Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

clean up the retinotopy/fmriprep submodule installation #33

Open
5 tasks
MarieStLaurent opened this issue Sep 6, 2024 · 0 comments
Open
5 tasks

clean up the retinotopy/fmriprep submodule installation #33

MarieStLaurent opened this issue Sep 6, 2024 · 0 comments
Assignees

Comments

@MarieStLaurent
Copy link
Collaborator

MarieStLaurent commented Sep 6, 2024

I do have the retinotopy.fmriprep repo (with_slicetiming branch) installed as a submodule named fmriprep under cneuromod-things/retinotopy, but my install is messy (I made changes to the stimuli sub-submodule that I can't push). Might be simplest to remove and reinstall cleanly.

  • I can't see the retinotopy.fmriprep repo on the cneuromod github (is it private?). I worked from the with_slicetiming branch, would it make sense to merge it into main? Or leave it as-is?
  • I also can't see the fmriprep/sourcedata/retinotopy submodule which should point to the cneuromod.retinotopy repo on github; my current version on beluga points to a detached head at 1758b9f. Can we validate that this is up-to-date (both the links within the cneuromod-things repo, and the ones between repos on github)?
  • Can we also validate that cneuromod.retinotopy contains *events.tsv files under each sub-0*/ses-0*/func folder that contain trialwise metrics? I do have local .tsv files under cneuromod-things/retinotopy/fmriprep/sourcedada/retinotopy, some are local files and other are symbolic links (not sure why).
  • Apparently I modified my local fmriprep/sourcedata/retinotopy/stimuli sub-submodule but failed to update the head that the submodule points toward. Might be worth reinstalling fmriprep/sourcedata/retinotopy/ (cneuromod.retinotopy) and making sure its stimuli submodule points to the right branch from retino.stimuli (with the aperture masks).
  • Once the nested repo structure (fmriprep/sourcedata/retinotopy/stimuli) is validated on github, perhaps reinstall retinotopy.fmriprep as a submodule called fmriprep under cneuromod-things/retinotopy to replace the old one.
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants