AFNI (Analysis of Functional NeuroImages)
-----------------------------------------
https://afni.nimh.nih.gov

For customising the behaviour of AFNI tools with a :code:`~/.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 :doc:`Apptainer <apptainer>` container image. 
Binaries and scripts are run within the context of the container.

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

.. code-block:: bash

    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 :code:`apptainer run $APPTAINER_IMG/<apptainer_image.sif>`. 

To get an interactive shell into the container:

.. code-block:: bash
    
    apptainer run $APPTAINER_IMG/afni_24.2.03.sif /bin/bash
    
Within the container, you'll find the AFNI binaries and scripts in :code:`/opt/afni/install`

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

.. code-block:: bash

    apptainer run $APPTAINER_IMG/afni_24.2.03.sif <command>