yes On Thu, 15 Dec 2011, Alexopoulos, Dimitrios wrote:
> Just for clarification, the standard output value in the aseg.stats for total > cortical WM > is detremined with 'mris_wm_volume' which subtracts out the volume of non-wm > voxels based on the > aseg, correct? > > Jim > > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Thursday, December 15, 2011 3:02 PM > To: Cheryl McCreary > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Estimate Brain Volume Fraction > > total cortical WM should not include the ventricles. If the lateral > ventricles are not segmented properly, then they would be included, but > this would be an error. Otherwise, I think your equation is correct. > doug > > Cheryl McCreary wrote: >> Hi Doug, >> >> Thanks for the quick reply. I will re-run the mri_segstats as below to get >> the BrainSegNotVent volumes for consistency with the previous version. >> >> Just for my own understanding using the default output aseg.stats from >> recon-all, could whole brain parenchymal volume be calculated as [(total >> GM, total cortical WM, cerebellar GM, cerebellar WM + brain-stem)-2*(left >> lateral ventricle + left Inf Lat Vent + right lateral ventricle+ right inf >> lat vent) - CSF)]? I'm assuming that since both the white matter and pial >> surfaces include the lateral ventricle, the lateral ventricular volume needs >> to be subtracted, while the 3rd and 4th ventricles are not included in the >> surfaces and therefore would not need to be subtracted? >> >> Kind regards, >> Cheryl >> >> >> On 11-12-14 12:45 PM, "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> wrote: >> >> >>> 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. > > > The materials in this email are private and may contain Protected Health > Information. If you are not the intended recipient, be advised that any > unauthorized use, disclosure, copying, distribution or the taking of any > action in reliance on the contents of this information is strictly > prohibited. If you have received this email in error, please immediately > notify the sender via telephone or return email. > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
