This is a Pegasus workflow for running FreeSurfer on the Open Science Grid, and replaces the fsurf service. The workflow is set up to take a directory with .mgz files as input and process each subject in parallel, using multicore jobs where appropriate.
Please run the workflow from your OSG Connect account. Anybody with a U.S. research affiliation can get access.
You will need your own license file. See the FreeSurfer documentation for details on how to obtain the license. Once you have it, name it license.txt and put it in the same directory as you are submitting the workflow from, as Pegasus will pick up the file and send it with the jobs.
This is a community driven development effort - feel free to fork and submit pull requests if you have improvements you want to share with the community. Thank you!
$ ./submit.sh --help
usage: submit.sh [-h] --inputs-def INPUTS_DEF [--cores NUM_CORES]
[--skip-recon] [--single-job] [--serial-job]
[--hemi {rh,lh}] [--debug]
Generate a pegasus workflow
optional arguments:
-h, --help show this help message and exit
--inputs-def INPUTS_DEF
yaml based description of inputs
--cores NUM_CORES number of cores to use
--skip-recon Skip recon processing
--single-job Do all processing in a single job per subject
--debug Enable debugging output
What to process is specified in an YAML input file with the format:
samplename:
input: /some/path/to/input-mgz-or-nii
T2: /optional/path/to/T2
autorecon-options:
Only samplename and input is required. Multiple inputs can be provided.
An example is provided in the example-run.yml file:
THP0001:
input: tests/sub-THP0001_ses-THP0001UCI1_run-01_T1w.nii.gz
T2: tests/sub-THP0001_ses-THP0001UCI1_run-01_T2w.nii.gz
autorecon-options: -cw256
sample-001:
input: /cvmfs/singularity.opensciencegrid.org/opensciencegrid/osgvo-freesurfer:latest/opt/freesurfer-6.0.1/subjects/sample-001.mgz
Check out this repository to your OSG Connect account $HOME directory. Put your license.txt in the top level directory and run:
$ ./submit.sh --inputs-def example-run.yml
The workflow will pick up the two samples as specified in the example-run.yml file, create a workflow and submit it. Once the workflow is running, you can check the status with pegasus-status [wfdir].
Outputs will be staged to /local-scratch/$USER/workflows/outputs/
Please contact OSG Connect Support for any questions.