We have recently run a set of longitudinal data (FreeSurfer5.3) and are making edits to the base pial surfaces.  It is clear that there are two different ways of doing pial edits including: 1. editing the brainmask.mgz and 2. the brain.finalsurfs.mgz.  I recognize that they are specific ways to deal with different issues in the surface reconstruction.

My question is will the following command (recon-all -base <ID> -autorecon2-pial -autorecon3) pick up both edits in the -base rerun 

or

will you need to make the brainmask.mgz edits, rerun the -base recon command the make brain.finalsufs.mgz edits, rerun the -base command?

Thanks,

David

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Martin Reuter, Ph.D.
Assistant in Neuroscience - Massachusetts General Hospital
Instructor in Neurology   - Harvard Medical School
MGH / HMS / MIT

A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129

Phone: +1-617-724-5652
Email: 
   mreuter@nmr.mgh.harvard.edu
   reuter@mit.edu
Web  : http://reuter.mit.edu