Hi all,<br>
<br>
I am fairly new to FreeSurfer and I&#39;ve just finished initial runs on about 140 MRI <br>
images.&nbsp; Now, my job is to go through and do a little QC that helps ensure that the <br>
cortical thickness values are as accurate as possible.&nbsp; Now, I have a few questions:<br>
<br>
1.&nbsp; Am I right in assuming that cortical thickness values are calculated as a function of <br>
the distance between the white and pial surfaces?<br>
<br>
2.&nbsp; How exactly are the white and pial surfaces calculated?&nbsp; Do they utilize the wm <br>
segmentation?<br>
<br>
3.&nbsp; Since I thought this was the case, I have tried cleaning up a couple images by using <br>
control points (using case 4 in the tutorial as a guide), hoping that the white and pial <br>
surfaces would be redrawn in a more accurate way.&nbsp; However, the problem remains.&nbsp; The <br>
surfaces are not including parts that are obviously white matter and gray matter.<br>
<br>
So basically, I&#39;m thinking I&#39;m missing something on the best way to fix white and pial <br>
surfaces when they&#39;re not accurate enough.&nbsp; Could anyone offer me some advice/a link to a <br>
site which explains the best way to handle such problems?<br>
<br>
Thanks, and sorry for the looooong post.<br>
<br>
Ryan