mne-tools / mne-tools/mne-python
ENH: Use something other than FreeSurfer for BEM extraction
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Description
Dear MNE expert,
I am working with a EEG dataset and I wish to run source on that. Unfortunately the T1w are not FLASH and I know that in the absence of FLASH images, MNE offers a somewhat less accurate
solution based on the watershed algorithm (see Jas et al., 2018).
Indeed for some subjects in my dataset (see attached 1) I got the following error when I am going to run make_bem_model.
RuntimeError: Surface inner skull is not completely inside surface outer skull
For other subject instead the surfaces are simply wrong (see attached 2), even though make_bem_model hadn't give me any error
I was wondering whether if you have some tips on how to fix them.
Thanks
Dave
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
This is an investigation and design request rather than a localized change. Start with the make_bem_model entry point and the watershed and FreeSurfer approaches described in the issue, then examine the attached examples of invalid surfaces. Done would require an agreed alternative extraction approach and a reproducible implementation or documented resolution.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- backend
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 18/100