–Purcell–Meiboom–Gill echo trains to obtain images in which one species can be nulled and another species emphasized. In particular, we show an image in which only blood is visible. Such techniques greatly enhance the already high intrinsic T1 contrast obtainable at ULF. We further present 2D images of T1 and the transverse relaxation time T2 of the brain and show that, as expected at ULF, they exhibit similar contrast. Applications of brain ULFMRI include integration with systems for magnetoencephalography. More generally, these techniques may be applicable, for example, to the imaging of tumors without the need for a contrast agent and to modalities recently demonstrated with T1ρ contrast imaging (T1 in the rotating frame) at fields of 1.5 T and above. PMID:24255111

  6. 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

  7. 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. PMID:26254586

  8. Feasibility of 3-D MRI of Proximal Femur Microarchitecture at 3 T using 26 Receive Elements without and with Parallel Imaging

    PubMed Central

    Chang, Gregory; Deniz, Cem; Honig, Stephen; Rajapakse, Chamith S.; Egol, Kenneth; Regatte, Ravinder R.; Brown, Ryan

    2013-01-01

    Purpose High-resolution imaging of deeper anatomy such as the hip is challenging due to low signal-to-noise ratio (SNR), necessitating long scan times. Multi-element coils can increase SNR and reduce scan time through parallel imaging (PI). We assessed the feasibility of using a 26-element receive coil setup to perform 3 T MRI of proximal femur microarchitecture without and with PI. Materials and Methods This study had institutional review board approval. We scanned thirteen subjects on a 3 T scanner using 26 receive-elements and a 3-D FLASH sequence without and with PI (acceleration factors (AF) 2, 3, 4). We assessed SNR, depiction of individual trabeculae, PI performance (1/g-factor), and image quality with PI (1=non-visualization to 5=excellent). Results SNR maps demonstrate higher SNR for the 26-element setup compared to a 12-element setup for hip MRI. Without PI, individual proximal femur trabeculae were well-depicted, including microarchitectural deterioration in osteoporotic subjects. With PI, 1/g values for the 26-element/12-element receive-setup were 0.71/0.45, 0.56/0.25, and 0.44/0.08 at AF2, AF3, and AF4, respectively. Image quality was: AF1, excellent (4.8±0.4); AF2, good (4.2±1.0); AF3, average (3.3±1.0); AF4, non-visualization (1.4±0.9). Conclusion A 26-element receive-setup permits 3 T MRI of proximal femur microarchitecture with good image quality up to PI AF2. PMID:24711013

  9. 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

  10. 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.

  11. A brief report on MRI investigation of experimental traumatic brain injury

    PubMed Central

    Duong, Timothy Q.; Watts, Lora T.

    2016-01-01

    Traumatic brain injury is a major cause of death and disability. This is a brief report based on a symposium presentation to the 2014 Chinese Neurotrauma Association Meeting in San Francisco, USA. It covers the work from our laboratory in applying multimodal MRI to study experimental traumatic brain injury in rats with comparisons made to behavioral tests and histology. MRI protocols include structural, perfusion, manganese-enhanced, diffusion-tensor MRI, and MRI of blood-brain barrier integrity and cerebrovascular reactivity. PMID:26981069

  12. High frequency functional brain networks in neonates revealed by rapid acquisition resting state fMRI.

    PubMed

    Smith-Collins, Adam P R; Luyt, Karen; Heep, Axel; Kauppinen, Risto A

    2015-07-01

    Understanding how spatially remote brain regions interact to form functional brain networks, and how these develop during the neonatal period, provides fundamental insights into normal brain development, and how mechanisms of brain disorder and recovery may function in the immature brain. A key imaging tool in characterising functional brain networks is examination of T2*-weighted fMRI signal during rest (resting state fMRI, rs-fMRI). The majority of rs-fMRI studies have concentrated on slow signal fluctuations occurring at <0.1 Hz, even though neuronal rhythms, and haemodynamic responses to these fluctuate more rapidly, and there is emerging evidence for crucial information about functional brain connectivity occurring more rapidly than these limits. The characterisation of higher frequency components has been limited by the sampling frequency achievable with standard T2* echoplanar imaging (EPI) sequences. We describe patterns of neonatal functional brain network connectivity derived using accelerated T2*-weighted EPI MRI. We acquired whole brain rs-fMRI data, at subsecond sampling frequency, from preterm infants at term equivalent age and compared this to rs-fMRI data acquired with standard EPI acquisition protocol. We provide the first evidence that rapid rs-fMRI acquisition in neonates, and adoption of an extended frequency range for analysis, allows identification of a substantial proportion of signal power residing above 0.2 Hz. We thereby describe changes in brain connectivity associated with increasing maturity which are not evident using standard rs-fMRI protocols. Development of optimised neonatal fMRI protocols, including use of high speed acquisition sequences, is crucial for understanding the physiology and pathophysiology of the developing brain. PMID:25787931

  13. 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

  14. 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.

  15. 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

  16. MRI brain in monohalomethane toxic encephalopathy: A case report.

    PubMed

    Deshmukh, Yogeshwari S; Atre, Ashish; Shah, Darshan; Kothari, Sudhir

    2013-07-01

    Monohalomethanes are alkylating agents that have been used as methylating agents, laboratory reagents, refrigerants, aerosol propellants, pesticides, fumigants, fire-extinguishing agents, anesthetics, degreasers, blowing agents for plastic foams, and chemical intermediates. Compounds in this group are methyl chloride, methyl bromide, methyl iodide (MI), and methyl fluoride. MI is a colorless volatile liquid used as a methylating agent to manufacture a few pharmaceuticals and is also used as a fumigative insecticide. It is a rare intoxicant. Neurotoxicity is known with both acute and chronic exposure to MI. We present the characteristic magnetic resonance imaging (MRI) brain findings in a patient who developed neuropsychiatric symptoms weeks after occupational exposure to excessive doses of MI. PMID:24347845

  17. 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.

  18. 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

  19. 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

  20. Simultaneous fMRI-PET of the Opioidergic Pain System in Human Brain

    PubMed Central

    Wey, Hsiao-Ying; Catana, Ciprian; Hooker, Jacob M.; Dougherty, Darin D.; Knudsen, Gitte M.; Wang, Danny JJ.; Chonde, Daniel B; Rosen, Bruce R.; Gollub, Randy L.; Kong, Jian

    2015-01-01

    MRI and PET provide complementary information for studying brain function. While the potential use of simultaneous MRI/PET for clinical diagnostic and disease staging has been demonstrated recently; the biological relevance of concurrent functional MRI-PET brain imaging to dissect neurochemically distinct components of the blood oxygenation level dependent (BOLD) fMRI signal has not yet been shown. We obtained sixteen fMRI-PET data sets from eight healthy volunteers. Each subject participated in randomized order in a pain scan and a control (nonpainful pressure) scan on the same day. Dynamic PET data were acquired with an opioid radioligand, [11C]Diprenorphine, to detect endogenous opioid releases in response to pain. BOLD fMRI data were collected at the same time to capture hemodynamic responses. In this simultaneous human fMRI-PET imaging study, we show co-localized responses in thalamus and striatum related to pain processing, while modality specific brain networks were also found. Co-localized fMRI and PET signal changes in the thalamus were positively correlated suggesting pain-induced changes in opioid neurotransmission contribute a significant component of the fMRI signal change in this region. Simultaneous fMRI-PET provides unique opportunities allowing us to relate specific neurochemical events to functional hemodynamic activation and to investigate the impacts of neurotransmission on neurovascular coupling of the human brain in vivo. PMID:25107855

  1. MRI-guided 3D conformal arc micro-irradiation of a F98 glioblastoma rat model using the Small Animal Radiation Research Platform (SARRP).

    PubMed

    Bolcaen, Julie; Descamps, Benedicte; Deblaere, Karel; Boterberg, Tom; Hallaert, Giorgio; Van den Broecke, Caroline; Decrock, Elke; Vral, Anne; Leybaert, Luc; Vanhove, Christian; Goethals, Ingeborg

    2014-11-01

    Current glioblastoma (GB) small animal models for cranial radiation therapy (RT) use simple single beam technologies, which differ from the advanced conformal image-guided radiation techniques used in clinical practice. This technological disparity presents a major disadvantage for the development of new therapeutic approaches. Hence, we established a F98 GB rat model using magnetic resonance imaging (MRI)-guided three-dimensional (3D)-conformal arc RT with the Small Animal Radiation Research Platform (SARRP). Ten Fischer rats were inoculated with F98 tumor cells. When the tumor reached a volume of approximately 27 mm(3) on T2-weighted MR images, the animals were randomized into a treatment group (n = 5) receiving RT and concomitant temozolomide, and a sham group (n = 5) receiving control injections. For the treated animals, contrast-enhanced T1-weighted MR images were acquired followed by a cone-beam computed tomography (CBCT) on the SARRP system. Both scans were co-registered; MRI was used to define the target whereas CBCT was used for calculating a dose plan (20 Gy, three non-coplanar arc beams, 3 × 3 mm collimator). Tumor volumes were evaluated on follow-up contrast-enhanced T1-weighted MR images. Verification of treatment accuracy with γH2AX immunohistochemical staining was performed. Tumors in the control animals showed rapid proliferation during follow-up, encompassing almost the entire right cerebral hemisphere at day 12-15. Treated animals showed no significant tumor growth from 2 to 9 days post RT. γH2AX results confirmed the accuracy of dose delivery. This model, which is quite similar to the approach in the clinic, is valid for combined RT and chemotherapy of GB in rats. PMID:25069566

  2. Estimating subthreshold tumor on MRI using a 3D-DTI growth model for GBM: An adjunct to radiation therapy planning.

    PubMed

    Hathout, Leith; Patel, Vishal

    2016-08-01

    Mathematical modeling and serial magnetic resonance imaging (MRI) used to calculate patient-specific rates of tumor diffusion, D, and proliferation, ρ, can be combined to simulate glioblastoma multiforme (GBM) growth. We showed that the proportion and distribution of tumor cells below the MRI threshold are determined by the D/ρ ratio of the tumor. As most radiation fields incorporate a 1‑3 cm margin to account for subthreshold tumor, accurate characterization of subthreshold tumor aids the design of optimal radiation fields. This study compared two models: a standard one‑dimensional (1D) isotropic model and a three‑dimensional (3D) anisotropic model using the advanced imaging method of diffusion tensor imaging (DTI) ‑ with regards to the D/ρ ratio's effect on the proportion and spatial extent of the subthreshold tumor. A validated reaction‑diffusion equation accounting for tumor diffusion and proliferation modeled tumor concentration in time and space. For the isotropic and anisotropic models, nine tumors with different D/ρ ratios were grown to a T1 radius of 1.5 cm. For each tumor, the percent and extent of tumor cells beyond the T2 radius were calculated. For both models, higher D/ρ ratios were correlated with a greater proportion and extent of subthreshold tumor. Anisotropic modeling demonstrated a higher proportion and extent of subthreshold tumor than predicted by the isotropic modeling. Because the quantity and distribution of subthreshold tumor depended on the D/ρ ratio, this ratio should influence radiation field demarcation. Furthermore, the use of DTI data to account for anisotropic tumor growth allows for more refined characterization of the subthreshold tumor based on the patient-specific D/ρ ratio. PMID:27374420

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. Value of brain MRI in infective endocarditis: a narrative literature review.

    PubMed

    Champey, J; Pavese, P; Bouvaist, H; Kastler, A; Krainik, A; Francois, P

    2016-02-01

    The nervous system is frequently involved in patients with infective endocarditis (IE). A systematic review of the literature was realized in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA). This study sought to systematically evaluate the published evidence of the contribution of brain magnetic resonance imaging (MRI) in IE. The aim was to identify studies presenting the incidence and type of MRI brain lesions in IE. Fifteen relevant studies were isolated using the Medline, Embase, and Cochrane databases. Most of them were observational studies with a small number of patients. MRI studies demonstrated a wide variety and high frequency of cerebral lesions, around 80 % of which were mostly clinically occult. This review shows MRI's superiority compared to brain computed tomography (CT) for the diagnosis of neurologic complications. Recent developments of sensitive MRI sequences can detect microinfarction and cerebral microhemorrhages. However, the clinical significance of these microhemorrhages, also called cerebral microbleeds (CMBs), remains uncertain. Because some MRI neurological lesions are a distinctive IE feature, they can have a broader involvement in diagnosis and therapeutic decisions. Even if cerebral MRI offers new perspectives for better IE management, there is not enough scientific proof to recommend it in current guidelines. The literature remains incomplete regarding the impact of MRI on concerted decision-making. The long-term prognosis of CMBs has not been evaluated to date and requires further studies. Today, brain MRI can be used on a case-by-case basis based on a clinician's appraisal. PMID:26585337

  9. 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

  10. 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

  11. 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

  12. Learning Computational Models of Video Memorability from fMRI Brain Imaging.

    PubMed

    Han, Junwei; Chen, Changyuan; Shao, Ling; Hu, Xintao; Han, Jungong; Liu, Tianming

    2015-08-01

    Generally, various visual media are unequally memorable by the human brain. This paper looks into a new direction of modeling the memorability of video clips and automatically predicting how memorable they are by learning from brain functional magnetic resonance imaging (fMRI). We propose a novel computational framework by integrating the power of low-level audiovisual features and brain activity decoding via fMRI. Initially, a user study experiment is performed to create a ground truth database for measuring video memorability and a set of effective low-level audiovisual features is examined in this database. Then, human subjects' brain fMRI data are obtained when they are watching the video clips. The fMRI-derived features that convey the brain activity of memorizing videos are extracted using a universal brain reference system. Finally, due to the fact that fMRI scanning is expensive and time-consuming, a computational model is learned on our benchmark dataset with the objective of maximizing the correlation between the low-level audiovisual features and the fMRI-derived features using joint subspace learning. The learned model can then automatically predict the memorability of videos without fMRI scans. Evaluations on publically available image and video databases demonstrate the effectiveness of the proposed framework. PMID:25314715

  13. 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

  14. Recapitulation of Tumor Heterogeneity and Molecular Signatures in a 3D Brain Cancer Model with Decreased Sensitivity to Histone Deacetylase Inhibition

    PubMed Central

    Smith, Stuart J.; Wilson, Martin; Ward, Jennifer H.; Rahman, Cheryl V.; Peet, Andrew C.; Macarthur, Donald C.; Rose, Felicity R. A. J.; Grundy, Richard G.; Rahman, Ruman

    2012-01-01

    Introduction Physiologically relevant pre-clinical ex vivo models recapitulating CNS tumor micro-environmental complexity will aid development of biologically-targeted agents. We present comprehensive characterization of tumor aggregates generated using the 3D Rotary Cell Culture System (RCCS). Methods CNS cancer cell lines were grown in conventional 2D cultures and the RCCS and comparison with a cohort of 53 pediatric high grade gliomas conducted by genome wide gene expression and microRNA arrays, coupled with immunohistochemistry, ex vivo magnetic resonance spectroscopy and drug sensitivity evaluation using the histone deacetylase inhibitor, Vorinostat. Results Macroscopic RCCS aggregates recapitulated the heterogeneous morphology of brain tumors with a distinct proliferating rim, necrotic core and oxygen tension gradient. Gene expression and microRNA analyses revealed significant differences with 3D expression intermediate to 2D cultures and primary brain tumors. Metabolic profiling revealed differential profiles, with an increase in tumor specific metabolites in 3D. To evaluate the potential of the RCCS as a drug testing tool, we determined the efficacy of Vorinostat against aggregates of U87 and KNS42 glioblastoma cells. Both lines demonstrated markedly reduced sensitivity when assaying in 3D culture conditions compared to classical 2D drug screen approaches. Conclusions Our comprehensive characterization demonstrates that 3D RCCS culture of high grade brain tumor cells has profound effects on the genetic, epigenetic and metabolic profiles of cultured cells, with these cells residing as an intermediate phenotype between that of 2D cultures and primary tumors. There is a discrepancy between 2D culture and tumor molecular profiles, and RCCS partially re-capitulates tissue specific features, allowing drug testing in a more relevant ex vivo system. PMID:23272238

  15. Structural and functional effects of metastases in rat brain determined by multimodal MRI.

    PubMed

    Serres, Sébastien; Martin, Christopher J; Sarmiento Soto, Manuel; Bristow, Claire; O'Brien, Emma R; Connell, John J; Khrapitchev, Alexandre A; Sibson, Nicola R

    2014-02-15

    Metastasis to the brain results in significant impairment of brain function and poor patient survival. Currently, magnetic resonance imaging (MRI) is under-utilised in monitoring brain metastases and their effects on brain function. Here, we sought to establish a model of focal brain metastasis in the rat that enables serial multimodal structural and functional MRI studies, and to assess the sensitivity of these approaches to metastatic growth. Female Berlin-Druckrey-IX rats were injected intracerebrally with metastatic ENU1564 cells in the ventroposterior medial nucleus (VPM) of the thalamus, a relay node of the whisker-to-barrel cortex pathway. Animals underwent multimodal structural and vascular MRI, as well as functional MRI of the cortical blood oxygenation level dependent (BOLD) responses to whisker pad stimulation. T2 , diffusion, magnetisation transfer and perfusion weighted MRI enabled differentiation between a central area of more advanced metastatic growth and penumbral regions of co-optive perivascular micrometastatic growth, with magnetisation transfer MRI being the most sensitive to micrometastatic growth. Areas of cortical BOLD activation in response to whisker pad stimulation were significantly reduced in the hemisphere containing metastases in the VPM. The reduction in BOLD response correlated with metastatic burden in the thalamus, and was sensitive to the presence of smaller metastases than currently detectable clinically. Our findings suggest that multimodal MRI provides greater sensitivity to tumour heterogeneity and micrometastatic growth than single modality contrast-enhanced MRI. Understanding the relationships between these MRI parameters and the underlying pathology may greatly enhance the utility of MRI in diagnosis, staging and monitoring of brain metastasis. PMID:23913394

  16. 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

  17. Relating resting-state fMRI and EEG whole-brain connectomes across frequency bands

    PubMed Central

    Deligianni, Fani; Centeno, Maria; Carmichael, David W.; Clayden, Jonathan D.

    2014-01-01

    Whole brain functional connectomes hold promise for understanding human brain activity across a range of cognitive, developmental and pathological states. So called resting-state (rs) functional MRI studies have contributed to the brain being considered at a macroscopic scale as a set of interacting regions. Interactions are defined as correlation-based signal measurements driven by blood oxygenation level dependent (BOLD) contrast. Understanding the neurophysiological basis of these measurements is important in conveying useful information about brain function. Local coupling between BOLD fMRI and neurophysiological measurements is relatively well defined, with evidence that gamma (range) frequency EEG signals are the closest correlate of BOLD fMRI changes during cognitive processing. However, it is less clear how whole-brain network interactions relate during rest where lower frequency signals have been suggested to play a key role. Simultaneous EEG-fMRI offers the opportunity to observe brain network dynamics with high spatio-temporal resolution. We utilize these measurements to compare the connectomes derived from rs-fMRI and EEG band limited power (BLP). Merging this multi-modal information requires the development of an appropriate statistical framework. We relate the covariance matrices of the Hilbert envelope of the source localized EEG signal across bands to the covariance matrices derived from rs-fMRI with the means of statistical prediction based on sparse Canonical Correlation Analysis (sCCA). Subsequently, we identify the most prominent connections that contribute to this relationship. We compare whole-brain functional connectomes based on their geodesic distance to reliably estimate the performance of the prediction. The performance of predicting fMRI from EEG connectomes is considerably better than predicting EEG from fMRI across all bands, whereas the connectomes derived in low frequency EEG bands resemble best rs-fMRI connectivity. PMID:25221467

  18. Relating resting-state fMRI and EEG whole-brain connectomes across frequency bands.

    PubMed

    Deligianni, Fani; Centeno, Maria; Carmichael, David W; Clayden, Jonathan D

    2014-01-01

    Whole brain functional connectomes hold promise for understanding human brain activity across a range of cognitive, developmental and pathological states. So called resting-state (rs) functional MRI studies have contributed to the brain being considered at a macroscopic scale as a set of interacting regions. Interactions are defined as correlation-based signal measurements driven by blood oxygenation level dependent (BOLD) contrast. Understanding the neurophysiological basis of these measurements is important in conveying useful information about brain function. Local coupling between BOLD fMRI and neurophysiological measurements is relatively well defined, with evidence that gamma (range) frequency EEG signals are the closest correlate of BOLD fMRI changes during cognitive processing. However, it is less clear how whole-brain network interactions relate during rest where lower frequency signals have been suggested to play a key role. Simultaneous EEG-fMRI offers the opportunity to observe brain network dynamics with high spatio-temporal resolution. We utilize these measurements to compare the connectomes derived from rs-fMRI and EEG band limited power (BLP). Merging this multi-modal information requires the development of an appropriate statistical framework. We relate the covariance matrices of the Hilbert envelope of the source localized EEG signal across bands to the covariance matrices derived from rs-fMRI with the means of statistical prediction based on sparse Canonical Correlation Analysis (sCCA). Subsequently, we identify the most prominent connections that contribute to this relationship. We compare whole-brain functional connectomes based on their geodesic distance to reliably estimate the performance of the prediction. The performance of predicting fMRI from EEG connectomes is considerably better than predicting EEG from fMRI across all bands, whereas the connectomes derived in low frequency EEG bands resemble best rs-fMRI connectivity. PMID:25221467

  19. The future of ultra-high field MRI and fMRI for study of the human brain

    PubMed Central

    Duyn, Jeff H.

    2011-01-01

    MRI and fMRI have been used for about three and two decades respectively and much has changed over this time period, both in the quality of the data and in the range of applications for studying the brain. Apart from resolution improvements from around 4 mm in the early days to below 0.5 mm with modern technology, novel uses of contrast have led to the ability to sensitize images to some of the brain’s structural properties at the cellular scale as well as study the localization and organization of brain function at the level of cortical columns. These developments have in part been facilitated by a continuing drive to increase the magnetic field strength. Will the next few decades see similar improvements? Here we will discuss current state of high field MRI, expected further increases in field strength, and improvements expected with these increases. PMID:22063093

  20. 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…

  1. Low-field MRI for studies of human pulmonary physiology and traumatic brain injury

    NASA Astrophysics Data System (ADS)

    Wilson, Alyssa; Devience, Stephen; Rosen, Matthew; Walsworth, Ronald

    2011-05-01

    We describe recent progress on the development of an open-access low-magnetic-field MRI system for studies of human pulmonary physiology and traumatic brain injury. Low-field MRI benefits from reduced magnetic susceptibility effects and can provide high-resolution images of the human body when used with hyperpolarized media such as 3He and 129Xe.

  2. Brain MRI in patients with diffuse psychiatric/neuropsychological syndromes in systemic lupus erythematosus

    PubMed Central

    Arinuma, Yoshiyuki; Kikuchi, Hirotoshi; Wada, Tatsuhiko; Nagai, Tatsuo; Tanaka, Sumiaki; Oba, Hiroshi; Hirohata, Shunsei

    2014-01-01

    Background Manifestations in neuropsychiatric systemic lupus erythematosus (NPSLE), especially active diffuse NPSLE syndromes, are some of the most difficult complications of the disease. For the evaluation and the diagnosis of central nervous system manifestations, including NPSLE, MRI is a very useful tool to detect the various abnormalities. However, the relationship between brain MRI findings and clinical variables has not yet been clarified in patients with diffuse NPSLE. Objectives The aim of this study is to investigate the pathogenesis of diffuse NPSLE, by comparing various parameters such as serum autoantibodies and cytokines in cerebrospinal fluid (CSF) with abnormal findings revealed on brain MRIs in patients with diffuse NPSLE. Methods Fifty-three patients with diffuse NPSLE admitted to our University Hospital from 1992 to 2012 were exhaustively enrolled in this study. Their medical charts and brain MRI scans were reviewed. The relationship of MRI abnormalities with various parameters was analysed. Results As many as 25 of 53 patients (47.2%) had abnormal MRI findings. MRI findings improved after treatment in 10 of 17 patients for whom follow-up studies were available. MRI abnormalities were not correlated with age at the onset of diffuse NPSLE. However, the disease duration of SLE was significantly longer in patients with abnormal MRI findings (p=0.0009). MRI abnormalities were not significantly associated with serum autoantibodies. However, there were significant elevations of the CSF protein level (p=0.0106) and the CSF interleukin 6 level (p=0.0225) in patients with abnormal MRI findings. Patients with MRI abnormalities showed significantly higher overall mortality (p=0.0348). Conclusions The results revealed that MRI abnormalities in diffuse NPSLE might be heterogeneous with regard to their reversibility. These data also indicate that patients with diffuse NPSLE and MRI abnormalities have more severe inflammation in the central nervous system

  3. Object categories specific brain activity classification with simultaneous EEG-fMRI.

    PubMed

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

    2015-08-01

    Any kind of visual information is encoded in terms of patterns of neural activity occurring inside the brain. Decoding neural patterns or its classification is a challenging task. Functional magnetic resonance imaging (fMRI) and Electroencephalography (EEG) are non-invasive neuroimaging modalities to capture the brain activity pattern in term of images and electric potential respectively. To get higher spatiotemporal resolution of human brain from these two complementary neuroimaging modalities, simultaneous EEG-fMRI can be helpful. In this paper, we proposed a framework for classifying the brain activity patterns with simultaneous EEG-fMRI. We have acquired five human participants' data with simultaneous EEG-fMRI by showing different object categories. Further, combined analysis of EEG and fMRI data was carried out. Extracted information through combine analysis is passed to support vector machine (SVM) classifier for classification purpose. We have achieved better classification accuracy using simultaneous EEG-fMRI i.e., 81.8% as compared to fMRI data standalone. This shows that multimodal neuroimaging can improve the classification accuracy of brain activity patterns as compared to individual modalities reported in literature. PMID:26736635

  4. 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. PMID:26037056

  5. 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

  6. Structural and Functional Brain Remodeling during Pregnancy with Diffusion Tensor MRI and Resting-State Functional MRI

    PubMed Central

    Chan, Russell W.; Ho, Leon C.; Zhou, Iris Y.; Gao, Patrick P.; Chan, Kevin C.; Wu, Ed X.

    2015-01-01

    Although pregnancy-induced hormonal changes have been shown to alter the brain at the neuronal level, the exact effects of pregnancy on brain at the tissue level remain unclear. In this study, diffusion tensor imaging (DTI) and resting-state functional MRI (rsfMRI) were employed to investigate and document the effects of pregnancy on the structure and function of the brain tissues. Fifteen Sprague-Dawley female rats were longitudinally studied at three days before mating (baseline) and seventeen days after mating (G17). G17 is equivalent to the early stage of the third trimester in humans. Seven age-matched nulliparous female rats served as non-pregnant controls and were scanned at the same time-points. For DTI, diffusivity was found to generally increase in the whole brain during pregnancy, indicating structural changes at microscopic levels that facilitated water molecular movement. Regionally, mean diffusivity increased more pronouncedly in the dorsal hippocampus while fractional anisotropy in the dorsal dentate gyrus increased significantly during pregnancy. For rsfMRI, bilateral functional connectivity in the hippocampus increased significantly during pregnancy. Moreover, fractional anisotropy increase in the dentate gyrus appeared to correlate with the bilateral functional connectivity increase in the hippocampus. These findings revealed tissue structural modifications in the whole brain during pregnancy, and that the hippocampus was structurally and functionally remodeled in a more marked manner. PMID:26658306

  7. 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

  8. 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

  9. 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.

  10. 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

  11. Atlas-based fuzzy connectedness segmentation and intensity nonuniformity correction applied to brain MRI.

    PubMed

    Zhou, Yongxin; Bai, Jing

    2007-01-01

    A framework that combines atlas registration, fuzzy connectedness (FC) segmentation, and parametric bias field correction (PABIC) is proposed for the automatic segmentation of brain magnetic resonance imaging (MRI). First, the atlas is registered onto the MRI to initialize the following FC segmentation. Original techniques are proposed to estimate necessary initial parameters of FC segmentation. Further, the result of the FC segmentation is utilized to initialize a following PABIC algorithm. Finally, we re-apply the FC technique on the PABIC corrected MRI to get the final segmentation. Thus, we avoid expert human intervention and provide a fully automatic method for brain MRI segmentation. Experiments on both simulated and real MRI images demonstrate the validity of the method, as well as the limitation of the method. Being a fully automatic method, it is expected to find wide applications, such as three-dimensional visualization, radiation therapy planning, and medical database construction. PMID:17260863

  12. Neurobiological origin of spurious brain morphological changes: A quantitative MRI study

    PubMed Central

    Lorio, Sara; Kherif, Ferath; Ruef, Anne; Melie‐Garcia, Lester; Frackowiak, Richard; Ashburner, John; Helms, Gunther

    2016-01-01

    Abstract The high gray‐white matter contrast and spatial resolution provided by T1‐weighted magnetic resonance imaging (MRI) has made it a widely used imaging protocol for computational anatomy studies of the brain. While the image intensity in T1‐weighted images is predominantly driven by T1, other MRI parameters affect the image contrast, and hence brain morphological measures derived from the data. Because MRI parameters are correlates of different histological properties of brain tissue, this mixed contribution hampers the neurobiological interpretation of morphometry findings, an issue which remains largely ignored in the community. We acquired quantitative maps of the MRI parameters that determine signal intensities in T1‐weighted images (R 1 (=1/T1), R 2*, and PD) in a large cohort of healthy subjects (n = 120, aged 18–87 years). Synthetic T1‐weighted images were calculated from these quantitative maps and used to extract morphometry features—gray matter volume and cortical thickness. We observed significant variations in morphometry measures obtained from synthetic images derived from different subsets of MRI parameters. We also detected a modulation of these variations by age. Our findings highlight the impact of microstructural properties of brain tissue—myelination, iron, and water content—on automated measures of brain morphology and show that microstructural tissue changes might lead to the detection of spurious morphological changes in computational anatomy studies. They motivate a review of previous morphological results obtained from standard anatomical MRI images and highlight the value of quantitative MRI data for the inference of microscopic tissue changes in the healthy and diseased brain. Hum Brain Mapp 37:1801–1815, 2016. © 2016 The Authors. Human Brain Mapping Published by Wiley Periodicals, Inc. PMID:26876452

  13. Neurobiological origin of spurious brain morphological changes: A quantitative MRI study.

    PubMed

    Lorio, Sara; Kherif, Ferath; Ruef, Anne; Melie-Garcia, Lester; Frackowiak, Richard; Ashburner, John; Helms, Gunther; Lutti, Antoine; Draganski, Bodgan

    2016-05-01

    The high gray-white matter contrast and spatial resolution provided by T1-weighted magnetic resonance imaging (MRI) has made it a widely used imaging protocol for computational anatomy studies of the brain. While the image intensity in T1-weighted images is predominantly driven by T1, other MRI parameters affect the image contrast, and hence brain morphological measures derived from the data. Because MRI parameters are correlates of different histological properties of brain tissue, this mixed contribution hampers the neurobiological interpretation of morphometry findings, an issue which remains largely ignored in the community. We acquired quantitative maps of the MRI parameters that determine signal intensities in T1-weighted images (R1 (=1/T1), R2 *, and PD) in a large cohort of healthy subjects (n = 120, aged 18-87 years). Synthetic T1-weighted images were calculated from these quantitative maps and used to extract morphometry features-gray matter volume and cortical thickness. We observed significant variations in morphometry measures obtained from synthetic images derived from different subsets of MRI parameters. We also detected a modulation of these variations by age. Our findings highlight the impact of microstructural properties of brain tissue-myelination, iron, and water content-on automated measures of brain morphology and show that microstructural tissue changes might lead to the detection of spurious morphological changes in computational anatomy studies. They motivate a review of previous morphological results obtained from standard anatomical MRI images and highlight the value of quantitative MRI data for the inference of microscopic tissue changes in the healthy and diseased brain. Hum Brain Mapp 37:1801-1815, 2016. © 2016 The Authors. Human Brain Mapping Published by Wiley Periodicals, Inc. PMID:26876452

  14. 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

  15. Structural MRI of Pediatric Brain Development: What Have We Learned and Where Are We Going?

    PubMed Central

    Giedd, Jay N.; Rapoport, Judith L.

    2012-01-01

    Magnetic resonance imaging (MRI) allows unprecedented access to the anatomy and physiology of the developing brain without the use of ionizing radiation. Over the past two decades, thousands of brain MRI scans from healthy youth and those with neuropsychiatric illness have been acquired and analyzed with respect to diagnosis, sex, genetics, and/or psychological variables such as IQ. Initial reports comparing size differences of various brain components averaged across large age spans have given rise to longitudinal studies examining trajectories of development over time and evaluations of neural circuitry as opposed to structures in isolation. Although MRI is still not of routine diagnostic utility for evaluation of pediatric neuropsychiatric disorders, patterns of typical versus atypical development have emerged that may elucidate pathologic mechanisms and suggest targets for intervention. In this review we summarize general contributions of structural MRI to our understanding of neurodevelopment in health and illness. PMID:20826305

  16. Profiles by Sex of Brain MRI and Cognitive Function in The Framingham Offspring Study

    PubMed Central

    Albert, Mark; Massaro, Joseph; DeCarli, Charles; Beiser, Alexa; Seshadri, Sudha; Wolf, Philip A.; Au, Rhoda

    2009-01-01

    Objective To examine whether there are sex-specific associations between brain MRI measures and neuropsychological test performance. Background Differences in cardiovascular risk factors (CVRF) have been linked to decreased total cerebral brain volume (TCBV) and white matter hyperintensities (WMH). Although brain morphology has been related to cognitive performance, few studies have addressed sex-specific effects in this relationship. Methods Framingham Offspring who were stroke and dementia-free underwent a brain MRI scan and neuropsychological (NP) testing (n=2,085; 978 men). Factor analysis identified four domain-specific neuropsychological factors. MRI participants were divided into four MRI subgroups based on measures of TCBV and combinations of the presence of WMH and silent cerebral infarcts (≥3mm; SCI). Results Overall, the relationship between MRI and NP measures was similar between the sexes. The exception was that only men showed a positive relationship between executive function (EF) and cerebrovascular disease defined as large white matter hyperintensity volume plus SCI. This finding was attributed only among men with FSRP scores > 90th percentile range (p=0.0019). Conclusions Measures of brain atrophy and subclinical markers of vascular disease showed that sex does not significantly alter the relationship between MRI and NP, except among men and women who are at high risk for stroke; these men show poorer performance on EF, whereas the women do not. PMID:20505436

  17. 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

  18. Measurement of physiological parameters during brain activation usingfMRI

    NASA Astrophysics Data System (ADS)

    Feng, Ching-Mei Janet

    The changes in cerebral metabolic rate of oxygen consumption (CMRO 2), cerebral blood flow (CBF) and cerebral blood volume (CBV) are correlated with the changes in blood deoxyhemoglobin content that determine the blood oxygen level-dependent (BOLD) signal. Both CBF and CBV have been widely measured and well understood by previous studies, while CMRO2 measurement is still in development. The central hypothesis of the proposed study is that those physiological parameters can be simulated by biophysical models with fixed parameters and measured directly. The goal of this proposal is to test the central hypothesis. In summary, this dissertation focused on measurements of physiological parameters in two image modalities. Cerebral blood flow (CBF), cerebral blood volume (CBV), blood oxygenation level dependent (BOLD) signal, and cerebral metabolic rate of oxygen consumption (CMRO2) were studied in chapters II to IV. It is going to help to understand human brain metabolism during neuronal activity. Chapter V compared two image modalities---MR and PET and furthermore determine beta* in existing MR model for clinic use. This dissertation shows that the characteristics of BOLD signal can be examined by balloon model in both block-designed and event-related designed paradigm. The dynamic change of CMRO2 and OER using event-related fMRI can be measured using existing biophysical model proposed by Kim and his coworker in 1999. Furthermore, PET experiment was used to determine the parameters contained in Kim's model. This dissertation verify the central hypothesis that we made early on and we expect CMRO2 model with fixed parameters will bring a big impact in research and clinical use.

  19. 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

  20. Repeated BOLD-fMRI Imaging of Deep Brain Stimulation Responses in Rats

    PubMed Central

    Chao, Tzu-Hao Harry; Chen, Jyh-Horng; Yen, Chen-Tung

    2014-01-01

    Functional magnetic resonance imaging (fMRI) provides a picture of the global spatial activation pattern of the brain. Interest is growing regarding the application of fMRI to rodent models to investigate adult brain plasticity. To date, most rodent studies used an electrical forepaw stimulation model to acquire fMRI data, with α-chloralose as the anesthetic. However, α-chloralose is harmful to animals, and not suitable for longitudinal studies. Moreover, peripheral stimulation models enable only a limited number of brain regions to be studied. Processing between peripheral regions and the brain is multisynaptic, and renders interpretation difficult and uncertain. In the present study, we combined the medetomidine-based fMRI protocol (a noninvasive rodent fMRI protocol) with chronic implantation of an MRI-compatible stimulation electrode in the ventroposterior (VP) thalamus to repetitively sample thalamocortical responses in the rat brain. Using this model, we scanned the forebrain responses evoked by the VP stimulation repeatedly of individual rats over 1 week. Cortical BOLD responses were compared between the 2 profiles obtained at day1 and day8. We discovered reproducible frequency- and amplitude-dependent BOLD responses in the ipsilateral somatosensory cortex (S1). The S1 BOLD responses during the 2 sessions were conserved in maximal response amplitude, area size (size ratio from 0.88 to 0.91), and location (overlap ratio from 0.61 to 0.67). The present study provides a long-term chronic brain stimulation protocol for studying the plasticity of specific neural circuits in the rodent brain by BOLD-fMRI. PMID:24825464

  1. Development of MRI-based atlases of non-human brains.

    PubMed

    Ullmann, Jeremy F P; Janke, Andrew L; Reutens, David; Watson, Charles

    2015-02-15

    Brain atlases are a fundamental resource for neuroscience research. In the past few decades they have undergone a transition from traditional printed histological atlases to digital atlases made up of multiple data sets from multiple modalities, and atlases based on magnetic resonance imaging (MRI) have become widespread. Here we discuss the methods involved in making an MRI brain atlas, including registration of multiple data sets into a model, ontological classification, segmentation of a minimum deformation model, dissemination strategies, and applications of these atlases. Finally, we discuss possible future directions in the development of brain atlases. PMID:25236843

  2. Robust Volume Assessment of Brain Tissues for 3-Dimensional Fourier Transformation MRI via a Novel Multispectral Technique

    PubMed Central

    Chai, Jyh-Wen; Chen, Clayton C.; Wu, Yi-Ying; Chen, Hung-Chieh; Tsai, Yi-Hsin; Chen, Hsian-Min; Lan, Tsuo-Hung; Ouyang, Yen-Chieh; Lee, San-Kan

    2015-01-01

    A new TRIO algorithm method integrating three different algorithms is proposed to perform brain MRI segmentation in the native coordinate space, with no need of transformation to a standard coordinate space or the probability maps for segmentation. The method is a simple voxel-based algorithm, derived from multispectral remote sensing techniques, and only requires minimal operator input to depict GM, WM, and CSF tissue clusters to complete classification of a 3D high-resolution multislice-multispectral MRI data. Results showed very high accuracy and reproducibility in classification of GM, WM, and CSF in multislice-multispectral synthetic MRI data. The similarity indexes, expressing overlap between classification results and the ground truth, were 0.951, 0.962, and 0.956 for GM, WM, and CSF classifications in the image data with 3% noise level and 0% non-uniformity intensity. The method particularly allows for classification of CSF with 0.994, 0.961 and 0.996 of accuracy, sensitivity and specificity in images data with 3% noise level and 0% non-uniformity intensity, which had seldom performed well in previous studies. As for clinical MRI data, the quantitative data of brain tissue volumes aligned closely with the brain morphometrics in three different study groups of young adults, elderly volunteers, and dementia patients. The results also showed very low rates of the intra- and extra-operator variability in measurements of the absolute volumes and volume fractions of cerebral GM, WM, and CSF in three different study groups. The mean coefficients of variation of GM, WM, and CSF volume measurements were in the range of 0.03% to 0.30% of intra-operator measurements and 0.06% to 0.45% of inter-operator measurements. In conclusion, the TRIO algorithm exhibits a remarkable ability in robust classification of multislice-multispectral brain MR images, which would be potentially applicable for clinical brain volumetric analysis and explicitly promising in cross

  3. A Window into the Brain: Advances in Psychiatric fMRI

    PubMed Central

    Zhan, Xiaoyan; Yu, Rongjun

    2015-01-01

    Functional magnetic resonance imaging (fMRI) plays a key role in modern psychiatric research. It provides a means to assay differences in brain systems that underlie psychiatric illness, treatment response, and properties of brain structure and function that convey risk factor for mental diseases. Here we review recent advances in fMRI methods in general use and progress made in understanding the neural basis of mental illness. Drawing on concepts and findings from psychiatric fMRI, we propose that mental illness may not be associated with abnormalities in specific local regions but rather corresponds to variation in the overall organization of functional communication throughout the brain network. Future research may need to integrate neuroimaging information drawn from different analysis methods and delineate spatial and temporal patterns of brain responses that are specific to certain types of psychiatric disorders. PMID:26413531

  4. 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

  5. High-Throughput, High-Frequency 3D Ultrasound for In Utero Analysis of Embryonic Mouse Brain Development

    PubMed Central

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

    2013-01-01

    With the emergence of the mouse as the predominant model system for studying mammalian brain development, in utero imaging methods are urgently required to analyze the dynamics of brain growth and patterning in mouse embryos. To address this need, we combined synthetic focusing with a high-frequency (38-MHz) annular-array ultrasound imaging system for extended depth-of-field, coded excitation for improved penetration, and respiratory-gated transmit-receive. This combination allowed noninvasive in utero acquisition of motion-free, three-dimensional data from individual embryos in approximately 2 minutes, and data from 4 or more embryos in a pregnant mouse in less than 30 minutes. Data were acquired from 148 embryos spanning 5 days of early-to-mid gestational stages of brain development. The results showed that brain anatomy and cerebral vasculature can be imaged with this system, and that quantitative analyses of segmented cerebral ventricles can be used to characterize volumetric changes associated with mouse brain development. PMID:24035625

  6. 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

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

    NASA Astrophysics Data System (ADS)

    Hogea, Cosmina; Biros, George; Abraham, Feby; Davatzikos, Christos

    2007-12-01

    We present a framework for black-box and flexible simulation of soft tissue deformation for medical imaging and surgical planning applications. Our main motivation in the present work is to develop robust algorithms that allow batch processing for registration of brains with tumors to statistical atlases of normal brains and construction of brain tumor atlases. We describe a fully Eulerian formulation able to handle large deformations effortlessly, with a level-set-based approach for evolving fronts. We use a regular grid—fictitious domain method approach, in which we approximate coefficient discontinuities, distributed forces and boundary conditions. This approach circumvents the need for unstructured mesh generation, which is often a bottleneck in the modeling and simulation pipeline. Our framework employs penalty approaches to impose boundary conditions and uses a matrix-free implementation coupled with a multigrid-accelerated Krylov solver. The overall scheme results in a scalable method with minimal storage requirements and optimal algorithmic complexity. We illustrate the potential of our framework to simulate realistic brain tumor mass effects at reduced computational cost, for aiding the registration process towards the construction of brain tumor atlases.

  8. Optimization of Free-Breathing Whole-Heart 3D Cardiac MRI at 3Tesla to Identify Coronary Vein Anatomy and to Compare with Multi-Detector Computed Tomography

    PubMed Central

    Ibrahim, Wael G.; El Khouli, Riham H.; Abd-Elmoniem, Khaled Z.; Matta, Jatin Raj; McAreavey, Dorothea; Gharib, Ahmed M

    2014-01-01

    Objective This study optimizes use of 3T MRI to delineate coronary venous anatomy, and compares 3T MRI with MDCT measurements. Methods The study population included 37 consecutive subjects (22 men, 19-71 years). Whole-heart contrast-enhanced MRI images at 3T were acquired using segmented k-space gradient echo with inversion recovery prepared technique. MDCT images were obtained using nonionic iodinated contrast. Results The coronary sinus, and great cardiac, posterior interventricular, and anterior interventricular veins were visualized in 100% of cases by both MRI and MDCT. Detection of the posterior vein of left ventricle and left marginal vein by MRI was 97% and 81% respectively. Bland Altman plots showed agreement in ostial diameter measured by both modalities with correlation coefficients ranging 0.5-0.76. Vein length and distances also agreed closely. Conclusion Free-breathing whole-heart 3D MRI at 3T provides high spatial resolution images and could offer an alternative imaging technique instead of MDCT scans. PMID:24983436

  9. 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

  10. From cartoon to real time MRI: in vivo monitoring of phagocyte migration in mouse brain.

    PubMed

    Mori, Yuki; Chen, Ting; Fujisawa, Tetsuya; Kobashi, Syoji; Ohno, Kohji; Yoshida, Shinichi; Tago, Yoshiyuki; Komai, Yutaka; Hata, Yutaka; Yoshioka, Yoshichika

    2014-01-01

    Recent studies have demonstrated that immune cells play an important role in the pathogenesis of many neurological conditions. Immune cells constantly survey the brain microvasculature for irregularities in levels of factors that signal homeostasis. Immune responses are initiated when necessary, resulting in mobilisation of the microglial cells resident in the central nervous system (CNS) and/or of infiltrating peripheral cells. However, little is known about the kinetics of immune cells in healthy and diseased CNS, because it is difficult to perform long-term visualisation of cell motility in live tissue with minimal invasion. Here, we describe highly sensitive in vivo MRI techniques for sequential monitoring of cell migration in the CNS at the single-cell level. We show that MRI combined with intravenous administration of super-paramagnetic particles of iron oxide (SPIO) can be used to monitor the transmigration of peripheral phagocytes into healthy or LPS-treated mouse brains. We also demonstrate dynamic cell migration in live animal brains with time-lapse MRI videos. Time-lapse MRI was used to visualise and track cells with low motility in a control mouse brain. High-sensitivity MRI cell tracking using SPIO offers new insights into immune cell kinetics in the brain and the mechanisms of CNS homeostasis. PMID:25385430

  11. 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

  12. Construction and tests of demonstrator modules for a 3-D axial PET system for brain or small animal imaging

    NASA Astrophysics Data System (ADS)

    Beltrame, P.; Bolle, E.; Braem, A.; Casella, C.; Chesi, E.; Clinthorne, N.; Cochran, E.; de Leo, R.; Dissertori, G.; Djambazov, G.; Fanti, V.; Honscheid, K.; Huh, S.; Johnson, I.; Joram, C.; Kagan, H.; Lustermann, W.; Meddi, F.; Nappi, E.; Nessi-Tedaldi, F.; Oliver, J. F.; Pauss, P.; Rafecas, M.; Renker, D.; Rudge, A.; Schinzel, D.; Schneider, T.; Seguinot, J.; Smith, S.; Solevi, P.; Stapnes, S.; Weilhammer, P.

    2011-04-01

    The design and construction of a PET camera module with high sensitivity, full 3-D spatial reconstruction and very good energy resolution is presented. The basic principle consists of an axial arrangement of long scintillation crystals around the Field Of View (FOV), providing a measurement of the transverse coordinates of the interacting 511 keV gamma ray. On top of each layer of crystals, an array of Wave-Length Shifter (WLS) strips, which collect the light leaving the crystals sideways, is positioned orthogonal to the crystal direction. The signals in the WLS strips allow a precise measurement of the z (axial) co-ordinate of the 511 keV γ-ray gamma impact. The construction of two modules used for demonstration of the concept is described. First preliminary results on spatial and energy resolution from one full module will be shown.

  13. 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

  14. Brain Activity During a Motor Learning Task: An fMRI and Skin Conductance Study

    PubMed Central

    MacIntosh, Bradley J.; Mraz, Richard; McIlroy, William E.; Graham, Simon J.

    2016-01-01

    Measuring electrodermal activity (EDA) during fMRI is an effective means of studying the influence of task-related arousal, inferred from autonomic nervous system activity, on brain activation patterns. The goals of this study were: (1) to measure reliable EDA from healthy individuals during fMRI involving an effortful unilateral motor task, (2) to explore how EDA recordings can be used to augment fMRI data analysis. In addition to conventional hemodynamic modeling, skin conductance time series data were used as model waveforms to generate activation images from fMRI data. Activations from the EDA model produced significantly different brain regions from those obtained with a standard hemodynamic model, primarily in the insula and cingulate cortices. Onsets of the EDA changes were synchronous with the hemodynamic model, but EDA data showed additional transient features, such as a decrease in amplitude with time, and helped to provide behavioral evidence suggesting task difficulty decreased with movement repetition. Univariate statistics also confirmed that several brain regions showed early versus late session effects. Partial least squares (PLS) multivariate analysis of EDA and fMRI data provided complimentary, additional insight on how the motor network varied over the course of a single fMRI session. Brain regions identified in this manner included the insula, cingulate gyrus, pre- and postcentral gyri, putamen and parietal cortices. These results suggest that recording EDA during motor fMRI experiments provides complementary information that can be used to improve the fMRI analysis, particularly when behavioral or task effects are difficult to model a priori. PMID:17318835

  15. Ultra-high spatial resolution basal and evoked cerebral blood flow MRI of the rat brain.

    PubMed

    Shen, Qiang; Huang, Shiliang; Duong, Timothy Q

    2015-03-01

    Cerebral blood flow (CBF) is tightly coupled to metabolism and neural activity under normal physiological conditions, and is often perturbed in disease states. The goals of this study were to implement a high-resolution (up to 50×38μm(2)) CBF MRI protocol of the rat brain, create a digital CBF atlas, report CBF values for 30+ brain structures based on the atlas, and explore applications of high-resolution CBF fMRI of forepaw stimulation. Excellent blood-flow contrasts were observed among different cortical and subcortical structures. CBF MRI showed column-like alternating bright and dark bands in the neocortices, reflecting the layout of descending arterioles and ascending venules, respectively. CBF MRI also showed lamina-like alternating bright and dark layers across the cortical thicknesses, consistent with the underlying vascular density. CBF profiles across the cortical thickness showed two peaks in layers IV and VI and a shallow trough in layer V. Whole-brain CBF was about 0.89ml/g/min, with the highest CBF values found amongst the neocortical structures (1ml/g/min, range: 0.89-1.16ml/g/min) and the lowest CBF values in the corpus callosum (0.32ml/g/min), yielding a gray:white matter CBF ratio of 3.1. CBF fMRI responses peaked across layers IV-V, whereas the BOLD fMRI responses showed a peak in the superficial layers II-III. High-resolution basal CBF MRI, evoked CBF fMRI, and CBF brain atlas can be used to study neurological disorders (such as ischemic stroke). PMID:25557404

  16. 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

  17. Brain MRI in neuropsychiatric lupus: associations with the 1999 ACR case definitions.

    PubMed

    Jeong, Hae Woong; Her, Minyoung; Bae, Jong Seok; Kim, Seong-Kyu; Lee, Sung Won; Kim, Ho Kyun; Kim, Dongyook; Park, Nayoung; Chung, Won Tae; Lee, Sang Yeob; Choe, Jung-Yoon; Kim, In Joo

    2015-05-01

    The purpose of this study was to identify the characteristic magnetic resonance imaging (MRI) findings in neuropsychiatric systemic lupus erythematosus (NPSLE) and to investigate the association between MRI findings and neuropsychiatric manifestations in SLE. Brain MRIs with a diagnosis of SLE from 2002 to 2013 from three tertiary university hospitals were screened. All clinical manifestations evaluated by brain MRI were retrospectively reviewed. If the clinical manifestations were compatible with the 1999 NPSLE American College of Rheumatology (ACR) nomenclature and case definitions, the brain MRIs were assessed for the presence of white matter hyperintensities, gray matter hyperintensities, parenchymal defects, atrophy, enhancement, and abnormalities in diffusion-weighted images (DWI). The number, size, and location of each lesion were evaluated. The neuropsychiatric manifestation of each brain MRI was classified according to the 1999 ACR NPSLE case definitions. The associations between MRI findings and NPSLE manifestations were examined. In total, 219 brain MRIs with a diagnosis of SLE were screened, and 133 brain MRIs met the inclusion criteria for NPSLE. The most common MRI abnormality was white matter hyperintensities, which were observed in 76 MRIs (57.1 %). Gray matter hyperintensities were observed in 41 MRIs (30.8 %). Parenchymal defects were found in 31 MRIs (23.3 %), and atrophy was detected in 20 MRIs (15.0 %). Patients who had seizures were more associated with gray matter hyperintensities than patients with other neuropsychiatric manifestations. Patients with cerebrovascular disease were more associated with gray matter hyperintensity, parenchymal defects, and abnormal DWI than patients with other neuropsychiatric manifestations. In addition to white matter hyperintensities, which were previously known as SLE findings, we also noted the presence of gray matter hyperintensities, parenchymal defects, and abnormal DWI in a substantial portion of SLE

  18. 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.

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

    PubMed Central

    Huang, W; Plyka, I; Li, H; Eisenstein, E M; Volkow, N D; Springer, C S

    1996-01-01

    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. Images Fig. 1 Fig. 4 PMID:8650215

  20. 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.

  1. 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

  2. Role of mitochondrial calcium uptake homeostasis in resting state fMRI brain networks.

    PubMed

    Kannurpatti, Sridhar S; Sanganahalli, Basavaraju G; Herman, Peter; Hyder, Fahmeed

    2015-11-01

    Mitochondrial Ca(2+) uptake influences both brain energy metabolism and neural signaling. Given that brain mitochondrial organelles are distributed in relation to vascular density, which varies considerably across brain regions, we hypothesized different physiological impacts of mitochondrial Ca(2+) uptake across brain regions. We tested the hypothesis by monitoring brain "intrinsic activity" derived from the resting state functional MRI (fMRI) blood oxygen level dependent (BOLD) fluctuations in different functional networks spanning the somatosensory cortex, caudate putamen, hippocampus and thalamus, in normal and perturbed mitochondrial Ca(2+) uptake states. In anesthetized rats at 11.7 T, mitochondrial Ca(2+) uptake was inhibited or enhanced respectively by treatments with Ru360 or kaempferol. Surprisingly, mitochondrial Ca(2+) uptake inhibition by Ru360 and enhancement by kaempferol led to similar dose-dependent decreases in brain-wide intrinsic activities in both the frequency domain (spectral amplitude) and temporal domain (resting state functional connectivity; RSFC). The fact that there were similar dose-dependent decreases in the frequency and temporal domains of the resting state fMRI-BOLD fluctuations during mitochondrial Ca(2+) uptake inhibition or enhancement indicated that mitochondrial Ca(2+) uptake and its homeostasis may strongly influence the brain's functional organization at rest. Interestingly, the resting state fMRI-derived intrinsic activities in the caudate putamen and thalamic regions saturated much faster with increasing dosage of either drug treatment than the drug-induced trends observed in cortical and hippocampal regions. Regional differences in how the spectral amplitude and RSFC changed with treatment indicate distinct mitochondrion-mediated spontaneous neuronal activity coupling within the various RSFC networks determined by resting state fMRI. PMID:26439799

  3. Brain extraction from cerebral MRI volume using a hybrid level set based active contour neighborhood model

    PubMed Central

    2013-01-01

    Background The extraction of brain tissue from cerebral MRI volume is an important pre-procedure for neuroimage analyses. The authors have developed an accurate and robust brain extraction method using a hybrid level set based active contour neighborhood model. Methods The method uses a nonlinear speed function in the hybrid level set model to eliminate boundary leakage. When using the new hybrid level set model an active contour neighborhood model is applied iteratively in the neighborhood of brain boundary. A slice by slice contour initial method is proposed to obtain the neighborhood of the brain boundary. The method was applied to the internet brain MRI data provided by the Internet Brain Segmentation Repository (IBSR). Results In testing, a mean Dice similarity coefficient of 0.95±0.02 and a mean Hausdorff distance of 12.4±4.5 were obtained when performing our method across the IBSR data set (18 × 1.5 mm scans). The results obtained using our method were very similar to those produced using manual segmentation and achieved the smallest mean Hausdorff distance on the IBSR data. Conclusions An automatic method of brain extraction from cerebral MRI volume was achieved and produced competitively accurate results. PMID:23587217

  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. 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

  6. An automatic method of brain tumor segmentation from MRI volume based on the symmetry of brain and level set method

    NASA Astrophysics Data System (ADS)

    Li, Xiaobing; Qiu, Tianshuang; Lebonvallet, Stephane; Ruan, Su

    2010-02-01

    This paper presents a brain tumor segmentation method which automatically segments tumors from human brain MRI image volume. The presented model is based on the symmetry of human brain and level set method. Firstly, the midsagittal plane of an MRI volume is searched, the slices with potential tumor of the volume are checked out according to their symmetries, and an initial boundary of the tumor in the slice, in which the tumor is in the largest size, is determined meanwhile by watershed and morphological algorithms; Secondly, the level set method is applied to the initial boundary to drive the curve evolving and stopping to the appropriate tumor boundary; Lastly, the tumor boundary is projected one by one to its adjacent slices as initial boundaries through the volume for the whole tumor. The experiment results are compared with hand tracking of the expert and show relatively good accordance between both.

  7. 3D Breath-Held Cardiac Function With Projection Reconstruction in Steady State Free Precession Validated Using 2D Cine MRI

    PubMed Central

    Peters, Dana C.; Ennis, Daniel B.; Rohatgi, Pratik; Syed, Mushabbar A.; McVeigh, Elliot R.; Arai, Andrew E.

    2007-01-01

    Purpose: To develop and validate a three-dimensional (3D) single breath-hold, projection reconstruction (PR), balanced steady state free precession (SSFP) method for cardiac function evaluation against a two-dimensional (2D) multislice Fourier (Cartesian) transform (FT) SSFP method. Materials and Methods: The 3D PR SSFP sequence used projections in the x-y plane and partitions in z, providing 70–80 msec temporal resolution and 1.7 × 1.7 × 8–10 mm in a 24-heartbeat breath hold. A total of 10 volunteers were imaged with both methods, and the measurements of global cardiac function were compared. Results: Mean signal-to-noise ratios (SNRs) for the blood and myocardium were 114 and 42 (2D) and 59 and 21 (3D). Bland-Altman analysis comparing the 2D and 3D ejection fraction (EF), left ventricular end diastolic volume (LVEDV) and end systolic volume (LVESV), and end diastolic myocardial mass (LVEDM) provided values of bias ±2 SD of 0.6% ± 7.7 % for LVEF, 5.9 mL ± 20 mL for LVEDV, −2.8 mL ± 12 mL for LVESV, and −0.61 g ± 13 g for LVEDM. 3D interobserver variability was greater than 2D for LVEDM and LVESV. Conclusion: In a single breath hold, the 3D PR method provides comparable information to the standard 2D FT method, which employs 10–12 breath holds. PMID:15332248

  8. 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

  9. 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

  10. Bayesian brain source imaging based on combined MEG/EEG and fMRI using MCMC

    PubMed Central

    Jun, Sung C.; George, John S.; Kim, Woohan; Paré-Blagoev, Juliana; Plis, Sergey; Ranken, Doug M.; Schmidt, David M.

    2010-01-01

    A number of brain imaging techniques have been developed in order to investigate brain function and to develop diagnostic tools for various brain disorders. Each modality has strengths as well as weaknesses compared to the others. Recent work has explored how multiple modalities can be integrated effectively so that they complement one another while maintaining their individual strengths. Bayesian inference employing Markov Chain Monte Carlo (MCMC) techniques provides a straightforward way to combine disparate forms of information while dealing with the uncertainty in each. In this paper we introduce methods of Bayesian inference as a way to integrate different forms of brain imaging data in a probabilistic framework. We formulate Bayesian integration of magnetoencephalography (MEG) data and functional magnetic resonance imaging (fMRI) data by incorporating fMRI data into a spatial prior. The usefulness and feasibility of the method are verified through testing with both simulated and empirical data. PMID:18314351

  11. Resting-State Blood Oxygen Level-Dependent Functional MRI: A Paradigm Shift in Preoperative Brain Mapping.

    PubMed

    Leuthardt, Eric C; Allen, Monica; Kamran, Mudassar; Hawasli, Ammar H; Snyder, Abraham Z; Hacker, Carl D; Mitchell, Timothy J; Shimony, Joshua S

    2015-01-01

    Currently, functional magnetic resonance imaging (fMRI) facilitates a preoperative awareness of an association of an eloquent region with a tumor. This information gives the neurosurgeon helpful information that can aid in creating a surgical strategy. Typically, task-based fMRI has been employed to preoperatively localize speech and motor function. Task-based fMRI depends on the patient's ability to comply with the task paradigm, which often is impaired in the setting of a brain tumor. This problem is overcome by using resting-state fMRI (rs-fMRI) to localize function. rs-fMRI measures spontaneous fluctuations in the blood oxygen level-dependent (BOLD) signal, representing the brain's functional organization. In a neurosurgical context, it allows noninvasive simultaneous assessment of multiple large-scale distributed networks. Compared with task-related fMRI, rs-fMRI provides more comprehensive information on the functional architecture of the brain and is applicable in settings where task-related fMRI may provide inadequate information or could not be performed. Taken together, rs-fMRI substantially expands the preoperative mapping capability in efficiency, effectiveness, and scope. In this article, a brief introduction into rs-fMRI processing methods is followed by a detailed discussion on the role rs-fMRI plays in presurgical planning. PMID:26784290

  12. 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.

  13. 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.

  14. 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. PMID:26216156

  15. Intensity based methods for brain MRI longitudinal registration. A study on multiple sclerosis patients.

    PubMed

    Diez, Yago; Oliver, Arnau; Cabezas, Mariano; Valverde, Sergi; Martí, Robert; Vilanova, Joan Carles; Ramió-Torrentà, Lluís; Rovira, Alex; Lladó, Xavier

    2014-07-01

    Registration is a key step in many automatic brain Magnetic Resonance Imaging (MRI) applications. In this work we focus on longitudinal registration of brain MRI for Multiple Sclerosis (MS) patients. First of all, we analyze the effect that MS lesions have on registration by synthetically eliminating some of the lesions. Our results show how a widely used method for longitudinal registration such as rigid registration is practically unconcerned by the presence of MS lesions while several non-rigid registration methods produce outputs that are significantly different. We then focus on assessing which is the best registration method for longitudinal MRI images of MS patients. In order to analyze the results obtained for all studied criteria, we use both descriptive statistics and statistical inference: one way ANOVA, pairwise t-tests and permutation tests. PMID:24338728

  16. 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.

  17. MRI-Related Heating near Deep Brain Stimulation Electrodes: More Data Are Needed

    PubMed Central

    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. PMID:21494064

  18. 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

  19. Oxytocin, brain physiology, and functional connectivity: a review of intranasal oxytocin fMRI studies.

    PubMed

    Bethlehem, Richard A I; van Honk, Jack; Auyeung, Bonnie; Baron-Cohen, Simon

    2013-07-01

    In recent years the neuropeptide oxytocin (OT) has become one of the most studied peptides of the human neuroendocrine system. Research has shown widespread behavioural effects and numerous potential therapeutic benefits. However, little is known about how OT triggers these effects in the brain. Here, we discuss some of the physiological properties of OT in the human brain including the long half-life of neuropeptides, the diffuse projections of OT throughout the brain and interactions with other systems such as the dopaminergic system. These properties indicate that OT acts without clear spatial and temporal specificity. Therefore, it is likely to have widespread effects on the brain's intrinsic functioning. Additionally, we review studies that have used functional magnetic resonance imaging (fMRI) concurrently with OT administration. These studies reveal a specific set of 'social' brain regions that are likely to be the strongest targets for OT's potential to influence human behaviour. On the basis of the fMRI literature and the physiological properties of the neuropeptide, we argue that OT has the potential to not only modulate activity in a set of specific brain regions, but also the functional connectivity between these regions. In light of the increasing knowledge of the behavioural effects of OT in humans, studies of the effects of OT administration on brain function can contribute to our understanding of the neural networks in the social brain. PMID:23159011

  20. Longitudinal fMRI studies: Exploring brain plasticity and repair in MS.

    PubMed

    Enzinger, Christian; Pinter, Daniela; Rocca, Maria A; De Luca, John; Sastre-Garriga, Jaume; Audoin, Bertrand; Filippi, Massimo

    2016-03-01

    Functional magnetic resonance imaging (fMRI) has greatly advanced our understanding of cerebral functional changes occurring in patients with multiple sclerosis (MS). However, most of our knowledge regarding brain plasticity and repair in MS as evidenced by fMRI has been extrapolated from cross-sectional studies across different phenotypes of the disease. This topical review provides an overview of this research, but also highlights limitations of existing fMRI studies with cross-sectional design. We then review the few existing longitudinal fMRI studies and discuss the feasibility and constraints of serial fMRI in individuals with MS. We further emphasize the potential to track fMRI changes in evolving disease and the insights this may give in terms of mechanisms of adaptation and repair, focusing on serial fMRI to monitor response to disease-modifying therapies or rehabilitation interventions. Finally, we offer recommendations for designing future research studies to overcome previous methodological shortcomings. PMID:26683590

  1. 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

  2. [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. PMID:26876086

  3. 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.

  4. 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

  5. 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. PMID:27043850

  6. Constructing and assessing brain templates from Chinese pediatric MRI data using SPM

    NASA Astrophysics Data System (ADS)

    Yin, Qingjie; Ye, Qing; Yao, Li; Chen, Kewei; Jin, Zhen; Liu, Gang; Wu, Xingchun; Wang, Tingting

    2005-04-01

    Spatial normalization is a very important step in the processing of magnetic resonance imaging (MRI) data. So the quality of brain templates is crucial for the accuracy of MRI analysis. In this paper, using the classical protocol and the optimized protocol plus nonlinear deformation, we constructed the T1 whole brain templates and apriori brain tissue data from 69 Chinese pediatric MRI data (age 7-16 years). Then we proposed a new assessment method to evaluate our templates. 10 pediatric subjects were chosen to do the assessment as the following steps. First, the cerebellum region, the region of interest (ROI), was located on both the pediatric volume and the template volume by an experienced neuroanatomist. Second, the pediatric whole brain was mapped to the template with affine and nonlinear deformation. Third, the parameter, derived from the second step, was used to only normalize the ROI of the child to the ROI of the template. Last, the overlapping ratio, which described the overlapping rate between the ROI of the template and the normalized ROI of the child, was calculated. The mean of overlapping ratio normalized to the classical template was 0.9687, and the mean normalized to the optimized template was 0.9713. The results show that the two Chinese pediatric brain templates are comparable and their accuracy is adequate to our studies.

  7. Reliability of brain volumes from multicenter MRI acquisition: a calibration study.

    PubMed

    Schnack, Hugo G; van Haren, Neeltje E M; Hulshoff Pol, Hilleke E; Picchioni, Marco; Weisbrod, Matthias; Sauer, Heinrich; Cannon, Tyrone; Huttunen, Matti; Murray, Robin; Kahn, René S

    2004-08-01

    Multicenter studies can provide additional information over single center studies because of their increased statistical power. Because similar acquisition protocols are being used internationally for structural magnetic resonance imaging (MRI) studies of the human brain, volumetric MRI data studies seem suitable for this purpose. Possible systematic differences between sites should be avoided, however, particularly when subtle differences in tissue volume are being searched for, such as in neuropsychiatric diseases. In this calibration study, the brains of six healthy volunteers were (re)scanned with MR scanners from four different manufacturers at five different sites, using the local acquisition protocols. The images were segmented at a central reference site. The intraclass correlation coefficient (ICC) was determined for the whole brain, gray and white matter, cerebellum, and lateral and third ventricle volumes. When required, the processing algorithms were calibrated for each site. Calibration of the histogram analysis was needed for segmentation of total brain volume at one site and for gray and white matter volume at all sites. No (additional) calibration was needed for cerebellum and ventricle volumes. The ICCs were > or = 0.96 for total brain, > or = 0.92 for cerebellum, > or = 0.96 for lateral ventricle, > or = 0.21 for third ventricle, > or = 0.84 for gray matter, and > or = 0.78 for white matter volume. Calibration of segmentation procedures allows morphologic MRI data acquired at different research sites to be combined reliably in multicenter studies. PMID:15202109

  8. Brain correlates of discourse processing: An fMRI investigation of irony and conventional metaphor comprehension

    PubMed Central

    Eviatar, Zohar; Just, Marcel Adam

    2006-01-01

    Higher levels of discourse processing evoke patterns of cognition and brain activation that extend beyond the literal comprehension of sentences. We used fMRI to examine brain activation patterns while 16 healthy participants read brief three-sentence stories that concluded with either a literal, metaphoric, or ironic sentence. The fMRI images acquired during the reading of the critical sentence revealed a selective response of the brain to the two types of nonliteral utterances. Metaphoric utterances resulted in significantly higher levels of activation in the left inferior frontal gyrus and in bilateral inferior temporal cortex than the literal and ironic utterances. Ironic statements resulted in significantly higher activation levels than literal statements in the right superior and middle temporal gyri, with metaphoric statements resulting in intermediate levels in these regions. The findings show differential hemispheric sensitivity to these aspects of figurative language, and are relevant to models of the functional cortical architecture of language processing in connected discourse. PMID:16806316

  9. Topology of whole-brain functional MRI networks: Improving the truncated scale-free model

    NASA Astrophysics Data System (ADS)

    Ruiz Vargas, E.; Mitchell, D. G. V.; Greening, S. G.; Wahl, L. M.

    2014-07-01

    Networks of connections within the human brain have been the subject of intense recent research, yet their topology is still only partially understood. We analyze weighted networks calculated from functional magnetic resonance imaging (fMRI) data acquired during task performance. Expanding previous work in the area, our analysis retains all of the connections between all of the voxels in the full brain fMRI data, computing correlations between approximately 200,000 voxels per subject for 10 subjects. We evaluate the extent to which this rich dataset can be described by existing models of scale-free or exponentially truncated scale-free topology, comparing results across a large number of more complex topological models as well. Our results suggest that the novel “log quadratic” model presented in this paper offers a significantly better fit to networks of functional connections at the voxel level in the human brain.

  10. A survey of current trends in diffusion MRI for structural brain connectivity

    NASA Astrophysics Data System (ADS)

    Ghosh, Aurobrata; Deriche, Rachid

    2016-02-01

    In this paper, we review the state of the art in diffusion magnetic resonance imaging (dMRI) and we present current trends in modelling the brain's tissue microstructure and the human connectome. dMRI is today the only tool that can probe the brain's axonal architecture in vivo and non-invasively, and has grown in leaps and bounds in the last two decades since its conception. A plethora of models with increasing complexity and better accuracy have been proposed to characterise the integrity of the cerebral tissue, to understand its microstructure and to infer its connectivity. Here, we discuss a wide range of the most popular, important and well-established local microstructure models and biomarkers that have been proposed from these models. Finally, we briefly present the state of the art in tractography techniques that allow us to understand the architecture of the brain's connectivity.

  11. 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

  12. Prediction of brain tumor progression using multiple histogram matched MRI scans

    NASA Astrophysics Data System (ADS)

    Banerjee, Debrup; Tran, Loc; Li, Jiang; Shen, Yuzhong; McKenzie, Frederic; Wang, Jihong

    2011-03-01

    In a recent study [1], we investigated the feasibility of predicting brain tumor progression based on multiple MRI series and we tested our methods on seven patients' MRI images scanned at three consecutive visits A, B and C. Experimental results showed that it is feasible to predict tumor progression from visit A to visit C using a model trained by the information from visit A to visit B. However, the trained model failed when we tried to predict tumor progression from visit B to visit C, though it is clinically more important. Upon a closer look at the MRI scans revealed that histograms of MRI scans such as T1, T2, FLAIR etc taken at different times have slight shifts or different shapes. This is because those MRI scans are qualitative instead of quantitative so MRI scans taken at different times or by different scanners might have slightly different scales or have different homogeneities in the scanning region. In this paper, we proposed a method to overcome this difficulty. The overall goal of this study is to assess brain tumor progression by exploring seven patients' complete MRI records scanned during their visits in the past two years. There are ten MRI series in each visit, including FLAIR, T1-weighted, post-contrast T1-weighted, T2-weighted and five DTI derived MRI volumes: ADC, FA, Max, Min and Middle Eigen Values. After registering all series to the corresponding DTI scan at the first visit, we applied a histogram matching algorithm to non-DTI MRI scans to match their histograms to those of the corresponding MRI scans at the first visit. DTI derived series are quantitative and do not require the histogram matching procedure. A machine learning algorithm was then trained using the data containing information from visit A to visit B, and the trained model was used to predict tumor progression from visit B to visit C. An average of 72% pixel-wise accuracy was achieved for tumor progression prediction from visit B to visit C.

  13. Spatial embedding of fMRI for investigating local coupling in human brain

    NASA Astrophysics Data System (ADS)

    Deshpande, Gopikrishna; LaConte, Stephen M.; Peltier, Scott; Hu, Xiaoping

    2005-04-01

    In this paper, we have investigated local spatial couplings in the human brain by applying nonlinear dynamical techniques on fMRI data. We have recorded BOLD-contrast echo-planar fMRI data along with high-resolution T1-weighted anatomical images from the resting brain of healthy human subjects and performed physiological correction on the functional data. The corrected data from resting subjects is spatially embedded into its phase space and the largest Lyapunov exponent of the resulting attractor is calculated and whole slice maps are obtained. In addition, we segment the high-resolution anatomical image and obtain a down sampled mask corresponding to gray and white matter, which is used to obtain mean indices of the exponents for both the tissues separately. The results show the existence of local couplings, its tissue specificity (more local coupling in gray matter than white matter) and dependence on the size of the neighborhood (larger the neighborhood, lesser the coupling). We believe that these techniques capture the information of a nonlinear and evolving system like the brain that may not be evident from static linear methods. The results show that there is evidence of spatio-temporal chaos in the brain, which is a significant finding hitherto not reported in literature to the best of our knowledge. We try to interpret our results from healthy resting subjects based on our knowledge of the native low frequency fluctuations in the resting brain and obtain a better understanding of the local spatial behavior of fMRI. This exploratory study has demonstrated the utility of nonlinear dynamical techniques like spatial embedding in analyzing fMRI data to gain meaningful insights into the working of human brain.

  14. An empirical comparison of different LDA methods in fMRI-based brain states decoding.

    PubMed

    Xia, Maogeng; Song, Sutao; Yao, Li; Long, Zhiying

    2015-01-01

    Decoding brain states from response patterns with multivariate pattern recognition techniques is a popular method for detecting multivoxel patterns of brain activation. These patterns are informative with respect to a subject's perceptual or cognitive states. Linear discriminant analysis (LDA) cannot be directly applied to fMRI data analysis because of the "few samples and large features" nature of functional magnetic resonance imaging (fMRI) data. Although several improved LDA methods have been used in fMRI-based decoding, little is known regarding the relative performance of different LDA classifiers on fMRI data. In this study, we compared five LDA classifiers using both simulated data with varied noise levels and real fMRI data. The compared LDA classifiers include LDA combined with PCA (LDA-PCA), LDA with three types of regularizations (identity matrix, diagonal matrix and scaled identity matrix) and LDA with optimal-shrinkage covariance estimator using Ledoit and Wolf lemma (LDA-LW). The results indicated that LDA-LW was the most robust to noises. Moreover, LDA-LW and LDA with scaled identity matrix showed better stability and classification accuracy than the other methods. LDA-LW demonstrated the best overall performance. PMID:26405876

  15. Rotarod training in mice is associated with changes in brain structure observable with multimodal MRI.

    PubMed

    Scholz, Jan; Niibori, Yosuke; Frankland, Paul W; Lerch, Jason P

    2015-02-15

    The brain has been shown to remain structurally plastic even throughout adulthood. However, little is known how motor-skill training affects different MRI modalities in the adult mouse brain. The aim of this study is to investigate whether rotarod training, a simple motor training task taken from the standard test battery, is associated with structural plasticity observable with different MRI modalities in adult C57BL/6 mice. The rotarod is a standard test that taxes motor coordination and balance. We use T2-weighted MRI followed by deformation-based morphometry to assess local volume and fractional anisotropy (FA) derived from diffusion MRI to assess microstructure ex-vivo. Using deformation-based morphometry we found that the hippocampus, frontal cortex and amygdala are larger in rotarod-trained mice compared to untrained controls. Surprisingly, the cerebellum and white matter in the corpus callosum underlying the primary motor cortex are smaller after training. We also found that the volume of the motor cortex is positively correlated with better rotarod performance. Diffusion imaging indicates group differences and behavioral correlations with FA, a measure of microstructure. Trained mice have higher FA in the hippocampus. Better rotarod performance is associated with higher FA in the hippocampus and lower FA in the primary visual cortex. This is the first study to reveal the substantial structural reorganization of the adult mouse brain following only a relatively brief period of motor-skill training by using complementary measures of microstructure and volume. PMID:25497397

  16. Nonlinear Complexity Analysis of Brain fMRI Signals in Schizophrenia

    PubMed Central

    Sokunbi, Moses O.; Gradin, Victoria B.; Waiter, Gordon D.; Cameron, George G.; Ahearn, Trevor S.; Murray, Alison D.; Steele, Douglas J.; Staff, Roger T.

    2014-01-01

    We investigated the differences in brain fMRI signal complexity in patients with schizophrenia while performing the Cyberball social exclusion task, using measures of Sample entropy and Hurst exponent (H). 13 patients meeting diagnostic and Statistical Manual of Mental Disorders, 4th Edition (DSM IV) criteria for schizophrenia and 16 healthy controls underwent fMRI scanning at 1.5 T. The fMRI data of both groups of participants were pre-processed, the entropy characterized and the Hurst exponent extracted. Whole brain entropy and H maps of the groups were generated and analysed. The results after adjusting for age and sex differences together show that patients with schizophrenia exhibited higher complexity than healthy controls, at mean whole brain and regional levels. Also, both Sample entropy and Hurst exponent agree that patients with schizophrenia have more complex fMRI signals than healthy controls. These results suggest that schizophrenia is associated with more complex signal patterns when compared to healthy controls, supporting the increase in complexity hypothesis, where system complexity increases with age or disease, and also consistent with the notion that schizophrenia is characterised by a dysregulation of the nonlinear dynamics of underlying neuronal systems. PMID:24824731

  17. 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 i