Hi Yuliya

they are included if they are inside of the ?h.pial surface. We don't use the cortex aseg label as it is in general less accurate than the surfaces.

cheers
Bruce

On Sun, 5 Jan 2014, Yuliya Yoncheva wrote:

Dear FreeSurfer community,
I am visually inspecting the quality of my recon -all output for a large
dataset and have a rookie question.

In some instances, when skull stripping ended up leaving some of the skull,
these voxels are associated with a "sgmtn label" (cerebral cortex). In other
instances, although there are a small number of skull voxels that were not
removed automatically, these voxels do not have an associated "sgmnt label"
available in TkMedit Tools.

Is it the case that only the voxels for which there is a segmentation label
are actually added to the total grey volume estimate? 

Thus, voxels, which have not been automatically labelled would not impact
volume computations?

Thank you kindly for your help.

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