Re: [Freesurfer] Total GM and WM volumes

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:

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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:

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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

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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

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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:

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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

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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

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