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