dcm2niix

Overview

dcm2niix is a program to convert neuroimaging data from the DICOM format to the NIfTI format.

Version 1.0.20220720 is installed on the CSF.

Restrictions on use

There are no restrictions on accessing this software on the CSF. All usage must adhere to the software licenses provided in the license.txt file (in the github repo).

Set up procedure

We now recommend loading modulefiles within your jobscript so that you have a full record of how the job was run. See the example jobscript below for how to do this. Alternatively, you may load modulefiles on the login node and let the job inherit these settings.

Load one of the following modulefiles:

module load apps/binapps/dcm2niix/1.0.20220720

Running the application

Please do not run dcmi2niix on the login node. Jobs should be submitted to the compute nodes via batch.

Serial batch job submission

Create a batch submission script (which will load the modulefile in the jobscript), for example:

#!/bin/bash --login
#$ -cwd             # Job will run from the current directory
                    # NO -V line - we load modulefiles in the jobscript

module load apps/binapps/dcm2niix/1.0.20220720

dcm2niix args ...
  #
  # Alternatively the dcmi2niibatch executable is also available

Submit the jobscript using:

qsub scriptname

where scriptname is the name of your jobscript.

Further info

• dcm2niix manual
• dcm2niix manual

Updates

None.