AFNI (Analysis of Functional NeuroImages)

https://afni.nimh.nih.gov

For customising the behaviour of AFNI tools with a ~/.afnirc config or via environment variables, see https://afni.nimh.nih.gov/pub/dist/doc/program_help/README.environment.html

GUI

The AFNI GUI can be accessed via the Open OnDemand Applications - https://ondemand.otago.ac.nz/pun/sys/dashboard/batch_connect/sys/ood_afni_apptainer.

Command line

The AFNI suite is made available on the cluster as a shared Apptainer container image. Binaries and scripts are run within the context of the container.

You can use the apptainer/AFNI module to add convenient aliases to running any of the AFNI binaries and scripts within the container:

Terminnal

module avail afni module load apptainer/AFNI

The following is required to use aliases in a non-interactive/SLURM batch script:

shopt -s expand_aliases afni......

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/afni_24.2.03.sif /bin/bash

Within the container, you'll find the AFNI binaries and scripts in /opt/afni/install

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

Terminal

apptainer run $APPTAINER_IMG/afni_24.2.03.sif