I deleted some extra dura that was included in the pial surface. I recompiled using recon-all -autorecon-pial -subjid <subject_name>. The wm.mgz file, however, was still wrong. Do you think I should edit it as well?

The wm.mgz before and after manual editing are shown on the left and right panels of the attachment. 

Thank you very much!

Sincerely,

Ye