Hi Freesurfer experts,
I would like to determine brain parenchymal fraction (ie brain tissue volume/estimated ICV) as an estimate of global atrophy. In previous versions of FS, I used the BrianVolNotVent/ICV. Is this correct?
I am now using freesurfer version 5.0.0 and BrainVolNotVent is not longer available.
My understanding is that the total gray matter and total cortical white matter volumes are determined from the pial and white surfaces (thickness *surface area). Do these volumes include or exclude the ventricular volumes? Can the total brain volume be calculated as the sum of the total GM, total cortical WM, brain stem, cerebellar GM and WM minus the CSF. Or do the volumes of the ventricles need to be subtracted as well?
Thanks for your help.
Cheryl
Hi Cheryl, You can regenerate the asseg.stats file with BrianVolNotVent with:
cd $SUBJECTS_DIR/yoursubject mri_segstats --subject yoursubject --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /usr/local/freesurfer/dev/ASegStatsLUT.txt --brain-vol-from-seg
This is the same command that generated the existing aseg.stats file with "--brain-vol-from-seg" added.
doug
Cheryl McCreary wrote:
Hi Freesurfer experts,
I would like to determine brain parenchymal fraction (ie brain tissue volume/estimated ICV) as an estimate of global atrophy. In previous versions of FS, I used the BrianVolNotVent/ICV. Is this correct?
I am now using freesurfer version 5.0.0 and BrainVolNotVent is not longer available.
My understanding is that the total gray matter and total cortical white matter volumes are determined from the pial and white surfaces (thickness *surface area). Do these volumes include or exclude the ventricular volumes? Can the total brain volume be calculated as the sum of the total GM, total cortical WM, brain stem, cerebellar GM and WM minus the CSF. Or do the volumes of the ventricles need to be subtracted as well?
Thanks for your help.
Cheryl
Hi Doug,
Thanks for the quick reply. I will re-run the mri_segstats as below to get the BrainSegNotVent volumes for consistency with the previous version.
Just for my own understanding using the default output aseg.stats from recon-all, could whole brain parenchymal volume be calculated as [(total GM, total cortical WM, cerebellar GM, cerebellar WM + brain-stem)-2*(left lateral ventricle + left Inf Lat Vent + right lateral ventricle+ right inf lat vent) - CSF)]? I'm assuming that since both the white matter and pial surfaces include the lateral ventricle, the lateral ventricular volume needs to be subtracted, while the 3rd and 4th ventricles are not included in the surfaces and therefore would not need to be subtracted?
Kind regards, Cheryl
On 11-12-14 12:45 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
Hi Cheryl, You can regenerate the asseg.stats file with BrianVolNotVent with:
cd $SUBJECTS_DIR/yoursubject mri_segstats --subject yoursubject --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /usr/local/freesurfer/dev/ASegStatsLUT.txt --brain-vol-from-seg
This is the same command that generated the existing aseg.stats file with "--brain-vol-from-seg" added.
doug
Cheryl McCreary wrote:
Hi Freesurfer experts,
I would like to determine brain parenchymal fraction (ie brain tissue volume/estimated ICV) as an estimate of global atrophy. In previous versions of FS, I used the BrianVolNotVent/ICV. Is this correct?
I am now using freesurfer version 5.0.0 and BrainVolNotVent is not longer available.
My understanding is that the total gray matter and total cortical white matter volumes are determined from the pial and white surfaces (thickness *surface area). Do these volumes include or exclude the ventricular volumes? Can the total brain volume be calculated as the sum of the total GM, total cortical WM, brain stem, cerebellar GM and WM minus the CSF. Or do the volumes of the ventricles need to be subtracted as well?
Thanks for your help.
Cheryl
total cortical WM should not include the ventricles. If the lateral ventricles are not segmented properly, then they would be included, but this would be an error. Otherwise, I think your equation is correct. doug
Cheryl McCreary wrote:
Hi Doug,
Thanks for the quick reply. I will re-run the mri_segstats as below to get the BrainSegNotVent volumes for consistency with the previous version.
Just for my own understanding using the default output aseg.stats from recon-all, could whole brain parenchymal volume be calculated as [(total GM, total cortical WM, cerebellar GM, cerebellar WM + brain-stem)-2*(left lateral ventricle + left Inf Lat Vent + right lateral ventricle+ right inf lat vent) - CSF)]? I'm assuming that since both the white matter and pial surfaces include the lateral ventricle, the lateral ventricular volume needs to be subtracted, while the 3rd and 4th ventricles are not included in the surfaces and therefore would not need to be subtracted?
Kind regards, Cheryl
On 11-12-14 12:45 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
Hi Cheryl, You can regenerate the asseg.stats file with BrianVolNotVent with:
cd $SUBJECTS_DIR/yoursubject mri_segstats --subject yoursubject --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /usr/local/freesurfer/dev/ASegStatsLUT.txt --brain-vol-from-seg
This is the same command that generated the existing aseg.stats file with "--brain-vol-from-seg" added.
doug
Cheryl McCreary wrote:
Hi Freesurfer experts,
I would like to determine brain parenchymal fraction (ie brain tissue volume/estimated ICV) as an estimate of global atrophy. In previous versions of FS, I used the BrianVolNotVent/ICV. Is this correct?
I am now using freesurfer version 5.0.0 and BrainVolNotVent is not longer available.
My understanding is that the total gray matter and total cortical white matter volumes are determined from the pial and white surfaces (thickness *surface area). Do these volumes include or exclude the ventricular volumes? Can the total brain volume be calculated as the sum of the total GM, total cortical WM, brain stem, cerebellar GM and WM minus the CSF. Or do the volumes of the ventricles need to be subtracted as well?
Thanks for your help.
Cheryl
Just for clarification, the standard output value in the aseg.stats for total cortical WM is detremined with 'mris_wm_volume' which subtracts out the volume of non-wm voxels based on the aseg, correct?
Jim
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Thursday, December 15, 2011 3:02 PM To: Cheryl McCreary Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Estimate Brain Volume Fraction
total cortical WM should not include the ventricles. If the lateral ventricles are not segmented properly, then they would be included, but this would be an error. Otherwise, I think your equation is correct. doug
Cheryl McCreary wrote:
Hi Doug,
Thanks for the quick reply. I will re-run the mri_segstats as below to get the BrainSegNotVent volumes for consistency with the previous version.
Just for my own understanding using the default output aseg.stats from recon-all, could whole brain parenchymal volume be calculated as [(total GM, total cortical WM, cerebellar GM, cerebellar WM + brain-stem)-2*(left lateral ventricle + left Inf Lat Vent + right lateral ventricle+ right inf lat vent) - CSF)]? I'm assuming that since both the white matter and pial surfaces include the lateral ventricle, the lateral ventricular volume needs to be subtracted, while the 3rd and 4th ventricles are not included in the surfaces and therefore would not need to be subtracted?
Kind regards, Cheryl
On 11-12-14 12:45 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
Hi Cheryl, You can regenerate the asseg.stats file with BrianVolNotVent with:
cd $SUBJECTS_DIR/yoursubject mri_segstats --subject yoursubject --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /usr/local/freesurfer/dev/ASegStatsLUT.txt --brain-vol-from-seg
This is the same command that generated the existing aseg.stats file with "--brain-vol-from-seg" added.
doug
Cheryl McCreary wrote:
Hi Freesurfer experts,
I would like to determine brain parenchymal fraction (ie brain tissue volume/estimated ICV) as an estimate of global atrophy. In previous versions of FS, I used the BrianVolNotVent/ICV. Is this correct?
I am now using freesurfer version 5.0.0 and BrainVolNotVent is not longer available.
My understanding is that the total gray matter and total cortical white matter volumes are determined from the pial and white surfaces (thickness *surface area). Do these volumes include or exclude the ventricular volumes? Can the total brain volume be calculated as the sum of the total GM, total cortical WM, brain stem, cerebellar GM and WM minus the CSF. Or do the volumes of the ventricles need to be subtracted as well?
Thanks for your help.
Cheryl
-- 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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email.
Yes.
Alexopoulos, Dimitrios wrote:
Just for clarification, the standard output value in the aseg.stats for total cortical WM is detremined with 'mris_wm_volume' which subtracts out the volume of non-wm voxels based on the aseg, correct?
Jim
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Thursday, December 15, 2011 3:02 PM To: Cheryl McCreary Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Estimate Brain Volume Fraction
total cortical WM should not include the ventricles. If the lateral ventricles are not segmented properly, then they would be included, but this would be an error. Otherwise, I think your equation is correct. doug
Cheryl McCreary wrote:
Hi Doug,
Thanks for the quick reply. I will re-run the mri_segstats as below to get the BrainSegNotVent volumes for consistency with the previous version.
Just for my own understanding using the default output aseg.stats from recon-all, could whole brain parenchymal volume be calculated as [(total GM, total cortical WM, cerebellar GM, cerebellar WM + brain-stem)-2*(left lateral ventricle + left Inf Lat Vent + right lateral ventricle+ right inf lat vent) - CSF)]? I'm assuming that since both the white matter and pial surfaces include the lateral ventricle, the lateral ventricular volume needs to be subtracted, while the 3rd and 4th ventricles are not included in the surfaces and therefore would not need to be subtracted?
Kind regards, Cheryl
On 11-12-14 12:45 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
Hi Cheryl, You can regenerate the asseg.stats file with BrianVolNotVent with:
cd $SUBJECTS_DIR/yoursubject mri_segstats --subject yoursubject --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /usr/local/freesurfer/dev/ASegStatsLUT.txt --brain-vol-from-seg
This is the same command that generated the existing aseg.stats file with "--brain-vol-from-seg" added.
doug
Cheryl McCreary wrote:
Hi Freesurfer experts,
I would like to determine brain parenchymal fraction (ie brain tissue volume/estimated ICV) as an estimate of global atrophy. In previous versions of FS, I used the BrianVolNotVent/ICV. Is this correct?
I am now using freesurfer version 5.0.0 and BrainVolNotVent is not longer available.
My understanding is that the total gray matter and total cortical white matter volumes are determined from the pial and white surfaces (thickness *surface area). Do these volumes include or exclude the ventricular volumes? Can the total brain volume be calculated as the sum of the total GM, total cortical WM, brain stem, cerebellar GM and WM minus the CSF. Or do the volumes of the ventricles need to be subtracted as well?
Thanks for your help.
Cheryl
-- 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email.
Ok. So then if ventricular volume is already excluded, the brain parenchymal volume should be:
Total GM + total cortical WM +cerebellar GM + cerebellar WM + brain stem - CSF?
Cheryl
On 11-12-15 2:58 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
Yes.
Alexopoulos, Dimitrios wrote:
Just for clarification, the standard output value in the aseg.stats for total cortical WM is detremined with 'mris_wm_volume' which subtracts out the volume of non-wm voxels based on the aseg, correct?
Jim
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Thursday, December 15, 2011 3:02 PM To: Cheryl McCreary Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Estimate Brain Volume Fraction
total cortical WM should not include the ventricles. If the lateral ventricles are not segmented properly, then they would be included, but this would be an error. Otherwise, I think your equation is correct. doug
Cheryl McCreary wrote:
Hi Doug,
Thanks for the quick reply. I will re-run the mri_segstats as below to get the BrainSegNotVent volumes for consistency with the previous version.
Just for my own understanding using the default output aseg.stats from recon-all, could whole brain parenchymal volume be calculated as [(total GM, total cortical WM, cerebellar GM, cerebellar WM + brain-stem)-2*(left lateral ventricle + left Inf Lat Vent + right lateral ventricle+ right inf lat vent) - CSF)]? I'm assuming that since both the white matter and pial surfaces include the lateral ventricle, the lateral ventricular volume needs to be subtracted, while the 3rd and 4th ventricles are not included in the surfaces and therefore would not need to be subtracted?
Kind regards, Cheryl
On 11-12-14 12:45 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
Hi Cheryl, You can regenerate the asseg.stats file with BrianVolNotVent with:
cd $SUBJECTS_DIR/yoursubject mri_segstats --subject yoursubject --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /usr/local/freesurfer/dev/ASegStatsLUT.txt --brain-vol-from-seg
This is the same command that generated the existing aseg.stats file with "--brain-vol-from-seg" added.
doug
Cheryl McCreary wrote:
Hi Freesurfer experts,
I would like to determine brain parenchymal fraction (ie brain tissue volume/estimated ICV) as an estimate of global atrophy. In previous versions of FS, I used the BrianVolNotVent/ICV. Is this correct?
I am now using freesurfer version 5.0.0 and BrainVolNotVent is not longer available.
My understanding is that the total gray matter and total cortical white matter volumes are determined from the pial and white surfaces (thickness *surface area). Do these volumes include or exclude the ventricular volumes? Can the total brain volume be calculated as the sum of the total GM, total cortical WM, brain stem, cerebellar GM and WM minus the CSF. Or do the volumes of the ventricles need to be subtracted as well?
Thanks for your help.
Cheryl
-- 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email.
yes On Thu, 15 Dec 2011, Alexopoulos, Dimitrios wrote:
Just for clarification, the standard output value in the aseg.stats for total cortical WM is detremined with 'mris_wm_volume' which subtracts out the volume of non-wm voxels based on the aseg, correct?
Jim
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: Thursday, December 15, 2011 3:02 PM To: Cheryl McCreary Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Estimate Brain Volume Fraction
total cortical WM should not include the ventricles. If the lateral ventricles are not segmented properly, then they would be included, but this would be an error. Otherwise, I think your equation is correct. doug
Cheryl McCreary wrote:
Hi Doug,
Thanks for the quick reply. I will re-run the mri_segstats as below to get the BrainSegNotVent volumes for consistency with the previous version.
Just for my own understanding using the default output aseg.stats from recon-all, could whole brain parenchymal volume be calculated as [(total GM, total cortical WM, cerebellar GM, cerebellar WM + brain-stem)-2*(left lateral ventricle + left Inf Lat Vent + right lateral ventricle+ right inf lat vent) - CSF)]? I'm assuming that since both the white matter and pial surfaces include the lateral ventricle, the lateral ventricular volume needs to be subtracted, while the 3rd and 4th ventricles are not included in the surfaces and therefore would not need to be subtracted?
Kind regards, Cheryl
On 11-12-14 12:45 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
Hi Cheryl, You can regenerate the asseg.stats file with BrianVolNotVent with:
cd $SUBJECTS_DIR/yoursubject mri_segstats --subject yoursubject --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /usr/local/freesurfer/dev/ASegStatsLUT.txt --brain-vol-from-seg
This is the same command that generated the existing aseg.stats file with "--brain-vol-from-seg" added.
doug
Cheryl McCreary wrote:
Hi Freesurfer experts,
I would like to determine brain parenchymal fraction (ie brain tissue volume/estimated ICV) as an estimate of global atrophy. In previous versions of FS, I used the BrianVolNotVent/ICV. Is this correct?
I am now using freesurfer version 5.0.0 and BrainVolNotVent is not longer available.
My understanding is that the total gray matter and total cortical white matter volumes are determined from the pial and white surfaces (thickness *surface area). Do these volumes include or exclude the ventricular volumes? Can the total brain volume be calculated as the sum of the total GM, total cortical WM, brain stem, cerebellar GM and WM minus the CSF. Or do the volumes of the ventricles need to be subtracted as well?
Thanks for your help.
Cheryl
-- 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Alexopoulos, Dimitrios -
Bruce Fischl -
Cheryl McCreary -
Douglas N Greve