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.
Allocate an interactive session and run the program. Sample session:
[user@biowulf]$ sinteractive salloc.exe: Pending job allocation 46116226 salloc.exe: job 46116226 queued and waiting for resources salloc.exe: job 46116226 has been allocated resources salloc.exe: Granted job allocation 46116226 salloc.exe: Waiting for resource configuration salloc.exe: Nodes cn3144 are ready for job [user@cn3144 ~]$ module load connectome-workbench [user@cn3144 ~]$ wb_command -help [user@cn3144 ~]$ wb_view -help [user@cn3144 ~]$ wb_import [user@cn3144 ~]$ exit salloc.exe: Relinquishing job allocation 46116226 [user@biowulf ~]$
Additionally, if you have X11 forwarding enabled you can use the workbench gui by entering wb_view with no arguments.
wb_command gives access to a wide variety of commands related to data analysis iand image processing that can be used in your scripts. Use the following argument to view the documentation.
[user@helix ~]$ wb_command -all-commands-help
After selecting the command(s) you want to run in a batch script, set it up like so.
#!/bin/bash # this file is called myjob.bat cd /data/$USER/my_workbench_data module load connectome-workbench wb_command ...my_command1... wb_command ...my_command2... wb_command ...my_command3... ... wb_command ...my_commandN...
Submit the job to SLURM with:
[user@helix ~]$ sbatch myjob.bat
If you need to run a large number of batch jobs, you can run them in parallel using the swarm program. For this example, imagine we have a large number of files to convert from cifti to nifti format. We would create a swarm file (called "workbench.swarm") that looked something like this:
wb_command -cifti-convert -to-nifti /path/to/file1.cifti /path/to/file1.nifti wb_command -cifti-convert -to-nifti /path/to/file2.cifti /path/to/file2.nifti wb_command -cifti-convert -to-nifti /path/to/file3.cifti /path/to/file3.nifti ... wb_command -cifti-convert -to-nifti /path/to/fileN.cifti /path/to/fileN.nifti
We would submit it to the queue with
[user@helix ~]$ swarm -f workbench.swarm --module connectome-workbench
See the swarm webpage for more information, or contact the Biowulf staff at staff@hpc.nih.gov