MRtrix3tissue is an extension of mrtrix3 that adds tools for three-tissue constrained spherical deconvolution, or 3-Tissue CSD. This approach separates diffusion MRI signals into white matter-like, gray matter-like, and cerebrospinal fluid-like components. It retains the broader image-processing and tractography features available in MRtrix3 while providing additional methods for analyzing complex brain tissue.

• mrtrix user documentation

• Module Name: mrtrix3tissue (see the modules page for more information)
• Multithreaded
• Environment variables set
  • MRTRIX3TISSUE_HOME

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load mrtrix3tissue
[+] Loading mrtrix3tissue  5.2.9  on cn3144

[user@cn3144 ~]$ wget https://github.com/MRtrix3/script_test_data/raw/master/BIDS/sub-02/dwi/sub-02_dwi.nii.gz
[user@cn3144 ~]$ wget https://github.com/MRtrix3/script_test_data/raw/master/BIDS/sub-02/dwi/sub-02_dwi.bval
[user@cn3144 ~]$ wget https://github.com/MRtrix3/script_test_data/raw/master/BIDS/sub-02/dwi/sub-02_dwi.bvec

[user@cn3144 ~]$ mrconvert sub-02_dwi.nii.gz dwi-prep.mif -fslgrad sub-02_dwi.bvec sub-02_dwi.bval
mrconvert: [100%] uncompressing image "sub-02_dwi.nii.gz"
mrconvert: [100%] copying from "sub-02_dwi.nii.gz" to "dwi-prep.mif"

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. mrtrix3tissue.sh). For example:

#!/bin/bash

module load mrtrix3tissue

wget https://github.com/MRtrix3/script_test_data/raw/master/BIDS/sub-02/dwi/sub-02_dwi.nii.gz
wget https://github.com/MRtrix3/script_test_data/raw/master/BIDS/sub-02/dwi/sub-02_dwi.bval
wget https://github.com/MRtrix3/script_test_data/raw/master/BIDS/sub-02/dwi/sub-02_dwi.bvec

mrconvert sub-02_dwi.nii.gz dwi-prep.mif -fslgrad sub-02_dwi.bvec sub-02_dwi.bval

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] mrtrix3tissue.sh

Create a swarmfile (e.g. mrtrix3tissue.swarm). For example:

mrconvert sub-01_dwi.nii.gz dwi-prep_sub-01.mif -fslgrad sub-01_dwi.bvec sub-01_dwi.bval
mrconvert sub-02_dwi.nii.gz dwi-prep_sub-02.mif -fslgrad sub-02_dwi.bvec sub-02_dwi.bval
mrconvert sub-03_dwi.nii.gz dwi-prep_sub-03.mif -fslgrad sub-03_dwi.bvec sub-03_dwi.bval

Submit this job using the swarm command.

swarm [-g #] [-t #] --module mrtrix3tissue mrtrix3tissue.swarm