MRtrix3 module for motion and distortion correction.

This module contains the SHARD reconstruction software for slice-level motion correction in multi-shell diffusion MRI, as described in

Daan Christiaens, Lucilio Cordero-Grande, Maximilian Pietsch, Jana Hutter, Anthony N. Price, Emer J. Hughes, Katy Vecchiato, Maria Deprez, A. David Edwards, Joseph V.Hajnal, and J-Donald Tournier, Scattered slice SHARD reconstruction for motion correction in multi-shell diffusion MRI, NeuroImage 117437 (2020). doi:10.1016/j.neuroimage.2020.117437

Setup & build

Prerequisites: MRtrix 3.0, Eigen 3.3.3, and python 3.x with numpy and scipy.

The code is built like any other MRtrix3 module, i.e., by setting up a symbolic link to the core build script:

$ git clone https://github.com/dchristiaens/shard-recon.git
$ cd shard-recon
$ ln -s /path/to/mrtrix3/build
$ ln -s /path/to/mrtrix3/bin/mrtrix3.py bin/
$ ./build

This will compile the code into shard-recon/bin, which then needs to be added to the PATH.

Help & support

Contact daan.christiaens@kcl.ac.uk