All of those except total brain volume are included in the aseg.stats. You can get total brain volume by running mri_binarize --i aparc+aseg.mgz --o junk.mgh --count brainvol.dat brainvol.dat will be a text file with the brain volume in it. You can delete junk.mgh doug

Bruce Fischl wrote:

Hi Dhinakaran.

I think we include this in one of the stats files. Allison or Doug would know.

cheers Bruce

On Fri, 9 Mar 2012, Dhinakaran Chinappen wrote:

...

Hi Prof. Fischl and Dr.Greve, I was wondering if you all got this email below? I sent in to the FS listserv early yesterday.

Would really appreciate your help on this matter of total WM and total GM.

Much thanks, Dhinakaran.

---------- Forwarded message ---------- From: Dhinakaran Chinappen dchinapp@seas.upenn.edu Date: Thu, Mar 8, 2012 at 1:20 PM Subject: Total WM and GM Vol in FS 5.0.0 To: Freesurfer Mailing List freesurfer@nmr.mgh.harvard.edu Cc: Professor Lynnae Schwartz schwartzl1@email.chop.edu

Hi all, I am using Freesurfer 5.0.0, before the outputs for cortical and subcortical GM and WM were made available in the final output files.

What is the best way to calculate total gray matter volume (cortical and subcortical)? Is it through mris_anatomical_stats or mri_segstats? Also, are there commands to calculate total cortical and total subcortical volumes of GM separately?

As for total white matter, is using the sum of the volumes of Left-Cerebral-White-Matter and Right-Cerebral-White-Matter considered acceptable practice? Or should I go to the command line and use mris_wm_volume?

Thanks in advance for the clarification, Dhinakaran.

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