Dear all, I have created a Docker image with Freesurfer distribution (and all required dependencies).
Features:
- Only requires Docker to run (works on Linux, Mac and Windows - does not suffer from the VirtualBox bug https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg42474.html ) - understands BIDS http://bids.neuroimaging.io/ formatted datasets - performs recon-all on all subjects - allows you to run each subject independently (and potentially in parallel) - automatically performs longitudinal analysis when multiple sessions are detected - creates custom group level template for your study - can be easily converted to a Singularity http://singularity.lbl.gov/ image using docker2singularity https://github.com/chrisfilo/docker2singularity tool and run on your local HPC/cluster
You can find more information here: https://github.com/BIDS-Apps/freesurfer
Please let me know what do you think!
Best, Chris