Kristina, you can also run defect-seg to create aseg segmentation of the defects. Follow the instructions in the --help to visualize. Look in that region for defects.
doug

On 2/8/13 5:56 PM, Bruce Fischl wrote:

Hi Kristina

I would guess you have a topological defect that is being fixed incorrectly. If you upload the subject I'm happy to take a look (in between rounds of shoveling)

Bruce
On Fri, 8 Feb 2013, Kristina Nalbandian wrote:

Hello,
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 "-autorecon-all
-autorecon2-cp -autorecon3 -subjid subject name" but I do not get a very
improved result. If there anything else I can try?

Thank you for all your help,
Kristina Nalbandyan
Neuroscience Undergraduate Interdepartmental Program, UCLA
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