Fastsurfer on conda / pip

[MariusCausemann]

Hi,
to ease installation of fastsurfer and its dependencies, especially, as part of a larger software stack, it would be very useful to have it installable via conda (or alternatively pip). Are there any plans to publish fastsurfer as a conda package, or is it something you would consider?
Thank you!

[dkuegler]

Hi Marius,

this wish has been asked previously in #262.

Eventually, this is intended, it is however not trivial because the structure of the project does not easily support this for multiple reasons.
Additionally, we recommend to use the official docker image (deepmi/fastsurfer) because that setup is tested and "certified" in quality. It will make it much easier for all to use (and for us to help users). In that context, singularity images are also available for security-restricted HPC environments.

Cheers

[MariusCausemann]

Hi David,
thanks, I somehow missed that issue. I see that there are several difficulties with packaging fastsurfer, but maybe it would be worth it to start with a minimal version, e.g. only cpu and only the segmentation, without the freesurfer parts. I think something like that could cover quite some use cases and would be valuable for many, coming with a much liter footprint and easier integration in other projects than container based solutions.
Maybe something to consider?

[dkuegler]

Thank you. I'll put this suggestion up for the next meetings :)

[m-reuter]

I am totally in favor of that. The only problem so far was, that the structure of the repo is not great for a package. There were some efforts in first restructuring the repo. I didn't see much progress on that end recently and think it makes sense to not wait for it and longer.

[finsberg]

I would also be very interested in this, and I would also be willing to help out if there is anything I can do to help.

[m-reuter]

thanks for offering your help, which is greatly appreciated. We will post here once we discussed the individual steps and what work items we have.

[MariusCausemann]

Hi @m-reuter and @dkuegler ,
we are still interested in getting fastsurfer on conda/pip. Are there any news?

[m-reuter]

Thanks for bringing this up again!
I guess there is never a perfect time for this (as we are constantly adding new modules etc). The question is, what should be part of a pip/conda release. All of FastSurfer (this would include FreeSurfer binaries, which are not compiled for all OSs), only the segmentation modules which are all python (including Cerebnet, Hypvinn etc) or only FastSurferVINN for the APARC-DKT full brain segmentation as a minimal solution?

Also I think we should not wait for a re-structuring of the code base. If we do, it will take forever.

So let's use this issue to define a work plan and split the workload, to at least have an initial release.