Can you upload the subject, the

500_lobes_1-in-fs.mgz file and lh.mask.mgz to

https://gate.nmr.mgh.harvard.edu/filedrop2

and I'll take a look

On 01/20/2017 12:08 PM, Eli Johnson wrote:

*Hi Doug,*

*Thanks a lot for your help!*

*I have run these commands and they complete with no problems. I can also view the region overlaid on a surface and this looks ok, however the volumes that are extracted from mri_segstats are much lower than expected - around half the volume expected, and they don't seem in line with the volumes automatically extracted (i.e. total cortical gm volume from the aseg.stats file). Any thoughts on why this might be?*

*Many thanks!*

*Eli

*Douglas N Greve*greve at nmr.mgh.harvard.edu mailto:freesurfer%40nmr.mgh.harvard.edu?Subject=Re:%20%5BFreesurfer%5D%20Cortical%20volume%20from%20masked%20region&In-Reply-To=%3C0ae71986-b91f-bdaa-c726-1db7cdd71830%40nmr.mgh.harvard.edu%3E /Wed Jan 18 15:30:45 EST 2017/

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I would probably map the mask to the surface,eg,

mri_vol2surf --regheadersubject --hemi lh --projfrac 0.5 --i scan500_std/mri/500_lobes_1-in-fs.mgz --interp nearest --o lh.mask.mgz

The run

mri_segstats --seg lh.mask.mgz --id 1 --accumulate --i lh.volume --o lh.vol.stats

---

*From:* Eli Johnson eli_g_123@hotmail.com *Sent:* Tuesday, 17 January 2017 4:24 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Cortical volume from masked region

Hi all,

I am trying to extract the volume from a FreeSurfer segmented scan within a pre-registered mask region, but only within the cortex, and wanted to check my command.

The mask is a binary mask (value of 1 across the mask) and is in the same space as the orig.mgz file. It covers part of the frontal lobe.

I have run:

mri_segstats --seg ./scan500_std/mri/500_lobes_1-in-fs.mgz --id 1 --i ./scan500_std/mri/aparc+aseg.mgz --accumulate --sum test.reg1.sum

This has output a text file with a value of 495563 mm3 in the last row.

I wanted to check whether this is the correct command to extract only cortical GM within this mask. If this is correct, should be adding other flags (e.g. -pv). I have searched the mailing list and the options for mri_segstats, but I'm not 100% confident in what I've done

• so any tips would be greatly appreciated.

Many thanks Eli

---

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

Hmm, I did not get an email. Did you put my email address on the upload?

On 1/25/17 4:55 AM, Eli Johnson wrote:

Hi Doug,

Thank you - I have uploaded the files for you.

Eli

---

*From:* Eli Johnson eli_g_123@hotmail.com *Sent:* Friday, 20 January 2017 5:08 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: Cortical volume from masked region

*Hi Doug,*

*Thanks a lot for your help!*

*I have run these commands and they complete with no problems. I can also view the region overlaid on a surface and this looks ok, however the volumes that are extracted from mri_segstats are much lower than expected - around half the volume expected, and they don't seem in line with the volumes automatically extracted (i.e. total cortical gm volume from the aseg.stats file). Any thoughts on why this might be?*

*Many thanks!*

*Eli

*Douglas N Greve*greve at nmr.mgh.harvard.edu mailto:freesurfer%40nmr.mgh.harvard.edu?Subject=Re:%20%5BFreesurfer%5D%20Cortical%20volume%20from%20masked%20region&In-Reply-To=%3C0ae71986-b91f-bdaa-c726-1db7cdd71830%40nmr.mgh.harvard.edu%3E /Wed Jan 18 15:30:45 EST 2017/

• Previous message: [Freesurfer] Cortical volume from masked region https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/049516.html
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• *Messages sorted by:* [ date ] https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/date.html#49559 [ thread ] https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/thread.html#49559 [ subject ] https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/subject.html#49559 [ author ] https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/author.html#49559

I would probably map the mask to the surface,eg,

mri_vol2surf --regheadersubject --hemi lh --projfrac 0.5 --i scan500_std/mri/500_lobes_1-in-fs.mgz --interp nearest --o lh.mask.mgz

The run

mri_segstats --seg lh.mask.mgz --id 1 --accumulate --i lh.volume --o lh.vol.stats

---

*From:* Eli Johnson eli_g_123@hotmail.com *Sent:* Tuesday, 17 January 2017 4:24 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Cortical volume from masked region

Hi all,

I am trying to extract the volume from a FreeSurfer segmented scan within a pre-registered mask region, but only within the cortex, and wanted to check my command.

The mask is a binary mask (value of 1 across the mask) and is in the same space as the orig.mgz file. It covers part of the frontal lobe.

I have run:

mri_segstats --seg ./scan500_std/mri/500_lobes_1-in-fs.mgz --id 1 --i ./scan500_std/mri/aparc+aseg.mgz --accumulate --sum test.reg1.sum

This has output a text file with a value of 495563 mm3 in the last row.

I wanted to check whether this is the correct command to extract only cortical GM within this mask. If this is correct, should be adding other flags (e.g. -pv). I have searched the mailing list and the options for mri_segstats, but I'm not 100% confident in what I've done

• so any tips would be greatly appreciated.

Many thanks Eli

---

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

I received your data but cannot find either

500_lobes_1-in-fs.mgz or lh.mask.mgz

On 01/25/2017 11:32 AM, Eli Johnson wrote:

Yes, I think I got the correct email. Attached is the notification I received upon upload.

Thanks Eli

You recently uploaded the following files to the Martinos Center FileDrop:

• 20001-013-1_std.zip (251.3 MiB)

Here are the people you sent these files to:

• greve@nmr.mgh.harvard.edu

In case you'd like to modify some of the above information, please use the link below:

http://gate.nmr.mgh.harvard.edu/filedrop2/?g=ahht5qz16h5

Cheers, The Martinos Center Web Team

---

*From:* Eli Johnson eli_g_123@hotmail.com *Sent:* Wednesday, 25 January 2017 9:55 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: Cortical volume from masked region

Hi Doug,

Thank you - I have uploaded the files for you.

Eli

---

*From:* Eli Johnson eli_g_123@hotmail.com *Sent:* Friday, 20 January 2017 5:08 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: Cortical volume from masked region

*Hi Doug,*

*Thanks a lot for your help!*

*I have run these commands and they complete with no problems. I can also view the region overlaid on a surface and this looks ok, however the volumes that are extracted from mri_segstats are much lower than expected - around half the volume expected, and they don't seem in line with the volumes automatically extracted (i.e. total cortical gm volume from the aseg.stats file). Any thoughts on why this might be?*

*Many thanks!*

*Eli

*Douglas N Greve*greve at nmr.mgh.harvard.edu mailto:freesurfer%40nmr.mgh.harvard.edu?Subject=Re:%20%5BFreesurfer%5D%20Cortical%20volume%20from%20masked%20region&In-Reply-To=%3C0ae71986-b91f-bdaa-c726-1db7cdd71830%40nmr.mgh.harvard.edu%3E /Wed Jan 18 15:30:45 EST 2017/

• Previous message: [Freesurfer] Cortical volume from masked region https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/049516.html
• Next message: [Freesurfer] installation fail :( https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/049518.html
• *Messages sorted by:* [ date ] https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/date.html#49559 [ thread ] https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/thread.html#49559 [ subject ] https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/subject.html#49559 [ author ] https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/author.html#49559

I would probably map the mask to the surface,eg,

mri_vol2surf --regheadersubject --hemi lh --projfrac 0.5 --i scan500_std/mri/500_lobes_1-in-fs.mgz --interp nearest --o lh.mask.mgz

The run

mri_segstats --seg lh.mask.mgz --id 1 --accumulate --i lh.volume --o lh.vol.stats

---

*From:* Eli Johnson eli_g_123@hotmail.com *Sent:* Tuesday, 17 January 2017 4:24 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Cortical volume from masked region

Hi all,

I am trying to extract the volume from a FreeSurfer segmented scan within a pre-registered mask region, but only within the cortex, and wanted to check my command.

The mask is a binary mask (value of 1 across the mask) and is in the same space as the orig.mgz file. It covers part of the frontal lobe.

I have run:

mri_segstats --seg ./scan500_std/mri/500_lobes_1-in-fs.mgz --id 1 --i ./scan500_std/mri/aparc+aseg.mgz --accumulate --sum test.reg1.sum

This has output a text file with a value of 495563 mm3 in the last row.

I wanted to check whether this is the correct command to extract only cortical GM within this mask. If this is correct, should be adding other flags (e.g. -pv). I have searched the mailing list and the options for mri_segstats, but I'm not 100% confident in what I've done

• so any tips would be greatly appreciated.

Many thanks Eli

---

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

Sent from my iPhone

On 26 Jan 2017, at 18:11, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:

In looking at your mask, it covers only half (or less) of the brain. This would explain why the total volume you get from the mask is much lesss than the total gm volume reported in aseg.stats.

...

On 01/20/2017 12:08 PM, Eli Johnson wrote:

*Hi Doug,*

*Thanks a lot for your help!*

*I have run these commands and they complete with no problems. I can also view the region overlaid on a surface and this looks ok, however the volumes that are extracted from mri_segstats are much lower than expected - around half the volume expected, and they don't seem in line with the volumes automatically extracted (i.e. total cortical gm volume from the aseg.stats file). Any thoughts on why this might be?*

*Many thanks!*

*Eli

*Douglas N Greve*greve at nmr.mgh.harvard.edu mailto:freesurfer%40nmr.mgh.harvard.edu?Subject=Re:%20%5BFreesurfer%5D%20Cortical%20volume%20from%20masked%20region&In-Reply-To=%3C0ae71986-b91f-bdaa-c726-1db7cdd71830%40nmr.mgh.harvard.edu%3E /Wed Jan 18 15:30:45 EST 2017/

• Previous message: [Freesurfer] Cortical volume from masked region https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/049516.html
• Next message: [Freesurfer] installation fail :( https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/049518.html
• *Messages sorted by:* [ date ] https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/date.html#49559 [ thread ] https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/thread.html#49559 [ subject ] https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/subject.html#49559 [ author ] https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/author.html#49559

I would probably map the mask to the surface,eg,

mri_vol2surf --regheadersubject --hemi lh --projfrac 0.5 --i scan500_std/mri/500_lobes_1-in-fs.mgz --interp nearest --o lh.mask.mgz

The run

mri_segstats --seg lh.mask.mgz --id 1 --accumulate --i lh.volume --o lh.vol.stats

---

*From:* Eli Johnson eli_g_123@hotmail.com *Sent:* Tuesday, 17 January 2017 4:24 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Cortical volume from masked region

Hi all,

I am trying to extract the volume from a FreeSurfer segmented scan within a pre-registered mask region, but only within the cortex, and wanted to check my command.

The mask is a binary mask (value of 1 across the mask) and is in the same space as the orig.mgz file. It covers part of the frontal lobe.

I have run:

mri_segstats --seg ./scan500_std/mri/500_lobes_1-in-fs.mgz --id 1 --i ./scan500_std/mri/aparc+aseg.mgz --accumulate --sum test.reg1.sum

This has output a text file with a value of 495563 mm3 in the last row.

I wanted to check whether this is the correct command to extract only cortical GM within this mask. If this is correct, should be adding other flags (e.g. -pv). I have searched the mailing list and the options for mri_segstats, but I'm not 100% confident in what I've done

• so any tips would be greatly appreciated.

Many thanks Eli

---

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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

---

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.

In that case please upload the actual data that is failing.

On 01/26/2017 01:22 PM, Eli Johnson wrote:

Hi Doug,

Yes, I have a series of masks that I have created to cover the whole cortex, but I want to examine the regions separately. Each region outputs a volume much smaller than I would expect given the volumes from aseg stats for the whole cortex. That is to say, when I combine the volume from each region although I would expect it to be different to the volume from aseg stats (aseg stats is of course highly optimized), it's a lot smaller than expected - around half the size.

Sorry for not being more clear! Thanks

...

On 26 Jan 2017, at 18:11,y Douglas N Greve greve@nmr.mgh.harvard.edu wrote:

In looking at your mask, it covers only half (or less) of the brain. This would explain why the total volume you get from the mask is much lesss than the total gm volume reported in aseg.stats.

...

On 01/20/2017 12:08 PM, Eli Johnson wrote:

*Hi Doug,*

*Thanks a lot for your help!*

*I have run these commands and they complete with no problems. I can also view the region overlaid on a surface and this looks ok, however the volumes that are extracted from mri_segstats are much lower than expected - around half the volume expected, and they don't seem in line with the volumes automatically extracted (i.e. total cortical gm volume from the aseg.stats file). Any thoughts on why this might be?*

*Many thanks!*

*Eli

*Douglas N Greve*greve at nmr.mgh.harvard.edu mailto:freesurfer%40nmr.mgh.harvard.edu?Subject=Re:%20%5BFreesurfer%5D%20Cortical%20volume%20from%20masked%20region&In-Reply-To=%3C0ae71986-b91f-bdaa-c726-1db7cdd71830%40nmr.mgh.harvard.edu%3E /Wed Jan 18 15:30:45 EST 2017/

• Previous message: [Freesurfer] Cortical volume from masked region https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/049516.html
• Next message: [Freesurfer] installation fail :( https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/049518.html
• *Messages sorted by:* [ date ] https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/date.html#49559 [ thread ] https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/thread.html#49559 [ subject ] https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/subject.html#49559 [ author ] https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/author.html#49559

I would probably map the mask to the surface,eg,

mri_vol2surf --regheadersubject --hemi lh --projfrac 0.5 --i scan500_std/mri/500_lobes_1-in-fs.mgz --interp nearest --o lh.mask.mgz

The run

mri_segstats --seg lh.mask.mgz --id 1 --accumulate --i lh.volume --o lh.vol.stats

---

*From:* Eli Johnson eli_g_123@hotmail.com *Sent:* Tuesday, 17 January 2017 4:24 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Cortical volume from masked region

Hi all,

I am trying to extract the volume from a FreeSurfer segmented scan within a pre-registered mask region, but only within the cortex, and wanted to check my command.

The mask is a binary mask (value of 1 across the mask) and is in the same space as the orig.mgz file. It covers part of the frontal lobe.

I have run:

mri_segstats --seg ./scan500_std/mri/500_lobes_1-in-fs.mgz --id 1 --i ./scan500_std/mri/aparc+aseg.mgz --accumulate --sum test.reg1.sum

This has output a text file with a value of 495563 mm3 in the last row.

I wanted to check whether this is the correct command to extract only cortical GM within this mask. If this is correct, should be adding other flags (e.g. -pv). I have searched the mailing list and the options for mri_segstats, but I'm not 100% confident in what I've done

• so any tips would be greatly appreciated.

Many thanks Eli

---

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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

---

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

Hi Doug,

I have re-uploaded the file (see bottom of this email for info):

Along with the default FS output, there are 5 masks, corresponding to frontal, temporal, parietal, occipital and insula regions (e.g. 20001-013-1_std/mri/20001_MNI_lobes_1-in-fs.mgz).

There are 10 surfs corresponding to lh & rh frontal,lh & rh temporal, lh & rh parietal,lh & rh occipital and lh & rh insula (e.g. 20001-013-1_std/surf/20001_MNI_lobes_1-in-fs_surfrh.mgz).

I ran the commands:

mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_1-in-fs_surfrh.mgz --id 1 --accumulate --i ./${i}-013-1_std/surf/rh.volume --sum ./${i}-013-1_std/rh.vol_region1.stats mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_2-in-fs_surfrh.mgz --id 1 --accumulate --i ./${i}-013-1_std/surf/rh.volume --sum ./${i}-013-1_std/rh.vol_region2.stats mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_3-in-fs_surfrh.mgz --id 1 --accumulate --i ./${i}-013-1_std/surf/rh.volume --sum ./${i}-013-1_std/rh.vol_region3.stats mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_4-in-fs_surfrh.mgz --id 1 --accumulate --i ./${i}-013-1_std/surf/rh.volume --sum ./${i}-013-1_std/rh.vol_region4.stats mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_5-in-fs_surfrh.mgz --id 1 --accumulate --i ./${i}-013-1_std/surf/rh.volume --sum ./${i}-013-1_std/rh.vol_region5.stats mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_1-in-fs_surf.mgz --id 1 --accumulate --i ./${i}-013-1_std/surf/lh.volume --sum ./${i}-013-1_std/lh.vol_region1.stats mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_2-in-fs_surf.mgz --id 1 --accumulate --i ./${i}-013-1_std/surf/lh.volume --sum ./${i}-013-1_std/lh.vol_region2.stats mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_3-in-fs_surf.mgz --id 1 --accumulate --i ./${i}-013-1_std/surf/lh.volume --sum ./${i}-013-1_std/lh.vol_region3.stats mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_4-in-fs_surf.mgz --id 1 --accumulate --i ./${i}-013-1_std/surf/lh.volume --sum ./${i}-013-1_std/lh.vol_region4.stats mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_5-in-fs_surf.mgz --id 1 --accumulate --i ./${i}-013-1_std/surf/lh.volume --sum ./${i}-013-1_std/lh.vol_region5.stats

to extract volumes from the 10 regions. The stats files are located as described in the command.

Also, in the ./20001-013-1_std/stats/ folder are the default FS lobular volumes for comparison.

Thanks again for all of your help, do let me know if I've missed anything again!!

Eli

You recently uploaded the following files to the Martinos Center FileDrop:

+ 20001-013-1_std.tar.gz (252.1 MiB)

Here are the people you sent these files to:

+ greve@nmr.mgh.harvard.edu

In case you'd like to modify some of the above information, please use the link below:

http://gate.nmr.mgh.harvard.edu/filedrop2/?g=7z2xk77v3ue

Cheers, The Martinos Center Web Team ________________________________ From: Eli Johnson eli_g_123@hotmail.com Sent: Thursday, 26 January 2017 7:13 PM To: Freesurfer support list Subject: Re: [Freesurfer] Cortical volume from masked region

Ok sure, I will do it tomorrow as I don't have access to the stats file right now

Many thanks!

________________________________ From: Eli Johnson eli_g_123@hotmail.com Sent: Thursday, 26 January 2017 6:22 PM To: Freesurfer support list Subject: Re: [Freesurfer] Cortical volume from masked region

Hi Doug,

Yes, I have a series of masks that I have created to cover the whole cortex, but I want to examine the regions separately. Each region outputs a volume much smaller than I would expect given the volumes from aseg stats for the whole cortex. That is to say, when I combine the volume from each region although I would expect it to be different to the volume from aseg stats (aseg stats is of course highly optimized), it's a lot smaller than expected - around half the size.

Sorry for not being more clear! Thanks

On 26 Jan 2017, at 18:11,y Douglas N Greve greve@nmr.mgh.harvard.edu wrote:

In looking at your mask, it covers only half (or less) of the brain. This would explain why the total volume you get from the mask is much lesss than the total gm volume reported in aseg.stats.

...

On 01/20/2017 12:08 PM, Eli Johnson wrote:

*Hi Doug,*

*Thanks a lot for your help!*

*I have run these commands and they complete with no problems. I can also view the region overlaid on a surface and this looks ok, however the volumes that are extracted from mri_segstats are much lower than expected - around half the volume expected, and they don't seem in line with the volumes automatically extracted (i.e. total cortical gm volume from the aseg.stats file). Any thoughts on why this might be?*

*Many thanks!*

*Eli

*Douglas N Greve*greve at nmr.mgh.harvard.edu mailto:freesurfer%40nmr.mgh.harvard.edu?Subject=Re:%20%5BFreesurfer%5D%20Cortical%20volume%20from%20masked%20region&In-Reply-To=%3C0ae71986-b91f-bdaa-c726-1db7cdd71830%40nmr.mgh.harvard.edu%3E /Wed Jan 18 15:30:45 EST 2017/

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I would probably map the mask to the surface,eg,

mri_vol2surf --regheadersubject --hemi lh --projfrac 0.5 --i scan500_std/mri/500_lobes_1-in-fs.mgz --interp nearest --o lh.mask.mgz

The run

mri_segstats --seg lh.mask.mgz --id 1 --accumulate --i lh.volume --o lh.vol.stats

---

*From:* Eli Johnson eli_g_123@hotmail.com *Sent:* Tuesday, 17 January 2017 4:24 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Cortical volume from masked region

Hi all,

I am trying to extract the volume from a FreeSurfer segmented scan within a pre-registered mask region, but only within the cortex, and wanted to check my command.

The mask is a binary mask (value of 1 across the mask) and is in the same space as the orig.mgz file. It covers part of the frontal lobe.

I have run:

mri_segstats --seg ./scan500_std/mri/500_lobes_1-in-fs.mgz --id 1 --i ./scan500_std/mri/aparc+aseg.mgz --accumulate --sum test.reg1.sum

This has output a text file with a value of 495563 mm3 in the last row.

I wanted to check whether this is the correct command to extract only cortical GM within this mask. If this is correct, should be adding other flags (e.g. -pv). I have searched the mailing list and the options for mri_segstats, but I'm not 100% confident in what I've done

• so any tips would be greatly appreciated.

Many thanks Eli

---

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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

---

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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.

Hi Doug,

I was reading the fourth column in the stats files as the volumes (highlighted in yellow), as that seems to correspond to the volume_mm3 label when the columns are lined up. Also, when I run asegstats2file with the 'rh.vol_region1.stats' file specified alongside 'volume' as the measure, the output is the fourth(highlighted) number in the stats files.

region 1 rh:

# ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max Range

1 1 49885 49885.0 Seg0001 88695.1094 1.1755 0.0000 19.4994 19.4994

region 2 rh:

# ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max Range

1 1 20761 20761.0 Seg0001 29523.0742 0.9522 0.0000 11.5547 11.5547

region 3 rh:

# ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max Range

1 1 35995 35995.0 Seg0001 57553.2656 1.0586 0.0000 10.9540 10.9540

region 4 rh:

# ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max Range

1 1 27060 27060.0 Seg0001 56422.7969 1.5332 0.0000 22.9446 22.9446

region 5 rh:

# ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max Range

1 1 2873 2873.0 Seg0001 5976.5181 1.4734 0.0424 11.5412 11.4987

If it's simply a case of me misinterpreting the stats file, and column 6 being the volume then I agree - there is no problem (and sorry for wasting so much time!). In that case, what does the fourth/highlighted column represent?

Many thanks

Eli

________________________________ From: Eli Johnson eli_g_123@hotmail.com Sent: Friday, 27 January 2017 10:24 AM To: Freesurfer support list Subject: Re: [Freesurfer] Cortical volume from masked region

Hi Doug,

I have re-uploaded the file (see bottom of this email for info):

Along with the default FS output, there are 5 masks, corresponding to frontal, temporal, parietal, occipital and insula regions (e.g. 20001-013-1_std/mri/20001_MNI_lobes_1-in-fs.mgz).

There are 10 surfs corresponding to lh & rh frontal,lh & rh temporal, lh & rh parietal,lh & rh occipital and lh & rh insula (e.g. 20001-013-1_std/surf/20001_MNI_lobes_1-in-fs_surfrh.mgz).

I ran the commands:

mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_1-in-fs_surfrh.mgz --id 1 --accumulate --i ./${i}-013-1_std/surf/rh.volume --sum ./${i}-013-1_std/rh.vol_region1.stats mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_2-in-fs_surfrh.mgz --id 1 --accumulate --i ./${i}-013-1_std/surf/rh.volume --sum ./${i}-013-1_std/rh.vol_region2.stats mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_3-in-fs_surfrh.mgz --id 1 --accumulate --i ./${i}-013-1_std/surf/rh.volume --sum ./${i}-013-1_std/rh.vol_region3.stats mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_4-in-fs_surfrh.mgz --id 1 --accumulate --i ./${i}-013-1_std/surf/rh.volume --sum ./${i}-013-1_std/rh.vol_region4.stats mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_5-in-fs_surfrh.mgz --id 1 --accumulate --i ./${i}-013-1_std/surf/rh.volume --sum ./${i}-013-1_std/rh.vol_region5.stats mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_1-in-fs_surf.mgz --id 1 --accumulate --i ./${i}-013-1_std/surf/lh.volume --sum ./${i}-013-1_std/lh.vol_region1.stats mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_2-in-fs_surf.mgz --id 1 --accumulate --i ./${i}-013-1_std/surf/lh.volume --sum ./${i}-013-1_std/lh.vol_region2.stats mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_3-in-fs_surf.mgz --id 1 --accumulate --i ./${i}-013-1_std/surf/lh.volume --sum ./${i}-013-1_std/lh.vol_region3.stats mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_4-in-fs_surf.mgz --id 1 --accumulate --i ./${i}-013-1_std/surf/lh.volume --sum ./${i}-013-1_std/lh.vol_region4.stats mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_5-in-fs_surf.mgz --id 1 --accumulate --i ./${i}-013-1_std/surf/lh.volume --sum ./${i}-013-1_std/lh.vol_region5.stats

to extract volumes from the 10 regions. The stats files are located as described in the command.

Also, in the ./20001-013-1_std/stats/ folder are the default FS lobular volumes for comparison.

Thanks again for all of your help, do let me know if I've missed anything again!!

Eli

You recently uploaded the following files to the Martinos Center FileDrop:

+ 20001-013-1_std.tar.gz (252.1 MiB)

Here are the people you sent these files to:

+ greve@nmr.mgh.harvard.edu

In case you'd like to modify some of the above information, please use the link below:

http://gate.nmr.mgh.harvard.edu/filedrop2/?g=7z2xk77v3ue

Cheers, The Martinos Center Web Team ________________________________ From: Eli Johnson eli_g_123@hotmail.com Sent: Thursday, 26 January 2017 7:13 PM To: Freesurfer support list Subject: Re: [Freesurfer] Cortical volume from masked region

Ok sure, I will do it tomorrow as I don't have access to the stats file right now

Many thanks!

________________________________ From: Eli Johnson eli_g_123@hotmail.com Sent: Thursday, 26 January 2017 6:22 PM To: Freesurfer support list Subject: Re: [Freesurfer] Cortical volume from masked region

Hi Doug,

Yes, I have a series of masks that I have created to cover the whole cortex, but I want to examine the regions separately. Each region outputs a volume much smaller than I would expect given the volumes from aseg stats for the whole cortex. That is to say, when I combine the volume from each region although I would expect it to be different to the volume from aseg stats (aseg stats is of course highly optimized), it's a lot smaller than expected - around half the size.

Sorry for not being more clear! Thanks

On 26 Jan 2017, at 18:11,y Douglas N Greve greve@nmr.mgh.harvard.edu wrote:

In looking at your mask, it covers only half (or less) of the brain. This would explain why the total volume you get from the mask is much lesss than the total gm volume reported in aseg.stats.

...

On 01/20/2017 12:08 PM, Eli Johnson wrote:

*Hi Doug,*

*Thanks a lot for your help!*

*I have run these commands and they complete with no problems. I can also view the region overlaid on a surface and this looks ok, however the volumes that are extracted from mri_segstats are much lower than expected - around half the volume expected, and they don't seem in line with the volumes automatically extracted (i.e. total cortical gm volume from the aseg.stats file). Any thoughts on why this might be?*

*Many thanks!*

*Eli

*Douglas N Greve*greve at nmr.mgh.harvard.edu mailto:freesurfer%40nmr.mgh.harvard.edu?Subject=Re:%20%5BFreesurfer%5D%20Cortical%20volume%20from%20masked%20region&In-Reply-To=%3C0ae71986-b91f-bdaa-c726-1db7cdd71830%40nmr.mgh.harvard.edu%3E /Wed Jan 18 15:30:45 EST 2017/

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I would probably map the mask to the surface,eg,

mri_vol2surf --regheadersubject --hemi lh --projfrac 0.5 --i scan500_std/mri/500_lobes_1-in-fs.mgz --interp nearest --o lh.mask.mgz

The run

mri_segstats --seg lh.mask.mgz --id 1 --accumulate --i lh.volume --o lh.vol.stats

---

*From:* Eli Johnson eli_g_123@hotmail.com *Sent:* Tuesday, 17 January 2017 4:24 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Cortical volume from masked region

Hi all,

I am trying to extract the volume from a FreeSurfer segmented scan within a pre-registered mask region, but only within the cortex, and wanted to check my command.

The mask is a binary mask (value of 1 across the mask) and is in the same space as the orig.mgz file. It covers part of the frontal lobe.

I have run:

mri_segstats --seg ./scan500_std/mri/500_lobes_1-in-fs.mgz --id 1 --i ./scan500_std/mri/aparc+aseg.mgz --accumulate --sum test.reg1.sum

This has output a text file with a value of 495563 mm3 in the last row.

I wanted to check whether this is the correct command to extract only cortical GM within this mask. If this is correct, should be adding other flags (e.g. -pv). I have searched the mailing list and the options for mri_segstats, but I'm not 100% confident in what I've done

• so any tips would be greatly appreciated.

Many thanks Eli

---

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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

---

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.

Great - that makes sense!

Thanks again for your help in resolving this.

Eli

________________________________ From: Eli Johnson eli_g_123@hotmail.com Sent: Friday, 27 January 2017 4:59 PM To: Freesurfer support list Subject: Re: [Freesurfer] Cortical volume from masked region

Hi Doug,

I was reading the fourth column in the stats files as the volumes (highlighted in yellow), as that seems to correspond to the volume_mm3 label when the columns are lined up. Also, when I run asegstats2file with the 'rh.vol_region1.stats' file specified alongside 'volume' as the measure, the output is the fourth(highlighted) number in the stats files.

region 1 rh:

# ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max Range

1 1 49885 49885.0 Seg0001 88695.1094 1.1755 0.0000 19.4994 19.4994

region 2 rh:

# ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max Range

1 1 20761 20761.0 Seg0001 29523.0742 0.9522 0.0000 11.5547 11.5547

region 3 rh:

# ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max Range

1 1 35995 35995.0 Seg0001 57553.2656 1.0586 0.0000 10.9540 10.9540

region 4 rh:

# ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max Range

1 1 27060 27060.0 Seg0001 56422.7969 1.5332 0.0000 22.9446 22.9446

region 5 rh:

# ColHeaders Index SegId NVoxels Volume_mm3 StructName Mean StdDev Min Max Range

1 1 2873 2873.0 Seg0001 5976.5181 1.4734 0.0424 11.5412 11.4987

If it's simply a case of me misinterpreting the stats file, and column 6 being the volume then I agree - there is no problem (and sorry for wasting so much time!). In that case, what does the fourth/highlighted column represent?

Many thanks

Eli

________________________________ From: Eli Johnson eli_g_123@hotmail.com Sent: Friday, 27 January 2017 10:24 AM To: Freesurfer support list Subject: Re: [Freesurfer] Cortical volume from masked region

Hi Doug,

I have re-uploaded the file (see bottom of this email for info):

Along with the default FS output, there are 5 masks, corresponding to frontal, temporal, parietal, occipital and insula regions (e.g. 20001-013-1_std/mri/20001_MNI_lobes_1-in-fs.mgz).

There are 10 surfs corresponding to lh & rh frontal,lh & rh temporal, lh & rh parietal,lh & rh occipital and lh & rh insula (e.g. 20001-013-1_std/surf/20001_MNI_lobes_1-in-fs_surfrh.mgz).

I ran the commands:

mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_1-in-fs_surfrh.mgz --id 1 --accumulate --i ./${i}-013-1_std/surf/rh.volume --sum ./${i}-013-1_std/rh.vol_region1.stats mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_2-in-fs_surfrh.mgz --id 1 --accumulate --i ./${i}-013-1_std/surf/rh.volume --sum ./${i}-013-1_std/rh.vol_region2.stats mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_3-in-fs_surfrh.mgz --id 1 --accumulate --i ./${i}-013-1_std/surf/rh.volume --sum ./${i}-013-1_std/rh.vol_region3.stats mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_4-in-fs_surfrh.mgz --id 1 --accumulate --i ./${i}-013-1_std/surf/rh.volume --sum ./${i}-013-1_std/rh.vol_region4.stats mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_5-in-fs_surfrh.mgz --id 1 --accumulate --i ./${i}-013-1_std/surf/rh.volume --sum ./${i}-013-1_std/rh.vol_region5.stats mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_1-in-fs_surf.mgz --id 1 --accumulate --i ./${i}-013-1_std/surf/lh.volume --sum ./${i}-013-1_std/lh.vol_region1.stats mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_2-in-fs_surf.mgz --id 1 --accumulate --i ./${i}-013-1_std/surf/lh.volume --sum ./${i}-013-1_std/lh.vol_region2.stats mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_3-in-fs_surf.mgz --id 1 --accumulate --i ./${i}-013-1_std/surf/lh.volume --sum ./${i}-013-1_std/lh.vol_region3.stats mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_4-in-fs_surf.mgz --id 1 --accumulate --i ./${i}-013-1_std/surf/lh.volume --sum ./${i}-013-1_std/lh.vol_region4.stats mri_segstats --seg ./${i}-013-1_std/surf/${i}_MNI_lobes_5-in-fs_surf.mgz --id 1 --accumulate --i ./${i}-013-1_std/surf/lh.volume --sum ./${i}-013-1_std/lh.vol_region5.stats

to extract volumes from the 10 regions. The stats files are located as described in the command.

Also, in the ./20001-013-1_std/stats/ folder are the default FS lobular volumes for comparison.

Thanks again for all of your help, do let me know if I've missed anything again!!

Eli

You recently uploaded the following files to the Martinos Center FileDrop:

+ 20001-013-1_std.tar.gz (252.1 MiB)

Here are the people you sent these files to:

+ greve@nmr.mgh.harvard.edu

In case you'd like to modify some of the above information, please use the link below:

http://gate.nmr.mgh.harvard.edu/filedrop2/?g=7z2xk77v3ue

Cheers, The Martinos Center Web Team ________________________________ From: Eli Johnson eli_g_123@hotmail.com Sent: Thursday, 26 January 2017 7:13 PM To: Freesurfer support list Subject: Re: [Freesurfer] Cortical volume from masked region

Ok sure, I will do it tomorrow as I don't have access to the stats file right now

Many thanks!

________________________________ From: Eli Johnson eli_g_123@hotmail.com Sent: Thursday, 26 January 2017 6:22 PM To: Freesurfer support list Subject: Re: [Freesurfer] Cortical volume from masked region

Hi Doug,

Yes, I have a series of masks that I have created to cover the whole cortex, but I want to examine the regions separately. Each region outputs a volume much smaller than I would expect given the volumes from aseg stats for the whole cortex. That is to say, when I combine the volume from each region although I would expect it to be different to the volume from aseg stats (aseg stats is of course highly optimized), it's a lot smaller than expected - around half the size.

Sorry for not being more clear! Thanks

On 26 Jan 2017, at 18:11,y Douglas N Greve greve@nmr.mgh.harvard.edu wrote:

In looking at your mask, it covers only half (or less) of the brain. This would explain why the total volume you get from the mask is much lesss than the total gm volume reported in aseg.stats.

...

On 01/20/2017 12:08 PM, Eli Johnson wrote:

*Hi Doug,*

*Thanks a lot for your help!*

*I have run these commands and they complete with no problems. I can also view the region overlaid on a surface and this looks ok, however the volumes that are extracted from mri_segstats are much lower than expected - around half the volume expected, and they don't seem in line with the volumes automatically extracted (i.e. total cortical gm volume from the aseg.stats file). Any thoughts on why this might be?*

*Many thanks!*

*Eli

*Douglas N Greve*greve at nmr.mgh.harvard.edu mailto:freesurfer%40nmr.mgh.harvard.edu?Subject=Re:%20%5BFreesurfer%5D%20Cortical%20volume%20from%20masked%20region&In-Reply-To=%3C0ae71986-b91f-bdaa-c726-1db7cdd71830%40nmr.mgh.harvard.edu%3E /Wed Jan 18 15:30:45 EST 2017/

• Previous message: [Freesurfer] Cortical volume from masked region https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/049516.html
• Next message: [Freesurfer] installation fail :( https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/049518.html
• *Messages sorted by:* [ date ] https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/date.html#49559 [ thread ] https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/thread.html#49559 [ subject ] https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/subject.html#49559 [ author ] https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-January/author.html#49559

I would probably map the mask to the surface,eg,

mri_vol2surf --regheadersubject --hemi lh --projfrac 0.5 --i scan500_std/mri/500_lobes_1-in-fs.mgz --interp nearest --o lh.mask.mgz

The run

mri_segstats --seg lh.mask.mgz --id 1 --accumulate --i lh.volume --o lh.vol.stats

---

*From:* Eli Johnson eli_g_123@hotmail.com *Sent:* Tuesday, 17 January 2017 4:24 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Cortical volume from masked region

Hi all,

I am trying to extract the volume from a FreeSurfer segmented scan within a pre-registered mask region, but only within the cortex, and wanted to check my command.

The mask is a binary mask (value of 1 across the mask) and is in the same space as the orig.mgz file. It covers part of the frontal lobe.

I have run:

mri_segstats --seg ./scan500_std/mri/500_lobes_1-in-fs.mgz --id 1 --i ./scan500_std/mri/aparc+aseg.mgz --accumulate --sum test.reg1.sum

This has output a text file with a value of 495563 mm3 in the last row.

I wanted to check whether this is the correct command to extract only cortical GM within this mask. If this is correct, should be adding other flags (e.g. -pv). I have searched the mailing list and the options for mri_segstats, but I'm not 100% confident in what I've done

• so any tips would be greatly appreciated.

Many thanks Eli

---

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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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