See if this answers your question http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats this is for v5.2 and beyond

On 06/03/2013 01:07 PM, Ritobrato Datta wrote:

ic thats right....I was getting confused. So the total gm vol includes cerebellar gm vol but the cortical wm vol only includes the wm vol under the cortical ribbon and around the subcortical gm structures....? Or does that include wm under the cerebellar cortex as well ?

Is there a table somewhere which specifies which of these freesurfer parcellated structures contribute to these combined measures such has supratentorial vol / whole gm vol etc etc....

That will be very helpful.

----- Original Message ----- From: Douglas N Greve greve@nmr.mgh.harvard.edu To: Ritobrato Datta ridatta@mail.med.upenn.edu, Freesurfer@nmr.mgh.harvard.edu Sent: Mon, 03 Jun 2013 12:59:30 -0400 (EDT) Subject: Re: [Freesurfer] Repost: question abt supratentorial vol and total brain vol.

Hi Rito, I don't think we report a total wm volume, do we? doug

On 06/03/2013 12:56 PM, Ritobrato Datta wrote:

...

Hi Doug,

Just following up on your reply sometime back - Does total white volume include cerebellar wm vol also ?

Please let me know.

Thanks

Rito

----- Original Message ----- From: Douglas N Greve greve@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Fri, 24 May 2013 17:36:18 -0400 (EDT) Subject: Re: [Freesurfer] Repost: question abt supratentorial vol and total brain vol.

Total Gray includes the cerebellar gray doug On 05/24/2013 03:51 PM, Ritobrato Datta wrote:

...

Hello All,

Can someone address the following ? I sent this query yesterday but it fell through the cracks.

I am using freesurfer 5.1 for my analysis.

I am interested in calculating the whole brain vol (total Gray vol + total WM vol) excluding the CSF volume and cerebellum.

Total Brain Vol = TotalGrayVol + CorticalWhiteMatterVol

In all of the 79 subjects, when I compare the Total Brain Vol to SupraTentorialVol, I find SupraTentorialVol is smaller than the Total Brain Vol I have calculated.

Here are some measures -

For 79 subjects -

Average Total Brain Vol = 1038395.291

Average SupraTentorialVol = 979996.4684

Is that expected ?

Is it possible that CSF vol is part of Total Brain Vol ?

Any insight will be helpful.

Thanks

Rito

---

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.

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

no, it does not include cerebellum On 06/03/2013 01:42 PM, Ritobrato Datta wrote:

In the website below, lhCorticalWhiteMatter,rhCorticalWhiteMatter,CorticalWhiteMatter - volume inside the white surface minus anything that is not WM. CorticalWhiteMatter includes hypointensities. This uses the surface-based volume computation for part of the calculation and counts voxels to subtract "anything not in WM". It is approximately equal to the count of WM voxels in aparc+aseg.mgz.

Since, cerebellar wm is in the aparc+aseg.mgz so that means its included in the CorticalWhiteMatter, correct ?

----- Original Message ----- From: Douglas N Greve greve@nmr.mgh.harvard.edu To: Ritobrato Datta ridatta@mail.med.upenn.edu Cc: Freesurfer@nmr.mgh.harvard.edu Sent: Mon, 03 Jun 2013 13:19:54 -0400 (EDT) Subject: Re: [Freesurfer] Repost: question abt supratentorial vol and total brain vol.

See if this answers your question http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats this is for v5.2 and beyond

On 06/03/2013 01:07 PM, Ritobrato Datta wrote:

...

ic thats right....I was getting confused. So the total gm vol includes cerebellar gm vol but the cortical wm vol only includes the wm vol under the cortical ribbon and around the subcortical gm structures....? Or does that include wm under the cerebellar cortex as well ?

Is there a table somewhere which specifies which of these freesurfer parcellated structures contribute to these combined measures such has supratentorial vol / whole gm vol etc etc....

That will be very helpful.

----- Original Message ----- From: Douglas N Greve greve@nmr.mgh.harvard.edu To: Ritobrato Datta ridatta@mail.med.upenn.edu, Freesurfer@nmr.mgh.harvard.edu Sent: Mon, 03 Jun 2013 12:59:30 -0400 (EDT) Subject: Re: [Freesurfer] Repost: question abt supratentorial vol and total brain vol.

Hi Rito, I don't think we report a total wm volume, do we? doug

On 06/03/2013 12:56 PM, Ritobrato Datta wrote:

...

Hi Doug,

Just following up on your reply sometime back - Does total white volume include cerebellar wm vol also ?

Please let me know.

Thanks

Rito

----- Original Message ----- From: Douglas N Greve greve@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Fri, 24 May 2013 17:36:18 -0400 (EDT) Subject: Re: [Freesurfer] Repost: question abt supratentorial vol and total brain vol.

Total Gray includes the cerebellar gray doug On 05/24/2013 03:51 PM, Ritobrato Datta wrote:

...

Hello All,

Can someone address the following ? I sent this query yesterday but it fell through the cracks.

I am using freesurfer 5.1 for my analysis.

I am interested in calculating the whole brain vol (total Gray vol + total WM vol) excluding the CSF volume and cerebellum.

Total Brain Vol = TotalGrayVol + CorticalWhiteMatterVol

In all of the 79 subjects, when I compare the Total Brain Vol to SupraTentorialVol, I find SupraTentorialVol is smaller than the Total Brain Vol I have calculated.

Here are some measures -

For 79 subjects -

Average Total Brain Vol = 1038395.291

Average SupraTentorialVol = 979996.4684

Is that expected ?

Is it possible that CSF vol is part of Total Brain Vol ?

Any insight will be helpful.

Thanks

Rito

---

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.

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

On 06/03/2013 02:03 PM, Ritobrato Datta wrote:

Hi Doug,

I looked that the morphometryStats table that you sent and looks like I need the following measure.

BrainSegNotVent - this I believe doesnt include cerebellum etc and no ventricles.

It does include cerebellum. It does exclude ventricles

But all my data are run through 5.1. How do I get this measure ? If I run the 5.2 version of mri_segstats on the data that has been run through 5.1, will it generate this volume ?

yes, you can run mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --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 --euler --ctab /usr/local/freesurfer/stable5/ASegStatsLUT.txt --subject subjectname

Please let me know and sorry to keep pestering this.

Thanks

Rito

----- Original Message ----- From: Douglas N Greve greve@nmr.mgh.harvard.edu To: Ritobrato Datta ridatta@mail.med.upenn.edu Cc: Freesurfer@nmr.mgh.harvard.edu Sent: Mon, 03 Jun 2013 13:54:01 -0400 (EDT) Subject: Re: [Freesurfer] Repost: question abt supratentorial vol and total brain vol.

no, it does not include cerebellum On 06/03/2013 01:42 PM, Ritobrato Datta wrote:

...

In the website below, lhCorticalWhiteMatter,rhCorticalWhiteMatter,CorticalWhiteMatter - volume inside the white surface minus anything that is not WM. CorticalWhiteMatter includes hypointensities. This uses the surface-based volume computation for part of the calculation and counts voxels to subtract "anything not in WM". It is approximately equal to the count of WM voxels in aparc+aseg.mgz.

Since, cerebellar wm is in the aparc+aseg.mgz so that means its included in the CorticalWhiteMatter, correct ?

----- Original Message ----- From: Douglas N Greve greve@nmr.mgh.harvard.edu To: Ritobrato Datta ridatta@mail.med.upenn.edu Cc: Freesurfer@nmr.mgh.harvard.edu Sent: Mon, 03 Jun 2013 13:19:54 -0400 (EDT) Subject: Re: [Freesurfer] Repost: question abt supratentorial vol and total brain vol.

See if this answers your question http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats this is for v5.2 and beyond

On 06/03/2013 01:07 PM, Ritobrato Datta wrote:

...

ic thats right....I was getting confused. So the total gm vol includes cerebellar gm vol but the cortical wm vol only includes the wm vol under the cortical ribbon and around the subcortical gm structures....? Or does that include wm under the cerebellar cortex as well ?

Is there a table somewhere which specifies which of these freesurfer parcellated structures contribute to these combined measures such has supratentorial vol / whole gm vol etc etc....

That will be very helpful.

----- Original Message ----- From: Douglas N Greve greve@nmr.mgh.harvard.edu To: Ritobrato Datta ridatta@mail.med.upenn.edu, Freesurfer@nmr.mgh.harvard.edu Sent: Mon, 03 Jun 2013 12:59:30 -0400 (EDT) Subject: Re: [Freesurfer] Repost: question abt supratentorial vol and total brain vol.

Hi Rito, I don't think we report a total wm volume, do we? doug

On 06/03/2013 12:56 PM, Ritobrato Datta wrote:

...

Hi Doug,

Just following up on your reply sometime back - Does total white volume include cerebellar wm vol also ?

Please let me know.

Thanks

Rito

----- Original Message ----- From: Douglas N Greve greve@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Fri, 24 May 2013 17:36:18 -0400 (EDT) Subject: Re: [Freesurfer] Repost: question abt supratentorial vol and total brain vol.

Total Gray includes the cerebellar gray doug On 05/24/2013 03:51 PM, Ritobrato Datta wrote:

...

Hello All,

Can someone address the following ? I sent this query yesterday but it fell through the cracks.

I am using freesurfer 5.1 for my analysis.

I am interested in calculating the whole brain vol (total Gray vol + total WM vol) excluding the CSF volume and cerebellum.

Total Brain Vol = TotalGrayVol + CorticalWhiteMatterVol

In all of the 79 subjects, when I compare the Total Brain Vol to SupraTentorialVol, I find SupraTentorialVol is smaller than the Total Brain Vol I have calculated.

Here are some measures -

For 79 subjects -

Average Total Brain Vol = 1038395.291

Average SupraTentorialVol = 979996.4684

Is that expected ?

Is it possible that CSF vol is part of Total Brain Vol ?

Any insight will be helpful.

Thanks

Rito

---

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.

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer