On 06/03/2013 02:03 PM, Ritobrato Datta wrote: > Hi Doug, > > I looked that the morphometryStats table that you sent and looks like I need > the following measure. > > BrainSegNotVent - this I believe doesnt include cerebellum etc and no > ventricles. It does include cerebellum. It does exclude ventricles > > But all my data are run through 5.1. How do I get this measure ? If I run the > 5.2 version of mri_segstats on the data that has been run through 5.1, will > it generate this volume ? yes, you can run mri_segstats --seg mri/aseg.mgz --sum stats/aseg.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
> > Please let me know and sorry to keep pestering this. > > Thanks > > Rito > > > ----- Original Message ----- > From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> > To: Ritobrato Datta <rida...@mail.med.upenn.edu> > Cc: Freesurfer@nmr.mgh.harvard.edu > Sent: Mon, 03 Jun 2013 13:54:01 -0400 (EDT) > Subject: Re: [Freesurfer] Repost: question abt supratentorial vol and total > brain vol. > > no, it does not include cerebellum > On 06/03/2013 01:42 PM, Ritobrato Datta wrote: >> In the website below, >> lhCorticalWhiteMatter,rhCorticalWhiteMatter,CorticalWhiteMatter - volume >> inside the white surface minus anything that is not WM. CorticalWhiteMatter >> includes hypointensities. This uses the surface-based volume computation for >> part of the calculation and counts voxels to subtract "anything not in WM". >> It is approximately equal to the count of WM voxels in aparc+aseg.mgz. >> >> Since, cerebellar wm is in the aparc+aseg.mgz so that means its included in >> the CorticalWhiteMatter, correct ? >> >> ----- Original Message ----- >> From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> >> To: Ritobrato Datta <rida...@mail.med.upenn.edu> >> Cc: Freesurfer@nmr.mgh.harvard.edu >> Sent: Mon, 03 Jun 2013 13:19:54 -0400 (EDT) >> Subject: Re: [Freesurfer] Repost: question abt supratentorial vol and total >> brain vol. >> >> >> See if this answers your question >> http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats >> this is for v5.2 and beyond >> >> On 06/03/2013 01:07 PM, Ritobrato Datta wrote: >>> ic thats right....I was getting confused. So the total gm vol includes >>> cerebellar gm vol but the cortical wm vol only includes the wm vol under >>> the cortical ribbon and around the subcortical gm structures....? Or does >>> that include wm under the cerebellar cortex as well ? >>> >>> Is there a table somewhere which specifies which of these freesurfer >>> parcellated structures contribute to these combined measures such has >>> supratentorial vol / whole gm vol etc etc.... >>> >>> That will be very helpful. >>> >>> >>> >>> ----- Original Message ----- >>> From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> >>> To: Ritobrato Datta <rida...@mail.med.upenn.edu>, >>> Freesurfer@nmr.mgh.harvard.edu >>> Sent: Mon, 03 Jun 2013 12:59:30 -0400 (EDT) >>> Subject: Re: [Freesurfer] Repost: question abt supratentorial vol and total >>> brain vol. >>> >>> >>> Hi Rito, I don't think we report a total wm volume, do we? >>> doug >>> >>> >>> >>> >>> On 06/03/2013 12:56 PM, Ritobrato Datta wrote: >>>> Hi Doug, >>>> >>>> Just following up on your reply sometime back - >>>> Does total white volume include cerebellar wm vol also ? >>>> >>>> Please let me know. >>>> >>>> Thanks >>>> >>>> Rito >>>> >>>> ----- Original Message ----- >>>> From: Douglas N Greve <gr...@nmr.mgh.harvard.edu> >>>> To: freesurfer@nmr.mgh.harvard.edu >>>> Sent: Fri, 24 May 2013 17:36:18 -0400 (EDT) >>>> Subject: Re: [Freesurfer] Repost: question abt supratentorial vol and >>>> total brain vol. >>>> >>>> Total Gray includes the cerebellar gray >>>> doug >>>> On 05/24/2013 03:51 PM, Ritobrato Datta wrote: >>>>> Hello All, >>>>> >>>>> Can someone address the following ? I sent this query yesterday but it >>>>> fell through the cracks. >>>>> >>>>> I am using freesurfer 5.1 for my analysis. >>>>> >>>>> I am interested in calculating the whole brain vol (total Gray vol + >>>>> total WM vol) excluding the CSF volume and cerebellum. >>>>> >>>>> Total Brain Vol = TotalGrayVol + CorticalWhiteMatterVol >>>>> >>>>> In all of the 79 subjects, when I compare the Total Brain Vol to >>>>> SupraTentorialVol, I find SupraTentorialVol is smaller than the Total >>>>> Brain Vol I have calculated. >>>>> >>>>> Here are some measures - >>>>> >>>>> For 79 subjects - >>>>> >>>>> Average Total Brain Vol = 1038395.291 >>>>> >>>>> Average SupraTentorialVol = 979996.4684 >>>>> >>>>> Is that expected ? >>>>> >>>>> Is it possible that CSF vol is part of Total Brain Vol ? >>>>> >>>>> Any insight will be helpful. >>>>> >>>>> Thanks >>>>> >>>>> Rito >>>>> >>>>> _______________________________________________ >>>>> 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. >>>>> >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
