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
On 9/9/2020 6:01 PM, Kadwani, Manorama wrote:
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=s...
Thanks, Manorama
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