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 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
Ed, can you send the recon-all.log file? The underlying code for mris_volume and the program that creates the stats file is identical. This other program (mri_segstats) prints out the values for the volumes inside the lh.pial, etc, and this will be captured by the recon-all.log file.
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
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 greve@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.
Hi Freesurfers,
I have created a binary mask of the ventricles using mri_binarize using data from aparc+aseg.mgz. I want to resample this mask into native functional space, but I want to include only functional voxels that are 100% covered by by the structural mask. Because the anatomical mask is written with voxels that are 1x1x1 and our functional data is re-sliced at 3x3x3, there are functional voxels that are more than 50% covered by the anatomical mask that I want to exclude. I used the command:
mri_vol2vol --mov brainmask.mgz --targ ventmask.nii --ing --reg register.dat --interp nearest --o func.ventmask.nii
This properly resampled the mask into functional space, and maintained its binary character, but it looks to be a bit too permissive -- although I could just be seeing things.
Any ideas?
Thanks for your help,
Andrew Ward Brigham and Women's Hospital (BBNG) Massachusetts General Hospital (GRU) Athinoula A. Martinos Center for Biomedical Imaging 149 13th St., Rm 2689C Charlestown, MA 02129 Phone: 617-726-6211 Fax: 617-726-5760
It is better to use mri_label2vol using the registration matrix for the functional. You can set the "fill threshold" to control the percent of a segmentation that must be present in a voxel to declare that voxel to be in that segment. I would not set this to 1 (ie, 100%) as this can lead to some artifacts since it just counts the number of anat voxels that land in the functional voxel. Set it to something like .85 or .9.
doug
Andrew Ward wrote:
Hi Freesurfers,
I have created a binary mask of the ventricles using mri_binarize using data from aparc+aseg.mgz. I want to resample this mask into native functional space, but I want to include only functional voxels that are 100% covered by by the structural mask. Because the anatomical mask is written with voxels that are 1x1x1 and our functional data is re-sliced at 3x3x3, there are functional voxels that are more than 50% covered by the anatomical mask that I want to exclude. I used the command:
mri_vol2vol --mov brainmask.mgz --targ ventmask.nii --ing --reg register.dat --interp nearest --o func.ventmask.nii
This properly resampled the mask into functional space, and maintained its binary character, but it looks to be a bit too permissive -- although I could just be seeing things.
Any ideas?
Thanks for your help,
Andrew Ward Brigham and Women's Hospital (BBNG) Massachusetts General Hospital (GRU) Athinoula A. Martinos Center for Biomedical Imaging 149 13th St., Rm 2689C Charlestown, MA 02129 Phone: 617-726-6211 Fax: 617-726-5760
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
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 greve@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
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
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 greve@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 greve@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
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-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 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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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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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.
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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
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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-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 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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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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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.
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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
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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-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 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 greve@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 greve@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
Hi Doug,
I'm sorry about using the term "subcortical white matter". It was due to misunderstanding your response, viz. "the white matter volume computed from the pial-white includes subcortical structures". It's settled now, see response by Michael Harms and my reponse to that.
Ed
On 4 Nov 2010, at 16:23, Douglas N Greve wrote:
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-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 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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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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
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