Hi Cheryl, You can regenerate the asseg.stats file with BrianVolNotVent with:
cd $SUBJECTS_DIR/yoursubject mri_segstats --subject yoursubject --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --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 --ctab /usr/local/freesurfer/dev/ASegStatsLUT.txt --brain-vol-from-seg
This is the same command that generated the existing aseg.stats file with "--brain-vol-from-seg" added.
doug
Cheryl McCreary wrote:
Hi Freesurfer experts,
I would like to determine brain parenchymal fraction (ie brain tissue volume/estimated ICV) as an estimate of global atrophy. In previous versions of FS, I used the BrianVolNotVent/ICV. Is this correct?
I am now using freesurfer version 5.0.0 and BrainVolNotVent is not longer available.
My understanding is that the total gray matter and total cortical white matter volumes are determined from the pial and white surfaces (thickness *surface area). Do these volumes include or exclude the ventricular volumes? Can the total brain volume be calculated as the sum of the total GM, total cortical WM, brain stem, cerebellar GM and WM minus the CSF. Or do the volumes of the ventricles need to be subtracted as well?
Thanks for your help.
Cheryl