Hi Ashkay,

if you are doing voxel-wise TBM it probably doesn't matter. The definition of gray matter should be consistent between the two, just the labels of what bit of cortex they are will change.

cheers Bruce On Fri, 22 Mar 2013, Akshay wrote:

Hello Freesurfer experts,

I am currently doing some TBM analysis and to compute whole brain atrophy I consider all the structures except ventricles and CSF from aseg.mgz in my definition. Should I also include the cortex definition from aparc+aseg? If yes, should I then use aparc+aseg or aparc.a2009s+aseg segmentation file?

Any help will be greatly appreciated.

Akshay

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