Closed maedoc closed 6 years ago
Docker might be worth using as well: the whole thing is lightweight and flexible compared to Vagrant. Once the image is built, one can practically run one off commands
docker run --rm -it tvb/recon -v /my_data:/work/data \
/work/env/freesurfer/bin/recon-all -s test -i /work/data/t1.nii.gz -all
without having to run the VM all the time.
And a a nice example of packaging FS inside a Docker container here
https://github.com/BIDS-Apps/freesurfer
where
Docker image has been created for this project, so i close this.
The scripts for setting up a VM are out of date,
https://github.com/ins-amu/bnm-recon-tools/tree/master/docs/setup-vm
and could be rewritten for Ansible to improve robustness. It's probably a good idea for us to be using a Vagrant (VBox) or Docker VM where possible, so that at least across dev machines, the environment is identical: