MRIcron

Overview

MRIcron is a NIfTI format image viewer. It can load multiple layers of images, generate volume renderings and draw volumes of interest. It also provides dcm2nii for converting DICOM images to NIfTI format and NPM for statistics.

Versions 190902 (2nd September 2019) and 160502 (2nd May 2016) are installed on the CSF.

Restrictions on use

There are no restrictions on accessing the software on the CSF. It is released under the BSD License and all usage must adhere to that license.

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/mricron/190902     # Provides: mricron, dcm2niix
module load apps/binapps/mricron/160502     # Provides: mricron, dcm2nii, dcm2niigui, npm

Running the application

Please do not run MRIcron on the login node. Jobs should be submitted to the compute nodes via batch or run interactively via the qrsh command.

Interactive usage via qrsh

To launch the MRIcron graphical user interface you should start an interactive session on a compute node using the qrsh command. This will log you in to a compute node so that you can run commands without using a batch jobscript. For example:

# First, load the modulefile on the login node:
module load apps/binapps/mricron/190902

# Now launch the MRIcron gui from the current folder, inheriting the modulefile settings
qrsh -l short -cwd -V mricron

When you exit the MRIcron GUI you will be returned to the login node. Please note that the -l short flag will allow you to run the GUI app for a maximum of 1 hour. This is needed for interactive sessions.

Serial batch job submission

To run the tools that do not require a GUI, in batch, 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

# Load the modulefile for the version you require
module load apps/binapps/mricron/190902

# Script to convert dicom files to niix format
dcm2niix -o outputdir inputdir

Submit the jobscript using:

qsub scriptname

where scriptname is the name of your jobscript.

Further info

• MRIcron website

Updates

None.