[Mne_analysis] BEM unaffected by edits to brainmask

[Kadwani, Manorama]

I should have asked this on the Freesurfer mailing list.
________________________________
From: mne_analysis-bounces at nmr.mgh.harvard.edu <mne_analysis-bounces at nmr.mgh.harvard.edu> on behalf of Kadwani, Manorama <MKADWANI at mgh.harvard.edu>
Sent: Wednesday, September 9, 2020 5:44 PM
To: Discussion and support forum for the users of MNE Software <mne_analysis at nmr.mgh.harvard.edu>
Subject: Re: [Mne_analysis] BEM unaffected by edits to brainmask

Hi Eric,

Yes, I tried those options and chose to go with editing the brainmask. After the brainmask was manually edited and recon-all process completed, the surfaces looked good.
But when I ran 'make_watershed_bem', the function 'mri_watershed' re-created a brainmask with the same errors that I had corrected earlier.
Is there a way to create BEM surfaces from the already corrected brainmask?

I saw there was a question on this topic already, but couldn't find answers: https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subject:%22%5C%5BFreesurfer%5C%5D+mri_watershed%22&o=newest&f=1

Thanks,
Manorama
________________________________
From: mne_analysis-bounces at nmr.mgh.harvard.edu <mne_analysis-bounces at nmr.mgh.harvard.edu> on behalf of Eric Larson <larson.eric.d at gmail.com>
Sent: Thursday, September 3, 2020 8:18 PM
To: Discussion and support forum for the users of MNE Software <mne_analysis at nmr.mgh.harvard.edu>
Subject: Re: [Mne_analysis] BEM unaffected by edits to brainmask


        External Email - Use Caution

Can you see if any of these ideas help?

https://mne.tools/dev/overview/faq.html#my-watershed-bem-meshes-look-incorrect

Eric


On Thu, Sep 3, 2020 at 6:58 PM Kadwani, Manorama <MKADWANI at mgh.harvard.edu<mailto:MKADWANI at mgh.harvard.edu>> wrote:
Hi,

While reconstructing cortical surface using Freesurfer, I encountered skull strip errors in the brainmask. I manually erased the dura mater, and then saved it as the main volume. Then re-ran the recon-all process. The pial and white matter surfaces came out correct, but the BEM surfaces were incorrect.
The innermost BEM surfaces, inner skull and brain, followed the old incorrect brainmask boundary for some reason. Are the BEM surfaces based on brainmask boundary or the white and pial surfaces? How to make the BEM brain surface follow the Freesurfer output pial surface?

Thanks!
Manorama
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