If you have 5.3 installed, you can just run

mri_segstats --seg mri/aseg.mgz --sum stats/aseg.v53.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /usr/local/freesurfer/stable5/ASegStatsLUT.txt --subject subjectname

this will only create a new stats file (aseg.v53.stats). If you just want to replace the one that is there, then spec aseg.stats instead of aseg.v53.stats

doug

On 06/03/2013 05:54 PM, Derek James Dean wrote:

Hello,

I am a novice, working with aseg.stats data that were processed using Freesurfer 5.1. A colleague requested a measure of total brain volume that does not include CSF for each subject. My understanding is that Freesurfer 5.2 and new versions provide BrainSegNotVent, which seems like the best measure for what my colleague requested. Is there a way to compute the BrainSegNotVent value with the Freesurfer 5.1 processed data? Do I need to re-run recon all with Freesurfer 5.3? Is there another way to get a total brain matter volume measure not including CSF?

Thank you in advance for your help with this question.

Best,

Derek Dean University of Colorado at Boulder Dept. of Psychology and Neuroscience

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