C3D is a command-line tool for converting 3D images between common file formats. The tool also includes a growing list of commands for image manipulation, such as thresholding and resampling.

Web site

• Home page

• C3D Documentation

• Module Name: c3d (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 c3d

[user@cn3144 ~]$ c3d -h

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

Create a batch input file (e.g. c3d_job.sh). For example:

#!/bin/bash
set -e
module load c3d
c3d minimal.nii output.img

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] c3d_job.sh

Create a swarmfile (e.g. c3d_jobs.swarm). For example:

c3d minimal.nii -interpolation Cubic -resample 50x30x40vox -o output_0.img
c3d minimal.nii -interpolation Cubic -resample 25x15x20vox -o output_1.img
c3d minimal.nii -interpolation Cubic -resample 12x7x10vox -o output_2.img

Submit this job using the swarm command.

swarm -f c3d_jobs.swarm [-g #] [-t #] --module c3d