Hi Gabor
run recon-all through to the mri_ca_label step. We do have some code for correcting the aseg with surface (which are typically more accurate), but I don't think we run it by default (Nick or Doug can correct me if I'm wrong)
cheers Bruce On Sat, 18 Jan 2014, Gabor Perlaki wrote:
Dear all,
Is there any commands in Freesurfer, which segment only the subcortical structures for me? The -autorecon2 calculates also the surfaces which seems unnecessary. However, I don't know whether the final surfaces have an effectt on subcortical volumes. There was a question about it on the Freesurfer's mailing list, but no answer(https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-July/031576.ht ml). Which is the most time-efficient way to get subcortical segmentation with Freesurfer?
Thanks, Gabor