CMTK is a set of command-line tools for computational morphometry of biomedical images. CMTK contains tools for (1) registration (affine and nonrigid, single and multichannel, pairwise and groupwise); (2) image correction (MR bias field estimation, interleaved image artifact correction, EPI unwarping); (3) processing (filters, combination of segmentations, shape-based averaging); and (4) statistics (t-tests and the general linear model).

Web site

• Home page

• CMTK Documents

• Module Name: cmtk (see the modules page for more information)

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 cmtk

[user@cn3144 ~]$  

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

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

#!/bin/bash
set -e
module load cmtk
cmtk registrationx --dofs 12 --min-stepsize 1 -o 2_rigid.xform minimal.nii minimal2.nii

Submit this job using the Slurm sbatch command.

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

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

cmtk registrationx --dofs 12 --min-stepsize 1 -o 2_rigid.xform minimal.nii minimal2.nii
cmtk registrationx --dofs 12 --min-stepsize 1 -o 2_rigid.xform minimal.nii minimal2.nii
cmtk registrationx --dofs 12 --min-stepsize 1 -o 2_rigid.xform minimal.nii minimal2.nii
cmtk registrationx --dofs 12 --min-stepsize 1 -o 2_rigid.xform minimal.nii minimal2.nii

Submit this job using the swarm command.

swarm -f cmtk_jobs.swarm [-g #] [-t #] --module cmtk