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Probabilistic white matter fiber tracking using particle filtering and von Mises–Fisher sampling

Fan Zhang, Edwin R. Hancock, Casey Goodlett, Guido Gerig
2009 Medical Image Analysis  
Finally, the importance density function for particle filtering is modeled using the von Mises-Fisher distribution on a unit sphere.  ...  Standard particle filtering technique have previously been applied to the problem of fiber tracking by Brun et al. (2002) and Bjornemo et al. (2002) .  ...  In this paper, we present a new and fast probabilistic fiber tracking algorithm which utilises the particle filtering technique and von Mises-Fisher sampling.  ... 
doi:10.1016/j.media.2008.05.001 pmid:18602332 pmcid:PMC2771420 fatcat:lvluw7e22jbmhc5zkrswjvqk6m

Outdoor human motion capture using inverse kinematics and von mises-fisher sampling

Gerard Pons-Moll, Andreas Baak, Juergen Gall, Laura Leal-Taixe, Meinard Muller, Hans-Peter Seidel, Bodo Rosenhahn
2011 2011 International Conference on Computer Vision  
Additionally, we introduce a novel sensor noise model to account for uncertainties based on the von Mises-Fisher distribution.  ...  Employing an annealing particle-based optimization scheme, our idea is to use orientation cues derived from the inertial input to sample particles from the manifold of valid poses.  ...  This work has been supported by the German Research Foundation (DFG CL 64/5-1 and DFG MU 2686/3-1). Meinard Müller is funded by the Cluster of Excellence on Multimodal Computing and Interaction.  ... 
doi:10.1109/iccv.2011.6126375 dblp:conf/iccv/Pons-MollBGLMSR11 fatcat:d4ugmhgu3jer7fl5cbhsgt4vni

Probabilistic Tractography Using Q-Ball Modeling and Particle Filtering [chapter]

Julien Pontabry, François Rousseau
2011 Lecture Notes in Computer Science  
In this paper, we investigate the use of an analytical Q-ball model for the diffusion data within a well-formalized particle filtering framework.  ...  The proposed method is validated and compared to other tracking algorithms on the MICCAI'09 contest Fiber Cup phantom and on in-vivo brain DWMRI data.  ...  Then, a non-linear state-model is used for the tracking modeling and the probabilistic maps of fibers are estimated using a particle filtering algorithm.  ... 
doi:10.1007/978-3-642-23629-7_26 fatcat:hdx2fiwtl5fjbbatd3wx3ro6iy

Adaptive Multi-modal Particle Filtering for Probabilistic White Matter Tractography [chapter]

Aymeric Stamm, Olivier Commowick, Christian Barillot, Patrick Pérez
2013 Lecture Notes in Computer Science  
Particle filtering has recently been introduced to perform probabilistic tractography in conjunction with DTI and Q-Ball models to estimate the diffusion information.  ...  For brain white matter tractography, this means that multiple fiber pathways are unlikely to be tracked over extended volumes.  ...  The von Mises & Fisher distribution on the sphere [14] is particularly well adapted to perform this sampling and has been used within a particle filter in which fiber pathways are reconstructed as first  ... 
doi:10.1007/978-3-642-38868-2_50 pmid:24684002 fatcat:cjzdgddrzzhtpo2jf2xtgkxiom

Data-Driven Manifolds for Outdoor Motion Capture [chapter]

Gerard Pons-Moll, Laura Leal-Taixé, Juergen Gall, Bodo Rosenhahn
2012 Lecture Notes in Computer Science  
Additionally, we introduce a novel sensor noise model to account for uncertainties based on the von Mises-Fisher distribution.  ...  Employing an annealing particle-based optimization scheme, our idea is to use orientation cues derived from the inertial input to sample particles from the manifold of valid poses.  ...  In the context of particle filters, the von Mises-Fisher distribution has been used as prior distribution for extracting white matter fiber pathways from MRI data [40] .  ... 
doi:10.1007/978-3-642-34091-8_14 fatcat:avmlwel5xrgx7na7gbh453puuu

TractoInferno: A large-scale, open-source, multi-site database for machine learning dMRI tractography [article]

Philippe Poulin, Guillaume Theaud, Francois Rheault, Etienne St-Onge, Arnaud Bore, Emmanuelle Renauld, Louis De Beaumont, Samuel Guay, Pierre-Marc Jodoin, Maxime Descoteaux
2021 bioRxiv   pre-print
Available data includes T1-weighted images, single-shell diffusion MRI (dMRI) acquisitions, spherical harmonics fitted to the dMRI signal, fiber ODFs, and reference streamlines for 30 delineated bundles  ...  generated using 4 tractography algorithms, as well as masks needed to run tractography algorithms.  ...  Probabilistic tracking and Particle-Filtered Tractography Probabilistic tracking [39] samples a new streamline direction inside a cone of evaluation aligned with the previous direction, with a probability  ... 
doi:10.1101/2021.11.29.470422 fatcat:botvws6xobdvrhrgacaztuf24e

Probabilistic tractography using Q-ball imaging and particle filtering: Application to adult and in-utero fetal brain studies

J. Pontabry, F. Rousseau, E. Oubel, C. Studholme, M. Koob, J.-L. Dietemann
2013 Medical Image Analysis  
In this paper, we investigate the use of an analytical Q-ball model for the diffusion data within a well-formalized particle filtering framework.  ...  The proposed method is validated and compared to other tracking algorithms on the MICCAI'09 contest Fiber Cup phantom.  ...  Then, a nonlinear state-model is used for the tracking modeling and the probabilistic maps of fibers are estimated using a particle filtering algorithm.  ... 
doi:10.1016/j.media.2012.11.004 pmid:23265801 fatcat:7d5sap5isvgqhfdex7y76hjqa4

Modeling Diffusion Directions of Corpus Callosum [chapter]

Safa Elsheikh, Andrew Fish, Roma Chakrabarti, Diwei Zhou, Mara Cercignani
2017 Communications in Computer and Information Science  
The von Mises-Fisher distribution (vmf) is a probability distribution for modeling directional data on the unit hypersphere.  ...  Diffusion Tensor Imaging (DTI) has been used to study the characteristics of Multiple Sclerosis (MS) in the brain.  ...  A probabilistic fiber tracking algorithm using a particle filtering technique and vmf sampling has been proposed in [6] .  ... 
doi:10.1007/978-3-319-60964-5_45 fatcat:uw4vcgmrevaylpudtrypctq65y

Estimation of Local Orientations in Fibrous Structures With Applications to the Purkinje System

Hasan E Çetingül, Gernot Plank, Natalia A Trayanova, René Vidal
2011 IEEE Transactions on Biomedical Engineering  
To deal with these challenges, we propose a framework that estimates local fiber orientations with high accuracy and reconstructs the fibers via tracking.  ...  The fiber/branch orientations are identified as the modes of the ODFs via spherical clustering and guide the extraction of the fiber centerlines.  ...  Institutes of Health (NIH) under Award HL082729, in part by the National Science Foundation (NSF) under Award CAREER IIS-0447739, in part by the Austrian Science Fund (FWF) under Grant SFB F3210-N18, and  ... 
doi:10.1109/tbme.2011.2116119 pmid:21335301 pmcid:PMC3130018 fatcat:a6mkwihwpnhgjhhkuboob3kcqu

Stochastic DT-MRI Connectivity Mapping on the GPU

Tim McGraw, Mariappan Nadar
2007 IEEE Transactions on Visualization and Computer Graphics  
A Bayesian formulation of the fiber model is given and it is shown that the inversion method can be used to construct plausible connectivity.  ...  Our implementation allows the user to interactively select regions of interest and observe the evolving connectivity results during computation.  ...  Brain dataset courtesy of Gordon Kindlmann at the Scientific Computing and Imaging Institute, University of Utah, and Andrew Alexander, W. M.  ... 
doi:10.1109/tvcg.2007.70597 pmid:17968103 fatcat:5lq2zt6pifcxnnczv6tpiix2ty

Probabilistic Fiber Tracking Using Particle Filtering [chapter]

Fan Zhang, Casey Goodlett, Edwin Hancock, Guido Gerig
Medical Image Computing and Computer-Assisted Intervention – MICCAI 2007  
Fast and efficient sampling is realised using the von Mises-Fisher distribution on unit spheres.  ...  The global tracking model is implemented using particle filtering, which allows us to recursively compute the posterior distribution of the potential fibers.  ...  Finally, we use the von Mises-Fisher distribution to model prior and the importance density for sampling particles.  ... 
doi:10.1007/978-3-540-75759-7_18 dblp:conf/miccai/ZhangGHG07 fatcat:awrtreapj5fk3aqmznl4n36fta

Feature Extraction for DW-MRI Visualization: The State of the Art and Beyond

Thomas Schultz, Marc Herbstritt
2011 Dagstuhl Publications  
In particular, it has been explored widely for imaging nerve fiber tracts in the human brain. Geometric features provide a quick visual overview of the complex datasets that arise from DW-MRI.  ...  It is the goal of this paper to survey contributions from all these fields, concentrating on streamline clustering, edge detection and segmentation, topological methods, and extraction of anisotropy creases  ...  Acknowledgement I would like to thank Gordon Kindlmann for helpful discussions about this paper, and Alfred Anwander (MPI CBS, Leipzig, Germany) for providing the DW-MRI dataset that was used to create  ... 
doi:10.4230/dfu.vol2.sciviz.2011.322 dblp:conf/dagstuhl/Schultz11 fatcat:4ovqks4gcbf5fadsjj3ts7b2nq

Anterior Cruciate Ligament: 3-D Fiber Anatomy, Fluorescence Arthroscopy & Healing

2016 Nederlands Tijdschrift voor Traumachirurgie  
Tom Gilbert and Cook Biotech for supplying the ECM-SIS, and the financial support of NIH #AR39683 and the Dutch Anna Fund is gratefully acknowledged.  ...  The study was sponsored by Mozaïek PhD training grant 017.004.076 from the Netherlands Organization for Scientific Research (NWO) and the Marti-Keuning Eckhart foundation.  ...  Goodlett, and G. Gerig. Probabilistic white matter fiber tracking using particle filtering and von Mises-Fisher sampling. Med Image Anal, 13(1):5-18, 2009.  ... 
doi:10.1007/s12506-016-0010-z fatcat:gxat5wblafhbbamhftuzpnqbre

Generation of 3D representative volume elements for heterogeneous materials: A review

Swantje Bargmann, Benjamin Klusemann, Jürgen Markmann, Jan Eike Schnabel, Konrad Schneider, Celal Soyarslan, Jana Wilmers
2018 Progress in Materials Science  
For completeness, relevant up-to-date software tools, used at various stages of RVE generation -either commercial or open-source -are summarized.  ...  Here, we divide heterogeneous solids into porous and non-porous media, with 0 < void volume fraction < 1 and void volume fraction = 0, respectively.  ...  Acknowledgements This work benefited from many fruitful discussions with co-workers and colleagues which is gratefully acknowledged.  ... 
doi:10.1016/j.pmatsci.2018.02.003 fatcat:aeie32pxmnfgdge2wmsnzadhvq

A Computational Approach to Understand Phenotypic Structure and Constitutive Mechanics Relationships of Single Cells

Scott T. Wood, Brian C. Dean, Delphine Dean
2012 Annals of Biomedical Engineering  
and actin stress fiber network of each cell.  ...  VSMCs are modeled here using a linear elastic material model together with truss elements, which simulate the cytoskeletal fiber network that provides the cells with much of their internal structural support  ...  REPRESENTATIVE VON MISES STRESS DISTRIBUTION (SHOWN IN CELL B)............................... 147 FIGURE 6.8.  ... 
doi:10.1007/s10439-012-0690-5 pmid:23180027 pmcid:PMC3594057 fatcat:c6hwpy5m25dvrgbp6hcscie4xe
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