FSL

FSL is a library of analysis tools for FMRI, MRI and diffusion brain imaging data.

via OnDemand

The FSL GUI tools (including FSLeyes) can be accessed via the Open OnDemand Applications. FSLeyes will be run with 3D hardware acceleration when started on a '3D-accelerated'/GPU partition (default); This should significantly improve rendering responsiveness.

via Apptainer

FSL is made available on the cluster as a shared Apptainer container image. You can use the apptainer/FSL module to add convenient aliases to running any of the FSL binaries within the container:

Terminal

module avail fsl
module load apptainer/FSL/6.0.7.6
# The following is required to use aliases in a non-interactive/SLURM batch script:
shopt -s expand_aliases
fsl......

Alternatively run with apptainer directly; i.e. to run binaries within the container, prefix any command with apptainer run $APPTAINER_IMG/<apptainer_image.sif>.

To get an interactive shell into the container:

Terminal

apptainer run $APPTAINER_IMG/fsl.sif /bin/bash

Within the container, you'll find the FSL binaries in /home/fsl/fsl/bin

These can also be invoked directly within the context of the container, with:

Terminal

apptainer run $APPTAINER_IMG/fsl.sif <fsl_binary>

via Spack

Alternatively FSL (fsl) can also be self-installed using Spack.