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
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