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!

--
John Sheppard
Undergraduate Student (Class of 2010)
Department of Biomedical Engineering
Northwestern University

Phone: (630) 957-8321
E-mail: john-sheppard@northwestern.edu