Hi Ryan,
1. Yes, it the average of the shortest distance between white and pial,
and between pial and white at each point.
2. Yes, in part although other things go into it. The wm.mgz is a
starting point (described in many technical papers).
3. The control points will only fix some issues. If the ?.orig doesn't
follow the filled.mgz volume then there is a topological defect this is
being fixed incorrectly, and you'll need to edit the wm.mgz to correct it
(I think there is a tutorial on this).
cheers,
Bruce
On Thu, 10 Jul 2008, Ryan Scotton
wrote:
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
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