Hello,
I would like to verify something regarding subcortical volume estimation in Freesurfer before we move forward with our analyses. From what I've read on the wiki and listserv, it seems the subcortical and cortical processing streams are largely independent. If one were only interested in subcortical volumes (e.g. hippocampus, striatum) is it sufficient to run recon-all -all on the participants, verify/correct any issues with the registration, verify that the segmentations look correct, and then move forward with statistical analyses on the subcortical volumes using aseg.stats, or will refinements in the surfaces (e.g. manually removing dura mater from the pial surface) have an effect on subcortical volume and thus it is necessary to check the surfaces as well, make the corrections, rerun autorecon 2 and 3, the and then perform stats on the subcortical volumes? Thank you in advance for your time.
Sincerely,
Jim Monti