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High-Fidelity Meshes from Tissue Samples for Diffusion MRI Simulations [chapter]

Eleftheria Panagiotaki, Matt G. Hall, Hui Zhang, Bernard Siow, Mark F. Lythgoe, Daniel C. Alexander
2010 Lecture Notes in Computer Science  
This paper presents a method for constructing detailed geometric models of tissue microstructure for synthesizing realistic diffusion MRI data.  ...  Randomwalk simulations within the resulting meshes provide synthetic diffusion MRI measurements.  ...  Thanks to Dr Chris Thrasivoulou for help with the confocal acquisition. Funded by EPSRC grants EP/E056938/1, EP/E007748, British Heart Foundation and BBSRC.  ... 
doi:10.1007/978-3-642-15745-5_50 fatcat:chy76hth4fbu5pqxawwiu67aca

A generative model of realistic brain cells with application to numerical simulation of diffusion-weighted MR signal [article]

Marco Palombo, Daniel C. Alexander, Hui Zhang
2018 arXiv   pre-print
Directly inspired by the advances in computational neuroscience for modelling brain cells, we propose a generative model that enables us to simulate molecular diffusion within realistic digitalised brain  ...  cells from available open-access databases.  ...  Here we demonstrated how this enables for the first time the design of numerical simulations for DW-MRI of digitalized ultra-realistic brain cell structures, achieving a new standard in fidelity.  ... 
arXiv:1806.07125v1 fatcat:mjpfscuvtva3tdqbqser42err4

Ex VivoFluorescence Molecular Tomography of the Spine

Monish Pimpalkhare, Jin Chen, Vivek Venugopal, Xavier Intes
2012 International Journal of Biomedical Imaging  
We investigated the potential of fluorescence molecular tomography to imageex vivosamples collected from a large animal model, in this case, a dog spine.  ...  Additionally, the incorporation of the heterogeneous nature of the tissue in the model to compute the Jacobians led to improved imaging performances.  ...  Linley to have provided support for the MRI imaging session.  ... 
doi:10.1155/2012/942326 pmid:23197973 pmcid:PMC3503328 fatcat:lacsomqs2rczren7udn23i2wuu

Multi-Scale Visual Analysis of Trauma Injury

Celina Imielinska, Andrzej Przekwas, XG Tan
2006 Information Visualization  
We propose a trauma injury simulation pipeline concept staring from anatomy and medical image-based high-fidelity 3D geometric modeling, extraction of tissue morphology, generation of computational grids  ...  We develop a multi-scale high-fidelity biomechanical and physiologically based modeling tools for trauma (ballistic/impact and blast) injury to brain, lung and spinal cord for resuscitation, treatment  ...  Udupa from University of Pennsylvania for letting us use 3DVIEWNIX to model head anatomy from the CT data and Autodesk for generous donation of Maya Software.  ... 
doi:10.1057/palgrave.ivs.9500137 fatcat:hkuxlqillvgqtgja7chdsmk33i

Impacts of Boundary Conforming Meshes on Electrical Cardiac Simulation [chapter]

Darrell J. Swenson, Joshua A. Levine, Jess D. Tate, Ross T. Whitaker, Rob S. MacLeod
2013 Proceedings of the 21st International Meshing Roundtable  
In the case of reaction diffusion simulations, by contrast, such meshing errors accounted for only an insignificant component of overall simulation uncertainty.  ...  The root mean squared error over the entire mesh was more modest, ranging from 1-6%.  ...  Simulations based on cardiac tissue also require a description of local muscle fiber direction, which was acquired using diffusion tensor MRI and applied to each mesh as anisotropic conductivity tensors  ... 
doi:10.1007/978-3-642-33573-0_34 dblp:conf/imr/SwensonLTWM12 fatcat:emckxveo6rdhxaxlrgvvyzng2a

Mathematical Methods in Biomedical Imaging

Wenxiang Cong, Kumar Durairaj, Peng Feng
2013 Computational and Mathematical Methods in Medicine  
Inverse Fast Fourier Transform (IFFT) is a standard method of image reconstruction in MRI from uniformly sampled K-space data.  ...  For MRI model, a mesh-deformation constraints based image registration algorithm was carefully investigated.  ...  Inverse Fast Fourier Transform (IFFT) is a standard method of image reconstruction in MRI from uniformly sampled K-space data.  ... 
doi:10.1155/2013/932794 pmid:24386007 pmcid:PMC3872393 fatcat:ylci4yktvbae5kg3e7pga6nhjy

Generation of histo-anatomically representative models of the individual heart: tools and application

G. Plank, R. A.B. Burton, P. Hales, M. Bishop, T. Mansoori, M. O. Bernabeu, A. Garny, A. J. Prassl, C. Bollensdorff, F. Mason, F. Mahmood, B. Rodriguez (+4 others)
2009 Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences  
The entire processing pipeline including image acquisition, image processing, mesh generation, model set-up and execution of computer simulations, and the underlying methods are described.  ...  The models are based on high-resolution three-dimensional anatomical and/or diffusion tensor magnetic resonance images, combined with serial histological sectioning data, and are used to investigate individualized  ...  Thus, optimal sample preparation for anatomical MRI scans involves doping of the tissue with gadodiamide to enhance contrast between extracellular space and myocardium.  ... 
doi:10.1098/rsta.2009.0056 pmid:19414455 pmcid:PMC2881535 fatcat:qh6v3rodsfbv3kwnsancv663je

Group-Wise Evaluation and Comparison of White Matter Fiber Strain and Maximum Principal Strain in Sports-Related Concussion

Songbai Ji, Wei Zhao, James C. Ford, Jonathan G. Beckwith, Richard P. Bolander, Richard M. Greenwald, Laura A. Flashman, Keith D. Paulsen, Thomas W. McAllister
2015 Journal of Neurotrauma  
Geometrically accurate subject-specific head models with high mesh quality were created based on the Dartmouth Head Injury Model (DHIM), which was successfully validated (performance categorized as "good  ...  with the percentage of WM voxels experiencing significant longitudinal changes of fractional anisotropy and mean diffusivity (3.2% and 3.44%, respectively) found from a separate independent study.  ...  Roth in the Brain Imaging Laboratory at the Geisel School of Medicine at Dartmouth College for assistance with image segmentation in MRI, and Drs. Philip V.  ... 
doi:10.1089/neu.2013.3268 pmid:24735430 pmcid:PMC4376290 fatcat:htt52cnl5net7nsmtxrvy2dm2a

Personalized computational modeling of left atrial geometry and transmural myofiber architecture

Thomas E. Fastl, Catalina Tobon-Gomez, Andrew Crozier, John Whitaker, Ronak Rajani, Karen P. McCarthy, Damian Sanchez-Quintana, Siew Y. Ho, Mark D. O'Neill, Gernot Plank, Martin J. Bishop, Steven A. Niederer
2018 Medical Image Analysis  
Personalized geometrical models included the heterogeneous thickness distribution of the left atrial myocardium and subsequent discretization led to high-fidelity tetrahedral FE meshes.  ...  ) meshes.  ...  Furthermore, important characteristics on the generated high-fidelity and high-resolution FE meshes are presented in Table 2 .  ... 
doi:10.1016/j.media.2018.04.001 pmid:29753182 pmcid:PMC6277816 fatcat:4m2v5vv3rbdsha4kptph7m5qvy

A Framework for the generation of digital twins of cardiac electrophysiology from clinical 12-leads ECGs

Karli Gillette, Matthias A.F. Gsell, Anton J. Prassl, Elias Karabelas, Ursula Reiter, Gert Reiter, Thomas Grandits, Christian Payer, Darko Štern, Martin Urschler, Jason D. Bayer, Christoph M. Augustin (+4 others)
2021 Medical Image Analysis  
bio-physically-detailed simulation required for parameter inference.  ...  Our study addresses three primary limitations impeding the routine generation of high-fidelity CDTs by introducing; a comprehensive parameter vector encapsulating all factors relating to the ventricular  ...  Simulations for this study were performed on the Vienna Scientific Cluster (VSC-4), which is maintained by the VSC Research Center in collaboration with the Information Technology Solutions of TU Wien.  ... 
doi:10.1016/j.media.2021.102080 pmid:33975097 fatcat:hbeko6s22re55htsb4nz4svwfe

A microstructurally based continuum model of cartilage viscoelasticity and permeability incorporating measured statistical fiber orientations

David M. Pierce, Michael J. Unterberger, Werner Trobin, Tim Ricken, Gerhard A. Holzapfel
2015 Biomechanics and Modeling in Mechanobiology  
By design, our modeling formulation accepts structural data on patient-specific collagen fiber networks as determined via diffusion tensor MRI.  ...  The remarkable mechanical properties of cartilage derive from an interplay of isotropically distributed, densely packed and negatively charged proteoglycans; a highly anisotropic and inhomogeneously oriented  ...  Eriksson from the University of Oxford, for help with ParFEAP; José Raya and Christian Glaser from the NYU Langone Medical Center for use of the diffusion tensor magnetic resonance imaging data; and Magnus  ... 
doi:10.1007/s10237-015-0685-x pmid:26001349 fatcat:fx5osxy5nzf5hn3ryflfviflq4

Using Cyber-Infrastructure for Dynamic Data Driven Laser Treatment of Cancer [chapter]

C. Bajaj, J. T. Oden, K. R. Diller, J. C. Browne, J. Hazle, I. Babuška, J. Bass, L. Bidaut, L. Demkowicz, A. Elliott, Y. Feng, D. Fuentes (+4 others)
2007 Lecture Notes in Computer Science  
region, higher intensity heat sources may be used to ablate the tissue.  ...  Hyperthermia based cancer treatments are used to increase the susceptibility of cancerous tissue to subsequent radiation or chemotherapy treatments, and in the case in which a tumor exists as a well-defined  ...  Figure 4 shows a quality hexahedral mesh obtained for finite element simulations from a set of MRI data (256x256x34 voxels) of a canine brain, Figure 3 .  ... 
doi:10.1007/978-3-540-72584-8_128 fatcat:mpzptmlbfbfpjm3bysidroidvm

Image-Based Personalization of Cardiac Anatomy for Coupled Electromechanical Modeling

A. Crozier, C. M. Augustin, A. Neic, A. J. Prassl, M. Holler, T. E. Fastl, A. Hennemuth, K. Bredies, T. Kuehne, M. J. Bishop, S. A. Niederer, G. Plank
2015 Annals of Biomedical Engineering  
Computational models of cardiac electromechanics (EM) are increasingly being applied to clinical problems, with patient-specific models being generated from high fidelity imaging and used to simulate patient  ...  Our method relies on using high resolution unstructured meshes for discretizing both physics, electrophysiology and mechanics, in combination with efficient, strongly scalable solvers necessary to deal  ...  generation of anatomical models for EM from medical images using existing mesh generation tools 54 with a high geometric fidelity.  ... 
doi:10.1007/s10439-015-1474-5 pmid:26424476 pmcid:PMC4690840 fatcat:5q7gu6fgqbbmrcal6fmquygnn4

Effects of Fibrosis Morphology on Reentrant Ventricular Tachycardia Inducibility and Simulation Fidelity in Patient-Derived Models

Jordan Ringenberg, Makarand Deo, David Filgueiras-Rama, Gonzalo Pizarro, Borja Ibañez, Rafael Peinado, José L. Merino, Omer Berenfeld, Vijay Devabhaktuni
2014 Clinical Medicine Insights: Cardiology  
We present a set of methods for constructing patient-specific computational models of human ventricles using in vivo MRI data for patients suffering from hypertension, hypercholesterolemia, and chronic  ...  Myocardial fibrosis detected via delayed-enhanced magnetic resonance imaging (MRI) has been shown to be a strong indicator for ventricular tachycardia (VT) inducibility.  ...  The authors would also like to acknowledge support from Dean Dr Nagi Naganathan of the College of Engineering at the University of Toledo in the form of graduate assistantship for PhD candidate Jordan  ... 
doi:10.4137/cmc.s15712 pmid:25368538 pmcid:PMC4210189 fatcat:cbsmekc2x5ckrkzpc5jhnimn7y

An Efficient Modelling-Simulation-Analysis Workflow to Investigate Stump-Socket Interaction Using Patient-Specific, Three-Dimensional, Continuum-Mechanical, Finite Element Residual Limb Models

Ellankavi Ramasamy, Okan Avci, Beate Dorow, Sook-Yee Chong, Leonardo Gizzi, Günter Steidle, Fritz Schick, Oliver Röhrle
2018 Frontiers in Bioengineering and Biotechnology  
The proposed approach is not only limited to modelling residual limbs but also has applications in predicting the impact of plastic surgery, for detailed forward-dynamics simulations of normal musculoskeletal  ...  AUTHOR CONTRIBUTIONS ER worked out most of the technical details, performed the numerical simulations and its analysis, and drafted the manuscript.  ...  S-YC and LG were in charge of the data collection, and GS and FS were in charge of the MRI imaging. OR devised, conceptualised and supervised the project and drafted parts of the manuscript.  ... 
doi:10.3389/fbioe.2018.00126 pmid:30283777 pmcid:PMC6156538 fatcat:el5ttk2np5gkdhup46ps5oywve
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