Hi Mike

our license lets you do pretty much whatever you want :). That said, the recon pipeline is complex and it isn't so easy to pick and choose steps, although I guess if you are just processing already datasets that have already been run through recon-all it should be pretty straightforward as all the files we expect to exist should be where we expect them to be Bruce

On Mon, 4 Nov 2019, Mike Schmidt wrote:

External Email - Use Caution

Cursory googling has not turned up a solution to this, but I expect it may have been asked before. I would like to use several FreeSurfer utilities (mri_convert, mri_binarize, mri_pretess, mri_tesselate, mris_convert) in a docker container to post-process existing FreeSurfer output files. Creating a full FreeSurfer docker container is easily done. But ideally, I'd like to keep the container as small as possible so I would like to avoid using the whole 6GB package.

While the license seems to legally allow derivative works like this, I'm not sure how the individual executables check for the license file, what the dependencies are, how tangled the web of dependencies may be, etc.

1. Is this a supported use and/or solved problem that I just haven't found in my searching?
2. If not, does anyone have a reason to warn me away from wasting time going down this road?

Thanks for the benefit of others' experience,     Mike Schmidt