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