Hi David,
recon-all -base <ID> -autorecon-pial should be enough to pick up both edits (probably you already looked at the tutorial at http://ftp.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial that describes most edits). Don't forget to re-run all longitudinals from scratch after you do this.
Best, Martin
On 06/06/2013 02:09 PM, David Tate wrote:
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
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