Hi Michael, Thanks for your explanation. It was rather confusing but the picture is now clear: for the total cerebral white matter I should take the measure "CorticalWhiteMatter" in the aseg.stats.
Ed On 4 Nov 2010, at 15:05, Michael Harms wrote: > > 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
