You can do: recon-all -cortparc -parcstats -s <subjid> which will create the cortical parcellations and the associated stats file. (Note: -cortparc2 and -parcstats2 will use the alternative atlas).
Steps like these can be found on the wiki, here: https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllStableTablev4
Allison
On Wed, 20 Feb 2008, Dan Dillon wrote:
Dear FreeSurfers,
I have several subjects who have fine inflated, white, and pial surfaces, as well as fine curvatures, but no cortical parcellations. Is there a directive I can pass to recon-all to generate the parcellation without having to run autorecon3 all over again? Something like "-autorecon3-parcellation"? I am running version 4.0.1.
Thanks!
Dan Dillon, Ph.D.
Post-doctoral Fellow
Affective Neuroscience Lab
Dept. of Psychology, Harvard University
Phone: (617) 495-1889
E-mail: dillon@wjh.harvard.edu