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Parallel Optimization of Fiber Bundle Segmentation for Massive Tractography Datasets

Andrea Vazquez, Narciso Lopez-Lopez, Nicole Labra, Miguel Figueroa, Cyril Poupon, Jean-Francois Mangin, Cecilia Hernandez, Pamela Guevara
2019 2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019)  
We present an optimized algorithm that performs automatic classification of white matter fibers based on a multi-subject bundle atlas.  ...  As a result, the segmentation of a subject of 4,145,000 fibers is reduced from about 14 minutes in the previous version to about 6 minutes, yielding an acceleration of 2.34.  ...  PARALLEL OPTIMIZATION OF FIBER BUNDLE SEGMENTATION FOR MASSIVE TRACTOGRAPHY DATASETS  ... 
doi:10.1109/isbi.2019.8759208 dblp:conf/isbi/VazquezLLFPMHG19 fatcat:46zgug3yc5dithw34epr7by7qm

ABrainVis: an android brain image visualization tool

Ignacio Osorio, Miguel Guevara, Danilo Bonometti, Diego Carrasco, Maxime Descoteaux, Cyril Poupon, Jean-François Mangin, Cecilia Hernández, Pamela Guevara
2021 BioMedical Engineering OnLine  
fiber bundles, MRI 3D images as rendered volumes and slices, and meshes.  ...  Results We present, ABrainVis, an Android mobile tool that allows users to visualize different types of brain images, such as white matter diffusion tractographies, represented as fibers in 3D, segmented  ...  Acknowledgements The authors thank Claudio Román and Liset González for pre-processing the data. Table 3 Page 22 of 23 Osorio et al. BioMed Eng OnLine (2021) 20:72  ... 
doi:10.1186/s12938-021-00909-0 pmid:34325693 pmcid:PMC8323223 fatcat:lehjftxyujdn5hbv6ig4shpvwy

Fiber Clustering Acceleration With a Modified Kmeans++ Algorithm Using Data Parallelism

Isaac Goicovich, Paulo Olivares, Claudio Román, Andrea Vázquez, Cyril Poupon, Jean-François Mangin, Pamela Guevara, Cecilia Hernández
2021 Frontiers in Neuroinformatics  
Fiber clustering methods are typically used in brain research to study the organization of white matter bundles from large diffusion MRI tractography datasets.  ...  This work proposes a parallel algorithm using a General Purpose Graphics Processing Unit (GPGPU) for fiber clustering based on the FFClust algorithm.  ...  For applications based on tractography datasets, some methods introduce parallelism using GPUs to improve the execution times for visualization of bundles and streamlines (Guevara et al., 2015; Combrisson  ... 
doi:10.3389/fninf.2021.727859 pmid:34539370 pmcid:PMC8445177 fatcat:mry5cozfinh4vc2fzvzbkunyvm

Robust clustering of massive tractography datasets

P. Guevara, C. Poupon, D. Rivière, Y. Cointepas, M. Descoteaux, B. Thirion, J.-F. Mangin
2011 NeuroImage  
This paper presents a clustering method that detects the fiber bundles embedded in any MR-diffusion based tractography dataset.  ...  For the sake of efficiency, part of the analysis is based on clustering the white matter (WM) voxels rather than the fibers.  ...  Adult HARDI datasets tractography: Streamline deterministic tractography was initiated from two seeds in each voxel of the propaga- Phantom datasets tractography: Two kinds of tractography for each diffusion  ... 
doi:10.1016/j.neuroimage.2010.10.028 pmid:20965259 fatcat:kockuz3zezexrjmp7r263uvu54

Tractography-based connectomes are dominated by false-positive connections [article]

Klaus Maier-Hein, Peter Neher, Jean-Christophe Houde, Marc-Alexandre Cote, Eleftherios Garyfallidis, Jidan Zhong, Maxime Chamberland, Fang-Cheng Yeh, Ying Chia Lin, Qing Ji, Wilburn E. Reddick, John O. Glass (+65 others)
2016 bioRxiv   pre-print
Fiber tractography based on non-invasive diffusion imaging is at the heart of connectivity studies of the human brain.  ...  Our results demonstrate fundamental ambiguities inherent to tract reconstruction methods based on diffusion orientation information, with critical consequences for the approach of diffusion tractography  ...  Such funnels embody hard bottlenecks for tractography, leading to massive combinatorial possibilities of plausible configurations for connecting the associated bundle endpoints as sketched in Figure 5c  ... 
doi:10.1101/084137 fatcat:c2s4nmf2kbdrrbpdde5y5afa44

Probabilistic Brain Fiber Tractography on GPUs

Mo Xu, Xiaorui Zhang, Yu Wang, Ling Ren, Ziyu Wen, Yi Xu, Gaolang Gong, Ningyi Xu, Huazhong Yang
2012 2012 IEEE 26th International Parallel and Distributed Processing Symposium Workshops & PhD Forum  
In this work we present a GPU-based probabilistic framework for brain fiber tractography.  ...  The probabilistic fiber tractography based on DT-MRI data behaves more robustly than deterministic approaches in the presence of fiber crossings, but requires more prohibitive computational time.  ...  The GPU, with massively parallel processors, proves suitable for general-purpose dataparallel scientific computation [16] .  ... 
doi:10.1109/ipdpsw.2012.92 dblp:conf/ipps/XuZWRWXGXY12 fatcat:khsy6ed5rrga3nkte52bqejqcu

Physical and digital phantoms for validating tractography and assessing artifacts

Ivana Drobnjak, Peter Neher, Cyril Poupon, Tabinda Sarwar
2021 NeuroImage  
, "What would the ideal phantom for validation fiber tractography look like?" and "What phantoms, phantom datasets and tools used for their creation are available to the research community?".  ...  Fiber tractography is widely used to non-invasively map white-matter bundles in vivo using diffusion-weighted magnetic resonance imaging (dMRI).  ...  Watanabe et al. (2006) proposed phantoms with parallel synthetic fibers along with curved and branched patterns to model the complex configuration of WM fiber bundles.  ... 
doi:10.1016/j.neuroimage.2021.118704 pmid:34748954 fatcat:zygzq576lnhqxekoixpnc4y3pq

COMMIT: Convex Optimization Modeling for Microstructure Informed Tractography

Alessandro Daducci, Alessandro Dal Palu, Alia Lemkaddem, Jean-Philippe Thiran
2015 IEEE Transactions on Medical Imaging  
Starting from an input set of candidate fiber-tracts, which are estimated from the data using standard fiber-tracking techniques, we model the diffusion MRI signal in each voxel of the image as a linear  ...  Then, we seek for the global weight of each of them, i.e. the effective contribution or volume, such that they globally fit the measured signal at best.  ...  ACKNOWLEDGMENTS The authors would like to thank Dr Yves Wiaux for many helpful discussions on convex optimization and Dr Marco Reisert for providing the code of GIBBS and suggesting the optimal parameters  ... 
doi:10.1109/tmi.2014.2352414 pmid:25167548 fatcat:cvvifjz7orhrhl6qyfr2htrl2e

Superficial white matter fiber systems impede detection of long-range cortical connections in diffusion MR tractography

Colin Reveley, Anil K. Seth, Carlo Pierpaoli, Afonso C. Silva, David Yu, Richard C. Saunders, David A. Leopold, Frank Q. Ye
2015 Proceedings of the National Academy of Sciences of the United States of America  
Here we demonstrate that the complex arrangement of white matter fibers residing just under the cortical sheet poses severe challenges for long-range tractography over roughly half of the brain.  ...  Because axonal projections originate and terminate in the gray matter but travel mainly through the deep white matter, the success of tractography hinges on the capacity to follow fibers across this transition  ...  Cibu Thomas for critical comments on the manuscript and Drs. Donna Dierker, Tim Coalson, and Matt Glasser for advice and discussion, and Drs.  ... 
doi:10.1073/pnas.1418198112 pmid:25964365 pmcid:PMC4450402 fatcat:5aw43erny5fshljhreksxecoti

AnatomiCuts: Hierarchical clustering of tractography streamlines based on anatomical similarity

Viviana Siless, Ken Chang, Bruce Fischl, Anastasia Yendiki
2018 NeuroImage  
The size of these datasets creates a need for automated clustering methods to group the streamlines into meaningful bundles.  ...  Diffusion MRI tractography produces massive sets of streamlines that contain a wealth of information on brain connections.  ...  Additional support was provided by the NIH Blueprint for Neuroscience Research (U01-MH093765; part of the multi-institutional Human Connectome Project, T90DA022759/R90DA023427).  ... 
doi:10.1016/j.neuroimage.2017.10.058 pmid:29100937 pmcid:PMC6152885 fatcat:mcp2h53etvdgberxqbscq5zpeq

Generalized Richardson-Lucy (GRL) for analyzing multi-shell diffusion MRI data [article]

Fenghua Guo, Alexander Leemans, Max A. Viergever, Flavio Dell'Acqua, Alberto De Luca
2020 arXiv   pre-print
The optimal weighting of multi-shell data in the fit and the robustness to noise and partial volume effects of GRL was studied with synthetic data.  ...  Subsequently, we investigated the performances of GRL in comparison to dRL on a high-resolution diffusion MRI dataset from the Human Connectome Project and on an MRI dataset acquired at 3T on a clinical  ...  F.D.A acknowledges funding from the Sackler Institute for Translational Neurodevelopment, Institute of  ... 
arXiv:1910.05372v3 fatcat:yb6o33xpqncjpa6bgqngqtebp4

Quantitative mapping of the brain's structural connectivity using diffusion MRI tractography: a review [article]

Fan Zhang, Alessandro Daducci, Yong He, Simona Schiavi, Caio Seguin, Robert Smith, Chun-Hung Yeh, Tengda Zhao, Lauren J. O'Donnell
2021 arXiv   pre-print
We first provide a review of methodology involved in three main processing steps that are common across most approaches for quantitative analysis of tractography, including methods for tractography correction  ...  , segmentation and quantification.  ...  CHY is grateful to the Ministry of Science and Technology of Taiwan (MOST 109-2222-E-182-001-MY3) for the support.  ... 
arXiv:2104.11644v1 fatcat:l3ixpcwu7jb7zcqo2sm5pswmja

Recognition of white matter bundles using local and global streamline-based registration and clustering

Eleftherios Garyfallidis, Marc-Alexandre Côté, Francois Rheault, Jasmeen Sidhu, Janice Hau, Laurent Petit, David Fortin, Stephen Cunanne, Maxime Descoteaux
2018 NeuroImage  
Having automated tools that can extract white matter bundles for tract-based studies of large numbers of people is of great interest for neuroscience and neurosurgical planning.  ...  The purpose of our proposed method, named RecoBundles, is to segment white matter bundles and make virtual dissection easier to perform.  ...  Descoteaux's Research Chair in Neuroinformatics for funding this research. We also thank Prof. David Fortin and Prof. Kevin Whittingstall for sharing some of the USherbrooke imaging data.  ... 
doi:10.1016/j.neuroimage.2017.07.015 pmid:28712994 fatcat:bpspukam5zeuxe6yu5ca3cqcmy

MaPPeRTrac: A Massively Parallel, Portable, and Reproducible Tractography Pipeline [article]

Joseph Moon, Peer-Timo Bremer, Pratik Mukherjee, Amy J Markowitz, Eva M Palacios, Alexis Rodriguez, Yuaki Xiao, Geoffrey T. Manley, Ravi Madduri
2020 bioRxiv   pre-print
The pipeline takes full advantage of HPC resources using the Parsl parallel programming framework, resulting in creation of connectome datasets of unprecedented size.  ...  It fully automates the entire tractography workflow, from management of raw MRI machine data to edge-density visualization of the connectome.  ...  To this end, we have developed MaPPeRTrac, a Massively Parallel, Portable, and Reproducible Tractography pipeline that is capable of: , 2016) .  ... 
doi:10.1101/2020.12.23.424191 fatcat:nbkkhkue5jbi5biduzqopxo2by

Using diffusion MRI data acquired with ultra-high gradients to improve tractography in routine-quality data [article]

C. Maffei, C. Lee, M. Planich, M. Ramprasad, N. Ravi, D. Trainor, Z. Urban, M. Kim, R.J. Jones, A. Henin, S.G. Hofmann, D.A. Pizzagalli (+6 others)
2021 bioRxiv   pre-print
In this study, we first update the classical protocols for tractography-based, manual annotation of major white-matter pathways, to adapt them to the much greater volume and variability of the streamlines  ...  for in vivo diffusion MRI acquisitions.  ...  Robust clustering of massive tractography datasets.  ... 
doi:10.1101/2021.06.28.450265 fatcat:laud55hjqzg6rhpd3cdqxsgyoa
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