Journal ArticleDOI
MRtrix: Diffusion tractography in crossing fiber regions
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This methodology is shown to provide superior delineations of a number of known white matter tracts, in a manner robust to crossing fiber effects, and has been compiled into a software package, called MRtrix, which has been made freely available for use by the scientific community.Abstract:
In recent years, diffusion-weighted magnetic resonance imaging has attracted considerable attention due to its unique potential to delineate the white matter pathways of the brain. However, methodologies currently available and in common use among neuroscientists and clinicians are typically based on the diffusion tensor model, which has comprehensively been shown to be inadequate to characterize diffusion in brain white matter. This is due to the fact that it is only capable of resolving a single fiber orientation per voxel, causing incorrect fiber orientations, and hence pathways, to be estimated through these voxels. Given that the proportion of affected voxels has been recently estimated at 90%, this is a serious limitation. Furthermore, most implementations use simple “deterministic” streamlines tracking algorithms, which have now been superseded by “probabilistic” approaches. In this study, we present a robust set of tools to perform tractography, using fiber orientations estimated using the validated constrained spherical deconvolution method, coupled with a probabilistic streamlines tracking algorithm. This methodology is shown to provide superior delineations of a number of known white matter tracts, in a manner robust to crossing fiber effects. These tools have been compiled into a software package, called MRtrix, which has been made freely available for use by the scientific community. © 2012 Wiley Periodicals, Inc. Int J Imaging Syst Technol, 22, 53–66, 2012 © 2012 Wiley Periodicals, Inc.read more
Citations
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Journal ArticleDOI
MRtrix3: A fast, flexible and open software framework for medical image processing and visualisation
Jacques-Donald Tournier,Robert E. Smith,Robert E. Smith,David Raffelt,Rami Tabbara,Thijs Dhollander,Thijs Dhollander,Maximilian Pietsch,Daan Christiaens,Ben Jeurissen,Chun-Hung Yeh,Chun-Hung Yeh,Alan Connelly,Alan Connelly +13 more
TL;DR: A high-level overview of the features of the MRtrix3 framework and general-purpose image processing applications provided with the software is provided.
Journal ArticleDOI
Denoising of diffusion MRI using random matrix theory
Jelle Veraart,Dmitry S. Novikov,Daan Christiaens,Benjamin Ades-Aron,Jan Sijbers,Els Fieremans +5 more
TL;DR: A post-processing technique for fast denoising of diffusion-weighted MR images is introduced and it is demonstrated that the technique suppresses local signal fluctuations that solely originate from thermal noise rather than from other sources such as anatomical detail.
Journal ArticleDOI
Multi-tissue constrained spherical deconvolution for improved analysis of multi-shell diffusion MRI data
TL;DR: The aim of this study is to incorporate support for multi-shell data into the CSD approach as well as to exploit the unique b-value dependencies of the different tissue types to estimate a multi-tissue ODF.
Journal ArticleDOI
The challenge of mapping the human connectome based on diffusion tractography
Klaus H. Maier-Hein,Peter F. Neher,Jean-Christophe Houde,Marc-Alexandre Côté,Eleftherios Garyfallidis,Jidan Zhong,Maxime Chamberland,Fang-Cheng Yeh,Ying-Chia Lin,Qing Ji,Wilburn E. Reddick,John O. Glass,David Qixiang Chen,Yuanjing Feng,Chengfeng Gao,Ye Wu,Jieyan Ma,H Renjie,Qiang Li,Carl-Fredrik Westin,Samuel Deslauriers-Gauthier,J. Omar Ocegueda Gonzalez,Michael Paquette,Samuel St-Jean,Gabriel Girard,François Rheault,Jasmeen Sidhu,Chantal M. W. Tax,Fenghua Guo,Hamed Y. Mesri,Szabolcs David,Martijn Froeling,Anneriet M. Heemskerk,Alexander Leemans,Arnaud Boré,Basile Pinsard,Christophe Bedetti,Matthieu Desrosiers,Simona M. Brambati,Julien Doyon,Alessia Sarica,Roberta Vasta,Antonio Cerasa,Aldo Quattrone,Jason D. Yeatman,Ali R. Khan,Wes Hodges,Simon Alexander,David Romascano,Muhamed Barakovic,Anna Auría,Oscar Esteban,Alia Lemkaddem,Jean-Philippe Thiran,Hasan Ertan Cetingul,Benjamin L. Odry,Boris Mailhe,Mariappan S. Nadar,Fabrizio Pizzagalli,Gautam Prasad,Julio E. Villalon-Reina,Justin Galvis,Paul M. Thompson,Francisco De Santiago Requejo,Pedro Luque Laguna,Luis Miguel Lacerda,Rachel Barrett,Flavio Dell'Acqua,Marco Catani,Laurent Petit,Emmanuel Caruyer,Alessandro Daducci,Tim B. Dyrby,Tim Holland-Letz,Claus C. Hilgetag,Bram Stieltjes,Maxime Descoteaux +76 more
TL;DR: The encouraging finding that most state-of-the-art algorithms produce tractograms containing 90% of the ground truth bundles (to at least some extent) is reported, however, the same tractograms contain many more invalid than valid bundles, and half of these invalid bundles occur systematically across research groups.
Journal ArticleDOI
Dipy, a library for the analysis of diffusion MRI data
Eleftherios Garyfallidis,Eleftherios Garyfallidis,Matthew Brett,Bagrat Amirbekian,Ariel Rokem,Stefan van der Walt,Maxime Descoteaux,Ian Nimmo-Smith +7 more
TL;DR: Dipy aims to provide transparent implementations for all the different steps of dMRI analysis with a uniform programming interface, and has implemented classical signal reconstruction techniques, such as the diffusion tensor model and deterministic fiber tractography.
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