Hello Freesurfers,
I ran recon-all on a subject's structural data like so: recon-all -autorecon-all -subjid subect_name
The resulting pial surface looked pretty good except that there were a few voxels of dura and cerebellum that were included in the pial surface. not a big deal. I deleted some voxels of dura from brainmask.mgz and deleted voxels of from the cerebellum by creating and saving a copy of brain.finalsurfs.mgz. /subject_name/mri/ cp brain.finalsurfs.mgz brain.finalsurfs.manedit.mgz
Then I ran recon all to regenerate the pial surface: recon-all -autorecon-pial -subjid subject_name
The results from the pial surface redrawing are now totally wrong and completely underestimated. The weird thing is that it looked perfectly fine before and removing some problematic voxels caused this result.
Any insights as to how/why this occurred and how to fix it? Images of the AFTER picture attached.
Thanks! -Ronny
