Hi Doug, This thread about GM and WM volumes was initiated by my question on how to get the total cerebral GM and WM volumes.
From what I understand now is that for the GM I should take the volume named "TotalGray" in the aseg.stats file. In the example below that would be 710389.282729. However, for the total cerebral WM volume I can't use the aseg.stats file because the measure "CorticalWhiteMatter" is ony the cortical white matter volume and does not include the subcortical white matter. Instead I should compute it by means of mris_volume lh.white + rh.white. Is that right? The alternative would be to derive the subcortical white matter volume from one of the stats files and add it to the cortical white matter. Is that possible and if so, how? Ed On 3 Nov 2010, at 15:58, Douglas N Greve wrote: > Ah, the "white matter" volume computed from the pial-white includes > the > subcortical structures. Once those are subtracted, you should get > the #s > in the aseg.stats file. > > doug > > Ed Gronenschild wrote: >> Hi Doug, >> >> I checked the numbers again and found the difference: >> >> The last occurrence in the recon-all.log reads: >> >> Getting Cerebral WM volumes from surface >> lh white matter volume 251139 >> rh white matter volume 254730 >> Getting Cerebral GM and WM volumes from surfaces >> lh surface-based volumes (mm3): wTot = 268878.928656, pTot = >> 532766.945301 c = 263888.016645 >> rh surface-based volumes (mm3): wTot = 270895.731618, pTot = >> 536126.997702 c = 265231.266084 >> >> Output from mris_volume: >> lh.pial = 532766.945301 >> rh.pial = 536126.997702 >> lh.white = 268878.928656 >> rh.white = 270895.731618 >> These numbers are exactly equal to those in recon-all.log (pTot and >> wTot, respectively). >> So far so good. >> >> Now I turn to the output in aseg.stats which read: >> # Measure lhCortex, lhCortexVol, Left hemisphere cortical gray matter >> volume, 263888.016645, mm^3 >> # Measure rhCortex, rhCortexVol, Right hemisphere cortical gray >> matter volume, 265231.266084, mm^3 >> # Measure Cortex, CortexVol, Total cortical gray matter volume, >> 529119.282729, mm^3 >> # Measure lhCorticalWhiteMatter, lhCorticalWhiteMatterVol, Left >> hemisphere cortical white matter volume, 251139.437500, mm^3 >> # Measure rhCorticalWhiteMatter, rhCorticalWhiteMatterVol, Right >> hemisphere cortical white matter volume, 254729.859375, mm^3 >> # Measure CorticalWhiteMatter, CorticalWhiteMatterVol, Total cortical >> white matter volume, 505869.296875, mm^3 >> # Measure SubCortGray, SubCortGrayVol, Subcortical gray matter >> volume, 181270.000000, mm^3 >> # Measure TotalGray, TotalGrayVol, Total gray matter volume, >> 710389.282729, mm^3 >> >> Now I get confused: >> The gray matter volumes "?hCortexVol" are equal to the volumes "c" in >> recon-all.log. >> But the white matter volumes "?hCorticalWhiteMatter" differ from >> "wTot" in recon-all.log. >> However, they are equal to the volumes listed below the line "Getting >> Cerebral WM volumes from surface" >> in recon-all.log. (these volumes are also equal to those computed >> with mris_wm_volume). >> What's the difference betwen these white matter volumes? >> >> In summary: the gray matter volumes in recon-all.log and aseg.stats >> are equal, >> but the white matter volumes differ. >> Which white matter volumes should I use? >> >> Ed >> >> >> On 29 Oct 2010, at 22:36, Douglas N Greve wrote: >> >> >>> Hi Ed, I can't replicate this. Can you double check your numbers >>> again? >>> In particular, can you compare them against numbers that are >>> printed in >>> the recon-all.log file? >>> >>> In recon-all.log, look for the lines >>> Getting Cerebral GM and WM volumes from surfaces >>> lh surface-based volumes (mm3): wTot = 244767.110356, pTot = >>> 436943.557923 c = 192176.447567 >>> rh surface-based volumes (mm3): wTot = 243959.351030, pTot = >>> 438113.303648 c = 194153.952618 >>> >>> These might be repeated through out the file if you're re-run. Make >>> sure >>> they are the last set. >>> >>> The wTot and pTot should give you the same values as mris_volume >>> ?h.white and mris_volume ?h.pial >>> It does when I run it here. >>> >>> doug >>> >>> >>> Ed Gronenschild wrote: >>> >>>> Dear Christian, >>>> >>>> Thanks for your suggestion. I followed the instructions to derive >>>> the >>>> GM and WM volumes. Here are the (rounded-off) results for one >>>> example: >>>> >>>> mris_volume lh.pial: 532767 >>>> mris_volume rh.pial: 536127 >>>> >>>> mris_wm_volume lh: 251139 >>>> mris_wm_volume rh: 254730 >>>> >>>> Accordingly: >>>> gm lh = 532767 - 251139 = 281628 >>>> gm rh = 536127 - 254730 = 281397 >>>> >>>> Left + right: >>>> total = 1068894 >>>> wm = 505869 >>>> gm = 563025 >>>> >>>> ------------ >>>> >>>> The aseg.stats file lists the following results: >>>> >>>> cortical wm lh: 251139 >>>> cortical wm rh: 254730 >>>> total wm: 505869 >>>> >>>> cortical gm lh: 263888 >>>> cortical gm rh: 265231 >>>> total cortical gm: 529119 >>>> subcortical gm: 181270 >>>> total gm: 710389 >>>> >>>> -------------- >>>> >>>> For wm both results are equal but for gm they are not. >>>> >>>> So now my question still exists: which wm and gm volumes should I >>>> take? >>>> >>>> Ed >>>> >>>> >>>> On 26 Oct 2010, at 20:40, freesurfer-requ...@nmr.mgh.harvard.edu >>>> <mailto:freesurfer-requ...@nmr.mgh.harvard.edu> wrote: >>>> >>>> >>>>> Dear Ed, >>>>> >>>>> to my knowledge, "mris_wm_volume" is the best option to determine >>>>> the >>>>> white matter volume. >>>>> >>>>> See this wiki page for usage: >>>>> http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats >>>>> >>>>> Best wishes, >>>>> Christian >>>>> >>>>> >>>>> --- >>>>> Christian Scheel >>>>> Department of Psychiatry >>>>> University of Cologne >>>>> >>>>> >>>>> >>>>> >>>>> Am 26.10.2010 15:22, schrieb Ed Gronenschild: >>>>> >>>>>> Hi, >>>>>> >>>>>> I post this once again because I didn't get any response. >>>>>> >>>>>> In the v5.0.0 aseg.stats file I can find the following volumes: >>>>>> >>>>>> - left/right cortical gray matter >>>>>> - subcortical gray matter >>>>>> - total cortical gray matter >>>>>> - total gray matter volume >>>>>> and >>>>>> - left/right cortical white matter >>>>>> - total cortical white matter >>>>>> >>>>>> How can I derive the total white matter volume? >>>>>> >>>>>> Ed >>>>>> >>>> --------------------------------------------------------------------- >>>> --- >>>> >>>> _______________________________________________ >>>> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> >>> >>> >>> 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: 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
