Hi Ed, What do you mean by subcortical white matter? Do you mean cerebellar white matter? The mris_volume command will give you the entire volume inside the white surface, which will include all gray matter structures. This will not include cerebellar white matter.
doug 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 >> > > -- 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
