MRtrix provides a large suite of tools for image processing, analysis and visualisation, with a focus on the analysis of white matter using diffusion-weighted MRI

• mrtrix user documentation

• Module Name: mrtrix (see the modules page for more information)
• Note that the GUI options have not been installed.
• Multithreaded
• Environment variables set
  • MRTRIX_HOME
• mrtrix 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 mrtrix
[+] Loading eigen 3.3.4  ...
[+] Loading Zlib 1.2.11  ...
[+] Loading GSL 2.4 for GCC 4.8.5 ...
[+] Loading FFTW 3.3.7 , compiled with gcc4.8.5  and openmpi2.1.2  ...
[+] Loading mrtrix 3.0_RC2  ...

[user@cn3144 ~]$ mrinfo /usr/local/apps/mrtrix/sample_data/data_slice_0000.nii.gz
mrinfo: [WARNING] transform matrix contains invalid entries - resetting to sane defaults
************************************************
Image:               "/usr/local/apps/mrtrix/sample_data/data_slice_0000.nii.gz"
************************************************
  Dimensions:        128 x 104 x 1 x 65
  Voxel size:        2 x 2 x 2 x 1
  Data strides:      [ 1 2 4 3 ]
  Format:            NIfTI-1.1 (GZip compressed)
  Data type:         signed 16 bit integer (little endian)
  Intensity scaling: offset = 0, multiplier = 1
  Transform:                    1           0           0        -127
                                0           1           0        -103
                                0           0           1          -0
  comments:          FSL5.0
  
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

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

#!/bin/bash
set -e
module load mrtrix
mrstats /usr/local/apps/mrtrix/sample_data/nodif_brain_mask.nii.gz
mrhistogram /usr/local/apps/mrtrix/sample_data/nodif.nii.gz  out.hist

Submit this job using the Slurm sbatch command.

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

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

mrstats file1.nii.gz
mrstats file2.nii.gz
mrstats file3.nii.gz
[...]

Submit this job using the swarm command.

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