mne-tools / mne-tools/mne-python
mkheadsurf with FS72 / subjdir undefined
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- Dominant language
- Python
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- Merged PRs (30d)
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Description
when estimating the high res head surface of subjects using freesurfer72 I get errors with
subjdir variable undefined. Just sourcing older freesurfer just works... grrr
wdyt about rewriting the shell script mkheadsurf in Python and call directly
freesurfer commands? Debugging these tcsh scripts makes me 😱
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by reproducing the mkheadsurf failure while estimating a high-resolution head surface with FreeSurfer 7.2, then inspect the mkheadsurf tcsh script and how subjdir is set. Compare this with the behavior when sourcing an older FreeSurfer version. Done means either resolving the undefined subjdir error or defining and validating the scope of a Python rewrite that invokes the FreeSurfer commands.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python, shell
- Domain
- tooling
- Issue type
- Bug
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 20/100