Hi Arsenije,
-autorecon-pial should not recreate the brainmask. Is the brainmask.mgz currently correct?
Bruce
On Tue, 21 Nov 2017, Arsenije Subotic wrote:
Dear experts,
I recently finished processing a subject for whom I had performed a skullstrip on the brainmask volume. I decreased the watershed parameter and re-examined the brainmask and the portion of the skull was gone, although some dura was left over. I did a recon-all using the following command:
recon-all -autorecon-pial -subjid <subject name>
However, when recon was finished, I noticed that the skull re-appeared and the surfaces were outlined on it. I went back and tried g-cut to remove the little dura that was left over, but that also did not work. I tried varying the watershed parameters again but I keep getting the same result. Is there any other underlying issue that may be at fault?
Thanks for your help,
Arsenije