MRIcroGL
Overview
MRIcroGL is a NIfTI format image viewer. It allows you to view 2D slices and renderings of your brain imaging data. It can display many image formats and includes a graphical interface for dcm2nii to convert DICOM images to NIfTI format. It allows you to draw regions of interest which can aid lesion mapping and fMRI analysis. It provides sophisticated rendering.
Version1.2 (v1.2.20210317, March 17th, 2021) is 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 the following modulefile:
module load apps/binapps/mricrogl/1.2
Running the application
Please do not run MRIcroGL 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 MRIcroGL 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/mricrogl/1.2
# Now launch the MRIcroGL gui from the current folder, inheriting the modulefile settings
qrsh -l short -cwd -V mricrogl
When you exit the MRIcroGL 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.
Further info
Updates
None.