Dana, Here's an approach that I use for total brain volume (without the cerebellum):

Compute the total volume enclosed within the pial surface (mris_volume lh.pial) and then subtract out the volume from the aseg.stats for the Lateral-Ventricle and choroid-plexus). Repeat for both hemispheres, and sum the total.

Note that the pial surface doesn't enclose the 3rd and 4th-ventricles, so those are already excluded. Also, it is my experience that most of the time the aseg.stats region "Int-Lat-Vent" also falls outside the pial surface, which is why I don't subtract that region from the above calculation either.

cheers, -MH

On Thu, 2009-06-11 at 14:41 -0400, Bruce Fischl wrote:

Hi Dana,

this will compute all supra-tentorial white matter and *cortical* gray matter volume. The mris_wm_volume binary computes the interior of the ?h.white surface, then throws out the volume of all the non-wm structures in the interior. I guess the BrainSetNotVen value is a reasonable one for total brain volume. You could probably get a more accurate one using surfaces, but not sure how big the difference would be.

cheers, Bruce

On Thu, 11 Jun 2009, Dana W. Moore wrote:

...

Hi all,

I am calculating total gray and white matter volumes using mrs_volume and mris_wm_volume, and I wanted to clarify what these are measuring. I am following the instructions on the morphometry stats wiki page, which say to use mris_volume and subract wm from pial volume to get total gray matter. Will this leave me with all gray matter including cortical and subcortical? Then I use mris_wm_volume to calculate total wm. Again, does this include all white matter in the brain?

Also, what would be the best way to calculate total brain volume? I could add the calculations for gray matter and white matter described above, or I could use BrainSetNotVen from the aseg stats file, or I could add all the structures in the aparc and aseg files. Any recommendation on which is best?

Thanks, Dana

Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuropsychology Service Weill Medical College of Cornell University New York Presbyterian Hospital Department of Neurology & Neuroscience 428 East 72nd Street, Suite 500 New York, NY 10021 Phone: 212-746-2441 Fax: 212-746-5584 Email: dwm2003@med.cornell.edu

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