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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  
RecoBundles leverages latest state-of-the-art streamline-based registration and clustering to recognize and extract bundles using prior bundle models.  ...  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.  ...  David Fortin and Prof. Kevin Whittingstall for sharing some of the USherbrooke imaging data. Finally, we are grateful to the Indiana University for providing Prof. Garyfallidis' startup fund.  ... 
doi:10.1016/j.neuroimage.2017.07.015 pmid:28712994 fatcat:bpspukam5zeuxe6yu5ca3cqcmy

Evaluating the Reliability of Human Brain White Matter Tractometry

John Kruper, Jason D. Yeatman, Adam Richie-Halford, David Bloom, Mareike Grotheer, Sendy Caffarra, Gregory Kiar, Iliana I. Karipidis, Ethan Roy, Bramsh Q. Chandio, Eleftherios Garyfallidis, Ariel Rokem
2021 Aperture Neuro  
We defined and assessed three dimensions of reliability in dMRI-based tractometry, an analysis technique that assesses the physical properties of white matter pathways: (1) reproducibility, (2) test-retest  ...  In recent years, there have been concerns about the validity of research that uses diffusion-weighted MRI (dMRI) to understand human brain white matter connections in vivo, in part based on the reliability  ...  Recognition of white matter bundles using local and global streamline-based registration and clustering. Neuroimage, July 2017. doi: 10.1016/j.neuroimage.2017.07.015. 9. Jason D. Yeatman, Robert F.  ... 
doi:10.52294/e6198273-b8e3-4b63-babb-6e6b0da10669 pmid:35079748 pmcid:PMC8785971 fatcat:rytvwmjxiffedd6qcoxgr3ptum

Quantifying indices of short- and long-range white matter connectivity at each cortical vertex

Maria Carmela Padula, Marie Schaer, Elisa Scariati, A. Kadir Mutlu, Daniela Zöller, Maude Schneider, Stephan Eliez, Hao Huang
2017 PLoS ONE  
Using these novel measures, we achieved a fine-grained visualization of the white matter connectivity patterns at each vertex of the cortical surface.  ...  In this study, we propose a novel methodology to compute and display metrics of white matter connectivity at each cortical point.  ...  Stephan Eliez [grant number: 324730_121996 and 324730_144260], and by the National Center of Competence in Research (NCCR) synapsy [grant number 51NF40_158776].  ... 
doi:10.1371/journal.pone.0187493 pmid:29141024 pmcid:PMC5687731 fatcat:6m33ctv6v5g2jcxgfl7d36rpye

Classifyber, a robust streamline-based linear classifier for white matter bundle segmentation

Giulia Bertò, Daniel Bullock, Pietro Astolfi, Soichi Hayashi, Luca Zigiotto, Luciano Annicchiarico, Francesco Corsini, Alessandro De Benedictis, Silvio Sarubbo, Franco Pestilli, Paolo Avesani, Emanuele Olivetti
2020 NeuroImage  
Virtual delineation of white matter bundles in the human brain is of paramount importance for multiple applications, such as pre-surgical planning and connectomics.  ...  In this work, we propose a novel, supervised streamline-based segmentation method, called Classifyber, which combines information from atlases, connectivity patterns, and the geometry of fiber paths into  ...  Set 1 and set 2 contain the distances (d MDF ) of the streamline with 100 global and 100 local landmarks, respectively.  ... 
doi:10.1016/j.neuroimage.2020.117402 pmid:32979520 fatcat:rufoeem5nzhlnezhyo6rkzvqhu

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  ...  Finally, we show that, when we use these manually annotated pathways as training data for global probabilistic tractography with anatomical neighborhood priors, we can perform highly accurate, automated  ...  “Recognition 1097 of white matter bundles using local and global streamline-based registration and clustering.” 1098 Academic Press Inc. https://doi.org/10.1016/j.neuroimage.2017.07.015. 1099  ... 
doi:10.1101/2021.06.28.450265 fatcat:laud55hjqzg6rhpd3cdqxsgyoa

BundleMAP: Anatomically localized classification, regression, and hypothesis testing in diffusion MRI

Mohammad Khatami, Tobias Schmidt-Wilcke, Pia C. Sundgren, Amin Abbasloo, Bernhard Schölkopf, Thomas Schultz
2017 Pattern Recognition  
Diffusion MRI (dMRI) provides rich information on the white matter of the human brain, enabling insight into neurological disease, normal aging, and neuroplasticity.  ...  Our features are based on aggregating measurements along nerve fiber bundles, enabling visualization and anatomical interpretation.  ...  PCS has, in part, been supported by funding from MICHR-02075, Alfred Österlunds Research Foundation, Sweden, and Skane University Research Funding, Sweden.  ... 
doi:10.1016/j.patcog.2016.09.020 fatcat:46tmphwnmjaw3jalv2c6enfgha

Prevalence of white matter pathways coming into a single white matter voxel orientation: The bottleneck issue in tractography

Kurt G. Schilling, Chantal M. W. Tax, Francois Rheault, Bennett A. Landman, Adam W. Anderson, Maxime Descoteaux, Laurent Petit
2021 Human Brain Mapping  
To do this, we use diffusion tractography to segment known white matter bundles of the brain, and assign each bundle to voxels they pass through and to specific orientations within those voxels (i.e. fixels  ...  We demonstrate that bottlenecks occur in greater than 50-70% of fixels in the white matter of the human brain.  ...  Bundle recognition was performed following streamline linear registration to the HCP842 (Yeh et al., 2018) bundle template (dipy_slr) and bundle recognition using default parameters of the RecoBundles  ... 
doi:10.1002/hbm.25697 pmid:34921473 pmcid:PMC8837578 fatcat:5vvylnrmend5vhsjg3eaeujuju

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.  ...  Recognition of white matter bundles using local and global streamline-based registration and clustering.  ... 
doi:10.3389/fninf.2022.777853 pmid:35250526 pmcid:PMC8891507 fatcat:hnow4nabwnagjkisqk3njqzoay

Classifyber, a robust streamline-based linear classifier for white matter bundle segmentation [article]

Giulia Bertò, Daniel Bullock, Pietro Astolfi, Siochi Hayashi, Luca Zigiotto, Luciano Annicchiarico, Francesco Corsini, Alessandro De Benedictis, Silvio Sarubbo, Franco Pestilli, Paolo Avesani, Emanuele Olivetti
2020 bioRxiv   pre-print
Virtual delineation of white matter bundles in the human brain is of paramount importance for multiple applications, such as pre-surgical planning and connectomics.  ...  In this work, we propose a novel, supervised streamline-based segmentation method, called Classifyber, which combines information from atlases, connectivity patterns, and the geometry of fiber paths into  ...  M DF ) and that did not use the local streamline linear registration (SLR), most probably because the bundles were already coregistered in MNI space.  ... 
doi:10.1101/2020.02.10.942714 fatcat:uaqiz7nhobe2begaqmtvlwtdce

Prevalence of white matter pathways coming into a single diffusion MRI voxel orientation: the bottleneck issue in tractography [article]

Kurt Schilling, Chantal M.W. Tax, Francois M.W. Rheault, Bennett A Landman, Adam W Anderson, Maxime Descoteaux, Laurent Petit
2021 bioRxiv   pre-print
To do this, we use diffusion tractography to segment known white matter bundles of the brain, and assign each bundle to voxels they pass through and to specific orientations within those voxels (i.e. fixels  ...  We demonstrate that bottlenecks occur in greater than 50-70% of fixels in the white matter of the human brain.  ...  Bundle recognition was performed following streamline linear registration to the HCP842 [36] bundle template (dipy_slr) and bundle recognition using default parameters of the RecoBundles algorithm [  ... 
doi:10.1101/2021.06.22.449454 fatcat:e7s2dkykprfyjfa26tnhvbxq3e

Altered structural network architecture is predictive of the presence of psychotic symptoms in patients with 22q11.2 deletion syndrome

Maria C. Padula, Elisa Scariati, Marie Schaer, Corrado Sandini, Marie Christine Ottet, Maude Schneider, Dimitri Van De Ville, Stephan Eliez
2017 NeuroImage: Clinical  
Different structural connectivity measures were used, including the number of streamlines connecting pairs of brain regions, graph theoretical measures, and diffusion measures.  ...  Our results point to alterations in structural network architecture and white matter microstructure in patients with 22q11DS with attenuated positive symptoms, mainly involving connections of the limbic  ...  We further thank Sarah Menghetti and Léa Chambaz for their involvement with the families and Frédérique Bena Sloan for the genetic analyses.  ... 
doi:10.1016/j.nicl.2017.07.023 pmid:28794975 pmcid:PMC5540832 fatcat:t4meywvqbfdijama3sjslxsz3e

White-Matter Connectivity between Face-Responsive Regions in the Human Brain

M. Gschwind, G. Pourtois, S. Schwartz, D. Van De Ville, P. Vuilleumier
2011 Cerebral Cortex  
We used functional magnetic resonance imaging to identify face-responsive regions in 22 participants and then employed diffusion tensor imaging with probabilistic tractography to establish the white-matter  ...  Face recognition is of major social importance and involves highly selective brain regions thought to be organized in a distributed functional network.  ...  Global white-matter connectivity probability of each ROI (analysis 1).  ... 
doi:10.1093/cercor/bhr226 pmid:21893680 fatcat:m56xlj2mf5f5flxd66p4a6b3ta

White matter correlates of cognitive domains in normal aging with diffusion tensor imaging

Efrat Sasson, Glen M. Doniger, Ofer Pasternak, Ricardo Tarrasch, Yaniv Assaf
2013 Frontiers in Neuroscience  
Different cognitive tasks employ distinctive white matter fiber bundles. The temporal lobe and its projections subserve a variety of key functions known to deteriorate during aging.  ...  The ability to perform complex as well as simple cognitive tasks engages a network of brain regions that is mediated by the white matter fiber bundles connecting them.  ...  the purchase and maintenance of the MRI system.  ... 
doi:10.3389/fnins.2013.00032 pmid:23493587 pmcid:PMC3595518 fatcat:kfispzfv6rfwbc6f7aqdr3m64u

Improving the Reliability of Network Metrics in Structural Brain Networks by Integrating Different Network Weighting Strategies into a Single Graph

Stavros I. Dimitriadis, Mark Drakesmith, Sonya Bells, Greg D. Parker, David E. Linden, Derek K. Jones
2017 Frontiers in Neuroscience  
Following a binary classification scheme, the classification performance based on ISWBN TF outperformed the nine different weighting strategies and the ISWBN.  ...  We also applied our methodology to a second dataset of diffusion-weighted MRI in healthy controls and individuals with psychotic experience.  ...  ACKNOWLEDGMENTS SD, DL, and DJ were supported by a MRC grant MR/K004360/1 (Behavioural and Neurophysiological Effects of Schizophrenia Risk Genes: A Multi-locus, Pathway Based Approach).  ... 
doi:10.3389/fnins.2017.00694 pmid:29311775 pmcid:PMC5742099 fatcat:6mhq5txjevgppjfjntslpouk6a

White matter structural bases for predictive tapping synchronization [article]

Pamela García-Saldivar, Cynthia de León, Luis Concha, Hugo Merchant
2022 bioRxiv   pre-print
of their superficial (SWM) and deep (dWM) white matter.  ...  are linked to the preferred tapping tempo, and the bundle properties of CC define an interval selective topography that has an anterior posterior gradient.  ...  Acknowledgements We thank Sonja Kotz and Florencia Assaneo for their fruitful comments on the manuscript.  ... 
doi:10.1101/2022.09.05.506691 fatcat:hksuhq3zpnc2lfckfc72nxapvy
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