[Mne_analysis] mne watershed: inner skull not inside the outer skull

[Mainak Jas]

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Depending on how your segmentation looks, the simplest solution might be to
run mri_expand in Freesurfer on the inner skull surface with a small
negative value.

Be sure to check the quality of the BEM afterwards.

Mainak

On Tue, Nov 19, 2019 at 2:03 PM Eric Larson <larson.eric.d at gmail.com> wrote:

>         External Email - Use Caution
>
> There are many options for computing the watershed bem, MNE only exposes
> some of them. You can try to fix it using Freesurfer commands. Check the
> archive for ideas here, such as:
>
>
> https://mail.nmr.mgh.harvard.edu/pipermail//mne_analysis/2019-April/005805.html
>
> Eric
>
>
> On Tue, Nov 19, 2019 at 7:13 AM Mina Jamshidi <jamshidi at cbs.mpg.de> wrote:
>
>>         External Email - Use Caution
>>
>> Dear All,
>>
>> what is the remedy when there is the following error for bem calculation
>> (with mne watershed_bem)?
>> Surface inner skull is not completely inside surface outer skull
>>
>> Best,
>> Mina
>> P.S. I plot the sufaces using mne.viz.plot_bem and see that the inner
>> skull is not inside in outer skull surface.
>>
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