You can do:
recon-all -cortparc -parcstats -s
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/ReconAllStable
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 "-auto
