Ok. So then if ventricular volume is already excluded, the brain parenchymal volume should be:
Total GM + total cortical WM +cerebellar GM + cerebellar WM + brain stem - CSF? Cheryl On 11-12-15 2:58 PM, "Douglas N Greve" <[email protected]> wrote: > Yes. > > 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: [email protected] >> [[email protected]] on behalf of Douglas N Greve >> [[email protected]] >> Sent: Thursday, December 15, 2011 3:02 PM >> To: Cheryl McCreary >> Cc: [email protected] >> 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" <[email protected]> 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 >> [email protected] >> 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 >> [email protected] >> 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. >> >> >> -- Cheryl McCreary Research Assistant Professor Seaman Family MR Research Centre Foothills Medical Centre 1403 29th Street NW Calgary, AB T2N 2T9 Phone: (403) 944-8781 FAX: (403) 270-7907 _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
