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?
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?