yes, Gabor already pointed this out to me :)

thanks to both of you

Bruce

On Tue, 26 Sep 2017, Antonin Skoch wrote:

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