Hi Aaron, probably the easiest thing to do is to re-run mri_segstats for each of your subjects giving it the option to save this measure into the output stats file. To do this, you can get the basic command from the recon-all.log file. To this add

--brainmask mri/brainmask.mgz --brain-vol-from-seg

Below are descriptions of the values that it produces.

doug

1. BrainSegNotVent - sum of the volume of the structures identified in the aseg.mgz volume this will include cerebellum but not ventricles, CSF and dura. Includes partial volume compensation with --pv. This is probably the number you want to report. 2. BrainMask - total volume of non-zero voxels in brainmask.mgz. This will include cerebellum, ventricles, and possibly dura. This is probably not what you want to report. 3. BrainSeg - sum of the volume of the structures identified in the aseg.mgz volume. This will include cerebellum and ventricles but should exclude dura. This does not include partial volume compensation, so this number might be different than the sum of the segmentation volumes. 4. IntraCranialVol (ICV) - estimate of the intracranial volume based on the talairach transform. See surfer.nmr.mgh.harvard.edu/fswiki/eTIV for more details. This is the same measure as Estimated Total Intracranial Volume (eTIV).

On 05/17/2012 04:56 PM, Goldman, Aaron (NIH/NIMH) [C] wrote:

Hello,

For an analysis, we’re trying to calculate a Total Brain Volume covariate based on the data in aseg.stats, generated using version 5.0.0. Basically, we want to include all WM and GM but not CSF.

I was thinking of doing Total GM + Cortical WM + L&R Cerebellum WM. Would this be the correct way to do it, or should we use some other combination?

Thanks,

Aaron

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