Hi Bruce,<br><br>I am trying to do cortical thickness on a few scans.&nbsp;
But on many of&nbsp; 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 :
<br><br><pre>recon-all -autorecon2-cp -autorecon3 -subjid subject</pre>-
which is supposed to do the trick and fix the pial surface as well.
Unfortunately, this didn&#39;t give me different results when I opened the
image using this command :
<br><br><pre>tkmedit subject brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white</pre>The image was the same,&nbsp; with contol points added, and the temporal region<span style="font-weight: bold;"><span style="font-weight: bold;">



 still</span> not included</span>. I have some images for you to look at ( <br><br>However,
I compared the stats ( lh &amp; rh .aparc.2005 and lh &amp; rh aparc )
before adding cp and after adding cp &amp; 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.&nbsp; Thank you for taking the time to help me
with this.
<br clear="all"><br clear="all">Deepa.<br clear="all"><br>-- <br>Deepa Ramasamy, MD<br>Research&nbsp;&nbsp;Assistant<br>Buffalo Neuroimaging Center<br>The Jacobs Neurological Institute<br>Department of Neurology<br>Buffalo General Hospital
<br>100 High St. Buffalo, NY 14203
<br>Work: 716-859-7038<br>Cell:&nbsp;&nbsp; 716-479- 3050<br>E-Mail: <a href="mailto:dramasamy@bnac.net" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">dramasamy@bnac.net</a>