I have an annotation file that covers the entire surface (each vertex has an annotation). When I run mris_anatomical_stats with the annotation file and sum the values from each annotation, I get a larger result for the surface area and a smaller value for the gray matter volume than if I run mris_anatomical_stats with just the surface (no annotation file specified on the command line).
[cuneus:kentron] (nmr-dev-env) mris_anatomical_stats -a 2859_4_ct/label/rh.cmaparc.annot -b 2859_4_ct/ rh
sum of each annotations' surface area: 112383 mm^2 sum of each annotations' gray matter volume: 375675 mm^3
[cuneus:kentron] (nmr-dev-env) mris_anatomical_stats 2859_4_ct/ rh
total surface area = 98400 mm^2 total gray matter volume = 401366 mm^3
-Jon