Hello, <br>    I am trying to run cortical thickness on a few scans. 
After the initial recon-all -all command not all regions of grey and 
white matter were included. I have attached a picture of the problem 
(the right side temporal lobe is not included, but the the left side 
is). I tried adding control points and re-running the process with the 
command &quot;-autorecon-all -autorecon2-cp -autorecon3 -subjid <i>subject name&quot; </i>but I do not get a very improved result. If there anything else I can try? <br>
<br>Thank you for all your help, <br>Kristina Nalbandyan <br>Neuroscience Undergraduate Interdepartmental Program, UCLA