Hi Octavian
if you want to regenerate the pial surface you have to run autorecon3 also.
And I don't think you want to edit the wm.mgz for wm edits. Probably you should edit brain.finalsurfs.mgz for both wm and pial. Can someone who has done more recent recons than I have confirm this?
cheers Bruce
On Thu, 9 Mar 2017, Octavian Lie wrote:
Dear All,
A simple issue of precedence. In the recon-all pipeline, wm edits take precedence to pial edits. If there are both wm and pial defects, should one apply edits sequentially, say on brainmask.mgz (first wm edits, rerun recon-all say recon-all -autorecon2 -wm, then do pial edits, rerun recon-all say recon-all -autorecon2 -pial) or to some extent pial edits influence the final surface generation in conjunction to wm edits (understood that the latter may influence more the final form than the former -pial- edits), in that case one may do both edits, then run -autorecon2 -wm only.
Please advise, Octavian