Hi Douglas,

This is the instruction I am using. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FuncOverlay

I cannot insert the picture in this email. I attach it. Hope it helps.

Thanks very much!

Yue

________________________________________ 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, June 09, 2016 3:38:43 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Resampling the parametric map of brain activations onto a surface

Sorry for the delay. I can't see the image. Also, what instructions are you following? They look pretty old.

check out our multimodal tutorial instead https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModal_freeview

On 06/09/2016 10:19 AM, Zhao, Yue wrote:

Hi All,

I am not sure if the question is successfully posted. If the post is there, does anyone has any idea? Thanks a lot!

Yue

---

*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Zhao, Yue zhao.y@wustl.edu *Sent:* Tuesday, June 07, 2016 4:15:20 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Resampling the parametric map of brain activations onto a surface

Hi All,

I am using a Ubuntu FreeSurfer v5.3.0 in the VirtualBox. I am trying to overlay a parametric map onto a FreeSurfer surface. Here are the tutorial codes I found:

1. To resample the paramatric map onto the individual's surface:

mri_vol2surf --src spm001.img --srcreg register.dat --hemi lh --projfrac 0.5 --out ./spm001-lh.w --out_type paint 2. Visualize and overlay: qsurfer -stat spm001 -hemi lh -subject bert-brf 3. Configure the image by selecting "View -> Configure -> Overlay" and play with the histogram

The image looks like this:

I assigned one single value to the voxels in each cortical parcellation. So the white matter and subcortical regions (e.g. caudate, putamen, hippocampus) are 0. The contrast represents the variations of the parameter across the cortex. Everything looks good to me except that I couldn't get rid of that green "noise" appearing at the hippocampus and occipital area. Does anyone have any idea why this is happening and how to get rid of it?

Another minor issue is that even though I play with the histogram in "Overlay" to get the best contrast, the colorbar looks less dynamic. Too much red but very little yellow. Any suggestion to improve that?

Thanks a lot!

Best,

Yue

---

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.

Thanks again. I will follow the new instructions!

Yue

________________________________________ 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, June 09, 2016 4:10:17 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Resampling the parametric map of brain activations onto a surface

That one is out of date; we'll delete it. Thanks for pointing it out and sorry for our wiki pointing you in the wrong direction. We're in the process of weeding it out...

On 06/09/2016 04:54 PM, Zhao, Yue wrote:

Hi Douglas,

This is the instruction I am using. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FuncOverlay

I cannot insert the picture in this email. I attach it. Hope it helps.

Thanks very much!

Yue

---

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, June 09, 2016 3:38:43 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Resampling the parametric map of brain activations onto a surface

Sorry for the delay. I can't see the image. Also, what instructions are you following? They look pretty old.

check out our multimodal tutorial instead https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModal_freeview

On 06/09/2016 10:19 AM, Zhao, Yue wrote:

...

Hi All,

I am not sure if the question is successfully posted. If the post is there, does anyone has any idea? Thanks a lot!

Yue

---

*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Zhao, Yue zhao.y@wustl.edu *Sent:* Tuesday, June 07, 2016 4:15:20 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Resampling the parametric map of brain activations onto a surface

Hi All,

I am using a Ubuntu FreeSurfer v5.3.0 in the VirtualBox. I am trying to overlay a parametric map onto a FreeSurfer surface. Here are the tutorial codes I found:

1. To resample the paramatric map onto the individual's surface:

mri_vol2surf --src spm001.img --srcreg register.dat --hemi lh --projfrac 0.5 --out ./spm001-lh.w --out_type paint 2. Visualize and overlay: qsurfer -stat spm001 -hemi lh -subject bert-brf 3. Configure the image by selecting "View -> Configure -> Overlay" and play with the histogram

The image looks like this:

I assigned one single value to the voxels in each cortical parcellation. So the white matter and subcortical regions (e.g. caudate, putamen, hippocampus) are 0. The contrast represents the variations of the parameter across the cortex. Everything looks good to me except that I couldn't get rid of that green "noise" appearing at the hippocampus and occipital area. Does anyone have any idea why this is happening and how to get rid of it?

Another minor issue is that even though I play with the histogram in "Overlay" to get the best contrast, the colorbar looks less dynamic. Too much red but very little yellow. Any suggestion to improve that?

Thanks a lot!

Best,

Yue

---

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