Connectome Workbench¶

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.

via commandline/Slurm¶

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

Terminal

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 apptainer run $APPTAINER_IMG/<apptainer_image.sif>.

To get an interactive shell into the container:

Terminal

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:

Terminal

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