Connectome Workbench
--------------------
`Connectome Workbench <https://humanconnectome.org/software/get-connectome-workbench>`_ is an open-source visualization and discovery tool used to explore data generated by the Human Connectome Project.


via OnDemand
^^^^^^^^^^^^
The Connectome Workbench wb_view GUI is `available as an Open OnDemand app <https://ondemand.otago.ac.nz/pun/sys/dashboard/batch_connect/sys/ood_connectome_workbench_apptainer>`_.


via commandline/Slurm
^^^^^^^^^^^^^^^^^^^^^
Connectome Workbench is made available on the cluster as a shared :doc:`Apptainer <apptainer>` container image.
You can use the :code:`apptainer/connectome_workbench` module to add convenient aliases to running any of the FSL binaries within the container:

.. code-block:: bash

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

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/connectome_workbench-<version>.sif /bin/bash
    
Within the container, you'll find the binaries under /opt/workbench/

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

.. code-block:: bash

    apptainer run $APPTAINER_IMG/connectome_workbench-<version>.sif wb_command ...