Hi everyone,
Quick question about how you can go about manual pial surface corrections.
This process is outlined at following page: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits
Following the manual edits, user runs following bit of autorecon2 (and autorecon3 again if you want subcortical segmentation):
recon-all -autorecon2-pial -autorecon3 -subjid subject3_before
My questions is simply whether Freesurfer takes the user's input for pial surface verbatim (i.e. does it make the *exact* changes that user specifies). Or, does Freesurfer take the users input but then make its own judgments on where the pial surface should be, combinining user input with intensity/morphometry considerations? Kind of like the way WM control points work (in a sense).
Thanks!