Hello,

Thank you for the very helpful replies! I have another quick question. Which commands would I use to generate images like the ones in Figure 1 (C) generated in the Salat paper (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2750073/#R57)?

Thank you Sabrina

________________________________________ 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: Tuesday, December 15, 2015 10:10 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Fw: Gray matter intensity

On 12/15/2015 01:00 PM, Sabrina Yu wrote:

Hi,

Just following up on my previous email (see below) as I have not yet heard back. I also have another question regarding the lh.wm.mgh and rh.wm.mgh generated by pctsurfcon. How do I view these as surface overlays on T1 brain scans?

If you want to view them on a volume instead of a surface, you can use mri_surf2vol

Thank you very much.

---

*From:* Sabrina Yu *Sent:* Thursday, December 10, 2015 2:47 PM *To:* Freesurfer support list *Subject:* Gray matter intensity

Hello,

I have been following the instructions in this email thread: https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-April/037240.html. https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-April/037240.html And have successfully gotten the wm-gm signal intensity contrast, but now have a few questions regarding signal intensity for white matter and gray matter intensity.

1. Does the wmparc.stats contain mean white matter intensity values

for each ROI?

Yes

2. Is it possible to extract these same mean intensity values for gray

matter? There is no gmparc.stats file. We know that it's possible to calculate these from the WM/GM ratio from pctsurfcon, but it'd be great if there was a more direct way to get this data.

There is not one by default that includes the cortical parcellation. You can create your own with mri_segstats passing it the aparc+aseg.mgz as the segmentation. Look in the recon-all.log file for the command line that creates the aseg.stats or wmparc.stats. You will probably need to change the --ctab flag to --ctab-default (no argument)

Thank you,

Sabrina Yu

---

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.

When I try to load the overlay in freeview, it crashes immediately. Any thoughts on why this happens?

Thanks

________________________________________ 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: Monday, December 21, 2015 10:08 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Fw: Gray matter intensity

freeview or tksurfer. Load the relevant map as an overlay

On 12/21/2015 12:57 PM, Sabrina Yu wrote:

Hello,

Thank you for the very helpful replies! I have another quick question. Which commands would I use to generate images like the ones in Figure 1 (C) generated in the Salat paper (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2750073/#R57)?

Thank you Sabrina

---

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: Tuesday, December 15, 2015 10:10 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Fw: Gray matter intensity

On 12/15/2015 01:00 PM, Sabrina Yu wrote:

...

Hi,

Just following up on my previous email (see below) as I have not yet heard back. I also have another question regarding the lh.wm.mgh and rh.wm.mgh generated by pctsurfcon. How do I view these as surface overlays on T1 brain scans?

If you want to view them on a volume instead of a surface, you can use mri_surf2vol

...

Thank you very much.

---

*From:* Sabrina Yu *Sent:* Thursday, December 10, 2015 2:47 PM *To:* Freesurfer support list *Subject:* Gray matter intensity

Hello,

I have been following the instructions in this email thread: https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-April/037240.html. https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-April/037240.html And have successfully gotten the wm-gm signal intensity contrast, but now have a few questions regarding signal intensity for white matter and gray matter intensity.

1. Does the wmparc.stats contain mean white matter intensity values

for each ROI?

Yes

...

2. Is it possible to extract these same mean intensity values for gray

matter? There is no gmparc.stats file. We know that it's possible to calculate these from the WM/GM ratio from pctsurfcon, but it'd be great if there was a more direct way to get this data.

There is not one by default that includes the cortical parcellation. You can create your own with mri_segstats passing it the aparc+aseg.mgz as the segmentation. Look in the recon-all.log file for the command line that creates the aseg.stats or wmparc.stats. You will probably need to change the --ctab flag to --ctab-default (no argument)

...

Thank you,

Sabrina Yu

---

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

-- 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

no way to help without more info.

On 12/21/2015 01:10 PM, Sabrina Yu wrote:

When I try to load the overlay in freeview, it crashes immediately. Any thoughts on why this happens?

Thanks

---

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: Monday, December 21, 2015 10:08 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Fw: Gray matter intensity

freeview or tksurfer. Load the relevant map as an overlay

On 12/21/2015 12:57 PM, Sabrina Yu wrote:

...

Hello,

Thank you for the very helpful replies! I have another quick question. Which commands would I use to generate images like the ones in Figure 1 (C) generated in the Salat paper (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2750073/#R57)?

Thank you Sabrina

---

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: Tuesday, December 15, 2015 10:10 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Fw: Gray matter intensity

On 12/15/2015 01:00 PM, Sabrina Yu wrote:

...

Hi,

Just following up on my previous email (see below) as I have not yet heard back. I also have another question regarding the lh.wm.mgh and rh.wm.mgh generated by pctsurfcon. How do I view these as surface overlays on T1 brain scans?

If you want to view them on a volume instead of a surface, you can use mri_surf2vol

...

Thank you very much.

---

*From:* Sabrina Yu *Sent:* Thursday, December 10, 2015 2:47 PM *To:* Freesurfer support list *Subject:* Gray matter intensity

Hello,

I have been following the instructions in this email thread: https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-April/037240.html. https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-April/037240.html And have successfully gotten the wm-gm signal intensity contrast, but now have a few questions regarding signal intensity for white matter and gray matter intensity.

1. Does the wmparc.stats contain mean white matter intensity values

for each ROI?

Yes

...

2. Is it possible to extract these same mean intensity values for gray

matter? There is no gmparc.stats file. We know that it's possible to calculate these from the WM/GM ratio from pctsurfcon, but it'd be great if there was a more direct way to get this data.

There is not one by default that includes the cortical parcellation. You can create your own with mri_segstats passing it the aparc+aseg.mgz as the segmentation. Look in the recon-all.log file for the command line that creates the aseg.stats or wmparc.stats. You will probably need to change the --ctab flag to --ctab-default (no argument)

...

Thank you,

Sabrina Yu

---

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

-- 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

---

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

which figure(s) in particular?

On 01/28/2016 01:41 PM, Sabrina Yu wrote:

Hi,

Sorry for bringing this thread up again. Referring back to the figure in the Salat paper, what map do I load as an overlay to get the intensity maps? How do I generate these maps?

Thank you, Sabrina

---

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: Monday, December 21, 2015 10:08 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Fw: Gray matter intensity

freeview or tksurfer. Load the relevant map as an overlay

On 12/21/2015 12:57 PM, Sabrina Yu wrote:

...

Hello,

Thank you for the very helpful replies! I have another quick question. Which commands would I use to generate images like the ones in Figure 1 (C) generated in the Salat paper (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2750073/#R57)?

Thank you Sabrina

---

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: Tuesday, December 15, 2015 10:10 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Fw: Gray matter intensity

On 12/15/2015 01:00 PM, Sabrina Yu wrote:

...

Hi,

Just following up on my previous email (see below) as I have not yet heard back. I also have another question regarding the lh.wm.mgh and rh.wm.mgh generated by pctsurfcon. How do I view these as surface overlays on T1 brain scans?

If you want to view them on a volume instead of a surface, you can use mri_surf2vol

...

Thank you very much.

---

*From:* Sabrina Yu *Sent:* Thursday, December 10, 2015 2:47 PM *To:* Freesurfer support list *Subject:* Gray matter intensity

Hello,

I have been following the instructions in this email thread: https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-April/037240.html. https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-April/037240.html And have successfully gotten the wm-gm signal intensity contrast, but now have a few questions regarding signal intensity for white matter and gray matter intensity.

1. Does the wmparc.stats contain mean white matter intensity values

for each ROI?

Yes

...

2. Is it possible to extract these same mean intensity values for gray

matter? There is no gmparc.stats file. We know that it's possible to calculate these from the WM/GM ratio from pctsurfcon, but it'd be great if there was a more direct way to get this data.

There is not one by default that includes the cortical parcellation. You can create your own with mri_segstats passing it the aparc+aseg.mgz as the segmentation. Look in the recon-all.log file for the command line that creates the aseg.stats or wmparc.stats. You will probably need to change the --ctab flag to --ctab-default (no argument)

...

Thank you,

Sabrina Yu

---

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

-- 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

---

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

Hi sorry, haven't heard back yet from Freesurfers. Just following up on how to generate gray matter & white matter intensity maps overlaid onto brain like in Salat paper.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2750073/#R57

Figure 1 (c). The mean maps of signal intensity.

Thanks! ________________________________________ From: Sabrina Yu Sent: Thursday, January 28, 2016 10:51 AM To: Freesurfer support list Subject: Re: [Freesurfer] Fw: Gray matter intensity

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2750073/#R57

Figure 1 (c). The mean maps of signal intensity.

________________________________________ 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, January 28, 2016 10:47 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Fw: Gray matter intensity

which figure(s) in particular?

On 01/28/2016 01:41 PM, Sabrina Yu wrote:

Hi,

Sorry for bringing this thread up again. Referring back to the figure in the Salat paper, what map do I load as an overlay to get the intensity maps? How do I generate these maps?

Thank you, Sabrina

---

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: Monday, December 21, 2015 10:08 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Fw: Gray matter intensity

freeview or tksurfer. Load the relevant map as an overlay

On 12/21/2015 12:57 PM, Sabrina Yu wrote:

...

Hello,

Thank you for the very helpful replies! I have another quick question. Which commands would I use to generate images like the ones in Figure 1 (C) generated in the Salat paper (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2750073/#R57)?

Thank you Sabrina

---

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: Tuesday, December 15, 2015 10:10 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Fw: Gray matter intensity

On 12/15/2015 01:00 PM, Sabrina Yu wrote:

...

Hi,

Just following up on my previous email (see below) as I have not yet heard back. I also have another question regarding the lh.wm.mgh and rh.wm.mgh generated by pctsurfcon. How do I view these as surface overlays on T1 brain scans?

If you want to view them on a volume instead of a surface, you can use mri_surf2vol

...

Thank you very much.

---

*From:* Sabrina Yu *Sent:* Thursday, December 10, 2015 2:47 PM *To:* Freesurfer support list *Subject:* Gray matter intensity

Hello,

I have been following the instructions in this email thread: https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-April/037240.html. https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-April/037240.html And have successfully gotten the wm-gm signal intensity contrast, but now have a few questions regarding signal intensity for white matter and gray matter intensity.

1. Does the wmparc.stats contain mean white matter intensity values

for each ROI?

Yes

...

2. Is it possible to extract these same mean intensity values for gray

matter? There is no gmparc.stats file. We know that it's possible to calculate these from the WM/GM ratio from pctsurfcon, but it'd be great if there was a more direct way to get this data.

There is not one by default that includes the cortical parcellation. You can create your own with mri_segstats passing it the aparc+aseg.mgz as the segmentation. Look in the recon-all.log file for the command line that creates the aseg.stats or wmparc.stats. You will probably need to change the --ctab flag to --ctab-default (no argument)

...

Thank you,

Sabrina Yu

---

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

-- 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

---

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

Hi Doug,

Thank you for taking the time to answer, I really appreciate it! I have completed this step for all subjects, and created the lh.wm.mgh and rh.wm.mgh files. What should be the next step for creating those maps? Unsure on how to overlay the mgh files.

Thanks, Sabrina

On Feb 4, 2016, at 4:48 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:

Hi Sabrina, sorry, I was working on a grant, and now I'm out of town until Monday. I can try to push you forward on this now, but I have to be brief. Those images where made from data created with the pctsurfcon scriopt. If you run it with --help, you will get some docs on it. This is already run by default with output {lr}h.w-g.pct.mgh which is the GM/WM intensity in Figure 1. This script will also create the GM and WM intensity files but deletes them by default. You can re-run it and specify the temporary folder with --tmp, and those files will be in there. I don't know what they will be called but hopefully it will be obvious.

doug

On 2/4/16 2:14 PM, Sabrina Yu wrote:

...

Hi sorry, haven't heard back yet from Freesurfers. Just following up on how to generate gray matter & white matter intensity maps overlaid onto brain like in Salat paper.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2750073/#R57

Figure 1 (c). The mean maps of signal intensity.

Thanks! ________________________________________ From: Sabrina Yu Sent: Thursday, January 28, 2016 10:51 AM To: Freesurfer support list Subject: Re: [Freesurfer] Fw: Gray matter intensity

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2750073/#R57

Figure 1 (c). The mean maps of signal intensity.

---

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, January 28, 2016 10:47 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Fw: Gray matter intensity

which figure(s) in particular?

On 01/28/2016 01:41 PM, Sabrina Yu wrote:

...

Hi,

Sorry for bringing this thread up again. Referring back to the figure in the Salat paper, what map do I load as an overlay to get the intensity maps? How do I generate these maps?

Thank you, Sabrina

---

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: Monday, December 21, 2015 10:08 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Fw: Gray matter intensity

freeview or tksurfer. Load the relevant map as an overlay

On 12/21/2015 12:57 PM, Sabrina Yu wrote:

...

Hello,

Thank you for the very helpful replies! I have another quick question. Which commands would I use to generate images like the ones in Figure 1 (C) generated in the Salat paper (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2750073/#R57)?

Thank you Sabrina

---

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: Tuesday, December 15, 2015 10:10 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Fw: Gray matter intensity

On 12/15/2015 01:00 PM, Sabrina Yu wrote:

...

Hi,

Just following up on my previous email (see below) as I have not yet heard back. I also have another question regarding the lh.wm.mgh and rh.wm.mgh generated by pctsurfcon. How do I view these as surface overlays on T1 brain scans?

If you want to view them on a volume instead of a surface, you can use mri_surf2vol

...

Thank you very much.

---

*From:* Sabrina Yu *Sent:* Thursday, December 10, 2015 2:47 PM *To:* Freesurfer support list *Subject:* Gray matter intensity

Hello,

I have been following the instructions in this email thread: https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-April/037240.html. https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-April/037240.html And have successfully gotten the wm-gm signal intensity contrast, but now have a few questions regarding signal intensity for white matter and gray matter intensity.

1. Does the wmparc.stats contain mean white matter intensity values

for each ROI?

Yes

...

2. Is it possible to extract these same mean intensity values for gray

matter? There is no gmparc.stats file. We know that it's possible to calculate these from the WM/GM ratio from pctsurfcon, but it'd be great if there was a more direct way to get this data.

There is not one by default that includes the cortical parcellation. You can create your own with mri_segstats passing it the aparc+aseg.mgz as the segmentation. Look in the recon-all.log file for the command line that creates the aseg.stats or wmparc.stats. You will probably need to change the --ctab flag to --ctab-default (no argument)

...

Thank you,

Sabrina Yu

---

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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: 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/

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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: 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/

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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: 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/

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Hi,

I know Doug is away, so he may correct me later, but I believe it doesn't matter, as long as it is consistent across runs, and you know what it is. It will just determine where the angle 0 activity goes (in a color map etc.). The way FS-FAST does the mapping it just may mean your colors don't line up with others.

hth d

On Thu, Feb 4, 2016 at 11:52 PM, m.abouelyazid@gmail.com wrote:

Dear all,

I am wondering about what the zero angle for retinotopy corresponds to in retinotopy analysis. I mean corresponding to the wedge being at zero angle in circular coordinate map (horizontal) or vertical up?

Thank you,

Best,

---

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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.

Yes, 0 is where the wedge starts. doug

On 2/7/16 7:56 AM, Mohamed Abdelhack wrote:

Does this mean that the zero angle is the one where the wedge starts rotating in the experiment? Does this apply to eccentricity experiment also (In my lab's protocol it doesn't start from zero)?

On Sat, Feb 6, 2016 at 2:20 AM, dgw <dgwakeman@gmail.com mailto:dgwakeman@gmail.com> wrote:

Hi,

I know Doug is away, so he may correct me later, but I believe it
doesn't matter, as long as it is consistent across runs, and you know
what it is. It will just determine where the angle 0 activity goes (in
a color map etc.). The way FS-FAST does the mapping it just may mean
your colors don't line up with others.

hth
d

On Thu, Feb 4, 2016 at 11:52 PM,  <m.abouelyazid@gmail.com
<mailto:m.abouelyazid@gmail.com>> wrote:
> Dear all,
>
>
>
> I am wondering about what the zero angle for retinotopy
corresponds to in
> retinotopy analysis. I mean corresponding to the wedge being at
zero angle
> in circular coordinate map (horizontal) or vertical up?
>
>
>
> Thank you,
>
> Best,
>
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
<mailto: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 <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

---

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Load them as an overlay in freeview or tksurfer. There should be examples on the wiki.

On 2/4/16 10:04 PM, Sabrina Yu wrote:

Hi Doug,

Thank you for taking the time to answer, I really appreciate it! I have completed this step for all subjects, and created the lh.wm.mgh and rh.wm.mgh files. What should be the next step for creating those maps? Unsure on how to overlay the mgh files.

Thanks, Sabrina

...

On Feb 4, 2016, at 4:48 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:

Hi Sabrina, sorry, I was working on a grant, and now I'm out of town until Monday. I can try to push you forward on this now, but I have to be brief. Those images where made from data created with the pctsurfcon scriopt. If you run it with --help, you will get some docs on it. This is already run by default with output {lr}h.w-g.pct.mgh which is the GM/WM intensity in Figure 1. This script will also create the GM and WM intensity files but deletes them by default. You can re-run it and specify the temporary folder with --tmp, and those files will be in there. I don't know what they will be called but hopefully it will be obvious.

doug

On 2/4/16 2:14 PM, Sabrina Yu wrote:

...

Hi sorry, haven't heard back yet from Freesurfers. Just following up on how to generate gray matter & white matter intensity maps overlaid onto brain like in Salat paper.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2750073/#R57

Figure 1 (c). The mean maps of signal intensity.

Thanks! ________________________________________ From: Sabrina Yu Sent: Thursday, January 28, 2016 10:51 AM To: Freesurfer support list Subject: Re: [Freesurfer] Fw: Gray matter intensity

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2750073/#R57

Figure 1 (c). The mean maps of signal intensity.

---

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, January 28, 2016 10:47 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Fw: Gray matter intensity

which figure(s) in particular?

On 01/28/2016 01:41 PM, Sabrina Yu wrote:

...

Hi,

Sorry for bringing this thread up again. Referring back to the figure in the Salat paper, what map do I load as an overlay to get the intensity maps? How do I generate these maps?

Thank you, Sabrina

---

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: Monday, December 21, 2015 10:08 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Fw: Gray matter intensity

freeview or tksurfer. Load the relevant map as an overlay

On 12/21/2015 12:57 PM, Sabrina Yu wrote:

...

Hello,

Thank you for the very helpful replies! I have another quick question. Which commands would I use to generate images like the ones in Figure 1 (C) generated in the Salat paper (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2750073/#R57)?

Thank you Sabrina

---

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: Tuesday, December 15, 2015 10:10 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Fw: Gray matter intensity

On 12/15/2015 01:00 PM, Sabrina Yu wrote:

...

Hi,

Just following up on my previous email (see below) as I have not yet heard back. I also have another question regarding the lh.wm.mgh and rh.wm.mgh generated by pctsurfcon. How do I view these as surface overlays on T1 brain scans?

If you want to view them on a volume instead of a surface, you can use mri_surf2vol

...

Thank you very much.

---

*From:* Sabrina Yu *Sent:* Thursday, December 10, 2015 2:47 PM *To:* Freesurfer support list *Subject:* Gray matter intensity

Hello,

I have been following the instructions in this email thread: https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-April/037240.html. https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-April/037240.html And have successfully gotten the wm-gm signal intensity contrast, but now have a few questions regarding signal intensity for white matter and gray matter intensity.

1. Does the wmparc.stats contain mean white matter intensity values

for each ROI?

Yes

...

2. Is it possible to extract these same mean intensity values for gray

matter? There is no gmparc.stats file. We know that it's possible to calculate these from the WM/GM ratio from pctsurfcon, but it'd be great if there was a more direct way to get this data.

There is not one by default that includes the cortical parcellation. You can create your own with mri_segstats passing it the aparc+aseg.mgz as the segmentation. Look in the recon-all.log file for the command line that creates the aseg.stats or wmparc.stats. You will probably need to change the --ctab flag to --ctab-default (no argument)

...

Thank you,

Sabrina Yu

---

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/

---

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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.

---

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/

---

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---

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/

---

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