Hi Amirhossein

which structures do you mean? Like the ventricles? We usually mask those regions out using the ?h.cortex.label. The surfaces should be "frozen" in those regions in any case, meaning that the white and pial are in the same location (and the thickness is 0)

cheers
Bruce

On Mon, 11 Aug 2014, amirhossein manzouri wrote:

Dear All, 
I wonder if you have experienced or there is any report on cortical segmentation reliability in the
mid-line structures of the brain, so one should take them into consideration in running group differences
with Qdec?

Best regards,
Amirhossein Manzouri 

 

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