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Sample records for 3d mri adaptive

  1. 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.

  2. 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

  3. 3D Structured Grid Adaptation

    NASA Technical Reports Server (NTRS)

    Banks, D. W.; Hafez, M. M.

    1996-01-01

    Grid adaptation for structured meshes is the art of using information from an existing, but poorly resolved, solution to automatically redistribute the grid points in such a way as to improve the resolution in regions of high error, and thus the quality of the solution. This involves: (1) generate a grid vis some standard algorithm, (2) calculate a solution on this grid, (3) adapt the grid to this solution, (4) recalculate the solution on this adapted grid, and (5) repeat steps 3 and 4 to satisfaction. Steps 3 and 4 can be repeated until some 'optimal' grid is converged to but typically this is not worth the effort and just two or three repeat calculations are necessary. They also may be repeated every 5-10 time steps for unsteady calculations.

  4. 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

  5. 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

  6. 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

  7. 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/.

  8. 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

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

    PubMed Central

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

    2014-01-01

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

  10. Adaptive fuzzy system for 3-D vision

    NASA Technical Reports Server (NTRS)

    Mitra, Sunanda

    1993-01-01

    An adaptive fuzzy system using the concept of the Adaptive Resonance Theory (ART) type neural network architecture and incorporating fuzzy c-means (FCM) system equations for reclassification of cluster centers was developed. The Adaptive Fuzzy Leader Clustering (AFLC) architecture is a hybrid neural-fuzzy system which learns on-line in a stable and efficient manner. The system uses a control structure similar to that found in the Adaptive Resonance Theory (ART-1) network to identify the cluster centers initially. The initial classification of an input takes place in a two stage process; a simple competitive stage and a distance metric comparison stage. The cluster prototypes are then incrementally updated by relocating the centroid positions from Fuzzy c-Means (FCM) system equations for the centroids and the membership values. The operational characteristics of AFLC and the critical parameters involved in its operation are discussed. The performance of the AFLC algorithm is presented through application of the algorithm to the Anderson Iris data, and laser-luminescent fingerprint image data. The AFLC algorithm successfully classifies features extracted from real data, discrete or continuous, indicating the potential strength of this new clustering algorithm in analyzing complex data sets. The hybrid neuro-fuzzy AFLC algorithm will enhance analysis of a number of difficult recognition and control problems involved with Tethered Satellite Systems and on-orbit space shuttle attitude controller.

  11. 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

  12. 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.

  13. Virtual view adaptation for 3D multiview video streaming

    NASA Astrophysics Data System (ADS)

    Petrovic, Goran; Do, Luat; Zinger, Sveta; de With, Peter H. N.

    2010-02-01

    Virtual views in 3D-TV and multi-view video systems are reconstructed images of the scene generated synthetically from the original views. In this paper, we analyze the performance of streaming virtual views over IP-networks with a limited and time-varying available bandwidth. We show that the average video quality perceived by the user can be improved with an adaptive streaming strategy aiming at maximizing the average video quality. Our adaptive 3D multi-view streaming can provide a quality improvement of 2 dB on the average - over non-adaptive streaming. We demonstrate that an optimized virtual view adaptation algorithm needs to be view-dependent and achieve an improvement of up to 0.7 dB. We analyze our adaptation strategies under dynamic available bandwidth in the network.

  14. Adapting 3D Equilibrium Reconstruction to Reconstruct Weakly 3D H-mode Tokamaks

    NASA Astrophysics Data System (ADS)

    Cianciosa, M. R.; Hirshman, S. P.; Seal, S. K.; Unterberg, E. A.; Wilcox, R. S.; Wingen, A.; Hanson, J. D.

    2015-11-01

    The application of resonant magnetic perturbations for edge localized mode (ELM) mitigation breaks the toroidal symmetry of tokamaks. In these scenarios, the axisymmetric assumptions of the Grad-Shafranov equation no longer apply. By extension, equilibrium reconstruction tools, built around these axisymmetric assumptions, are insufficient to fully reconstruct a 3D perturbed equilibrium. 3D reconstruction tools typically work on systems where the 3D components of signals are a significant component of the input signals. In nominally axisymmetric systems, applied field perturbations can be on the order of 1% of the main field or less. To reconstruct these equilibria, the 3D component of signals must be isolated from the axisymmetric portions to provide the necessary information for reconstruction. This presentation will report on the adaptation to V3FIT for application on DIII-D H-mode discharges with applied resonant magnetic perturbations (RMPs). Newly implemented motional stark effect signals and modeling of electric field effects will also be discussed. Work supported under U.S. DOE Cooperative Agreement DE-AC05-00OR22725.

  15. fMRI adaptation revisited.

    PubMed

    Larsson, Jonas; Solomon, Samuel G; Kohn, Adam

    2016-07-01

    Adaptation has been widely used in functional magnetic imaging (fMRI) studies to infer neuronal response properties in human cortex. fMRI adaptation has been criticized because of the complex relationship between fMRI adaptation effects and the multiple neuronal effects that could underlie them. Many of the longstanding concerns about fMRI adaptation have received empirical support from neurophysiological studies over the last decade. We review these studies here, and also consider neuroimaging studies that have investigated how fMRI adaptation effects are influenced by high-level perceptual processes. The results of these studies further emphasize the need to interpret fMRI adaptation results with caution, but they also provide helpful guidance for more accurate interpretation and better experimental design. In addition, we argue that rather than being used as a proxy for measurements of neuronal stimulus selectivity, fMRI adaptation may be most useful for studying population-level adaptation effects across cortical processing hierarchies. PMID:26703375

  16. 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…

  17. 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

  18. 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.

  19. 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

  20. Parallel 3D Mortar Element Method for Adaptive Nonconforming Meshes

    NASA Technical Reports Server (NTRS)

    Feng, Huiyu; Mavriplis, Catherine; VanderWijngaart, Rob; Biswas, Rupak

    2004-01-01

    High order methods are frequently used in computational simulation for their high accuracy. An efficient way to avoid unnecessary computation in smooth regions of the solution is to use adaptive meshes which employ fine grids only in areas where they are needed. Nonconforming spectral elements allow the grid to be flexibly adjusted to satisfy the computational accuracy requirements. The method is suitable for computational simulations of unsteady problems with very disparate length scales or unsteady moving features, such as heat transfer, fluid dynamics or flame combustion. In this work, we select the Mark Element Method (MEM) to handle the non-conforming interfaces between elements. A new technique is introduced to efficiently implement MEM in 3-D nonconforming meshes. By introducing an "intermediate mortar", the proposed method decomposes the projection between 3-D elements and mortars into two steps. In each step, projection matrices derived in 2-D are used. The two-step method avoids explicitly forming/deriving large projection matrices for 3-D meshes, and also helps to simplify the implementation. This new technique can be used for both h- and p-type adaptation. This method is applied to an unsteady 3-D moving heat source problem. With our new MEM implementation, mesh adaptation is able to efficiently refine the grid near the heat source and coarsen the grid once the heat source passes. The savings in computational work resulting from the dynamic mesh adaptation is demonstrated by the reduction of the the number of elements used and CPU time spent. MEM and mesh adaptation, respectively, bring irregularity and dynamics to the computer memory access pattern. Hence, they provide a good way to gauge the performance of computer systems when running scientific applications whose memory access patterns are irregular and unpredictable. We select a 3-D moving heat source problem as the Unstructured Adaptive (UA) grid benchmark, a new component of the NAS Parallel

  1. 3DSEM++: Adaptive and intelligent 3D SEM surface reconstruction.

    PubMed

    Tafti, Ahmad P; Holz, Jessica D; Baghaie, Ahmadreza; Owen, Heather A; He, Max M; Yu, Zeyun

    2016-08-01

    Structural analysis of microscopic objects is a longstanding topic in several scientific disciplines, such as biological, mechanical, and materials sciences. The scanning electron microscope (SEM), as a promising imaging equipment has been around for decades to determine the surface properties (e.g., compositions or geometries) of specimens by achieving increased magnification, contrast, and resolution greater than one nanometer. Whereas SEM micrographs still remain two-dimensional (2D), many research and educational questions truly require knowledge and facts about their three-dimensional (3D) structures. 3D surface reconstruction from SEM images leads to remarkable understanding of microscopic surfaces, allowing informative and qualitative visualization of the samples being investigated. In this contribution, we integrate several computational technologies including machine learning, contrario methodology, and epipolar geometry to design and develop a novel and efficient method called 3DSEM++ for multi-view 3D SEM surface reconstruction in an adaptive and intelligent fashion. The experiments which have been performed on real and synthetic data assert the approach is able to reach a significant precision to both SEM extrinsic calibration and its 3D surface modeling. PMID:27200484

  2. 3D Game Content Distributed Adaptation in Heterogeneous Environments

    NASA Astrophysics Data System (ADS)

    Morán, Francisco; Preda, Marius; Lafruit, Gauthier; Villegas, Paulo; Berretty, Robert-Paul

    2007-12-01

    Most current multiplayer 3D games can only be played on a single dedicated platform (a particular computer, console, or cell phone), requiring specifically designed content and communication over a predefined network. Below we show how, by using signal processing techniques such as multiresolution representation and scalable coding for all the components of a 3D graphics object (geometry, texture, and animation), we enable online dynamic content adaptation, and thus delivery of the same content over heterogeneous networks to terminals with very different profiles, and its rendering on them. We present quantitative results demonstrating how the best displayed quality versus computational complexity versus bandwidth tradeoffs have been achieved, given the distributed resources available over the end-to-end content delivery chain. Additionally, we use state-of-the-art, standardised content representation and compression formats (MPEG-4 AFX, JPEG 2000, XML), enabling deployment over existing infrastructure, while keeping hooks to well-established practices in the game industry.

  3. 3D Finite Element Trajectory Code with Adaptive Meshing

    NASA Astrophysics Data System (ADS)

    Ives, Lawrence; Bui, Thuc; Vogler, William; Bauer, Andy; Shephard, Mark; Beal, Mark; Tran, Hien

    2004-11-01

    Beam Optics Analysis, a new, 3D charged particle program is available and in use for the design of complex, 3D electron guns and charged particle devices. The code reads files directly from most CAD and solid modeling programs, includes an intuitive Graphical User Interface (GUI), and a robust mesh generator that is fully automatic. Complex problems can be set up, and analysis initiated in minutes. The program includes a user-friendly post processor for displaying field and trajectory data using 3D plots and images. The electrostatic solver is based on the standard nodal finite element method. The magnetostatic field solver is based on the vector finite element method and is also called during the trajectory simulation process to solve for self magnetic fields. The user imports the geometry from essentially any commercial CAD program and uses the GUI to assign parameters (voltages, currents, dielectric constant) and designate emitters (including work function, emitter temperature, and number of trajectories). The the mesh is generated automatically and analysis is performed, including mesh adaptation to improve accuracy and optimize computational resources. This presentation will provide information on the basic structure of the code, its operation, and it's capabilities.

  4. 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.

  5. 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

  6. 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

  7. 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.

  8. 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.

  9. 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

  10. 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.

  11. 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.

  12. 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.

  13. 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

  14. 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

  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. 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.

  17. 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.

  18. 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

  19. 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

  20. 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.

  1. 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

  2. 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

  3. 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

  4. 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

  5. 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

  6. Stereo 3D vision adapter using commercial DIY goods

    NASA Astrophysics Data System (ADS)

    Sakamoto, Kunio; Ohara, Takashi

    2009-10-01

    The conventional display can show only one screen, but it is impossible to enlarge the size of a screen, for example twice. Meanwhile the mirror supplies us with the same image but this mirror image is usually upside down. Assume that the images on an original screen and a virtual screen in the mirror are completely different and both images can be displayed independently. It would be possible to enlarge a screen area twice. This extension method enables the observers to show the virtual image plane and to enlarge a screen area twice. Although the displaying region is doubled, this virtual display could not produce 3D images. In this paper, we present an extension method using a unidirectional diffusing image screen and an improvement for displaying a 3D image using orthogonal polarized image projection.

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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.

  13. 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

  14. 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.

  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. Parallel adaptive mesh refinement within the PUMAA3D Project

    NASA Technical Reports Server (NTRS)

    Freitag, Lori; Jones, Mark; Plassmann, Paul

    1995-01-01

    To enable the solution of large-scale applications on distributed memory architectures, we are designing and implementing parallel algorithms for the fundamental tasks of unstructured mesh computation. In this paper, we discuss efficient algorithms developed for two of these tasks: parallel adaptive mesh refinement and mesh partitioning. The algorithms are discussed in the context of two-dimensional finite element solution on triangular meshes, but are suitable for use with a variety of element types and with h- or p-refinement. Results demonstrating the scalability and efficiency of the refinement algorithm and the quality of the mesh partitioning are presented for several test problems on the Intel DELTA.

  17. 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

  18. 3-D Adaptive Sparsity Based Image Compression with Applications to Optical Coherence Tomography

    PubMed Central

    Fang, Leyuan; Li, Shutao; Kang, Xudong; Izatt, Joseph A.; Farsiu, Sina

    2015-01-01

    We present a novel general-purpose compression method for tomographic images, termed 3D adaptive sparse representation based compression (3D-ASRC). In this paper, we focus on applications of 3D-ASRC for the compression of ophthalmic 3D optical coherence tomography (OCT) images. The 3D-ASRC algorithm exploits correlations among adjacent OCT images to improve compression performance, yet is sensitive to preserving their differences. Due to the inherent denoising mechanism of the sparsity based 3D-ASRC, the quality of the compressed images are often better than the raw images they are based on. Experiments on clinical-grade retinal OCT images demonstrate the superiority of the proposed 3D-ASRC over other well-known compression methods. PMID:25561591

  19. 3-D Adaptive Sparsity Based Image Compression With Applications to Optical Coherence Tomography.

    PubMed

    Fang, Leyuan; Li, Shutao; Kang, Xudong; Izatt, Joseph A; Farsiu, Sina

    2015-06-01

    We present a novel general-purpose compression method for tomographic images, termed 3D adaptive sparse representation based compression (3D-ASRC). In this paper, we focus on applications of 3D-ASRC for the compression of ophthalmic 3D optical coherence tomography (OCT) images. The 3D-ASRC algorithm exploits correlations among adjacent OCT images to improve compression performance, yet is sensitive to preserving their differences. Due to the inherent denoising mechanism of the sparsity based 3D-ASRC, the quality of the compressed images are often better than the raw images they are based on. Experiments on clinical-grade retinal OCT images demonstrate the superiority of the proposed 3D-ASRC over other well-known compression methods. PMID:25561591

  20. 3D Compressible Melt Transport with Adaptive Mesh Refinement

    NASA Astrophysics Data System (ADS)

    Dannberg, Juliane; Heister, Timo

    2015-04-01

    Melt generation and migration have been the subject of numerous investigations, but their typical time and length-scales are vastly different from mantle convection, which makes it difficult to study these processes in a unified framework. The equations that describe coupled Stokes-Darcy flow have been derived a long time ago and they have been successfully implemented and applied in numerical models (Keller et al., 2013). However, modelling magma dynamics poses the challenge of highly non-linear and spatially variable material properties, in particular the viscosity. Applying adaptive mesh refinement to this type of problems is particularly advantageous, as the resolution can be increased in mesh cells where melt is present and viscosity gradients are high, whereas a lower resolution is sufficient in regions without melt. In addition, previous models neglect the compressibility of both the solid and the fluid phase. However, experiments have shown that the melt density change from the depth of melt generation to the surface leads to a volume increase of up to 20%. Considering these volume changes in both phases also ensures self-consistency of models that strive to link melt generation to processes in the deeper mantle, where the compressibility of the solid phase becomes more important. We describe our extension of the finite-element mantle convection code ASPECT (Kronbichler et al., 2012) that allows for solving additional equations describing the behaviour of silicate melt percolating through and interacting with a viscously deforming host rock. We use the original compressible formulation of the McKenzie equations, augmented by an equation for the conservation of energy. This approach includes both melt migration and melt generation with the accompanying latent heat effects. We evaluate the functionality and potential of this method using a series of simple model setups and benchmarks, comparing results of the compressible and incompressible formulation and

  1. 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.

  2. 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

  3. 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.

  4. 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

  5. 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

  6. 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

  7. 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.

  8. 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.

  9. 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.

  10. 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

  11. 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

  12. 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

  13. 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.

  14. Electro-bending characterization of adaptive 3D fiber reinforced plastics based on shape memory alloys

    NASA Astrophysics Data System (ADS)

    Ashir, Moniruddoza; Hahn, Lars; Kluge, Axel; Nocke, Andreas; Cherif, Chokri

    2016-03-01

    The industrial importance of fiber reinforced plastics (FRPs) is growing steadily in recent years, which are mostly used in different niche products, has been growing steadily in recent years. The integration of sensors and actuators in FRP is potentially valuable for creating innovative applications and therefore the market acceptance of adaptive FRP is increasing. In particular, in the field of highly stressed FRP, structural integrated systems for continuous component parts monitoring play an important role. This presented work focuses on the electro-mechanical characterization of adaptive three-dimensional (3D)FRP with integrated textile-based actuators. Here, the friction spun hybrid yarn, consisting of shape memory alloy (SMA) in wire form as core, serves as an actuator. Because of the shape memory effect, the SMA-hybrid yarn returns to its original shape upon heating that also causes the deformation of adaptive 3D FRP. In order to investigate the influences of the deformation behavior of the adaptive 3D FRP, investigations in this research are varied according to the structural parameters such as radius of curvature of the adaptive 3D FRP, fabric types and number of layers of the fabric in the composite. Results show that reproducible deformations can be realized with adaptive 3D FRP and that structural parameters have a significant impact on the deformation capability.

  15. 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

  16. 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

  17. 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.

  18. 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

  19. 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

  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. Real-time 3D adaptive filtering for portable imaging systems

    NASA Astrophysics Data System (ADS)

    Bockenbach, Olivier; Ali, Murtaza; Wainwright, Ian; Nadeski, Mark

    2015-03-01

    Portable imaging devices have proven valuable for emergency medical services both in the field and hospital environments and are becoming more prevalent in clinical settings where the use of larger imaging machines is impractical. 3D adaptive filtering is one of the most advanced techniques aimed at noise reduction and feature enhancement, but is computationally very demanding and hence often not able to run with sufficient performance on a portable platform. In recent years, advanced multicore DSPs have been introduced that attain high processing performance while maintaining low levels of power dissipation. These processors enable the implementation of complex algorithms like 3D adaptive filtering, improving the image quality of portable medical imaging devices. In this study, the performance of a 3D adaptive filtering algorithm on a digital signal processor (DSP) is investigated. The performance is assessed by filtering a volume of size 512x256x128 voxels sampled at a pace of 10 MVoxels/sec.

  2. 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

  3. 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

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

    PubMed

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

    2016-04-01

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

  5. 3D-SoftChip: A Novel Architecture for Next-Generation Adaptive Computing Systems

    NASA Astrophysics Data System (ADS)

    Kim, Chul; Rassau, Alex; Lachowicz, Stefan; Lee, Mike Myung-Ok; Eshraghian, Kamran

    2006-12-01

    This paper introduces a novel architecture for next-generation adaptive computing systems, which we term 3D-SoftChip. The 3D-SoftChip is a 3-dimensional (3D) vertically integrated adaptive computing system combining state-of-the-art processing and 3D interconnection technology. It comprises the vertical integration of two chips (a configurable array processor and an intelligent configurable switch) through an indium bump interconnection array (IBIA). The configurable array processor (CAP) is an array of heterogeneous processing elements (PEs), while the intelligent configurable switch (ICS) comprises a switch block, 32-bit dedicated RISC processor for control, on-chip program/data memory, data frame buffer, along with a direct memory access (DMA) controller. This paper introduces the novel 3D-SoftChip architecture for real-time communication and multimedia signal processing as a next-generation computing system. The paper further describes the advanced HW/SW codesign and verification methodology, including high-level system modeling of the 3D-SoftChip using SystemC, being used to determine the optimum hardware specification in the early design stage.

  6. 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

  7. 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

  8. Grid-Adapted FUN3D Computations for the Second High Lift Prediction Workshop

    NASA Technical Reports Server (NTRS)

    Lee-Rausch, E. M.; Rumsey, C. L.; Park, M. A.

    2014-01-01

    Contributions of the unstructured Reynolds-averaged Navier-Stokes code FUN3D to the 2nd AIAA CFD High Lift Prediction Workshop are described, and detailed comparisons are made with experimental data. Using workshop-supplied grids, results for the clean wing configuration are compared with results from the structured code CFL3D Using the same turbulence model, both codes compare reasonably well in terms of total forces and moments, and the maximum lift is similarly over-predicted for both codes compared to experiment. By including more representative geometry features such as slat and flap brackets and slat pressure tube bundles, FUN3D captures the general effects of the Reynolds number variation, but under-predicts maximum lift on workshop-supplied grids in comparison with the experimental data, due to excessive separation. However, when output-based, off-body grid adaptation in FUN3D is employed, results improve considerably. In particular, when the geometry includes both brackets and the pressure tube bundles, grid adaptation results in a more accurate prediction of lift near stall in comparison with the wind-tunnel data. Furthermore, a rotation-corrected turbulence model shows improved pressure predictions on the outboard span when using adapted grids.

  9. Modeling and simulating the adaptive electrical properties of stochastic polymeric 3D networks

    NASA Astrophysics Data System (ADS)

    Sigala, R.; Smerieri, A.; Schüz, A.; Camorani, P.; Erokhin, V.

    2013-10-01

    Memristors are passive two-terminal circuit elements that combine resistance and memory. Although in theory memristors are a very promising approach to fabricate hardware with adaptive properties, there are only very few implementations able to show their basic properties. We recently developed stochastic polymeric matrices with a functionality that evidences the formation of self-assembled three-dimensional (3D) networks of memristors. We demonstrated that those networks show the typical hysteretic behavior observed in the ‘one input-one output’ memristive configuration. Interestingly, using different protocols to electrically stimulate the networks, we also observed that their adaptive properties are similar to those present in the nervous system. Here, we model and simulate the electrical properties of these self-assembled polymeric networks of memristors, the topology of which is defined stochastically. First, we show that the model recreates the hysteretic behavior observed in the real experiments. Second, we demonstrate that the networks modeled indeed have a 3D instead of a planar functionality. Finally, we show that the adaptive properties of the networks depend on their connectivity pattern. Our model was able to replicate fundamental qualitative behavior of the real organic 3D memristor networks; yet, through the simulations, we also explored other interesting properties, such as the relation between connectivity patterns and adaptive properties. Our model and simulations represent an interesting tool to understand the very complex behavior of self-assembled memristor networks, which can finally help to predict and formulate hypotheses for future experiments.

  10. 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.

  11. Adaptive image warping for hole prevention in 3D view synthesis.

    PubMed

    Plath, Nils; Knorr, Sebastian; Goldmann, Lutz; Sikora, Thomas

    2013-09-01

    Increasing popularity of 3D videos calls for new methods to ease the conversion process of existing monocular video to stereoscopic or multi-view video. A popular way to convert video is given by depth image-based rendering methods, in which a depth map that is associated with an image frame is used to generate a virtual view. Because of the lack of knowledge about the 3D structure of a scene and its corresponding texture, the conversion of 2D video, inevitably, however, leads to holes in the resulting 3D image as a result of newly-exposed areas. The conversion process can be altered such that no holes become visible in the resulting 3D view by superimposing a regular grid over the depth map and deforming it. In this paper, an adaptive image warping approach as an improvement to the regular approach is proposed. The new algorithm exploits the smoothness of a typical depth map to reduce the complexity of the underlying optimization problem that is necessary to find the deformation, which is required to prevent holes. This is achieved by splitting a depth map into blocks of homogeneous depth using quadtrees and running the optimization on the resulting adaptive grid. The results show that this approach leads to a considerable reduction of the computational complexity while maintaining the visual quality of the synthesized views. PMID:23782807

  12. Parallel Adaptive Computation of Blood Flow in a 3D ``Whole'' Body Model

    NASA Astrophysics Data System (ADS)

    Zhou, M.; Figueroa, C. A.; Taylor, C. A.; Sahni, O.; Jansen, K. E.

    2008-11-01

    Accurate numerical simulations of vascular trauma require the consideration of a larger portion of the vasculature than previously considered, due to the systemic nature of the human body's response. A patient-specific 3D model composed of 78 connected arterial branches extending from the neck to the lower legs is constructed to effectively represent the entire body. Recently developed outflow boundary conditions that appropriately represent the downstream vasculature bed which is not included in the 3D computational domain are applied at 78 outlets. In this work, the pulsatile blood flow simulations are started on a fairly uniform, unstructured mesh that is subsequently adapted using a solution-based approach to efficiently resolve the flow features. The adapted mesh contains non-uniform, anisotropic elements resulting in resolution that conforms with the physical length scales present in the problem. The effects of the mesh resolution on the flow field are studied, specifically on relevant quantities of pressure, velocity and wall shear stress.

  13. Generation and adaptation of 3-D unstructured grids for transient problems

    NASA Technical Reports Server (NTRS)

    Loehner, Rainald

    1990-01-01

    Grid generation and adaptive refinement techniques suitable for the simulation of strongly unsteady flows past geometrically complex bodies in 3-D are described. The grids are generated using the advancing front technique. Emphasis is placed not to generate elements that are too small, as this would severely increase the cost of simulations with explicit flow solvers. The grids are adapted to an evolving flowfield using simple h-refinement. A grid change is performed every 5 to 10 timesteps, and only one level of refinement/coarsening is allowed per mesh change.

  14. 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.

  15. 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.

  16. FUN3D Grid Refinement and Adaptation Studies for the Ares Launch Vehicle

    NASA Technical Reports Server (NTRS)

    Bartels, Robert E.; Vasta, Veer; Carlson, Jan-Renee; Park, Mike; Mineck, Raymond E.

    2010-01-01

    This paper presents grid refinement and adaptation studies performed in conjunction with computational aeroelastic analyses of the Ares crew launch vehicle (CLV). The unstructured grids used in this analysis were created with GridTool and VGRID while the adaptation was performed using the Computational Fluid Dynamic (CFD) code FUN3D with a feature based adaptation software tool. GridTool was developed by ViGYAN, Inc. while the last three software suites were developed by NASA Langley Research Center. The feature based adaptation software used here operates by aligning control volumes with shock and Mach line structures and by refining/de-refining where necessary. It does not redistribute node points on the surface. This paper assesses the sensitivity of the complex flow field about a launch vehicle to grid refinement. It also assesses the potential of feature based grid adaptation to improve the accuracy of CFD analysis for a complex launch vehicle configuration. The feature based adaptation shows the potential to improve the resolution of shocks and shear layers. Further development of the capability to adapt the boundary layer and surface grids of a tetrahedral grid is required for significant improvements in modeling the flow field.

  17. High performance 3D adaptive filtering for DSP based portable medical imaging systems

    NASA Astrophysics Data System (ADS)

    Bockenbach, Olivier; Ali, Murtaza; Wainwright, Ian; Nadeski, Mark

    2015-03-01

    Portable medical imaging devices have proven valuable for emergency medical services both in the field and hospital environments and are becoming more prevalent in clinical settings where the use of larger imaging machines is impractical. Despite their constraints on power, size and cost, portable imaging devices must still deliver high quality images. 3D adaptive filtering is one of the most advanced techniques aimed at noise reduction and feature enhancement, but is computationally very demanding and hence often cannot be run with sufficient performance on a portable platform. In recent years, advanced multicore digital signal processors (DSP) have been developed that attain high processing performance while maintaining low levels of power dissipation. These processors enable the implementation of complex algorithms on a portable platform. In this study, the performance of a 3D adaptive filtering algorithm on a DSP is investigated. The performance is assessed by filtering a volume of size 512x256x128 voxels sampled at a pace of 10 MVoxels/sec with an Ultrasound 3D probe. Relative performance and power is addressed between a reference PC (Quad Core CPU) and a TMS320C6678 DSP from Texas Instruments.

  18. 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

  19. Aeroacoustic Simulation of Nose Landing Gear on Adaptive Unstructured Grids With FUN3D

    NASA Technical Reports Server (NTRS)

    Vatsa, Veer N.; Khorrami, Mehdi R.; Park, Michael A.; Lockhard, David P.

    2013-01-01

    Numerical simulations have been performed for a partially-dressed, cavity-closed nose landing gear configuration that was tested in NASA Langley s closed-wall Basic Aerodynamic Research Tunnel (BART) and in the University of Florida's open-jet acoustic facility known as the UFAFF. The unstructured-grid flow solver FUN3D, developed at NASA Langley Research center, is used to compute the unsteady flow field for this configuration. Starting with a coarse grid, a series of successively finer grids were generated using the adaptive gridding methodology available in the FUN3D code. A hybrid Reynolds-averaged Navier-Stokes/large eddy simulation (RANS/LES) turbulence model is used for these computations. Time-averaged and instantaneous solutions obtained on these grids are compared with the measured data. In general, the correlation with the experimental data improves with grid refinement. A similar trend is observed for sound pressure levels obtained by using these CFD solutions as input to a FfowcsWilliams-Hawkings noise propagation code to compute the farfield noise levels. In general, the numerical solutions obtained on adapted grids compare well with the hand-tuned enriched fine grid solutions and experimental data. In addition, the grid adaption strategy discussed here simplifies the grid generation process, and results in improved computational efficiency of CFD simulations.

  20. 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.

  1. Parallel goal-oriented adaptive finite element modeling for 3D electromagnetic exploration

    NASA Astrophysics Data System (ADS)

    Zhang, Y.; Key, K.; Ovall, J.; Holst, M.

    2014-12-01

    We present a parallel goal-oriented adaptive finite element method for accurate and efficient electromagnetic (EM) modeling of complex 3D structures. An unstructured tetrahedral mesh allows this approach to accommodate arbitrarily complex 3D conductivity variations and a priori known boundaries. The total electric field is approximated by the lowest order linear curl-conforming shape functions and the discretized finite element equations are solved by a sparse LU factorization. Accuracy of the finite element solution is achieved through adaptive mesh refinement that is performed iteratively until the solution converges to the desired accuracy tolerance. Refinement is guided by a goal-oriented error estimator that uses a dual-weighted residual method to optimize the mesh for accurate EM responses at the locations of the EM receivers. As a result, the mesh refinement is highly efficient since it only targets the elements where the inaccuracy of the solution corrupts the response at the possibly distant locations of the EM receivers. We compare the accuracy and efficiency of two approaches for estimating the primary residual error required at the core of this method: one uses local element and inter-element residuals and the other relies on solving a global residual system using a hierarchical basis. For computational efficiency our method follows the Bank-Holst algorithm for parallelization, where solutions are computed in subdomains of the original model. To resolve the load-balancing problem, this approach applies a spectral bisection method to divide the entire model into subdomains that have approximately equal error and the same number of receivers. The finite element solutions are then computed in parallel with each subdomain carrying out goal-oriented adaptive mesh refinement independently. We validate the newly developed algorithm by comparison with controlled-source EM solutions for 1D layered models and with 2D results from our earlier 2D goal oriented

  2. 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

  3. 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

  4. Adaptive noise suppression technique for dense 3D point cloud reconstructions from monocular vision

    NASA Astrophysics Data System (ADS)

    Diskin, Yakov; Asari, Vijayan K.

    2012-10-01

    Mobile vision-based autonomous vehicles use video frames from multiple angles to construct a 3D model of their environment. In this paper, we present a post-processing adaptive noise suppression technique to enhance the quality of the computed 3D model. Our near real-time reconstruction algorithm uses each pair of frames to compute the disparities of tracked feature points to translate the distance a feature has traveled within the frame in pixels into real world depth values. As a result these tracked feature points are plotted to form a dense and colorful point cloud. Due to the inevitable small vibrations in the camera and the mismatches within the feature tracking algorithm, the point cloud model contains a significant amount of misplaced points appearing as noise. The proposed noise suppression technique utilizes the spatial information of each point to unify points of similar texture and color into objects while simultaneously removing noise dissociated with any nearby objects. The noise filter combines all the points of similar depth into 2D layers throughout the point cloud model. By applying erosion and dilation techniques we are able to eliminate the unwanted floating points while retaining points of larger objects. To reverse the compression process, we transform the 2D layer back into the 3D model allowing points to return to their original position without the attached noise components. We evaluate the resulting noiseless point cloud by utilizing an unmanned ground vehicle to perform obstacle avoidance tasks. The contribution of the noise suppression technique is measured by evaluating the accuracy of the 3D reconstruction.

  5. Object-adaptive depth compensated inter prediction for depth video coding in 3D video system

    NASA Astrophysics Data System (ADS)

    Kang, Min-Koo; Lee, Jaejoon; Lim, Ilsoon; Ho, Yo-Sung

    2011-01-01

    Nowadays, the 3D video system using the MVD (multi-view video plus depth) data format is being actively studied. The system has many advantages with respect to virtual view synthesis such as an auto-stereoscopic functionality, but compression of huge input data remains a problem. Therefore, efficient 3D data compression is extremely important in the system, and problems of low temporal consistency and viewpoint correlation should be resolved for efficient depth video coding. In this paper, we propose an object-adaptive depth compensated inter prediction method to resolve the problems where object-adaptive mean-depth difference between a current block, to be coded, and a reference block are compensated during inter prediction. In addition, unique properties of depth video are exploited to reduce side information required for signaling decoder to conduct the same process. To evaluate the coding performance, we have implemented the proposed method into MVC (multiview video coding) reference software, JMVC 8.2. Experimental results have demonstrated that our proposed method is especially efficient for depth videos estimated by DERS (depth estimation reference software) discussed in the MPEG 3DV coding group. The coding gain was up to 11.69% bit-saving, and it was even increased when we evaluated it on synthesized views of virtual viewpoints.

  6. 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

  7. Adaptive multi-GPU Exchange Monte Carlo for the 3D Random Field Ising Model

    NASA Astrophysics Data System (ADS)

    Navarro, Cristóbal A.; Huang, Wei; Deng, Youjin

    2016-08-01

    This work presents an adaptive multi-GPU Exchange Monte Carlo approach for the simulation of the 3D Random Field Ising Model (RFIM). The design is based on a two-level parallelization. The first level, spin-level parallelism, maps the parallel computation as optimal 3D thread-blocks that simulate blocks of spins in shared memory with minimal halo surface, assuming a constant block volume. The second level, replica-level parallelism, uses multi-GPU computation to handle the simulation of an ensemble of replicas. CUDA's concurrent kernel execution feature is used in order to fill the occupancy of each GPU with many replicas, providing a performance boost that is more notorious at the smallest values of L. In addition to the two-level parallel design, the work proposes an adaptive multi-GPU approach that dynamically builds a proper temperature set free of exchange bottlenecks. The strategy is based on mid-point insertions at the temperature gaps where the exchange rate is most compromised. The extra work generated by the insertions is balanced across the GPUs independently of where the mid-point insertions were performed. Performance results show that spin-level performance is approximately two orders of magnitude faster than a single-core CPU version and one order of magnitude faster than a parallel multi-core CPU version running on 16-cores. Multi-GPU performance is highly convenient under a weak scaling setting, reaching up to 99 % efficiency as long as the number of GPUs and L increase together. The combination of the adaptive approach with the parallel multi-GPU design has extended our possibilities of simulation to sizes of L = 32 , 64 for a workstation with two GPUs. Sizes beyond L = 64 can eventually be studied using larger multi-GPU systems.

  8. 3-D inversion of airborne electromagnetic data parallelized and accelerated by local mesh and adaptive soundings

    NASA Astrophysics Data System (ADS)

    Yang, Dikun; Oldenburg, Douglas W.; Haber, Eldad

    2014-03-01

    Airborne electromagnetic (AEM) methods are highly efficient tools for assessing the Earth's conductivity structures in a large area at low cost. However, the configuration of AEM measurements, which typically have widely distributed transmitter-receiver pairs, makes the rigorous modelling and interpretation extremely time-consuming in 3-D. Excessive overcomputing can occur when working on a large mesh covering the entire survey area and inverting all soundings in the data set. We propose two improvements. The first is to use a locally optimized mesh for each AEM sounding for the forward modelling and calculation of sensitivity. This dedicated local mesh is small with fine cells near the sounding location and coarse cells far away in accordance with EM diffusion and the geometric decay of the signals. Once the forward problem is solved on the local meshes, the sensitivity for the inversion on the global mesh is available through quick interpolation. Using local meshes for AEM forward modelling avoids unnecessary computing on fine cells on a global mesh that are far away from the sounding location. Since local meshes are highly independent, the forward modelling can be efficiently parallelized over an array of processors. The second improvement is random and dynamic down-sampling of the soundings. Each inversion iteration only uses a random subset of the soundings, and the subset is reselected for every iteration. The number of soundings in the random subset, determined by an adaptive algorithm, is tied to the degree of model regularization. This minimizes the overcomputing caused by working with redundant soundings. Our methods are compared against conventional methods and tested with a synthetic example. We also invert a field data set that was previously considered to be too large to be practically inverted in 3-D. These examples show that our methodology can dramatically reduce the processing time of 3-D inversion to a practical level without losing resolution

  9. The image adaptive method for solder paste 3D measurement system

    NASA Astrophysics Data System (ADS)

    Xiaohui, Li; Changku, Sun; Peng, Wang

    2015-03-01

    The extensive application of Surface Mount Technology (SMT) requires various measurement methods to evaluate the circuit board. The solder paste 3D measurement system utilizing laser light projecting on the printed circuit board (PCB) surface is one of the critical methods. The local oversaturation, arising from the non-consistent reflectivity of the PCB surface, will lead to inaccurate measurement. The paper reports a novel optical image adaptive method of remedying the local oversaturation for solder paste measurement. The liquid crystal on silicon (LCoS) and image sensor (CCD or CMOS) are combined as the high dynamic range image (HDRI) acquisition system. The significant characteristic of the new method is that the image after adjustment is captured by specially designed HDRI acquisition system programmed by the LCoS mask. The formation of the LCoS mask, depending on a HDRI combined with the image fusion algorithm, is based on separating the laser light from the local oversaturated region. Experimental results demonstrate that the method can significantly improve the accuracy for the solder paste 3D measurement system with local oversaturation.

  10. 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

  11. A 3D approach for object recognition in illuminated scenes with adaptive correlation filters

    NASA Astrophysics Data System (ADS)

    Picos, Kenia; Díaz-Ramírez, Víctor H.

    2015-09-01

    In this paper we solve the problem of pose recognition of a 3D object in non-uniformly illuminated and noisy scenes. The recognition system employs a bank of space-variant correlation filters constructed with an adaptive approach based on local statistical parameters of the input scene. The position and orientation of the target are estimated with the help of the filter bank. For an observed input frame, the algorithm computes the correlation process between the observed image and the bank of filters using a combination of data and task parallelism by taking advantage of a graphics processing unit (GPU) architecture. The pose of the target is estimated by finding the template that better matches the current view of target within the scene. The performance of the proposed system is evaluated in terms of recognition accuracy, location and orientation errors, and computational performance.

  12. Model-based adaptive 3D sonar reconstruction in reverberating environments.

    PubMed

    Saucan, Augustin-Alexandru; Sintes, Christophe; Chonavel, Thierry; Caillec, Jean-Marc Le

    2015-10-01

    In this paper, we propose a novel model-based approach for 3D underwater scene reconstruction, i.e., bathymetry, for side scan sonar arrays in complex and highly reverberating environments like shallow water areas. The presence of multipath echoes and volume reverberation generates false depth estimates. To improve the resulting bathymetry, this paper proposes and develops an adaptive filter, based on several original geometrical models. This multimodel approach makes it possible to track and separate the direction of arrival trajectories of multiple echoes impinging the array. Echo tracking is perceived as a model-based processing stage, incorporating prior information on the temporal evolution of echoes in order to reject cluttered observations generated by interfering echoes. The results of the proposed filter on simulated and real sonar data showcase the clutter-free and regularized bathymetric reconstruction. Model validation is carried out with goodness of fit tests, and demonstrates the importance of model-based processing for bathymetry reconstruction. PMID:25974936

  13. MMW and THz images denoising based on adaptive CBM3D

    NASA Astrophysics Data System (ADS)

    Dai, Li; Zhang, Yousai; Li, Yuanjiang; Wang, Haoxiang

    2014-04-01

    Over the past decades, millimeter wave and terahertz radiation has received a lot of interest due to advances in emission and detection technologies which allowed the widely application of the millimeter wave and terahertz imaging technology. This paper focuses on solving the problem of this sort of images existing stripe noise, block effect and other interfered information. A new kind of nonlocal average method is put forward. Suitable level Gaussian noise is added to resonate with the image. Adaptive color block-matching 3D filtering is used to denoise. Experimental results demonstrate that it improves the visual effect and removes interference at the same time, making the analysis of the image and target detection more easily.

  14. Dynamic Implicit 3D Adaptive Mesh Refinement for Non-Equilibrium Radiation Diffusion

    SciTech Connect

    Philip, Bobby; Wang, Zhen; Berrill, Mark A; Rodriguez Rodriguez, Manuel; Pernice, Michael

    2014-01-01

    The time dependent non-equilibrium radiation diffusion equations are important for solving the transport of energy through radiation in optically thick regimes and find applications in several fields including astrophysics and inertial confinement fusion. The associated initial boundary value problems that are encountered exhibit a wide range of scales in space and time and are extremely challenging to solve. To efficiently and accurately simulate these systems we describe our research on combining techniques that will also find use more broadly for long term time integration of nonlinear multiphysics systems: implicit time integration for efficient long term time integration of stiff multiphysics systems, local control theory based step size control to minimize the required global number of time steps while controlling accuracy, dynamic 3D adaptive mesh refinement (AMR) to minimize memory and computational costs, Jacobian Free Newton Krylov methods on AMR grids for efficient nonlinear solution, and optimal multilevel preconditioner components that provide level independent linear solver convergence.

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

    NASA Astrophysics Data System (ADS)

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

    2006-08-01

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

  16. 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

  17. 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.

  18. 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

  19. 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.

  20. 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

  1. 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.

  2. 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

  3. Adaptive volume rendering of cardiac 3D ultrasound images: utilizing blood pool statistics

    NASA Astrophysics Data System (ADS)

    Åsen, Jon Petter; Steen, Erik; Kiss, Gabriel; Thorstensen, Anders; Rabben, Stein Inge

    2012-03-01

    In this paper we introduce and investigate an adaptive direct volume rendering (DVR) method for real-time visualization of cardiac 3D ultrasound. DVR is commonly used in cardiac ultrasound to visualize interfaces between tissue and blood. However, this is particularly challenging with ultrasound images due to variability of the signal within tissue as well as variability of noise signal within the blood pool. Standard DVR involves a global mapping of sample values to opacity by an opacity transfer function (OTF). While a global OTF may represent the interface correctly in one part of the image, it may result in tissue dropouts, or even artificial interfaces within the blood pool in other parts of the image. In order to increase correctness of the rendered image, the presented method utilizes blood pool statistics to do regional adjustments of the OTF. The regional adaptive OTF was compared with a global OTF in a dataset of apical recordings from 18 subjects. For each recording, three renderings from standard views (apical 4-chamber (A4C), inverted A4C (IA4C) and mitral valve (MV)) were generated for both methods, and each rendering was tuned to the best visual appearance by a physician echocardiographer. For each rendering we measured the mean absolute error (MAE) between the rendering depth buffer and a validated left ventricular segmentation. The difference d in MAE between the global and regional method was calculated and t-test results are reported with significant improvements for the regional adaptive method (dA4C = 1.5 +/- 0.3 mm, dIA4C = 2.5 +/- 0.4 mm, dMV = 1.7 +/- 0.2 mm, d.f. = 17, all p < 0.001). This improvement by the regional adaptive method was confirmed through qualitative visual assessment by an experienced physician echocardiographer who concluded that the regional adaptive method produced rendered images with fewer tissue dropouts and less spurious structures inside the blood pool in the vast majority of the renderings. The algorithm has been

  4. Capabilities of wind tunnels with two-adaptive walls to minimize boundary interference in 3-D model testing

    NASA Technical Reports Server (NTRS)

    Rebstock, Rainer; Lee, Edwin E., Jr.

    1989-01-01

    An initial wind tunnel test was made to validate a new wall adaptation method for 3-D models in test sections with two adaptive walls. First part of the adaptation strategy is an on-line assessment of wall interference at the model position. The wall induced blockage was very small at all test conditions. Lift interference occurred at higher angles of attack with the walls set aerodynamically straight. The adaptation of the top and bottom tunnel walls is aimed at achieving a correctable flow condition. The blockage was virtually zero throughout the wing planform after the wall adjustment. The lift curve measured with the walls adapted agreed very well with interference free data for Mach 0.7, regardless of the vertical position of the wing in the test section. The 2-D wall adaptation can significantly improve the correctability of 3-D model data. Nevertheless, residual spanwise variations of wall interference are inevitable.

  5. 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

  6. 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.

  7. 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

  8. 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

  9. 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.

  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

    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.

  12. 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

  13. 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

  14. 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

  15. 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

  16. Detection and Reconstruction of an Implicit Boundary Surface by Adaptively Expanding A Small Surface Patch in a 3D Image.

    PubMed

    Wang, Lisheng; Wang, Pai; Cheng, Liuhang; Ma, Yu; Wu, Shenzhi; Wang, Yu-Ping; Xu, Zongben

    2014-11-01

    In this paper we propose a novel and easy to use 3D reconstruction method. With the method, users only need to specify a small boundary surface patch in a 2D section image, and then an entire continuous implicit boundary surface (CIBS) can be automatically reconstructed from a 3D image. In the method, a hierarchical tracing strategy is used to grow the known boundary surface patch gradually in the 3D image. An adaptive detection technique is applied to detect boundary surface patches from different local regions. The technique is based on both context dependence and adaptive contrast detection as in the human vision system. A recognition technique is used to distinguish true boundary surface patches from the false ones in different cubes. By integrating these different approaches, a high-resolution CIBS model can be automatically reconstructed by adaptively expanding the small boundary surface patch in the 3D image. The effectiveness of our method is demonstrated by its applications to a variety of real 3D images, where the CIBS with complex shapes/branches and with varying gray values/gradient magnitudes can be well reconstructed. Our method is easy to use, which provides a valuable tool for 3D image visualization and analysis as needed in many applications. PMID:26355329

  17. Novel multiresolution mammographic density segmentation using pseudo 3D features and adaptive cluster merging

    NASA Astrophysics Data System (ADS)

    He, Wenda; Juette, Arne; Denton, Erica R. E.; Zwiggelaar, Reyer

    2015-03-01

    Breast cancer is the most frequently diagnosed cancer in women. Early detection, precise identification of women at risk, and application of appropriate disease prevention measures are by far the most effective ways to overcome the disease. Successful mammographic density segmentation is a key aspect in deriving correct tissue composition, ensuring an accurate mammographic risk assessment. However, mammographic densities have not yet been fully incorporated with non-image based risk prediction models, (e.g. the Gail and the Tyrer-Cuzick model), because of unreliable segmentation consistency and accuracy. This paper presents a novel multiresolution mammographic density segmentation, a concept of stack representation is proposed, and 3D texture features were extracted by adapting techniques based on classic 2D first-order statistics. An unsupervised clustering technique was employed to achieve mammographic segmentation, in which two improvements were made; 1) consistent segmentation by incorporating an optimal centroids initialisation step, and 2) significantly reduced the number of missegmentation by using an adaptive cluster merging technique. A set of full field digital mammograms was used in the evaluation. Visual assessment indicated substantial improvement on segmented anatomical structures and tissue specific areas, especially in low mammographic density categories. The developed method demonstrated an ability to improve the quality of mammographic segmentation via clustering, and results indicated an improvement of 26% in segmented image with good quality when compared with the standard clustering approach. This in turn can be found useful in early breast cancer detection, risk-stratified screening, and aiding radiologists in the process of decision making prior to surgery and/or treatment.

  18. Dynamic implicit 3D adaptive mesh refinement for non-equilibrium radiation diffusion

    SciTech Connect

    B. Philip; Z. Wang; M.A. Berrill; M. Birke; M. Pernice

    2014-04-01

    The time dependent non-equilibrium radiation diffusion equations are important for solving the transport of energy through radiation in optically thick regimes and find applications in several fields including astrophysics and inertial confinement fusion. The associated initial boundary value problems that are encountered often exhibit a wide range of scales in space and time and are extremely challenging to solve. To efficiently and accurately simulate these systems we describe our research on combining techniques that will also find use more broadly for long term time integration of nonlinear multi-physics systems: implicit time integration for efficient long term time integration of stiff multi-physics systems, local control theory based step size control to minimize the required global number of time steps while controlling accuracy, dynamic 3D adaptive mesh refinement (AMR) to minimize memory and computational costs, Jacobian Free Newton–Krylov methods on AMR grids for efficient nonlinear solution, and optimal multilevel preconditioner components that provide level independent solver convergence.

  19. Stereoscopic-3D display design: a new paradigm with Intel Adaptive Stable Image Technology [IA-SIT

    NASA Astrophysics Data System (ADS)

    Jain, Sunil

    2012-03-01

    Stereoscopic-3D (S3D) proliferation on personal computers (PC) is mired by several technical and business challenges: a) viewing discomfort due to cross-talk amongst stereo images; b) high system cost; and c) restricted content availability. Users expect S3D visual quality to be better than, or at least equal to, what they are used to enjoying on 2D in terms of resolution, pixel density, color, and interactivity. Intel Adaptive Stable Image Technology (IA-SIT) is a foundational technology, successfully developed to resolve S3D system design challenges and deliver high quality 3D visualization at PC price points. Optimizations in display driver, panel timing firmware, backlight hardware, eyewear optical stack, and synch mechanism combined can help accomplish this goal. Agnostic to refresh rate, IA-SIT will scale with shrinking of display transistors and improvements in liquid crystal and LED materials. Industry could profusely benefit from the following calls to action:- 1) Adopt 'IA-SIT S3D Mode' in panel specs (via VESA) to help panel makers monetize S3D; 2) Adopt 'IA-SIT Eyewear Universal Optical Stack' and algorithm (via CEA) to help PC peripheral makers develop stylish glasses; 3) Adopt 'IA-SIT Real Time Profile' for sub-100uS latency control (via BT Sig) to extend BT into S3D; and 4) Adopt 'IA-SIT Architecture' for Monitors and TVs to monetize via PC attach.

  20. Adaptive Iterative Dose Reduction Using Three Dimensional Processing (AIDR3D) Improves Chest CT Image Quality and Reduces Radiation Exposure

    PubMed Central

    Yamashiro, Tsuneo; Miyara, Tetsuhiro; Honda, Osamu; Kamiya, Hisashi; Murata, Kiyoshi; Ohno, Yoshiharu; Tomiyama, Noriyuki; Moriya, Hiroshi; Koyama, Mitsuhiro; Noma, Satoshi; Kamiya, Ayano; Tanaka, Yuko; Murayama, Sadayuki

    2014-01-01

    Objective To assess the advantages of Adaptive Iterative Dose Reduction using Three Dimensional Processing (AIDR3D) for image quality improvement and dose reduction for chest computed tomography (CT). Methods Institutional Review Boards approved this study and informed consent was obtained. Eighty-eight subjects underwent chest CT at five institutions using identical scanners and protocols. During a single visit, each subject was scanned using different tube currents: 240, 120, and 60 mA. Scan data were converted to images using AIDR3D and a conventional reconstruction mode (without AIDR3D). Using a 5-point scale from 1 (non-diagnostic) to 5 (excellent), three blinded observers independently evaluated image quality for three lung zones, four patterns of lung disease (nodule/mass, emphysema, bronchiolitis, and diffuse lung disease), and three mediastinal measurements (small structure visibility, streak artifacts, and shoulder artifacts). Differences in these scores were assessed by Scheffe's test. Results At each tube current, scans using AIDR3D had higher scores than those without AIDR3D, which were significant for lung zones (p<0.0001) and all mediastinal measurements (p<0.01). For lung diseases, significant improvements with AIDR3D were frequently observed at 120 and 60 mA. Scans with AIDR3D at 120 mA had significantly higher scores than those without AIDR3D at 240 mA for lung zones and mediastinal streak artifacts (p<0.0001), and slightly higher or equal scores for all other measurements. Scans with AIDR3D at 60 mA were also judged superior or equivalent to those without AIDR3D at 120 mA. Conclusion For chest CT, AIDR3D provides better image quality and can reduce radiation exposure by 50%. PMID:25153797

  1. 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

  2. A semi-automatic 2D-to-3D video conversion with adaptive key-frame selection

    NASA Astrophysics Data System (ADS)

    Ju, Kuanyu; Xiong, Hongkai

    2014-11-01

    To compensate the deficit of 3D content, 2D to 3D video conversion (2D-to-3D) has recently attracted more attention from both industrial and academic communities. The semi-automatic 2D-to-3D conversion which estimates corresponding depth of non-key-frames through key-frames is more desirable owing to its advantage of balancing labor cost and 3D effects. The location of key-frames plays a role on quality of depth propagation. This paper proposes a semi-automatic 2D-to-3D scheme with adaptive key-frame selection to keep temporal continuity more reliable and reduce the depth propagation errors caused by occlusion. The potential key-frames would be localized in terms of clustered color variation and motion intensity. The distance of key-frame interval is also taken into account to keep the accumulated propagation errors under control and guarantee minimal user interaction. Once their depth maps are aligned with user interaction, the non-key-frames depth maps would be automatically propagated by shifted bilateral filtering. Considering that depth of objects may change due to the objects motion or camera zoom in/out effect, a bi-directional depth propagation scheme is adopted where a non-key frame is interpolated from two adjacent key frames. The experimental results show that the proposed scheme has better performance than existing 2D-to-3D scheme with fixed key-frame interval.

  3. Locally adaptive 2D-3D registration using vascular structure model for liver catheterization.

    PubMed

    Kim, Jihye; Lee, Jeongjin; Chung, Jin Wook; Shin, Yeong-Gil

    2016-03-01

    Two-dimensional-three-dimensional (2D-3D) registration between intra-operative 2D digital subtraction angiography (DSA) and pre-operative 3D computed tomography angiography (CTA) can be used for roadmapping purposes. However, through the projection of 3D vessels, incorrect intersections and overlaps between vessels are produced because of the complex vascular structure, which makes it difficult to obtain the correct solution of 2D-3D registration. To overcome these problems, we propose a registration method that selects a suitable part of a 3D vascular structure for a given DSA image and finds the optimized solution to the partial 3D structure. The proposed algorithm can reduce the registration errors because it restricts the range of the 3D vascular structure for the registration by using only the relevant 3D vessels with the given DSA. To search for the appropriate 3D partial structure, we first construct a tree model of the 3D vascular structure and divide it into several subtrees in accordance with the connectivity. Then, the best matched subtree with the given DSA image is selected using the results from the coarse registration between each subtree and the vessels in the DSA image. Finally, a fine registration is conducted to minimize the difference between the selected subtree and the vessels of the DSA image. In experimental results obtained using 10 clinical datasets, the average distance errors in the case of the proposed method were 2.34±1.94mm. The proposed algorithm converges faster and produces more correct results than the conventional method in evaluations on patient datasets. PMID:26824922

  4. 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

  5. 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

  6. The relationship between fMRI adaptation and repetition priming.

    PubMed

    Ganel, Tzvi; Gonzalez, Claudia L R; Valyear, Kenneth F; Culham, Jody C; Goodale, Melvyn A; Köhler, Stefan

    2006-09-01

    Neuroimaging investigations of the cortically defined fMRI adaptation effect and of the behaviorally defined repetition priming effect have provided useful insights into how visual information is perceived and stored in the brain. Yet, although both phenomena are typically associated with reduced activation in visually responsive brain regions as a result of stimulus repetition, it is presently unknown whether they rely on common or dissociable neural mechanisms. In an event-related fMRI experiment, we manipulated fMRI adaptation and repetition priming orthogonally. Subjects made comparative size judgments for pairs of stimuli that depicted either the same or different objects; some of the pairs presented during scanning had been shown previously and others were new. This design allowed us to examine whether object-selective regions in occipital and temporal cortex were sensitive to adaptation, priming, or both. Critically, it also allowed us to test whether any region showing sensitivity to both manipulations displayed interactive or additive effects. Only a partial overlap was found between areas that were sensitive to fMRI adaptation and those sensitive to repetition priming. Moreover, in most of the object-selective regions that showed both effects, the reduced activation associated with the two phenomena were additive rather than interactive. Together, these findings suggest that fMRI adaptation and repetition priming can be dissociated from one another in terms of their neural mechanisms. PMID:16854597

  7. Cell type-specific adaptation of cellular and nuclear volume in micro-engineered 3D environments.

    PubMed

    Greiner, Alexandra M; Klein, Franziska; Gudzenko, Tetyana; Richter, Benjamin; Striebel, Thomas; Wundari, Bayu G; Autenrieth, Tatjana J; Wegener, Martin; Franz, Clemens M; Bastmeyer, Martin

    2015-11-01

    Bio-functionalized three-dimensional (3D) structures fabricated by direct laser writing (DLW) are structurally and mechanically well-defined and ideal for systematically investigating the influence of three-dimensionality and substrate stiffness on cell behavior. Here, we show that different fibroblast-like and epithelial cell lines maintain normal proliferation rates and form functional cell-matrix contacts in DLW-fabricated 3D scaffolds of different mechanics and geometry. Furthermore, the molecular composition of cell-matrix contacts forming in these 3D micro-environments and under conventional 2D culture conditions is identical, based on the analysis of several marker proteins (paxillin, phospho-paxillin, phospho-focal adhesion kinase, vinculin, β1-integrin). However, fibroblast-like and epithelial cells differ markedly in the way they adapt their total cell and nuclear volumes in 3D environments. While fibroblast-like cell lines display significantly increased cell and nuclear volumes in 3D substrates compared to 2D substrates, epithelial cells retain similar cell and nuclear volumes in 2D and 3D environments. Despite differential cell volume regulation between fibroblasts and epithelial cells in 3D environments, the nucleus-to-cell (N/C) volume ratios remain constant for all cell types and culture conditions. Thus, changes in cell and nuclear volume during the transition from 2D to 3D environments are strongly cell type-dependent, but independent of scaffold stiffness, while cells maintain the N/C ratio regardless of culture conditions. PMID:26283159

  8. 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

  9. A mesh adaptivity scheme on the Landau-de Gennes functional minimization case in 3D, and its driving efficiency

    NASA Astrophysics Data System (ADS)

    Bajc, Iztok; Hecht, Frédéric; Žumer, Slobodan

    2016-09-01

    This paper presents a 3D mesh adaptivity strategy on unstructured tetrahedral meshes by a posteriori error estimates based on metrics derived from the Hessian of a solution. The study is made on the case of a nonlinear finite element minimization scheme for the Landau-de Gennes free energy functional of nematic liquid crystals. Newton's iteration for tensor fields is employed with steepest descent method possibly stepping in. Aspects relating the driving of mesh adaptivity within the nonlinear scheme are considered. The algorithmic performance is found to depend on at least two factors: when to trigger each single mesh adaptation, and the precision of the correlated remeshing. Each factor is represented by a parameter, with its values possibly varying for every new mesh adaptation. We empirically show that the time of the overall algorithm convergence can vary considerably when different sequences of parameters are used, thus posing a question about optimality. The extensive testings and debugging done within this work on the simulation of systems of nematic colloids substantially contributed to the upgrade of an open source finite element-oriented programming language to its 3D meshing possibilities, as also to an outer 3D remeshing module.

  10. 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

  11. 3D dynamic rupture with anelastic wave propagation using an hp-adaptive Discontinuous Galerkin method

    NASA Astrophysics Data System (ADS)

    Tago, J.; Cruz-Atienza, V. M.; Etienne, V.; Virieux, J.; Benjemaa, M.; Sanchez-Sesma, F. J.

    2010-12-01

    Simulating any realistic seismic scenario requires incorporating physical basis into the model. Considering both the dynamics of the rupture process and the anelastic attenuation of seismic waves is essential to this purpose and, therefore, we choose to extend the hp-adaptive Discontinuous Galerkin finite-element method to integrate these physical aspects. The 3D elastodynamic equations in an unstructured tetrahedral mesh are solved with a second-order time marching approach in a high-performance computing environment. The first extension incorporates the viscoelastic rheology so that the intrinsic attenuation of the medium is considered in terms of frequency dependent quality factors (Q). On the other hand, the extension related to dynamic rupture is integrated through explicit boundary conditions over the crack surface. For this visco-elastodynamic formulation, we introduce an original discrete scheme that preserves the optimal code performance of the elastodynamic equations. A set of relaxation mechanisms describes the behavior of a generalized Maxwell body. We approximate almost constant Q in a wide frequency range by selecting both suitable relaxation frequencies and anelastic coefficients characterizing these mechanisms. In order to do so, we solve an optimization problem which is critical to minimize the amount of relaxation mechanisms. Two strategies are explored: 1) a least squares method and 2) a genetic algorithm (GA). We found that the improvement provided by the heuristic GA method is negligible. Both optimization strategies yield Q values within the 5% of the target constant Q mechanism. Anelastic functions (i.e. memory variables) are introduced to efficiently evaluate the time convolution terms involved in the constitutive equations and thus to minimize the computational cost. The incorporation of anelastic functions implies new terms with ordinary differential equations in the mathematical formulation. We solve these equations using the same order

  12. First steps toward 3D high resolution imaging using adaptive optics and full-field optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Blanco, Leonardo; Blavier, Marie; Glanc, Marie; Pouplard, Florence; Tick, Sarah; Maksimovic, Ivan; Chenegros, Guillaume; Mugnier, Laurent; Lacombe, Francois; Rousset, Gérard; Paques, Michel; Le Gargasson, Jean-François; Sahel, Jose-Alain

    2008-09-01

    We describe here two parts of our future 3D fundus camera coupling Adaptive Optics and full-field Optical Coherence Tomography. The first part is an Adaptive Optics flood imager installed at the Quinze-Vingts Hospital, regularly used on healthy and pathological eyes. A posteriori image reconstruction is performed, increasing the final image quality and field of view. The instrument lateral resolution is better than 2 microns. The second part is a full-field Optical Coherence Tomograph, which has demonstrated capability of performing a simple kind of "4 phases" image reconstruction of non biological samples and ex situ retinas. Final aim is to couple both parts in order to achieve 3D high resolution mapping of in vivo retinas.

  13. 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

  14. Adaptive optofluidic lens(es) for switchable 2D and 3D imaging

    NASA Astrophysics Data System (ADS)

    Huang, Hanyang; Wei, Kang; Zhao, Yi

    2016-03-01

    The stereoscopic image is often captured using dual cameras arranged side-by-side and optical path switching systems such as two separate solid lenses or biprism/mirrors. The miniaturization of the overall size of current stereoscopic devices down to several millimeters is at a sacrifice of further device size shrinkage. The limited light entry worsens the final image resolution and brightness. It is known that optofluidics offer good re-configurability for imaging systems. Leveraging this technique, we report a reconfigurable optofluidic system whose optical layout can be swapped between a singlet lens with 10 mm in diameter and a pair of binocular lenses with each lens of 3 mm in diameter for switchable two-dimensional (2D) and three-dimensional (3D) imaging. The singlet and the binoculars share the same optical path and the same imaging sensor. The singlet acquires a 3D image with better resolution and brightness, while the binoculars capture stereoscopic image pairs for 3D vision and depth perception. The focusing power tuning capability of the singlet and the binoculars enable image acquisition at varied object planes by adjusting the hydrostatic pressure across the lens membrane. The vari-focal singlet and binoculars thus work interchangeably and complementarily. The device is thus expected to have applications in robotic vision, stereoscopy, laparoendoscopy and miniaturized zoom lens system.

  15. 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

  16. Arbitrary-level hanging nodes for adaptive hphp-FEM approximations in 3D

    SciTech Connect

    Pavel Kus; Pavel Solin; David Andrs

    2014-11-01

    In this paper we discuss constrained approximation with arbitrary-level hanging nodes in adaptive higher-order finite element methods (hphp-FEM) for three-dimensional problems. This technique enables using highly irregular meshes, and it greatly simplifies the design of adaptive algorithms as it prevents refinements from propagating recursively through the finite element mesh. The technique makes it possible to design efficient adaptive algorithms for purely hexahedral meshes. We present a detailed mathematical description of the method and illustrate it with numerical examples.

  17. 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.

  18. Parallel Implementation of an Adaptive Scheme for 3D Unstructured Grids on the SP2

    NASA Technical Reports Server (NTRS)

    Oliker, Leonid; Biswas, Rupak; Strawn, Roger C.

    1996-01-01

    Dynamic mesh adaption on unstructured grids is a powerful tool for computing unsteady flows that require local grid modifications to efficiently resolve solution features. For this work, we consider an edge-based adaption scheme that has shown good single-processor performance on the C90. We report on our experience parallelizing this code for the SP2. Results show a 47.OX speedup on 64 processors when 10% of the mesh is randomly refined. Performance deteriorates to 7.7X when the same number of edges are refined in a highly-localized region. This is because almost all mesh adaption is confined to a single processor. However, this problem can be remedied by repartitioning the mesh immediately after targeting edges for refinement but before the actual adaption takes place. With this change, the speedup improves dramatically to 43.6X.

  19. Parallel implementation of an adaptive scheme for 3D unstructured grids on the SP2

    NASA Technical Reports Server (NTRS)

    Strawn, Roger C.; Oliker, Leonid; Biswas, Rupak

    1996-01-01

    Dynamic mesh adaption on unstructured grids is a powerful tool for computing unsteady flows that require local grid modifications to efficiently resolve solution features. For this work, we consider an edge-based adaption scheme that has shown good single-processor performance on the C90. We report on our experience parallelizing this code for the SP2. Results show a 47.0X speedup on 64 processors when 10 percent of the mesh is randomly refined. Performance deteriorates to 7.7X when the same number of edges are refined in a highly-localized region. This is because almost all the mesh adaption is confined to a single processor. However, this problem can be remedied by repartitioning the mesh immediately after targeting edges for refinement but before the actual adaption takes place. With this change, the speedup improves dramatically to 43.6X.

  20. Adaptation of video game UVW mapping to 3D visualization of gene expression patterns

    NASA Astrophysics Data System (ADS)

    Vize, Peter D.; Gerth, Victor E.

    2007-01-01

    Analysis of gene expression patterns within an organism plays a critical role in associating genes with biological processes in both health and disease. During embryonic development the analysis and comparison of different gene expression patterns allows biologists to identify candidate genes that may regulate the formation of normal tissues and organs and to search for genes associated with congenital diseases. No two individual embryos, or organs, are exactly the same shape or size so comparing spatial gene expression in one embryo to that in another is difficult. We will present our efforts in comparing gene expression data collected using both volumetric and projection approaches. Volumetric data is highly accurate but difficult to process and compare. Projection methods use UV mapping to align texture maps to standardized spatial frameworks. This approach is less accurate but is very rapid and requires very little processing. We have built a database of over 180 3D models depicting gene expression patterns mapped onto the surface of spline based embryo models. Gene expression data in different models can easily be compared to determine common regions of activity. Visualization software, both Java and OpenGL optimized for viewing 3D gene expression data will also be demonstrated.

  1. 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

  2. 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

  3. 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

  4. 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

  5. Accessible bioprinting: adaptation of a low-cost 3D-printer for precise cell placement and stem cell differentiation.

    PubMed

    Reid, John A; Mollica, Peter A; Johnson, Garett D; Ogle, Roy C; Bruno, Robert D; Sachs, Patrick C

    2016-01-01

    The precision and repeatability offered by computer-aided design and computer-numerically controlled techniques in biofabrication processes is quickly becoming an industry standard. However, many hurdles still exist before these techniques can be used in research laboratories for cellular and molecular biology applications. Extrusion-based bioprinting systems have been characterized by high development costs, injector clogging, difficulty achieving small cell number deposits, decreased cell viability, and altered cell function post-printing. To circumvent the high-price barrier to entry of conventional bioprinters, we designed and 3D printed components for the adaptation of an inexpensive 'off-the-shelf' commercially available 3D printer. We also demonstrate via goal based computer simulations that the needle geometries of conventional commercially standardized, 'luer-lock' syringe-needle systems cause many of the issues plaguing conventional bioprinters. To address these performance limitations we optimized flow within several microneedle geometries, which revealed a short tapered injector design with minimal cylindrical needle length was ideal to minimize cell strain and accretion. We then experimentally quantified these geometries using pulled glass microcapillary pipettes and our modified, low-cost 3D printer. This systems performance validated our models exhibiting: reduced clogging, single cell print resolution, and maintenance of cell viability without the use of a sacrificial vehicle. Using this system we show the successful printing of human induced pluripotent stem cells (hiPSCs) into Geltrex and note their retention of a pluripotent state 7 d post printing. We also show embryoid body differentiation of hiPSC by injection into differentiation conducive environments, wherein we observed continuous growth, emergence of various evaginations, and post-printing gene expression indicative of the presence of all three germ layers. These data demonstrate an

  6. Radiation dose reduction for coronary artery calcium scoring at 320-detector CT with adaptive iterative dose reduction 3D.

    PubMed

    Tatsugami, Fuminari; Higaki, Toru; Fukumoto, Wataru; Kaichi, Yoko; Fujioka, Chikako; Kiguchi, Masao; Yamamoto, Hideya; Kihara, Yasuki; Awai, Kazuo

    2015-06-01

    To assess the possibility of reducing the radiation dose for coronary artery calcium (CAC) scoring by using adaptive iterative dose reduction 3D (AIDR 3D) on a 320-detector CT scanner. Fifty-four patients underwent routine- and low-dose CT for CAC scoring. Low-dose CT was performed at one-third of the tube current used for routine-dose CT. Routine-dose CT was reconstructed with filtered back projection (FBP) and low-dose CT was reconstructed with AIDR 3D. We compared the calculated Agatston-, volume-, and mass scores of these images. The overall percentage difference in the Agatston-, volume-, and mass scores between routine- and low-dose CT studies was 15.9, 11.6, and 12.6%, respectively. There were no significant differences in the routine- and low-dose CT studies irrespective of the scoring algorithms applied. The CAC measurements of both imaging modalities were highly correlated with respect to the Agatston- (r = 0.996), volume- (r = 0.996), and mass score (r = 0.997; p < 0.001, all); the Bland-Altman limits of agreement scores were -37.4 to 51.4, -31.2 to 36.4 and -30.3 to 40.9%, respectively, suggesting that AIDR 3D was a good alternative for FBP. The mean effective radiation dose for routine- and low-dose CT was 2.2 and 0.7 mSv, respectively. The use of AIDR 3D made it possible to reduce the radiation dose by 67% for CAC scoring without impairing the quantification of coronary calcification. PMID:25754302

  7. Amoeboid migration mode adaption in quasi-3D spatial density gradients of varying lattice geometry

    NASA Astrophysics Data System (ADS)

    Gorelashvili, Mari; Emmert, Martin; Hodeck, Kai F.; Heinrich, Doris

    2014-07-01

    Cell migration processes are controlled by sensitive interaction with external cues such as topographic structures of the cell’s environment. Here, we present systematically controlled assays to investigate the specific effects of spatial density and local geometry of topographic structure on amoeboid migration of Dictyostelium discoideum cells. This is realized by well-controlled fabrication of quasi-3D pillar fields exhibiting a systematic variation of inter-pillar distance and pillar lattice geometry. By time-resolved local mean-squared displacement analysis of amoeboid migration, we can extract motility parameters in order to elucidate the details of amoeboid migration mechanisms and consolidate them in a two-state contact-controlled motility model, distinguishing directed and random phases. Specifically, we find that directed pillar-to-pillar runs are found preferably in high pillar density regions, and cells in directed motion states sense pillars as attractive topographic stimuli. In contrast, cell motion in random probing states is inhibited by high pillar density, where pillars act as obstacles for cell motion. In a gradient spatial density, these mechanisms lead to topographic guidance of cells, with a general trend towards a regime of inter-pillar spacing close to the cell diameter. In locally anisotropic pillar environments, cell migration is often found to be damped due to competing attraction by different pillars in close proximity and due to lack of other potential stimuli in the vicinity of the cell. Further, we demonstrate topographic cell guidance reflecting the lattice geometry of the quasi-3D environment by distinct preferences in migration direction. Our findings allow to specifically control amoeboid cell migration by purely topographic effects and thus, to induce active cell guidance. These tools hold prospects for medical applications like improved wound treatment, or invasion assays for immune cells.

  8. SU-E-J-153: MRI Based, Daily Adaptive Radiotherapy for Rectal Cancer: Contour Adaptation

    SciTech Connect

    Kleijnen, J; Burbach, M; Verbraeken, T; Weggers, R; Zoetelief, A; Reerink, O; Lagendijk, J; Raaymakers, B; Asselen, B

    2014-06-01

    Purpose: A major hurdle in adaptive radiotherapy is the adaptation of the planning MRI's delineations to the daily anatomy. We therefore investigate the accuracy and time needed for online clinical target volume (CTV) adaptation by radiation therapists (RTT), to be used in MRI-guided adaptive treatments on a MRI-Linac (MRL). Methods: Sixteen patients, diagnosed with early stage rectal cancer, underwent a T2-weighted MRI prior to each fraction of short-course radiotherapy, resulting in 4–5 scans per patient. On these scans, the CTV was delineated according to guidelines by an experienced radiation oncologist (RO) and considered to be the gold standard. For each patient, the first MRI was considered as the planning MRI and matched on bony anatomy to the 3–4 daily MRIs. The planning MRI's CTV delineation was rigidly propagated to the daily MRI scans as a proposal for adaptation. Three RTTs in training started the adaptation of the CTV conform guidelines, after a two hour training lecture and a two patient (n=7) training set. To assess the inter-therapist variation, all three RTTs altered delineations of 3 patients (n=12). One RTT altered the CTV delineations (n=53) of the remaining 11 patients. Time needed for adaptation of the CTV to guidelines was registered.As a measure of agreement, the conformity index (CI) was determined between the RTTs' delineations as a group. Dice similarity coefficients were determined between delineations of the RTT and the RO. Results: We found good agreement between RTTs' and RO's delineations (average Dice=0.91, SD=0.03). Furthermore, the inter-observer agreement between the RTTs was high (average CI=0.94, SD=0.02). Adaptation time reduced from 10:33 min (SD= 3:46) to 2:56 min (SD=1:06) between the first and last ten delineations, respectively. Conclusion: Daily CTV adaptation by RTTs, seems a feasible and safe way to introduce daily, online MRI-based plan adaptation for a MRL.

  9. Wavelet-based adaptive numerical simulation of unsteady 3D flow around a bluff body

    NASA Astrophysics Data System (ADS)

    de Stefano, Giuliano; Vasilyev, Oleg

    2012-11-01

    The unsteady three-dimensional flow past a two-dimensional bluff body is numerically simulated using a wavelet-based method. The body is modeled by exploiting the Brinkman volume-penalization method, which results in modifying the governing equations with the addition of an appropriate forcing term inside the spatial region occupied by the obstacle. The volume-penalized incompressible Navier-Stokes equations are numerically solved by means of the adaptive wavelet collocation method, where the non-uniform spatial grid is dynamically adapted to the flow evolution. The combined approach is successfully applied to the simulation of vortex shedding flow behind a stationary prism with square cross-section. The computation is conducted at transitional Reynolds numbers, where fundamental unstable three-dimensional vortical structures exist, by well-predicting the unsteady forces arising from fluid-structure interaction.

  10. Biophysically Defined and Cytocompatible Covalently Adaptable Networks as Viscoelastic 3D Cell Culture Systems

    PubMed Central

    McKinnon, Daniel D.; Domaille, Dylan W.; Cha, Jennifer N.; Anseth, Kristi S.

    2015-01-01

    Presented here is a cytocompatible covalently adaptable hydrogel uniquely capable of mimicking the complex biophysical properties of native tissue and enabling natural cell functions without matrix degradation. Demonstrated is both the ability to control elastic modulus and stress relaxation time constants by more than an order of magnitude while predicting these values based on fundamental theoretical understanding and the simulation of muscle tissue and the encapsulation of myoblasts. PMID:24127293

  11. A 3-D adaptive mesh refinement algorithm for multimaterial gas dynamics

    SciTech Connect

    Puckett, E.G. ); Saltzman, J.S. )

    1991-08-12

    Adaptive Mesh Refinement (AMR) in conjunction with high order upwind finite difference methods has been used effectively on a variety of problems. In this paper we discuss an implementation of an AMR finite difference method that solves the equations of gas dynamics with two material species in three dimensions. An equation for the evolution of volume fractions augments the gas dynamics system. The material interface is preserved and tracked from the volume fractions using a piecewise linear reconstruction technique. 14 refs., 4 figs.

  12. 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

  13. Adaptive enhancement and visualization techniques for 3D THz images of breast cancer tumors

    NASA Astrophysics Data System (ADS)

    Wu, Yuhao; Bowman, Tyler; Gauch, John; El-Shenawee, Magda

    2016-03-01

    This paper evaluates image enhancement and visualization techniques for pulsed terahertz (THz) images of tissue samples. Specifically, our research objective is to effectively differentiate between heterogeneous regions of breast tissues that contain tumors diagnosed as triple negative infiltrating ductal carcinoma (IDC). Tissue slices and blocks of varying thicknesses were prepared and scanned using our lab's THz pulsed imaging system. One of the challenges we have encountered in visualizing the obtained images and differentiating between healthy and cancerous regions of the tissues is that most THz images have a low level of details and narrow contrast, making it difficult to accurately identify and visualize the margins around the IDC. To overcome this problem, we have applied and evaluated a number of image processing techniques to the scanned 3D THz images. In particular, we employed various spatial filtering and intensity transformation techniques to emphasize the small details in the images and adjust the image contrast. For each of these methods, we investigated how varying filter sizes and parameters affect the amount of enhancement applied to the images. Our experimentation shows that several image processing techniques are effective in producing THz images of breast tissue samples that contain distinguishable details, making further segmentation of the different image regions promising.

  14. Electrowetting-based adaptive vari-focal liquid lens array for 3D display

    NASA Astrophysics Data System (ADS)

    Won, Yong Hyub

    2014-10-01

    Electrowetting is a phenomenon that can control the surface tension of liquid when a voltage is applied. This paper introduces the fabrication method of liquid lens array by the electrowetting phenomenon. The fabricated 23 by 23 lens array has 1mm diameter size with 1.6 mm interval distance between adjacent lenses. The diopter of each lens was - 24~27 operated at 0V to 50V. The lens array chamber fabricated by Deep Reactive-Ion Etching (DRIE) is deposited with IZO and parylene C and tantalum oxide. To prevent water penetration and achieve high dielectric constant, parylene C and tantalum oxide (ɛ = 23 ~ 25) are used respectively. Hydrophobic surface which enables the range of contact angle from 60 to 160 degree is coated to maximize the effect of electrowetting causing wide band of dioptric power. Liquid is injected into each lens chamber by two different ways. First way was self water-oil dosing that uses cosolvent and diffusion effect, while the second way was micro-syringe by the hydrophobic surface properties. To complete the whole process of the lens array fabrication, underwater sealing was performed using UV adhesive that does not dissolve in water. The transient time for changing from concave to convex lens was measured <33ms (at frequency of 1kHz AC voltage.). The liquid lens array was tested unprecedentedly for integral imaging to achieve more advanced depth information of 3D image.

  15. 3D positional control of magnetic levitation system using adaptive control: improvement of positioning control in horizontal plane

    NASA Astrophysics Data System (ADS)

    Nishino, Toshimasa; Fujitani, Yasuhiro; Kato, Norihiko; Tsuda, Naoaki; Nomura, Yoshihiko; Matsui, Hirokazu

    2012-01-01

    The objective of this paper is to establish a technique that levitates and conveys a hand, a kind of micro-robot, by applying magnetic forces: the hand is assumed to have a function of holding and detaching the objects. The equipment to be used in our experiments consists of four pole-pieces of electromagnets, and is expected to work as a 4DOF drive unit within some restricted range of 3D space: the three DOF are corresponding to 3D positional control and the remaining one DOF, rotational oscillation damping control. Having used the same equipment, Khamesee et al. had manipulated the impressed voltages on the four electric magnetics by a PID controller by the use of the feedback signal of the hand's 3D position, the controlled variable. However, in this system, there were some problems remaining: in the horizontal direction, when translating the hand out of restricted region, positional control performance was suddenly degraded. The authors propose a method to apply an adaptive control to the horizontal directional control. It is expected that the technique to be presented in this paper contributes not only to the improvement of the response characteristic but also to widening the applicable range in the horizontal directional control.

  16. A low order flow/acoustics interaction method for the prediction of sound propagation using 3D adaptive hybrid grids

    SciTech Connect

    Kallinderis, Yannis; Vitsas, Panagiotis A.; Menounou, Penelope

    2012-07-15

    A low-order flow/acoustics interaction method for the prediction of sound propagation and diffraction in unsteady subsonic compressible flow using adaptive 3-D hybrid grids is investigated. The total field is decomposed into the flow field described by the Euler equations, and the acoustics part described by the Nonlinear Perturbation Equations. The method is shown capable of predicting monopole sound propagation, while employment of acoustics-guided adapted grid refinement improves the accuracy of capturing the acoustic field. Interaction of sound with solid boundaries is also examined in terms of reflection, and diffraction. Sound propagation through an unsteady flow field is examined using static and dynamic flow/acoustics coupling demonstrating the importance of the latter.

  17. Adaptive multi-resolution 3D Hartree-Fock-Bogoliubov solver for nuclear structure

    NASA Astrophysics Data System (ADS)

    Pei, J. C.; Fann, G. I.; Harrison, R. J.; Nazarewicz, W.; Shi, Yue; Thornton, S.

    2014-08-01

    Background: Complex many-body systems, such as triaxial and reflection-asymmetric nuclei, weakly bound halo states, cluster configurations, nuclear fragments produced in heavy-ion fusion reactions, cold Fermi gases, and pasta phases in neutron star crust, are all characterized by large sizes and complex topologies in which many geometrical symmetries characteristic of ground-state configurations are broken. A tool of choice to study such complex forms of matter is an adaptive multi-resolution wavelet analysis. This method has generated much excitement since it provides a common framework linking many diversified methodologies across different fields, including signal processing, data compression, harmonic analysis and operator theory, fractals, and quantum field theory. Purpose: To describe complex superfluid many-fermion systems, we introduce an adaptive pseudospectral method for solving self-consistent equations of nuclear density functional theory in three dimensions, without symmetry restrictions. Methods: The numerical method is based on the multi-resolution and computational harmonic analysis techniques with a multi-wavelet basis. The application of state-of-the-art parallel programming techniques include sophisticated object-oriented templates which parse the high-level code into distributed parallel tasks with a multi-thread task queue scheduler for each multi-core node. The internode communications are asynchronous. The algorithm is variational and is capable of solving coupled complex-geometric systems of equations adaptively, with functional and boundary constraints, in a finite spatial domain of very large size, limited by existing parallel computer memory. For smooth functions, user-defined finite precision is guaranteed. Results: The new adaptive multi-resolution Hartree-Fock-Bogoliubov (HFB) solver madness-hfb is benchmarked against a two-dimensional coordinate-space solver hfb-ax that is based on the B-spline technique and a three-dimensional solver

  18. Vertical Scan (V-SCAN) for 3-D Grid Adaptive Mesh Refinement for an atmospheric Model Dynamical Core

    NASA Astrophysics Data System (ADS)

    Andronova, N. G.; Vandenberg, D.; Oehmke, R.; Stout, Q. F.; Penner, J. E.

    2009-12-01

    One of the major building blocks of a rigorous representation of cloud evolution in global atmospheric models is a parallel adaptive grid MPI-based communication library (an Adaptive Blocks for Locally Cartesian Topologies library -- ABLCarT), which manages the block-structured data layout, handles ghost cell updates among neighboring blocks and splits a block as refinements occur. The library has several modules that provide a layer of abstraction for adaptive refinement: blocks, which contain individual cells of user data; shells - the global geometry for the problem, including a sphere, reduced sphere, and now a 3D sphere; a load balancer for placement of blocks onto processors; and a communication support layer which encapsulates all data movement. A major performance concern with adaptive mesh refinement is how to represent calculations that have need to be sequenced in a particular order in a direction, such as calculating integrals along a specific path (e.g. atmospheric pressure or geopotential in the vertical dimension). This concern is compounded if the blocks have varying levels of refinement, or are scattered across different processors, as can be the case in parallel computing. In this paper we describe an implementation in ABLCarT of a vertical scan operation, which allows computing along vertical paths in the correct order across blocks transparent to their resolution and processor location. We test this functionality on a 2D and a 3D advection problem, which tests the performance of the model’s dynamics (transport) and physics (sources and sinks) for different model resolutions needed for inclusion of cloud formation.

  19. Quantitative Evaluation of Tissue Surface Adaption of CAD-Designed and 3D Printed Wax Pattern of Maxillary Complete Denture

    PubMed Central

    Chen, Hu; Wang, Han; Lv, Peijun; Wang, Yong; Sun, Yuchun

    2015-01-01

    Objective. To quantitatively evaluate the tissue surface adaption of a maxillary complete denture wax pattern produced by CAD and 3DP. Methods. A standard edentulous maxilla plaster cast model was used, for which a wax pattern of complete denture was designed using CAD software developed in our previous study and printed using a 3D wax printer, while another wax pattern was manufactured by the traditional manual method. The cast model and the two wax patterns were scanned in the 3D scanner as “DataModel,” “DataWaxRP,” and “DataWaxManual.” After setting each wax pattern on the plaster cast, the whole model was scanned for registration. After registration, the deviations of tissue surface between “DataModel” and “DataWaxRP” and between “DataModel” and “DataWaxManual” were measured. The data was analyzed by paired t-test. Results. For both wax patterns produced by the CAD&RP method and the manual method, scanning data of tissue surface and cast surface showed a good fit in the majority. No statistically significant (P > 0.05) difference was observed between the CAD&RP method and the manual method. Conclusions. Wax pattern of maxillary complete denture produced by the CAD&3DP method is comparable with traditional manual method in the adaption to the edentulous cast model. PMID:26583108

  20. 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

  1. The development of a solution-adaptive 3D Navier-Stokes solver for turbomachinery

    NASA Astrophysics Data System (ADS)

    Dawes, W. N.

    1991-06-01

    This paper describes the early stages in the development of a solution-adaptive fully three-dimensional Navier-Stokes solver. The compressible, Navier-Stokes equations, closed with k-epsiton turbulence modeling, are discretized on an unstructured mesh formed from tetrahedral computational control volumes. At the mesh generation stage and at stages during the solution process itself, mesh refinement is carried out by flagging cells which satisfy particular critera. These criteria include geometric features such as proximity to wetted surfaces and features associated with the particular flowfield, such as fractional variation of a flow variable over cell faces. Solutions are presented for the highly three-dimensional flows associated with a truncated cylinder in a cross flow, a three-dimensional swept transonic bump, and the corner stall and secondary flow in a transonic compressor cascade.

  2. Automatic window size selection in Windowed Fourier Transform for 3D reconstruction using adapted mother wavelets

    NASA Astrophysics Data System (ADS)

    Fernandez, Sergio; Gdeisat, Munther A.; Salvi, Joaquim; Burton, David

    2011-06-01

    Fringe pattern analysis in coded structured light constitutes an active field of research. Techniques based on first projecting a sinusoidal pattern and then recovering the phase deviation permit the computation of the phase map and its corresponding depth map, leading to a dense acquisition of the measuring object. Among these techniques, the ones based on time-frequency analysis permit to extract the depth map from a single image, thus having potential applications measuring moving objects. The main techniques are Fourier Transform (FT), Windowed Fourier Transform (WFT) and Wavelet Transform (WT). This paper first analyzes the pros and cons of these three techniques, then a new algorithm for the automatic selection of the window size in WFT is proposed. This algorithm is compared to the traditional WT using adapted mother wavelet signals both with simulated and real objects, showing the performance results for quantitative and qualitative evaluations of the new method.

  3. Adaptive model based pulmonary artery segmentation in 3D chest CT

    NASA Astrophysics Data System (ADS)

    Feuerstein, Marco; Kitasaka, Takayuki; Mori, Kensaku

    2010-03-01

    The extraction and analysis of the pulmonary artery in computed tomography (CT) of the chest can be an important, but time-consuming step for the diagnosis and treatment of lung disease, in particular in non-contrast data, where the pulmonary artery has low contrast and frequently merges with adjacent tissue of similar intensity. We here present a new method for the automatic segmentation of the pulmonary artery based on an adaptive model, Hough and Euclidean distance transforms, and spline fitting, which works equally well on non-contrast and contrast enhanced data. An evaluation on 40 patient data sets and a comparison to manual segmentations in terms of Jaccard index, sensitivity, specificity, and minimum mean distance shows its overall robustness.

  4. A parallel dynamic load balancing algorithm for 3-D adaptive unstructured grids

    NASA Technical Reports Server (NTRS)

    Vidwans, A.; Kallinderis, Y.; Venkatakrishnan, V.

    1993-01-01

    Adaptive local grid refinement and coarsening results in unequal distribution of workload among the processors of a parallel system. A novel method for balancing the load in cases of dynamically changing tetrahedral grids is developed. The approach employs local exchange of cells among processors in order to redistribute the load equally. An important part of the load balancing algorithm is the method employed by a processor to determine which cells within its subdomain are to be exchanged. Two such methods are presented and compared. The strategy for load balancing is based on the Divide-and-Conquer approach which leads to an efficient parallel algorithm. This method is implemented on a distributed-memory MIMD system.

  5. Adaptive optics SLO/OCT for 3D imaging of human photoreceptors in vivo

    PubMed Central

    Felberer, Franz; Kroisamer, Julia-Sophie; Baumann, Bernhard; Zotter, Stefan; Schmidt-Erfurth, Ursula; Hitzenberger, Christoph K.; Pircher, Michael

    2014-01-01

    We present a new instrument that is capable of imaging human photoreceptors in three dimensions. To achieve high lateral resolution, the system incorporates an adaptive optics system. The high axial resolution is achieved through the implementation of optical coherence tomography (OCT). The instrument records simultaneously both, scanning laser ophthalmoscope (SLO) and OCT en-face images, with a pixel to pixel correspondence. The information provided by the SLO is used to correct for transverse eye motion in post-processing. In order to correct for axial eye motion, the instrument is equipped with a high speed axial eye tracker. In vivo images of foveal cones as well as images recorded at an eccentricity from the fovea showing cones and rods are presented. PMID:24575339

  6. 3D Adaptive Mesh Refinement Simulations of Pellet Injection in Tokamaks

    SciTech Connect

    R. Samtaney; S.C. Jardin; P. Colella; D.F. Martin

    2003-10-20

    We present results of Adaptive Mesh Refinement (AMR) simulations of the pellet injection process, a proven method of refueling tokamaks. AMR is a computationally efficient way to provide the resolution required to simulate realistic pellet sizes relative to device dimensions. The mathematical model comprises of single-fluid MHD equations with source terms in the continuity equation along with a pellet ablation rate model. The numerical method developed is an explicit unsplit upwinding treatment of the 8-wave formulation, coupled with a MAC projection method to enforce the solenoidal property of the magnetic field. The Chombo framework is used for AMR. The role of the E x B drift in mass redistribution during inside and outside pellet injections is emphasized.

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

    NASA Astrophysics Data System (ADS)

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

    2001-07-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2009-02-01

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

  9. 3D Boltzmann Simulation of the Io's Plasma Environment with Adaptive Mesh and Particle Refinement

    NASA Astrophysics Data System (ADS)

    Lipatov, A. S.; Combi, M. R.

    2002-12-01

    The global dynamics of the ionized and neutral components in the environment of Io plays an important role in the interaction of Jupiter's corotating magnetospheric plasma with Io [Combi et al., 2002; 1998; Kabin et al., 2001]. The stationary simulation of this problem was done in the MHD [Combi et al., 1998; Linker et al, 1998; Kabin et al., 2001] and the electrodynamic [Saur et al., 1999] approaches. In this report, we develop a method of kinetic ion-neutral simulation, which is based on a multiscale adaptive mesh, particle and algorithm refinement. This method employs the fluid description for electrons whereas for ions the drift-kinetic and particle approaches are used. This method takes into account charge-exchange and photoionization processes. The first results of such simulation of the dynamics of ions in the Io's environment are discussed in this report. ~ M R Combi et al., J. Geophys. Res., 103, 9071, 1998. M R Combi, T I Gombosi, K Kabin, Atmospheres in the Solar System: Comparative\\ Aeronomy. Geophys. Monograph Series, 130, 151, 2002. K Kabin et al., Planetary and Space Sci., 49, 337, 2001. J A Linker et al., J. Geophys. Res., 103(E9), 19867, 1998. J Saur et al., J. Geophys. Res., 104, 25105, 1999.

  10. Parametric Characterization of Porous 3D Bioscaffolds Fabricated by an Adaptive Foam Reticulation Technique

    NASA Astrophysics Data System (ADS)

    Winnett, James; Mallick, Kajal K.

    2014-04-01

    Commercially pure titanium (Ti) and its alloys, in particular, titanium-vanadium-aluminium (Ti-6Al-4V), have been used as biomaterials due to their mechanical similarities to bone, good biocompatibility, and inertness in vivo. The introduction of porosity to the scaffolds leads to optimized mechanical properties and enhanced biological activity. The adaptive foam reticulation (AFR) technique has been previously used to generate hydroxyapatite bioscaffolds with enhanced cell behavior due to the generation of macroporous structures with microporous struts that provided routes for cell infiltration as well as attachment sites. Sacrificial polyurethane templates of 45 ppi and 90 ppi were coated in biomaterial-based slurries containing either Ti or Ti-6Al-4V as the biomaterial and camphene as the porogen. The resultant macropore sizes of 100-550 μm corresponded well with the initial template pore sizes while camphene produced micropores of 1-10 μm, with the level of microporosity related to the amount of porogen inclusion.

  11. Data-adapted moving least squares method for 3-D image interpolation

    NASA Astrophysics Data System (ADS)

    Jang, Sumi; Nam, Haewon; Lee, Yeon Ju; Jeong, Byeongseon; Lee, Rena; Yoon, Jungho

    2013-12-01

    In this paper, we present a nonlinear three-dimensional interpolation scheme for gray-level medical images. The scheme is based on the moving least squares method but introduces a fundamental modification. For a given evaluation point, the proposed method finds the local best approximation by reproducing polynomials of a certain degree. In particular, in order to obtain a better match to the local structures of the given image, we employ locally data-adapted least squares methods that can improve the classical one. Some numerical experiments are presented to demonstrate the performance of the proposed method. Five types of data sets are used: MR brain, MR foot, MR abdomen, CT head, and CT foot. From each of the five types, we choose five volumes. The scheme is compared with some well-known linear methods and other recently developed nonlinear methods. For quantitative comparison, we follow the paradigm proposed by Grevera and Udupa (1998). (Each slice is first assumed to be unknown then interpolated by each method. The performance of each interpolation method is assessed statistically.) The PSNR results for the estimated volumes are also provided. We observe that the new method generates better results in both quantitative and visual quality comparisons.

  12. HIFI-C: a robust and fast method for determining NMR couplings from adaptive 3D to 2D projections.

    PubMed

    Cornilescu, Gabriel; Bahrami, Arash; Tonelli, Marco; Markley, John L; Eghbalnia, Hamid R

    2007-08-01

    We describe a novel method for the robust, rapid, and reliable determination of J couplings in multi-dimensional NMR coupling data, including small couplings from larger proteins. The method, "High-resolution Iterative Frequency Identification of Couplings" (HIFI-C) is an extension of the adaptive and intelligent data collection approach introduced earlier in HIFI-NMR. HIFI-C collects one or more optimally tilted two-dimensional (2D) planes of a 3D experiment, identifies peaks, and determines couplings with high resolution and precision. The HIFI-C approach, demonstrated here for the 3D quantitative J method, offers vital features that advance the goal of rapid and robust collection of NMR coupling data. (1) Tilted plane residual dipolar couplings (RDC) data are collected adaptively in order to offer an intelligent trade off between data collection time and accuracy. (2) Data from independent planes can provide a statistical measure of reliability for each measured coupling. (3) Fast data collection enables measurements in cases where sample stability is a limiting factor (for example in the presence of an orienting medium required for residual dipolar coupling measurements). (4) For samples that are stable, or in experiments involving relatively stronger couplings, robust data collection enables more reliable determinations of couplings in shorter time, particularly for larger biomolecules. As a proof of principle, we have applied the HIFI-C approach to the 3D quantitative J experiment to determine N-C' RDC values for three proteins ranging from 56 to 159 residues (including a homodimer with 111 residues in each subunit). A number of factors influence the robustness and speed of data collection. These factors include the size of the protein, the experimental set up, and the coupling being measured, among others. To exhibit a lower bound on robustness and the potential for time saving, the measurement of dipolar couplings for the N-C' vector represents a realistic

  13. NOTE: Adaptation of a 3D prostate cancer atlas for transrectal ultrasound guided target-specific biopsy

    NASA Astrophysics Data System (ADS)

    Narayanan, R.; Werahera, P. N.; Barqawi, A.; Crawford, E. D.; Shinohara, K.; Simoneau, A. R.; Suri, J. S.

    2008-10-01

    when TRUS guided biopsies are assisted by the 3D prostate cancer atlas compared to the current standard of care. The fast registration algorithm we have developed can easily be adapted for clinical applications for the improved diagnosis of prostate cancer.

  14. A region-appearance-based adaptive variational model for 3D liver segmentation

    SciTech Connect

    Peng, Jialin; Dong, Fangfang; Chen, Yunmei; Kong, Dexing

    2014-04-15

    Purpose: Liver segmentation from computed tomography images is a challenging task owing to pixel intensity overlapping, ambiguous edges, and complex backgrounds. The authors address this problem with a novel active surface scheme, which minimizes an energy functional combining both edge- and region-based information. Methods: In this semiautomatic method, the evolving surface is principally attracted to strong edges but is facilitated by the region-based information where edge information is missing. As avoiding oversegmentation is the primary challenge, the authors take into account multiple features and appearance context information. Discriminative cues, such as multilayer consecutiveness and local organ deformation are also implicitly incorporated. Case-specific intensity and appearance constraints are included to cope with the typically large appearance variations over multiple images. Spatially adaptive balancing weights are employed to handle the nonuniformity of image features. Results: Comparisons and validations on difficult cases showed that the authors’ model can effectively discriminate the liver from adhering background tissues. Boundaries weak in gradient or with no local evidence (e.g., small edge gaps or parts with similar intensity to the background) were delineated without additional user constraint. With an average surface distance of 0.9 mm and an average volume overlap of 93.9% on the MICCAI data set, the authors’ model outperformed most state-of-the-art methods. Validations on eight volumes with different initial conditions had segmentation score variances mostly less than unity. Conclusions: The proposed model can efficiently delineate ambiguous liver edges from complex tissue backgrounds with reproducibility. Quantitative validations and comparative results demonstrate the accuracy and efficacy of the model.

  15. 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

  16. 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

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

    PubMed

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

    2009-05-01

    A novel super-resolution reconstruction (SRR) framework in magnetic resonance imaging (MRI) is proposed. Its purpose is to produce images of both high resolution and high contrast desirable for image-guided minimally invasive brain surgery. The input data are multiple 2-D multislice inversion recovery MRI scans acquired at orientations with regular angular spacing rotated around a common frequency encoding axis. The output is a 3-D volume of isotropic high resolution. The inversion process resembles a localized projection reconstruction problem. Iterative algorithms for reconstruction are based on the projection onto convex sets (POCS) formalism. Results demonstrate resolution enhancement in simulated phantom studies, and ex vivo and in vivo human brain scans, carried out on clinical scanners. A comparison with previously published SRR methods shows favorable characteristics in the proposed approach. PMID:19272995

  18. 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

  19. 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

  20. Parametric 3D Atmospheric Reconstruction in Highly Variable Terrain with Recycled Monte Carlo Paths and an Adapted Bayesian Inference Engine

    NASA Technical Reports Server (NTRS)

    Langmore, Ian; Davis, Anthony B.; Bal, Guillaume; Marzouk, Youssef M.

    2012-01-01

    We describe a method for accelerating a 3D Monte Carlo forward radiative transfer model to the point where it can be used in a new kind of Bayesian retrieval framework. The remote sensing challenge is to detect and quantify a chemical effluent of a known absorbing gas produced by an industrial facility in a deep valley. The available data is a single low resolution noisy image of the scene in the near IR at an absorbing wavelength for the gas of interest. The detected sunlight has been multiply reflected by the variable terrain and/or scattered by an aerosol that is assumed partially known and partially unknown. We thus introduce a new class of remote sensing algorithms best described as "multi-pixel" techniques that call necessarily for a 3D radaitive transfer model (but demonstrated here in 2D); they can be added to conventional ones that exploit typically multi- or hyper-spectral data, sometimes with multi-angle capability, with or without information about polarization. The novel Bayesian inference methodology uses adaptively, with efficiency in mind, the fact that a Monte Carlo forward model has a known and controllable uncertainty depending on the number of sun-to-detector paths used.

  1. A novel method of target recognition based on 3D-color-space locally adaptive regression kernels model

    NASA Astrophysics Data System (ADS)

    Liu, Jiaqi; Han, Jing; Zhang, Yi; Bai, Lianfa

    2015-10-01

    Locally adaptive regression kernels model can describe the edge shape of images accurately and graphic trend of images integrally, but it did not consider images' color information while the color is an important element of an image. Therefore, we present a novel method of target recognition based on 3-D-color-space locally adaptive regression kernels model. Different from the general additional color information, this method directly calculate the local similarity features of 3-D data from the color image. The proposed method uses a few examples of an object as a query to detect generic objects with incompact, complex and changeable shapes. Our method involves three phases: First, calculating the novel color-space descriptors from the RGB color space of query image which measure the likeness of a voxel to its surroundings. Salient features which include spatial- dimensional and color -dimensional information are extracted from said descriptors, and simplifying them to construct a non-similar local structure feature set of the object class by principal components analysis (PCA). Second, we compare the salient features with analogous features from the target image. This comparison is done using a matrix generalization of the cosine similarity measure. Then the similar structures in the target image are obtained using local similarity structure statistical matching. Finally, we use the method of non-maxima suppression in the similarity image to extract the object position and mark the object in the test image. Experimental results demonstrate that our approach is effective and accurate in improving the ability to identify targets.

  2. 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.

  3. 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

  4. 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

  5. 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

  6. Adaptive 4D MR Imaging Using Navigator-Based Respiratory Signal for MRI-Guided Therapy

    PubMed Central

    Tokuda, Junichi; Morikawa, Shigehiro; Haque, Hasnine A.; Tsukamoto, Tetsuji; Matsumiya, Kiyoshi; Liao, Hongen; Masamune, Ken; Dohi, Takeyoshi

    2010-01-01

    For real-time 3D visualization of respiratory organ motion for MRI-guided therapy, a new adaptive 4D MR imaging method based on navigator echo and multiple gating windows was developed. This method was designed to acquire a time series of volumetric 3D images of a cyclically moving organ, enabling therapy to be guided by synchronizing the 4D image with the actual organ motion in real time. The proposed method was implemented in an open-configuration 0.5T clinical MR scanner. To evaluate the feasibility and determine optimal imaging conditions, studies were conducted with a phantom, volunteers, and a patient. In the phantom study the root mean square (RMS) position error in the 4D image of the cyclically moving phantom was 1.9 mm and the imaging time was ≈10 min when the 4D image had six frames. In the patient study, 4D images were successfully acquired under clinical conditions and a liver tumor was discriminated in the series of frames. The image quality was affected by the relations among the encoding direction, the slice orientation, and the direction of motion of the target organ. In conclusion, this study has shown that the proposed method is feasible and capable of providing a real-time dynamic 3D atlas for surgical navigation with sufficient accuracy and image quality. PMID:18429011

  7. 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.

  8. 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.

  9. 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

  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. 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

  14. 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

  15. Robust Adaptive 3-D Segmentation of Vessel Laminae From Fluorescence Confocal Microscope Images and Parallel GPU Implementation

    PubMed Central

    Narayanaswamy, Arunachalam; Dwarakapuram, Saritha; Bjornsson, Christopher S.; Cutler, Barbara M.; Shain, William

    2010-01-01

    This paper presents robust 3-D algorithms to segment vasculature that is imaged by labeling laminae, rather than the lumenal volume. The signal is weak, sparse, noisy, nonuniform, low-contrast, and exhibits gaps and spectral artifacts, so adaptive thresholding and Hessian filtering based methods are not effective. The structure deviates from a tubular geometry, so tracing algorithms are not effective. We propose a four step approach. The first step detects candidate voxels using a robust hypothesis test based on a model that assumes Poisson noise and locally planar geometry. The second step performs an adaptive region growth to extract weakly labeled and fine vessels while rejecting spectral artifacts. To enable interactive visualization and estimation of features such as statistical confidence, local curvature, local thickness, and local normal, we perform the third step. In the third step, we construct an accurate mesh representation using marching tetrahedra, volume-preserving smoothing, and adaptive decimation algorithms. To enable topological analysis and efficient validation, we describe a method to estimate vessel centerlines using a ray casting and vote accumulation algorithm which forms the final step of our algorithm. Our algorithm lends itself to parallel processing, and yielded an 8× speedup on a graphics processor (GPU). On synthetic data, our meshes had average error per face (EPF) values of (0.1–1.6) voxels per mesh face for peak signal-to-noise ratios from (110–28 dB). Separately, the error from decimating the mesh to less than 1% of its original size, the EPF was less than 1 voxel/face. When validated on real datasets, the average recall and precision values were found to be 94.66% and 94.84%, respectively. PMID:20199906

  16. 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

  17. 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

  18. 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

  19. 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.

  20. 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

  1. 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

  2. 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.

  3. 3D imaging of cone photoreceptors over extended time periods using optical coherence tomography with adaptive optics

    NASA Astrophysics Data System (ADS)

    Kocaoglu, Omer P.; Lee, Sangyeol; Jonnal, Ravi S.; Wang, Qiang; Herde, Ashley E.; Besecker, Jason; Gao, Weihua; Miller, Donald T.

    2011-03-01

    Optical coherence tomography with adaptive optics (AO-OCT) is a highly sensitive, noninvasive method for 3D imaging of the microscopic retina. The purpose of this study is to advance AO-OCT technology by enabling repeated imaging of cone photoreceptors over extended periods of time (days). This sort of longitudinal imaging permits monitoring of 3D cone dynamics in both normal and diseased eyes, in particular the physiological processes of disc renewal and phagocytosis, which are disrupted by retinal diseases such as age related macular degeneration and retinitis pigmentosa. For this study, the existing AO-OCT system at Indiana underwent several major hardware and software improvements to optimize system performance for 4D cone imaging. First, ultrahigh speed imaging was realized using a Basler Sprint camera. Second, a light source with adjustable spectrum was realized by integration of an Integral laser (Femto Lasers, λc=800nm, ▵λ=160nm) and spectral filters in the source arm. For cone imaging, we used a bandpass filter with λc=809nm and ▵λ=81nm (2.6 μm nominal axial resolution in tissue, and 167 KHz A-line rate using 1,408 px), which reduced the impact of eye motion compared to previous AO-OCT implementations. Third, eye motion artifacts were further reduced by custom ImageJ plugins that registered (axially and laterally) the volume videos. In two subjects, cone photoreceptors were imaged and tracked over a ten day period and their reflectance and outer segment (OS) lengths measured. High-speed imaging and image registration/dewarping were found to reduce eye motion to a fraction of a cone width (1 μm root mean square). The pattern of reflections in the cones was found to change dramatically and occurred on a spatial scale well below the resolution of clinical instruments. Normalized reflectance of connecting cilia (CC) and OS posterior tip (PT) of an exemplary cone was 54+/-4, 47+/-4, 48+/-6, 50+/-5, 56+/-1% and 46+/-4, 53+/-4, 52+/-6, 50+/-5, 44

  4. Image Quality and Radiation Dose of CT Coronary Angiography with Automatic Tube Current Modulation and Strong Adaptive Iterative Dose Reduction Three-Dimensional (AIDR3D)

    PubMed Central

    Shen, Hesong; Dai, Guochao; Luo, Mingyue; Duan, Chaijie; Cai, Wenli; Liang, Dan; Wang, Xinhua; Zhu, Dongyun; Li, Wenru; Qiu, Jianping

    2015-01-01

    Purpose To investigate image quality and radiation dose of CT coronary angiography (CTCA) scanned using automatic tube current modulation (ATCM) and reconstructed by strong adaptive iterative dose reduction three-dimensional (AIDR3D). Methods Eighty-four consecutive CTCA patients were collected for the study. All patients were scanned using ATCM and reconstructed with strong AIDR3D, standard AIDR3D and filtered back-projection (FBP) respectively. Two radiologists who were blinded to the patients' clinical data and reconstruction methods evaluated image quality. Quantitative image quality evaluation included image noise, signal-to-noise ratio (SNR), and contrast-to-noise ratio (CNR). To evaluate image quality qualitatively, coronary artery is classified into 15 segments based on the modified guidelines of the American Heart Association. Qualitative image quality was evaluated using a 4-point scale. Radiation dose was calculated based on dose-length product. Results Compared with standard AIDR3D, strong AIDR3D had lower image noise, higher SNR and CNR, their differences were all statistically significant (P<0.05); compared with FBP, strong AIDR3D decreased image noise by 46.1%, increased SNR by 84.7%, and improved CNR by 82.2%, their differences were all statistically significant (P<0.05 or 0.001). Segments with diagnostic image quality for strong AIDR3D were 336 (100.0%), 486 (96.4%), and 394 (93.8%) in proximal, middle, and distal part respectively; whereas those for standard AIDR3D were 332 (98.8%), 472 (93.7%), 378 (90.0%), respectively; those for FBP were 217 (64.6%), 173 (34.3%), 114 (27.1%), respectively; total segments with diagnostic image quality in strong AIDR3D (1216, 96.5%) were higher than those of standard AIDR3D (1182, 93.8%) and FBP (504, 40.0%); the differences between strong AIDR3D and standard AIDR3D, strong AIDR3D and FBP were all statistically significant (P<0.05 or 0.001). The mean effective radiation dose was (2.55±1.21) mSv. Conclusion

  5. 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

  6. 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

  7. The Impact of Different Levels of Adaptive Iterative Dose Reduction 3D on Image Quality of 320-Row Coronary CT Angiography: A Clinical Trial

    PubMed Central

    Feger, Sarah; Rief, Matthias; Zimmermann, Elke; Martus, Peter; Schuijf, Joanne Désirée; Blobel, Jörg; Richter, Felicitas; Dewey, Marc

    2015-01-01

    Purpose The aim of this study was the systematic image quality evaluation of coronary CT angiography (CTA), reconstructed with the 3 different levels of adaptive iterative dose reduction (AIDR 3D) and compared to filtered back projection (FBP) with quantum denoising software (QDS). Methods Standard-dose CTA raw data of 30 patients with mean radiation dose of 3.2 ± 2.6 mSv were reconstructed using AIDR 3D mild, standard, strong and compared to FBP/QDS. Objective image quality comparison (signal, noise, signal-to-noise ratio (SNR), contrast-to-noise ratio (CNR), contour sharpness) was performed using 21 measurement points per patient, including measurements in each coronary artery from proximal to distal. Results Objective image quality parameters improved with increasing levels of AIDR 3D. Noise was lowest in AIDR 3D strong (p≤0.001 at 20/21 measurement points; compared with FBP/QDS). Signal and contour sharpness analysis showed no significant difference between the reconstruction algorithms for most measurement points. Best coronary SNR and CNR were achieved with AIDR 3D strong. No loss of SNR or CNR in distal segments was seen with AIDR 3D as compared to FBP. Conclusions On standard-dose coronary CTA images, AIDR 3D strong showed higher objective image quality than FBP/QDS without reducing contour sharpness. Trial Registration Clinicaltrials.gov NCT00967876 PMID:25945924

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. Adaptive step ODE algorithms for the 3D simulation of electric heart activity with graphics processing units.

    PubMed

    Garcia-Molla, V M; Liberos, A; Vidal, A; Guillem, M S; Millet, J; Gonzalez, A; Martinez-Zaldivar, F J; Climent, A M

    2014-01-01

    In this paper we studied the implementation and performance of adaptive step methods for large systems of ordinary differential equations systems in graphics processing units, focusing on the simulation of three-dimensional electric cardiac activity. The Rush-Larsen method was applied in all the implemented solvers to improve efficiency. We compared the adaptive methods with the fixed step methods, and we found that the fixed step methods can be faster while the adaptive step methods are better in terms of accuracy and robustness. PMID:24377685

  14. Development of a solution adaptive unstructured scheme for quasi-3D inviscid flows through advanced turbomachinery cascades

    NASA Technical Reports Server (NTRS)

    Usab, William J., Jr.; Jiang, Yi-Tsann

    1991-01-01

    The objective of the present research is to develop a general solution adaptive scheme for the accurate prediction of inviscid quasi-three-dimensional flow in advanced compressor and turbine designs. The adaptive solution scheme combines an explicit finite-volume time-marching scheme for unstructured triangular meshes and an advancing front triangular mesh scheme with a remeshing procedure for adapting the mesh as the solution evolves. The unstructured flow solver has been tested on a series of two-dimensional airfoil configurations including a three-element analytic test case presented here. Mesh adapted quasi-three-dimensional Euler solutions are presented for three spanwise stations of the NASA rotor 67 transonic fan. Computed solutions are compared with available experimental data.

  15. A parallelized surface extraction algorithm for large binary image data sets based on an adaptive 3D delaunay subdivision strategy.

    PubMed

    Ma, Yingliang; Saetzler, Kurt

    2008-01-01

    In this paper we describe a novel 3D subdivision strategy to extract the surface of binary image data. This iterative approach generates a series of surface meshes that capture different levels of detail of the underlying structure. At the highest level of detail, the resulting surface mesh generated by our approach uses only about 10% of the triangles in comparison to the marching cube algorithm (MC) even in settings were almost no image noise is present. Our approach also eliminates the so-called "staircase effect" which voxel based algorithms like the MC are likely to show, particularly if non-uniformly sampled images are processed. Finally, we show how the presented algorithm can be parallelized by subdividing 3D image space into rectilinear blocks of subimages. As the algorithm scales very well with an increasing number of processors in a multi-threaded setting, this approach is suited to process large image data sets of several gigabytes. Although the presented work is still computationally more expensive than simple voxel-based algorithms, it produces fewer surface triangles while capturing the same level of detail, is more robust towards image noise and eliminates the above-mentioned "staircase" effect in anisotropic settings. These properties make it particularly useful for biomedical applications, where these conditions are often encountered. PMID:17993710

  16. 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

  17. Adaptation, Commissioning, and Evaluation of a 3D Treatment Planning System for High-Resolution Small-Animal Irradiation.

    PubMed

    Jeong, Jeho; Chen, Qing; Febo, Robert; Yang, Jie; Pham, Hai; Xiong, Jian-Ping; Zanzonico, Pat B; Deasy, Joseph O; Humm, John L; Mageras, Gig S

    2016-06-01

    Although spatially precise systems are now available for small-animal irradiations, there are currently limited software tools available for treatment planning for such irradiations. We report on the adaptation, commissioning, and evaluation of a 3-dimensional treatment planning system for use with a small-animal irradiation system. The 225-kV X-ray beam of the X-RAD 225Cx microirradiator (Precision X-Ray) was commissioned using both ion-chamber and radiochromic film for 10 different collimators ranging in field size from 1 mm in diameter to 40 × 40 mm(2) A clinical 3-dimensional treatment planning system (Metropolis) developed at our institution was adapted to small-animal irradiation by making it compatible with the dimensions of mice and rats, modeling the microirradiator beam orientations and collimators, and incorporating the measured beam data for dose calculation. Dose calculations in Metropolis were verified by comparison with measurements in phantoms. Treatment plans for irradiation of a tumor-bearing mouse were generated with both the Metropolis and the vendor-supplied software. The calculated beam-on times and the plan evaluation tools were compared. The dose rate at the central axis ranges from 74 to 365 cGy/min depending on the collimator size. Doses calculated with Metropolis agreed with phantom measurements within 3% for all collimators. The beam-on times calculated by Metropolis and the vendor-supplied software agreed within 1% at the isocenter. The modified 3-dimensional treatment planning system provides better visualization of the relationship between the X-ray beams and the small-animal anatomy as well as more complete dosimetric information on target tissues and organs at risk. It thereby enhances the potential of image-guided microirradiator systems for evaluation of dose-response relationships and for preclinical experimentation generally. PMID:25948321

  18. Evaluation of a prototype 3D ultrasound system for multimodality imaging of cervical nodes for adaptive radiation therapy

    NASA Astrophysics Data System (ADS)

    Fraser, Danielle; Fava, Palma; Cury, Fabio; Vuong, Te; Falco, Tony; Verhaegen, Frank

    2007-03-01

    Sonography has good topographic accuracy for superficial lymph node assessment in patients with head and neck cancers. It is therefore an ideal non-invasive tool for precise inter-fraction volumetric analysis of enlarged cervical nodes. In addition, when registered with computed tomography (CT) images, ultrasound information may improve target volume delineation and facilitate image-guided adaptive radiation therapy. A feasibility study was developed to evaluate the use of a prototype ultrasound system capable of three dimensional visualization and multi-modality image fusion for cervical node geometry. A ceiling-mounted optical tracking camera recorded the position and orientation of a transducer in order to synchronize the transducer's position with respect to the room's coordinate system. Tracking systems were installed in both the CT-simulator and radiation therapy treatment rooms. Serial images were collected at the time of treatment planning and at subsequent treatment fractions. Volume reconstruction was performed by generating surfaces around contours. The quality of the spatial reconstruction and semi-automatic segmentation was highly dependent on the system's ability to track the transducer throughout each scan procedure. The ultrasound information provided enhanced soft tissue contrast and facilitated node delineation. Manual segmentation was the preferred method to contour structures due to their sonographic topography.

  19. Development 3D model of adaptation of the Azerbaijan coastal zone at the various levels of Caspian Sea

    NASA Astrophysics Data System (ADS)

    Mammadov, Ramiz

    2013-04-01

    coastal areas at hydraulic engineering projects the sea level should be considered as multistage process, what we have considered by development of adaptation of a coastal zone The exact three-dimensional map of a coastal zone has been created. For different scenario sea levels, or example, -30.0; -29.0; -28.0; -27.0; -26.0; -25.0 and -24.0 exact coastal lines have been certain. Further maps of a vegetative cover, ground, social and economic and ecological conditions have been developed for different level and respective alterations are certain. More vulnerable coastal zone, flooded area and socio-economic damage were estimated.

  20. 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

  1. 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

  2. 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

  3. Adaptive thresholding for reliable topological inference in single subject fMRI analysis.

    PubMed

    Gorgolewski, Krzysztof J; Storkey, Amos J; Bastin, Mark E; Pernet, Cyril R

    2012-01-01

    Single subject fMRI has proved to be a useful tool for mapping functional areas in clinical procedures such as tumor resection. Using fMRI data, clinicians assess the risk, plan and execute such procedures based on thresholded statistical maps. However, because current thresholding methods were developed mainly in the context of cognitive neuroscience group studies, most single subject fMRI maps are thresholded manually to satisfy specific criteria related to single subject analyzes. Here, we propose a new adaptive thresholding method which combines Gamma-Gaussian mixture modeling with topological thresholding to improve cluster delineation. In a series of simulations we show that by adapting to the signal and noise properties, the new method performs well in terms of total number of errors but also in terms of the trade-off between false negative and positive cluster error rates. Similarly, simulations show that adaptive thresholding performs better than fixed thresholding in terms of over and underestimation of the true activation border (i.e., higher spatial accuracy). Finally, through simulations and a motor test-retest study on 10 volunteer subjects, we show that adaptive thresholding improves reliability, mainly by accounting for the global signal variance. This in turn increases the likelihood that the true activation pattern can be determined offering an automatic yet flexible way to threshold single subject fMRI maps. PMID:22936908

  4. Reduction of EEG artifacts in simultaneous EEG-fMRI: Reference layer adaptive filtering (RLAF).

    PubMed

    Steyrl, David; Patz, Franz; Krausz, Gunther; Edlinger, Günter; Müller-Putz, Gernot R

    2015-08-01

    Although simultaneous measurement of electroencephalography (EEG) and functional magnetic resonance imaging (fMRI) is one of the most valuable methods for studying human brain activity non-invasively, it remains challenging to measure high quality EEG inside the MRI scanner. Recently, a new approach for minimizing residual MRI scanner artifacts in the EEG was presented: reference layer artifact subtraction (RLAS). Here, reference electrodes capture only the artifacts, which are subsequently subtracted from the measurement electrodes. With the present work we demonstrate that replacing the subtraction by adaptive filtering statistically significantly outperforms RLAS. Reference layer adaptive filtering (RLAF) attenuates the average artifact root-mean-square (RMS) voltage of the passive MRI scanner to 0.7 μV (-14.4 dB). RLAS achieves 0.78 μV (-13.5 dB). The combination of average artifact subtraction (AAS) and RLAF reduces the residual average gradient artifact RMS voltage to 2.3 μV (-49.2 dB). AAS alone achieves 5.7 μV (-39.0 dB). All measurements were conducted with an MRI phantom, as the reference layer cap available to us was a prototype. PMID:26737122

  5. Bayesian symmetrical EEG/fMRI fusion with spatially adaptive priors

    PubMed Central

    Luessi, Martin; Babacan, S. Derin; Molina, Rafael; Booth, James R.; Katsaggelos, Aggelos K.

    2011-01-01

    In this paper, we propose a novel symmetrical EEG/fMRI fusion method which combines EEG and fMRI by means of a common generative model. We use a total variation (TV) prior to model the spatial distribution of the cortical current responses and hemodynamic response functions, and utilize spatially adaptive temporal priors to model their temporal shapes. The spatial adaptivity of the prior model allows for adaptation to the local characteristics of the estimated responses and leads to high estimation performance for the cortical current distribution and the hemodynamic response functions. We utilize a Bayesian formulation with a variational Bayesian framework and obtain a fully automatic fusion algorithm. Simulations with synthetic data and experiments with real data from a multimodal study on face perception demonstrate the performance of the proposed method. PMID:21130173

  6. Adaptation of a haptic robot in a 3T fMRI.

    PubMed

    Snider, Joseph; Plank, Markus; May, Larry; Liu, Thomas T; Poizner, Howard

    2011-01-01

    .6 lbs) but extremely stiff 3/4" graphite and well balanced on the 3DoF joint in the middle. The end result is an fMRI compatible, haptic system with about 1 cubic foot of working space, and, when combined with virtual reality, it allows for a new set of experiments to be performed in the fMRI environment including naturalistic reaching, passive displacement of the limb and haptic perception, adaptation learning in varying force fields, or texture identification. PMID:21989084

  7. A novel adaptive biogeochemical model, and its 3-D application for a decadal hindcast simulation of the biogeochemistry of the southern North Sea

    NASA Astrophysics Data System (ADS)

    Kerimoglu, Onur; Hofmeister, Richard; Wirtz, Kai

    2016-04-01

    Adaptation and acclimation processes are often ignored in ecosystem-scale model implementations, despite the long-standing recognition of their importance. Here we present a novel adaptive phytoplankton growth model where acclimation of the community to the changes in external resource ratios is accounted for, using optimality principles and dynamic physiological traits. We show that the model can reproduce the internal stoichiometries obtained at marginal supply ratios in chemostat experiments. The model is applied in a decadal hindcast simulation of the southern North Sea, where it is coupled to a 2-D benthic model and a 3-D hydrodynamic model in an approximately 1.5km horizontal resolution at the German Bight coast. The model is shown to have good skill in capturing the steep, coastal gradients in the German Bight, suggested by the match between the estimated and observed dissolved nutrient and chlorophyll concentrations. We then analyze the differential sensitivity of the coastal and off-shore zones to major drivers of the system, such as riverine nutrient loads. We demonstrate that the relevance of phytoplankton acclimation varies across coastal gradients and can become particularly significant in terms of summer nutrient depletion.

  8. An adaptive 3D region growing algorithm to automatically segment and identify thoracic aorta and its centerline using computed tomography angiography scans

    NASA Astrophysics Data System (ADS)

    Ferreira, F.; Dehmeshki, J.; Amin, H.; Dehkordi, M. E.; Belli, A.; Jouannic, A.; Qanadli, S.

    2010-03-01

    Thoracic Aortic Aneurysm (TAA) is a localized swelling of the thoracic aorta. The progressive growth of an aneurysm may eventually cause a rupture if not diagnosed or treated. This necessitates the need for an accurate measurement which in turn calls for the accurate segmentation of the aneurysm regions. Computer Aided Detection (CAD) is a tool to automatically detect and segment the TAA in the Computer tomography angiography (CTA) images. The fundamental major step of developing such a system is to develop a robust method for the detection of main vessel and measuring its diameters. In this paper we propose a novel adaptive method to simultaneously segment the thoracic aorta and to indentify its center line. For this purpose, an adaptive parametric 3D region growing is proposed in which its seed will be automatically selected through the detection of the celiac artery and the parameters of the method will be re-estimated while the region is growing thorough the aorta. At each phase of region growing the initial center line of aorta will also be identified and modified through the process. Thus the proposed method simultaneously detect aorta and identify its centerline. The method has been applied on CT images from 20 patients with good agreement with the visual assessment by two radiologists.

  9. 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.

  10. MRI-guided prostate adaptive radiotherapy - A systematic review.

    PubMed

    McPartlin, A J; Li, X A; Kershaw, L E; Heide, U; Kerkmeijer, L; Lawton, C; Mahmood, U; Pos, F; van As, N; van Herk, M; Vesprini, D; van der Voort van Zyp, J; Tree, A; Choudhury, A

    2016-06-01

    Dose escalated radiotherapy improves outcomes for men with prostate cancer. A plateau for benefit from dose escalation using EBRT may not have been reached for some patients with higher risk disease. The use of increasingly conformal techniques, such as step and shoot IMRT or more recently VMAT, has allowed treatment intensification to be achieved whilst minimising associated increases in toxicity to surrounding normal structures. To support further safe dose escalation, the uncertainties in the treatment target position will need be minimised using optimal planning and image-guided radiotherapy (IGRT). In particular the increasing usage of profoundly hypo-fractionated stereotactic therapy is predicated on the ability to confidently direct treatment precisely to the intended target for the duration of each treatment. This article reviews published studies on the influences of varies types of motion on daily prostate position and how these may be mitigated to improve IGRT in future. In particular the role that MRI has played in the generation of data is discussed and the potential role of the MR-Linac in next-generation IGRT is discussed. PMID:27162159