Diffusion MRI Analysis with MRtrix: An Interactive Three-Part Series on Neurodesk

This project stores the results of a three-part interactive example series on NeurodeskEDU (https://neurodesk.org/edu/intro.html) demonstrating diffusion MRI analysis with MRtrix. The notebooks cover essential steps: Preprocessing (Part 1), Constrained Spherical Deconvolution (CSD) methods and tissue estimation (Part 2) as well as registration and streamline fitting (Part 3). Results from each part are saved here and can be downloaded for use in subsequent notebooks. This project provides a simple, hands-on approach to learning diffusion MRI processing. Primary subject: sub-CON02 (ses-preop) from OpenNeuro dataset ds001226, the multi-shell (b=0/700/1200/2800) diffusion tutorial subject. Contents (osfstorage): - preprocessed/ — denoised DWI (sub-02_den.mif), distortion+eddy corrected (sub-02_den_preproc.mif), fully preprocessed/bias-corrected (sub-02_den_preproc_unbiased.mif), brain mask (mask.mif), T1w, gradient tables - fod/ — normalized FODs (wmfod_norm/gmfod_norm/csffod_norm.mif), tissue segmentation (5tt_nocoreg/5tt_coreg.mif), seed (gmwmSeed_coreg.mif), CSD peaks (peaks.mif) - dti/ — DTI scalar maps (FA, MD, AD, RD) - tractography/ — track-density image (tdi.mif)