Hi Ed, Is there a distinction in FreeSurfer between "cortical" and "subcortical" white matter? I thought that white matter was simply white matter...
You wrote that the white matter values in aseg.stats are identical to the output of mris_wm_volume, which is exactly what I would expect. You do NOT want to use the output of mris_volume on lh.white and rh.white as a measure of white matter volume, as that will include subcortical gray as well as the ventricles. (mris_volume simply returns the total volume enclosed within the input surface, and since the lh/rh.white surfaces also "enclose" the subcortical gray and ventricles, those would be included in the total. The whole purpose of mris_wm_volume is to remove those structures from the WM volume calculation). cheers, -MH On Thu, 2010-11-04 at 10:15 +0100, Ed Gronenschild wrote: > 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
