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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  
This paper presents a method for automatic segmentation of some short association fiber bundles from massive dMRI tractography datasets.  ...  The method is based on a multi-subject bundle atlas derived from a two-level intra-subject and inter-subject clustering strategy.  ...  However, short fibers of superficial white matter (SWM) have been barely considered, probably because these are more variable across sujects.  ... 
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.  ...  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.  ...  Valenzuela, et al., “Clustering matter fibers, based on probabilistic tractography, which can of whole-brain white matter short association bundles using  ... 
doi:10.1109/isbi.2019.8759208 dblp:conf/isbi/VazquezLLFPMHG19 fatcat:46zgug3yc5dithw34epr7by7qm

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

Miguel Guevara, Pamela Guevara, Claudio Román, Jean-François Mangin
2020 NeuroImage  
Unlike deep white matter (DWM), which has been extensively studied and well documented, superficial white matter (SWM) has been often left aside.  ...  The shape and localization of these short bundles present a high variability across subjects.  ...  A posterior refinement of this method was presented in , adapting the clustering specifically to short fibers and removing from the analysis the long white matter bundles already identified in the same  ... 
doi:10.1016/j.neuroimage.2020.116673 pmid:32114152 fatcat:onw3cxzkvzau7lng54dtgzlwga

Automatic group-wise whole-brain short association fiber bundle labeling based on clustering and cortical surface information

Andrea Vázquez, Narciso López-López, Josselin Houenou, Cyril Poupon, Jean-François Mangin, Susana Ladra, Pamela Guevara
2020 BioMedical Engineering OnLine  
Tractography datasets contain 3D streamlines that can be analyzed to study the main brain white matter tracts.  ...  We present an automatic method for labeling of short association bundles on a group of subjects. The method is based on an intra-subject fiber clustering that generates compact fiber clusters.  ...  QB is a clustering method specialized in grouping white matter fibers from tractography datasets quickly and with good quality.  ... 
doi:10.1186/s12938-020-00786-z pmid:32493483 fatcat:hapmy6vbe5ajlhs2luo4iua3gu

Robust clustering of massive tractography datasets

P. Guevara, C. Poupon, D. Rivière, Y. Cointepas, M. Descoteaux, B. Thirion, J.-F. Mangin
2011 NeuroImage  
For the sake of efficiency, part of the analysis is based on clustering the white matter (WM) voxels rather than the fibers.  ...  This paper presents a clustering method that detects the fiber bundles embedded in any MR-diffusion based tractography dataset.  ...  Results Adult HARDI datasets: Twelve fiber datasets from the adult HARDI brain database (cf. section 2.1) were clustered with our method.  ... 
doi:10.1016/j.neuroimage.2010.10.028 pmid:20965259 fatcat:kockuz3zezexrjmp7r263uvu54

Cortical surface parcellation based on intra-subject white matter fiber clustering [article]

Narciso López-López, Andrea Vázquez, Cyril Poupon, Jean-François Mangin, Pamela Guevara
2020 arXiv   pre-print
We present a hybrid method that performs the complete parcellation of the cerebral cortex of an individual, based on the connectivity information of the white matter fibers from a whole-brain tractography  ...  The method consists of five steps, first intra-subject clustering is performed on the brain tractography.  ...  STEP 1: Fiber clustering: We apply an intra-subject clustering to all the fibers of the whole-brain tractography dataset.  ... 
arXiv:2002.09034v1 fatcat:m5534eypkvb4zmde7rpgepftau

Automatic clustering and population analysis of white matter tracts using maximum density paths

Gautam Prasad, Shantanu H. Joshi, Neda Jahanshad, Julio Villalon-Reina, Iman Aganj, Christophe Lenglet, Guillermo Sapiro, Katie L. McMahon, Greig I. de Zubicaray, Nicholas G. Martin, Margaret J. Wright, Arthur W. Toga (+1 others)
2014 NeuroImage  
The framework enables extraction of fibers from high angular resolution diffusion images (HARDI); clustering of the fibers based partly on prior knowledge from an atlas; representation of the fiber bundles  ...  We demonstrate our method on 4-Tesla HARDI scans from 565 young adults to compute localized statistics across 50 white matter tracts based on fractional anisotropy (FA).  ...  The paths are derived from tractography fibers, clustered into white matter tracts, and then represented as paths that follow points in these white matter bundles of maximum density of fibers.  ... 
doi:10.1016/j.neuroimage.2014.04.033 pmid:24747738 pmcid:PMC4065851 fatcat:ymcxjw2lgjai7k7yklijmsnrqm

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 paper presents a method inferring a model of the brain white matter organisation from HARDI tractography results computed for a group of subjects.  ...  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.  ...  Until now, short fibers of superficial white matter (SWM) have been barely considered. The cartography of fiber bundles of SWM is a complex and unachieved task for the human brain.  ... 
doi:10.1007/978-3-642-15705-9_67 fatcat:g562krujkzdufd7coieqbiuug4

Test-retest reliability of high angular resolution diffusion imaging acquisition within medial temporal lobe connections assessed via tract based spatial statistics, probabilistic tractography and a novel graph theory metric

T. Kuhn, J. M. Gullett, P. Nguyen, A. E. Boutzoukas, A. Ford, L. M. Colon-Perez, W. Triplett, P. R. Carney, T. H. Mareci, C. C. Price, R. M. Bauer
2015 Brain Imaging and Behavior  
Conclusions-By confirming the test retest reliability of HARDI data acquisition, support for the validity of significant results derived from diffusion data can be obtained.  ...  Tractography-derived metrics displayed larger ranges of scanner-to-scanner variability.  ...  This research was also conducted while Taylor Kuhn was a Graduate Fellow in the Clinical and Health Psychology Department at the University of Florida.  ... 
doi:10.1007/s11682-015-9425-1 pmid:26189060 pmcid:PMC4718901 fatcat:b5td2lwmanbezajqrr2ags6624

Investigating The Functional Consequence Of White Matter Damage: An Automatic Pipeline To Create Longitudinal Disconnection Tractograms [article]

Kesshi Marin Jordan, Anisha Keshavan, Eduardo Caverzasi, Joseph Osorio, Nico Papinutto, Bagrat Amirbekian, Mitchel S. Berger, Roland G. Henry
2017 bioRxiv   pre-print
This two-part approach includes (i) automatic segmentation of focal white matter injury from anisotropic power differences, and (ii) modeling disconnection using tractography on the single-subject level  ...  The advantages of this approach stem from (1) objective and automatic lesion segmentation and tractogram generation, (2) objective and precise segmentation of affected tissue likely to be associated with  ...  Tractography has been used extensively to study the clinical consequence of white matter disconnection by modeling the white matter connectivity on a single-subject level and associating damage to white  ... 
doi:10.1101/140137 fatcat:zo32kpgdhfeilkzsqdltxuemzu

Automatic clustering of white matter fibers in brain diffusion MRI with an application to genetics

Yan Jin, Yonggang Shi, Liang Zhan, Boris A. Gutman, Greig I. de Zubicaray, Katie L. McMahon, Margaret J. Wright, Arthur W. Toga, Paul M. Thompson
2014 NeuroImage  
To understand factors that affect brain connectivity and integrity, it is beneficial to automatically cluster white matter (WM) fibers into anatomically recognizable tracts.  ...  We illustrate our method in a genetic study of white matter tract heritability in twins.  ...  Acknowledgments This study was supported by Grant R01 HD050735 from the National Institutes of  ... 
doi:10.1016/j.neuroimage.2014.04.048 pmid:24821529 pmcid:PMC4255631 fatcat:gkfru53xxzajdhzl4gyif7t6k4

Assessing the Reliability of Template-Based Clustering for Tractography in Healthy Human Adults

Jason Kai, Ali R. Khan
2022 Frontiers in Neuroinformatics  
The effect of intersubject variability on template-based clustering reliability was investigated, as well as the reliability of both deep and superficial white matter tracts.  ...  The two different template-based approaches exhibited similar reliability for identifying both deep white matter tracts and the superficial white matter.  ...  Clustering of whole-brain white matter short association bundles using HARDI data. Front.  ... 
doi:10.3389/fninf.2022.777853 pmid:35250526 pmcid:PMC8891507 fatcat:hnow4nabwnagjkisqk3njqzoay

Semi-Automatic Segmentation of Optic Radiations and LGN, and Their Relationship to EEG Alpha Waves

Emmanuelle Renauld, Maxime Descoteaux, Michaël Bernier, Eleftherios Garyfallidis, Kevin Whittingstall, Maurice Ptito
2016 PLoS ONE  
Given the widespread use of EEG alpha in basic and clinical research, addressing this is important, though difficult given the problems associated with reliably segmenting the LGN and OR.  ...  For the former, we developed a new, semiautomated approach for segmenting the OR and LGN, from which we extracted several structural metrics such as volume, position and diffusivity.  ...  As a result, one could determine a nucleus by clustering the voxels belonging to an associated fiber [44, 45] .  ... 
doi:10.1371/journal.pone.0156436 pmid:27383146 pmcid:PMC4934857 fatcat:7crm6kin75cs7g4o5se5i5hycy

Track Orientation Density Imaging (TODI) and Track Orientation Distribution (TOD) based tractography

Thijs Dhollander, Louise Emsell, Wim Van Hecke, Frederik Maes, Stefan Sunaert, Paul Suetens
2014 NeuroImage  
This in turn motivated us to explore the idea of TOD-based fiber tractography.  ...  Ever since the introduction of the concept of fiber tractography, methods to generate better and more plausible tractograms have become available.  ...  fractions of underlying white matter fiber populations.  ... 
doi:10.1016/j.neuroimage.2013.12.047 pmid:24389015 fatcat:mwqychjadzgpvdsrgzbaexpcdu

Free water modeling of peritumoral edema using multi-fiber tractography: Application to tracking the arcuate fasciculus for neurosurgical planning

Shun Gong, Fan Zhang, Isaiah Norton, Walid I. Essayed, Prashin Unadkat, Laura Rigolo, Ofer Pasternak, Yogesh Rathi, Lijun Hou, Alexandra J. Golby, Lauren J. O'Donnell, Pew-Thian Yap
2018 PLoS ONE  
The purpose of this study is to investigate the effect of incorporating a free water (FW) model of edema for white matter tractography in the presence of edema. fraction was significantly larger in tracts  ...  Purpose Peritumoral edema impedes the full delineation of fiber tracts due to partial volume effects in image voxels that contain a mixture of cerebral parenchyma and extracellular water.  ...  Automatically detected arcuate fasciculus tract clusters in example datasets from patients with edema.  ... 
doi:10.1371/journal.pone.0197056 pmid:29746544 pmcid:PMC5944935 fatcat:stgso2i4rvdtfhmza7pw2ztxwm
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