Dear Bruce, Gabor,
while reading this thread, I think that there is misunderstanding.
-noaseg flag of recon-all indeed disables using aseg.presurf,
whereas -autorecon2-noaseg does the same thing as -autorecon2-cp
(at least in dev version, looking at the recon-all code).
Antonin Skoch
Hi Gabor
you don't want to specify -noaseg. That tells recon-all not to use the aseg. I think autorecon2-cp and autorecon3 should do the trick
cheers Bruce On Tue, 26 Sep 2017, Gabor Perlaki wrote:
Dear Bruce,
I've corrected the lateral ventricles in the aseg.presurf.mgz and ran "recon-all -autorecon2-noaseg -autorecon3 -subjid". Although the labels in aseg.mgz is fine the surfaces (and midline cut) remained bad. Any other idea how to correct this type of error?
Best Regards, Gabor