Thank you, I got a brain surface using the mri_binarize function.

Is there a function for expanding the surface radially by a few millimeters? I want to create the inner skull surface as an expansion of the brain surface.

Thanks,
Manorama

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edu>
Sent: Wednesday, September 9, 2020 6:25 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Make BEM with corrected brainmask

I'm not sure, but you might be able to just create a surface from the brain mask with
mri_binarize --i brainmask.mgz --min 0.5 --surf brainmask.surf
You can smooth it a bit if you add --surf-smooth 2
where 2 is the number of iterations (more for smoother)
Try that

Hi,

Why does the "mri_watershed" function create a new brainmask? Is there a way to create BEM surfaces from an existing or already corrected brainmask?

I had manually edited the brainmask during recon-all process. After the recon-all process completed, the pial surfaces looked good.

But when I ran 'make_watershed_bem', the BEM surfaces came out incorrect. The function 'mri_watershed' re-created a brainmask with the same errors that I had corrected earlier.

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

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