Connectome Workbench wb_command

Connectome Workbench is an open source, freely available visualization and discovery tool used to map neuroimaging data, especially data generated by the Human Connectome Project. The distribution includes wb_view, a GUI-based visualiation platform, and wb_command, a command-line program for performing a variety of algorithmic tasks using volume, surface, and grayordinate data.

• wb_command is a powerful suite of commands used for performing operations on all sorts of neuroimaging data. It is necessary for running HCP data processing pipelines.
• wb_view is a GUI-based viewer. It has a lot of features, but is not especially popular in our lab. You can see more details, including tutorials, in the appropriate section below.

wb_command

wb_command is a suite of command-line programs for performing a variety of algorithmic tasks using volume, surface, and grayordinate data. wb_command is necessary for running HCP data processing pipelines. A full list of commands and documentation for wb_command can be found here

Starting wb_command

To use Connectome Workbench on MASSIVE, open a terminal and type > module load connectome. You can use > module list to see what version of the Workbench has been loaded, or > wb_command -help for more information. You'll probably be using version 1.5.XX or version 2.XX.

Using commands

• To use commands in Workbench in terminal, enter the line > wb_command SUBPROGRAM_NAME OTHER_ARGUMENTS
  • e.g. wb_command -cifti-reduce inputfile.dtseries.nii MEAN mean.dscalar.nii
• You can see the full list of subprograms here and some common ones are listed below
• When reading the documentation, arguments in angle brackets are mandatory, order-dependent, and do not have the name specified; arguments in square brackets are optional and need to have the flag specified
  • for example, if you wanted to change the direction of the cifti-reduce call above, you would use
    wb_command -cifti-reduce inputfile.dtseries.nii MEAN mean.dscalar.nii -direction COLUMN
• See wbcommand_example.sh in the wb_command folder of the repo for a comprehensive example!

Common functions

-metric-resample -surface-geodesic-distance -surface-geodesic-distance-all-to-all -cifti-convert -cifti-math -cifti-reduce -cifti-parcellate

wb_view

Workbench also includes a GUI based viewer in the package. This is a nice viewer but is not especially popular (at least not in NSB). If you want more details, you can have a look at the v1.5 tutorial [here].(https://www.humanconnectome.org/storage/app/media/documentation/tutorials/Connectome_WB_Tutorial_v1.5.pdf), or find out more about annotations here.

Tutorials

• The HCP has released a comprehensive tutorial that primarily focusses on wb_view. You can access that here, or find out more about annotations here.
  • Note: to access some of their example data, you may need to create an account with the HCP here.
• There is a series of tutorials by Dr Jo Etzel here. This runs through many different aspects of the Workbench, again primarily focussing on the viewer.