did you check the skull stripping? And the talairach? On Wed, 21 Mar 2007, 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 regionstillnot 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.