Hi Vy,

not sure what it going on in your data. Surfaces are copied from the base and if they are not accurate there you need to fix it there. It seems you did that and you worked the edits in the right order.

What exactly happened? You fixed cross and base and everything look fine. When you run long it looks fine, but when you edit long and run it again it messes up?

Did you edit only the brain.finalsurfs or also other things at the same time? Also, if you edited long, these edits will be kept and not replaced with new edits from base or cross. So if cross or base get edited it may be good to rename or remove the edit file in the long and run long without edits again. This way the cross and base edits get transferred to long automatically. Only if that is not sufficient you need to do edits in the long.

Sorry I cannot say more right now without knowing what you did.

Best, Martin

On Fri, Mar 29, 2013 at 10:13 AM, Vy Dinh <vy_dinh@rush.edu> wrote:

BTW, we are using Freesurfer 5.1: freesurfer-i686-apple-darwin9.8.0-stable5-20110525

On Fri, Mar 29, 2013 at 10:08 AM, Vy Dinh <vy_dinh@rush.edu> wrote:

Dear Developers, 

I have a significant problem when rerunning the pial edits for the longitudinal data. Our dataset consists of subjects & a followup scan (for each sub). To be thorough, we edited brain.finalsurfs.manedit.mgz (as it was further in the processing stream) for the cross-sectional scans, the base scans, and the longitudinal scans. The longitudinal data were created only after the base has been edited and rerun. Likewise, the base was only created and rerun after the cross-sectionals were finalized. 

We work with a clinical population so minor edits do show up on the longitudinal scans. However, after editing and recreating the surfaces from these longitudinal scans, the pial surfaces has extended to include dura & other voxels that were not previously included within the pial surface (during the initial creation of the longitudinal data). We tried both commands (listed below) and get this same problem:

recon-all -autorecon2-pial -autorecon3 -long tpN tp_base (http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits)

or recon-all -autorecon3-pial -long tpN tp_base  (http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial)

Could you please help us figure out why the pial surface extends to include nonbrain regions when recreating the surfaces? 

What solutions would you suggest in resolving this problem?

Thank you,

Vy Dinh

Research Associate

Department of Neurological Sciences 

Rush University Medical Center

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-- 
Dr. Martin Reuter
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 

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

-- 
Dr. Martin Reuter
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