This is a jupyter notebook with all the basic and necessary steps for dwi preprocessing.
Algorithm used is constrained spherical deconvolution (CSD). Code can also be modified for DTI
This is basically a transcript/notebook version of Dr. Andrew Jahn's YouTube tutorials (https://youtube.com/playlist?list=PLIQIswOrUH68Zi9SVDAdcUExpq2i6A2eD&feature=shared). All rights reserved to them.
Requirements:
- mrtrix3 (https://www.mrtrix.org)
- freesurfer (https://surfer.nmr.mgh.harvard.edu)
- fsl (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/)
- ants (https://github.com/ANTsX/ANTs)