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Inference of a HARDI Fiber Bundle Atlas Using a Two-Level Clustering Strategy [chapter]

Pamela Guevara, Cyril Poupon, Denis Rivière, Yann Cointepas, Linda Marrakchi, Maxime Descoteaux, Pierre Fillard, Bertrand Thirion, Jean-François Mangin
2010 Lecture Notes in Computer Science  
This model is made up of a set of generic fiber bundles that can be detected in most of the population. Our approach is based on a two-level clustering strategy.  ...  The second level is an intersubject clustering over fiber bundle centroids from all the subjects using a pairwise distance computed after spatial normalization.  ...  generated tracts to infer atlases of the fiber bundles.  ... 
doi:10.1007/978-3-642-15705-9_67 fatcat:g562krujkzdufd7coieqbiuug4

Segmentation of Short Association Bundles in Massive Tractography Datasets Using a Multi-subject Bundle Atlas [chapter]

Pamela Guevara, Delphine Duclap, Cyril Poupon, Linda Marrakchi-Kacem, Josselin Houenou, Marion Leboyer, Jean-François Mangin
2011 Lecture Notes in Computer Science  
The method is based on a multi-subject bundle atlas derived from a two-level intra-subject and inter-subject clustering strategy.  ...  An atlas of 47 bundles is inferred from a first database of 12 brains, and used to segment the same bundles in a second database of 10 brains.  ...  HARDI Multi-subject Fiber Bundle Atlas The two-level clustering was performed using the method described in [11] applied on database DB1, with some improvements.  ... 
doi:10.1007/978-3-642-25085-9_83 fatcat:ygne5rvcnvebja4lqyjnixxsp4

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.  ...  Our new version uses the local memory of each processor, which leads to a reduction in execution time. Hence, it allows the analysis of bigger subject and/or atlas datasets.  ...  The second strategy uses a fiber bundle atlas.  ... 
doi:10.1109/isbi.2019.8759208 dblp:conf/isbi/VazquezLLFPMHG19 fatcat:46zgug3yc5dithw34epr7by7qm

Robust clustering of massive tractography datasets

P. Guevara, C. Poupon, D. Rivière, Y. Cointepas, M. Descoteaux, B. Thirion, J.-F. Mangin
2011 NeuroImage  
The resulting regions of interest are used to define subset of fibers that are subdivided further into consistent bundles using a clustering of the fiber extremities.  ...  The dataset is reduced from more than one million fiber tracts to about two thousand fiber bundles. Validations are provided using simulated data and a physical phantom.  ...  of subjects to infer an atlas.  ... 
doi:10.1016/j.neuroimage.2010.10.028 pmid:20965259 fatcat:kockuz3zezexrjmp7r263uvu54

Automated multi-subject fiber clustering of mouse brain using dominant sets

Luca Dodero, Sebastiano Vascon, Vittorio Murino, Angelo Bifone, Alessandro Gozzi, Diego Sona
2015 Frontiers in Neuroinformatics  
Here we propose an automatic multi-subject fiber clustering method that enables retrieval of group-wise WM fiber bundles.  ...  The approach serves the final goal of detecting WM bundles at a population level, thus paving the way to the study of the WM organization across groups.  ...  This technique can be used to estimate the orientation of fibers at the voxel level, which can in turn be used by a number of tractography algorithms to build global fiber trajectories (Basser and Jones  ... 
doi:10.3389/fninf.2014.00087 pmid:25628561 pmcid:PMC4290731 fatcat:2qhdlvjwq5dihlle2z7h7lzx7y

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  ...  some of the figures.  ... 
doi:10.4230/dfu.vol2.sciviz.2011.322 dblp:conf/dagstuhl/Schultz11 fatcat:4ovqks4gcbf5fadsjj3ts7b2nq

Superficial white matter: A review on the dMRI analysis methods and applications

Miguel Guevara, Pamela Guevara, Claudio Román, Jean-François Mangin
2020 NeuroImage  
Therefore, the mapping of SWM bundles and the use of the resulting atlases for clinical studies requiere dedicated methodologies that are reviewed in this paper.  ...  The shape and localization of these short bundles present a high variability across subjects.  ...  All the clusters within these sub-categories were compared to the bundles in the other two atlases. The three atlas were transformed to MNI space.  ... 
doi:10.1016/j.neuroimage.2020.116673 pmid:32114152 fatcat:onw3cxzkvzau7lng54dtgzlwga

Active fibers: Matching deformable tract templates to diffusion tensor images

Ilya Eckstein, David W. Shattuck, Jason L. Stein, Katie L. McMahon, Greig de Zubicaray, Margaret J. Wright, Paul M. Thompson, Arthur W. Toga
2009 NeuroImage  
In the proposed method, a deformable fiber-bundle model is aligned directly with the subject tensor field, skipping the fiber tracking step.  ...  Furthermore, the use of a common template eliminates the need for tractography segmentation and defines intersubject shape correspondence.  ...  Acknowledgements This work is funded by the National Institutes of Health through the NIH Roadmap for Medical Research, Grant U54 RR021813.  ... 
doi:10.1016/j.neuroimage.2009.01.065 pmid:19457360 pmcid:PMC2720421 fatcat:76mq7755cncg3jhvnnqixfnora

Simultaneous ODF estimation and tractography in HARDI

H. E. Cetingul, M. Nadar, P. Thompson, G. Sapiro, C. Lenglet
2012 2012 Annual International Conference of the IEEE Engineering in Medicine and Biology Society  
In simulations, our method outperforms filtered two-tensor tractography at different levels of noise by achieving a reduction in mean Chamfer error of 0.05 to 0.27 voxels; it also produced in vivo fiber  ...  We consider the problem of tracking white matter fibers in high angular resolution diffusion imaging (HARDI) data while simultaneously estimating the local fiber orientation profile.  ...  As a result, we obtain configurations at different levels of complexity, which include intersecting linear or curved fibers (see Fig. 1(a) ).  ... 
doi:10.1109/embc.2012.6345877 pmid:23365838 dblp:conf/embc/CetingulNTSL12 fatcat:t6cujdb33jdr7fx4uoblwp77ua

The CONNECT project: Combining macro- and micro-structure

Yaniv Assaf, Daniel C. Alexander, Derek K. Jones, Albero Bizzi, Tim E.J. Behrens, Chris A. Clark, Yoram Cohen, Tim B. Dyrby, Petra S. Huppi, Thomas R. Knoesche, Denis LeBihan, Geoff J.M. Parker (+1 others)
2013 NeuroImage  
Recent applications of diffusion MRI aimed to characterize the structural connectome using tractography to infer connectivity between brain regions.  ...  in order to obtain a better estimate of the connectome, while also striving to extend validation of these measurements.  ...  Connectivity atlas. Rendering of the long WM fiber bundles (A,B,C) and of the short WM fiber bundles (D,E,F) for subject 1 of the ARCHI database.  ... 
doi:10.1016/j.neuroimage.2013.05.055 pmid:23727318 fatcat:2hlmflqpmnc3piswo6mybzai64

Ontology-based approach for in vivo human connectomics: the medial Brodmann area 6 case study

Tristan Moreau, Bernard Gibaud
2015 Frontiers in Neuroinformatics  
The aim of this study was to create a neuroanatomical ontology, called "Human Connectomics Ontology" (HCO), in order to represent macroscopic gray matter regions connected with fiber bundles assessed by  ...  Brodmann Area 6 was achieved using a set of queries.  ...  Poupon for the brain datasets used in this paper which were part of the NMR public database (Poupon et al., 2006) . We would like to thank Pr. X. Morandi and R.  ... 
doi:10.3389/fninf.2015.00009 pmid:25914640 pmcid:PMC4392700 fatcat:5hao2rthfjafpfwkpct2obcwoe

Post-mortem inference of the human hippocampal connectivity and microstructure using ultra-high field diffusion MRI at 11.7 T

Justine Beaujoin, Nicola Palomero-Gallagher, Fawzi Boumezbeur, Markus Axer, Jeremy Bernard, Fabrice Poupon, Daniel Schmitz, Jean-François Mangin, Cyril Poupon
2018 Brain Structure and Function  
High Angular Resolution Diffusion Imaging estimates allowed us to obtain an accurate tractography resolving more complex fiber architecture than DTI models, and subsequently provided a map of the cross-regional  ...  reconstruct elements of the polysynaptic intra-hippocampal pathway using fiber tractography techniques at very high spatial/angular resolutions.  ...  Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creat iveco mmons .org/licen ses/by/4.0/), which permits unrestricted use,  ... 
doi:10.1007/s00429-018-1617-1 pmid:29387938 pmcid:PMC5968081 fatcat:4cttfy7ienhrxex4ra43xngsly

Alterations in fiber pathways reveal brain tumor typology: a diffusion tractography study

Martina Campanella, Tamara Ius, Miran Skrap, Luciano Fadiga
2014 PeerJ  
We used deterministic multi-fiber tractography to analyze 16 cases of histologically classified brain tumors (meningioma, low-grade glioma, high-grade glioma) to evaluate the integrity of WM bundles in  ...  In this study, we used Diffusion-Weighted (DW) MRI tractography to explore tumor-induced alterations of WM architecture without any a priori knowledge about the fiber paths under consideration.  ...  In the latter, the range of probable fiber orientations is probed with a Monte Carlo strategy and the total number of fiber trajectories passing through each voxel provides a confidence level of that voxel  ... 
doi:10.7717/peerj.497 pmid:25250209 pmcid:PMC4168762 fatcat:zcs4dtkb3jbs7m2dwmd7epgwpu

A methodological scoping review of the integration of fMRI to guide dMRI tractography. What has been done and what can be improved; a 20-year perspective

Julien Jarret, Arnaud Bore, Christophe Bedetti, Maxime Descoteaux, Simona Maria Brambati
2021 Journal of Neuroscience Methods  
A quick glimpse of the literature on this topic reveals that this technique is challenging, and no consensus or "best practices" currently exist, at least not within a single document.  ...  We present the first attempt to systematically analyze and summarize the literature of 80 studies that integrated task-based fMRI results to guide tractography, over the last two decades.  ...  fiber bundle defined by an anatomical atlas.  ... 
doi:10.1016/j.jneumeth.2021.109435 pmid:34915047 fatcat:ofsuzwg57zcxdkh4xezcyo7gga

Fusing DTI and fMRI data: A survey of methods and applications

Dajiang Zhu, Tuo Zhang, Xi Jiang, Xintao Hu, Hanbo Chen, Ning Yang, Jinglei Lv, Junwei Han, Lei Guo, Tianming Liu
2014 NeuroImage  
Given the intrinsic integration of WM/GM and the complementary information embedded in DTI/fMRI data, it is natural and well-justified to combine these two neuroimaging modalities together to investigate  ...  The relationship between brain structure and function has been one of the centers of research in neuroimaging for decades.  ...  Acknowledgments D Zhu and T Liu were supported by the NIH Career Award (NIH EB 006878), NSF CAREER Award IIS-1149260, NIH R01 DA033393, and the University of Georgia start-up research funding.  ... 
doi:10.1016/j.neuroimage.2013.09.071 pmid:24103849 pmcid:PMC4012015 fatcat:f6swsx2dnfbxdp3uifg3k3wfw4
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