MRtrix3Tissue is an application for 3-Tissue CSD modelling and analysis (based on mrtrix).

• MRtrix3tissue user documentation

• Module Name: mrtrix3tissue (see the modules page for more information)
• Note that the GUI options have not been installed.
• Multithreaded
• mrtrix3tissue configuration: Users can set up a file /home/$USER/.mrtrix.conf containing mrtrix configuration options with default options that they desire. The list of possible settings for the mrtrix config file is detailed here. A sample config file is available in /usr/local/apps/mrtrix/mrtrix.conf.

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 ~]$ ss3t_csd_beta1 -help
Version 3Tissue_v5.2.9           ss3t_csd_beta1
using MRtrix3 3Tissue_v5.2.9

     ss3t_csd_beta1: external MRtrix3 project

SYNOPSIS

     SS3T-CSD: beta 1 implementation

USAGE

     ss3t_csd_beta1 [ options ] in_dMRI_data in_SFWM_resp out_WM_FOD in_GM_resp
     out_GM in_CSF_resp out_CSF

        in_dMRI_data Input dMRI dataset

        in_SFWM_resp Input single-fibre WM response function text file

        out_WM_FOD   Output WM FOD image

        in_GM_resp   Input GM response function text file

        out_GM       Output GM image

        in_CSF_resp  Input CSF response function text file

        out_CSF      Output CSF image

DESCRIPTION

     This is an implementation of SS3T-CSD for beta testing and distribution.
     Use with caution and check all results carefully.

     For more information on how to use SS3T-CSD, please visit
     https://3Tissue.github.io/doc/ss3t-csd.html

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

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

#!/bin/bash
set -e
module load mrtrix3tissue

cd /data/${USER}

dwi2response dhollander dwi-prep.mif response_wm.txt response_gm.txt response_csf.txt
ss3t_csd_beta1 dwi-prep.mif response_wm.txt wmfod.mif response_gm.txt gm.mif response_csf.txt csf.mif -mask mask.mif

Submit this job using the Slurm sbatch command.

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

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

cd /data/${USER}/dataset01;\ 
   ss3t_csd_beta1 dwi-prep.mif response_wm.txt wmfod.mif response_gm.txt gm.mif response_csf.txt csf.mif -mask mask.mif
cd /data/${USER}/dataset02;\
   ss3t_csd_beta1 dwi-prep.mif response_wm.txt wmfod.mif response_gm.txt gm.mif response_csf.txt csf.mif -mask mask.mif
[...]

Submit this job using the swarm command.

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