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 > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
