Processing multi-­shell diffusion MRI data using MRtrix3

Abstract

Event Abstract Back to Event Processing multi-­shell diffusion MRI data using MRtrix3 Ben Jeurissen1* 1 University of Antwerp, Dept. of Physics, Belgium MRtrix3 (https://github.com/MRtrix3/) provides a comprehensive set of tools to perform diffusion-weighted MRI white matter (WM) tractography in the presence of crossing fibers using constrained spherical deconvolution and a probabilistic streamlines algorithm [1]. It is written entirely in C++, using multi-threading throughout for maximum performance. It is primarily command-line driven, allowing for easy scripting and chaining of commands via Unix pipes. It provides native support throughout for DICOM, NIfTI. MRtrix can be installed on Microsoft Windows, Mac OS X, and most recent GNU/Linux distributions, and is available free of charge under an open-source license. Until recently, MRtrix only supported data acquired on a single shell in q-space. However, a recent extension of constrained spherical deconvolution to multi-shell acquisitions has shown great promise as it allows simultaneous estimation of the WM fiber orientation distribution function (fODF) and the apparent densities of the main tissue types of the brain (cerebrospinal fluid (CSF), gray matter (GM) and WM) [2]. It has been shown that this approach avoids the overestimation of apparent WM density in voxels containing GM and/or CSF, as was the case with single-tissue CSD. In addition, it substantially increases the precision of the fODF fiber orientations and reduces the presence of spurious fODF peaks in voxels containing GM and/or CSF. This lecture will give an overview of the MRtrix3 toolbox with a focus on its new multi-shell capabilities. Acknowledgements Ben Jeurissen is a post-doctoral fellow supported by the Research Foundation Flanders (FWO Vlaanderen).