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-request@nmr.mgh.harvard.edu mailto:freesurfer-request@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 mattersubcortical gray mattertotal cortical gray mattertotal gray matter volumeand
left/right cortical white mattertotal cortical white matterHow can I derive the total white matter volume?
Ed
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