Gray Matter and White Matter Volume
Estimation of the gray matter and white matter volumes should be taken from the surfaces, and not from the aseg. If the data is of very poor quality and surfaces cannot be reconstructed, but the aseg is fairly accurate, then gm and wm volume can be taken from the aseg.
Surface-based measures of cortical gray matter and white matter volume can be found in the header of the aseg.stats file:
lhCortex & rhCortex - per hemi gray matter volume based on the pial surface
Cortex - total gray matter volume based on the pial surface
lhCorticalWhiteMatter & rhCorticalWhiteMatter - per hemi white matter volume based on the white surface
CorticalWhiteMatter - total white matter volume based on the white surface
Here is how the above are calculated:
Volume = Surface Area x Thickness
More specifically, the CorticalWhiteMatter measurement is calculated by determining which voxels are within the WM surface. Only the voxels with the following labels in the aseg are counted: Left_Cerebral_Cortex, Right_Cerebral_Cortex, Left_Cerebral_White_Matter, Right_Cerebral_White_Matter, Left_WM_hypointensities, Right_WM_hypointensities, CC_Posterior, CC_Mid_Posterior, CC_Central, CC_Mid_Anterior, and CC_Anterior.
Note: The *_Cortex labels are included when calculating the CorticalWhiteMatter measurement to catch the partially volumed voxels.
The volume for all the subcortical structures segmented by the aseg.mgz can also be found in the aseg.stats file. For each structure, you will find the number of voxels, mean intensity across the structure, the standard deviation, Min, Max and Range of the intensity across the structure. The structures that are segmented are:
In the aseg.stats header, you will also find the following volumes:
SubCortGray - volume-based measure of subcortical gray matter
TotalGray - Cortex + SubCortGray
SupraTentorial - Cortex + CorticalWhiteMatter + SubCortGray (essentially, everything above the tentorium within the pial surface plus the subcortical volumes)
IntraCranialVol - estimated Total Intracranial vol (eTIV)