hi,

I've read through the list, and searched over the last few days, and can't quite seem to find what I'm looking for. My first message wasn't clear at all either (my apologies), it was one of those days where your brain ends up in a bit of a fog.

I am trying to get a heat map style visual output based on the destrieux 72 region map using cortical thickness as our measure. I'm using FS 6.0 and the edits and outputs have all gone great. We are doing the analysis of the cortical thickness outside of FS and would like to create a heat-map style visual output of the areas that show a large effect size. My original idea was to create a custom color map and somehow load that in place of the default destrieux color map but I couldn't get that to work. Tried replacing the FS LUT table as well and when loaded the colors remained the same as well.

Hope that clarifies what I'm trying to do.

Thanks,

Peter ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of dg wakeman [dgwakeman@gmail.com] Sent: Tuesday, April 04, 2017 12:11 PM To: Freesurfer support list Subject: Re: [Freesurfer] Custom color maps

Hi Peter,

We will need a lot more details to help. I suggest you look through the e-mail list a bit. I spent a lot of time helping a user or two with a similar issue. The key details are what are you trying to show (an annotation, a single label, or values)?

hth d

On Wed, Mar 29, 2017 at 11:15 AM, Senften, Peter peter.senften@ubc.ca wrote:

Hello,

I am wondering if it is possible to create a custom color map that will be visible in freeview using the 3D viewer - not the coronal, axial, or sagital views. I created a copy of the LUT file and then replaced the RGB values the ones I wanted but haven't been able to get it to load at all.

In the end I am trying to make pretty 3D pictures to see our regions of interest better for our data. I am open to other ways of doing this.

Thanks,

Peter

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Thanks, I'll take a look at it and let you know how it goes.

Peter ________________________________________ 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, April 06, 2017 1:00 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Custom color maps

See if annotval2surfoverlay.m does what you want. It is in v6. If you have v5.x, I can send you the mfile separtely

On 04/06/2017 01:00 PM, Senften, Peter wrote:

hi,

I've read through the list, and searched over the last few days, and can't quite seem to find what I'm looking for. My first message wasn't clear at all either (my apologies), it was one of those days where your brain ends up in a bit of a fog.

I am trying to get a heat map style visual output based on the destrieux 72 region map using cortical thickness as our measure. I'm using FS 6.0 and the edits and outputs have all gone great. We are doing the analysis of the cortical thickness outside of FS and would like to create a heat-map style visual output of the areas that show a large effect size. My original idea was to create a custom color map and somehow load that in place of the default destrieux color map but I couldn't get that to work. Tried replacing the FS LUT table as well and when loaded the colors remained the same as well.

Hope that clarifies what I'm trying to do.

Thanks,

Peter ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of dg wakeman [dgwakeman@gmail.com] Sent: Tuesday, April 04, 2017 12:11 PM To: Freesurfer support list Subject: Re: [Freesurfer] Custom color maps

Hi Peter,

We will need a lot more details to help. I suggest you look through the e-mail list a bit. I spent a lot of time helping a user or two with a similar issue. The key details are what are you trying to show (an annotation, a single label, or values)?

hth d

On Wed, Mar 29, 2017 at 11:15 AM, Senften, Peter peter.senften@ubc.ca wrote:

...

Hello,

I am wondering if it is possible to create a custom color map that will be visible in freeview using the 3D viewer - not the coronal, axial, or sagital views. I created a copy of the LUT file and then replaced the RGB values the ones I wanted but haven't been able to get it to load at all.

In the end I am trying to make pretty 3D pictures to see our regions of interest better for our data. I am open to other ways of doing this.

Thanks,

Peter

---

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

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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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