Hi Mike,
you need to exclude non-cortical regions (e.g. hippocampus) from the pial volume. I think mris_anatomical_stats -l $subject/label/$hemi.cortex should be the right measure.
cheers, Bruce
On Fri, 20 Apr 2007, Michael Harms wrote:
Hello FS-list,
Could you please confirm the recommended current approach for calculating the total cortical gray matter volume.
Based on the following Wiki page http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats? action=highlight&value=mris_volume I presume that the recommended calculation (illustrated using tcsh syntax) is:
@ total_cort_gm_vol = `mris_volume ?h.pial` - `mris_volume ?h.white`
My only hesitation is that I noticed the resulting value doesn't quite match the value of "total gray matter volume" that is output by mris_anatomical_stats. Is this because mris_anatomical_stats uses a older approach that is no longer considered quite as accurate?
thanks, Mike Harms
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer