Deepa,

How different were the values? The stats will differ about 0.02% from run-to-run on the same subject due to randomness present in some of the processing algorithms.

Nick

On Wed, 2007-03-21 at 11:17 -0400, deepa preeti wrote:

Hi Bruce,

I am trying to do cortical thickness on a few scans. But on many of the subjects after autorecon2, I found temporal regions were not included. When I browsed the archive, it was suggested to add a few control points in the temporal lobe wm, saving the control points and rerunning using the command :

recon-all -autorecon2-cp -autorecon3 -subjid subject

• which is supposed to do the trick and fix the pial surface as well.

Unfortunately, this didn't give me different results when I opened the image using this command :

tkmedit subject brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white The image was the same, with contol points added, and the temporal region still not included. I have some images for you to look at (

However, I compared the stats ( lh & rh .aparc.2005 and lh & rh aparc ) before adding cp and after adding cp & rerunning eveything --- the values are different. Although the second image still did not include the temporal region, the stats nevertheless gave me different values. I am relatively new to Freesurfer and I appreciate your suggestions and thoughts on this dilemma. Thank you for taking the time to help me with this.

Deepa.

-- Deepa Ramasamy, MD Research Assistant Buffalo Neuroimaging Center The Jacobs Neurological Institute Department of Neurology Buffalo General Hospital 100 High St. Buffalo, NY 14203 Work: 716-859-7038 Cell: 716-479- 3050 E-Mail: dramasamy@bnac.net _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer