Hi Brianna
If the white surface is correct and you can't get watershed/graph cuts to
do any better, it may be that erasing voxels from the brainmask or
brain.finalsurfs is your only option. If you had multi-echo MPRAGE you
might be able to get rid of it also.
sorry,
Bruce
On Tue, 3 Jul 2012, Kolody, Brianna wrote:
Hi,
We are having problems with some of our pial surfaces extending into the
sagittal sinus. We are interested in cortical thickness around the
precuneus, etc. I attached a couple screen shots to describe. The error is
not repaired by adjusting watershed parameters. How do you suggest we
proceed? Should we erase voxels from brainmask? We are concerned since these
errors extend for a significant number of slices, in many subjects, and
include such a large amount of the sinus.
As a second part to this question, I am unclear on how cortical thickness is
calculated and whether the statistics are directly derived from the visible
surfaces. For instance, when there is an error with the cortical surface
image including the sagittal sinus, it also visibly appears as an error in
aseg and aparc. However, the mistaken area doesn't have an associated region
label in aseg or aparc when we move the cursor over it. Are the cortical
thickness statistics reflected by the parcellation, which possibly does not
include the sinus, or the surfaces, which do seem to include the sinus?
Brianna
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