Freesurfer image

[brandmaier]

How to install FreeSurfer in a container? It requires a license that is free but has to be obtained first. See here: https://surfer.nmr.mgh.harvard.edu/fswiki/LinuxInstall

[brandmaier]

Here is a solution: https://hub.docker.com/r/vistalab/freesurfer/dockerfile
How would we best integrate this into our solution?

[aaronpeikert]

Users may freely add any Docker statements to the file .repro/Dockerfile_manual so they could paste the relevant lines from the freesurfer dockerfile you linked to and it would work.
However, I guess including the licence file via COPY in the docker image and then distributing the image violates the licence agreement.

Anyway when the user has already acquired a licence file and it is available at runtime because the standard repro makefile makes the project files available inside docker. Setting some environment variable so that free surver finds the licence should do the trick. It probably would require some tinkering to find out how to not violate the licence agreement and still make it technically work.