Skip to content
A Pegasus workflow for running FreeSurfer on the Open Science Grid
Python Shell
Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
scripts
tests
.gitignore
README.md
example-run.yml
pegasus.conf
sites.xml.template
submit.sh
workflow-generator.py

README.md

FreeSurfer workflow for Open Science Grid

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 usage

$ ./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

Specifying Inputs

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

Submitting an Example Workflow

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/

Getting Help

Please contact OSG Connect Support for any questions.

You can’t perform that action at this time.