[Mne_analysis] Inconsistent surfaces extracted using watershed

[Eric Larson]

        External Email - Use Caution        

Can you see if any of the tips in these old posts help? This looks like a
Freesurfer reconstruction / function problem.

https://mail.nmr.mgh.harvard.edu/pipermail//mne_analysis/2019-February/005561.html
https://mail.nmr.mgh.harvard.edu/pipermail//mne_analysis/2019-April/005805.html
https://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/2019-November/006317.html

In this particular case I'm guessing that your `brainmask.mgz` does not
look correct. I would tweak the freesurfer reconstruction before working on
BEM mesh extraction.

HTH,
Eric



On Tue, Jan 21, 2020 at 10:11 AM Davide Momi <momi.davide89 at gmail.com>
wrote:

>         External Email - Use Caution
>
> 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
>
>
>
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