freesurfer parcellation lookup table

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freesurfer parcellation lookup table

Gregory Book
Is there a way in Slicer to view a freesurfer surface (*.pial) and assign a different colors to each of the parcellations instead of the default random colors?

I'm able to load a surface and view that, but how do I
a) create a custom parcellation color lookup table
b) view it on a surface

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Re: freesurfer parcellation lookup table

Nicole Aucoin
Hi Gregory,

When you load a *.aparc.annot overlay onto a surface file, Slicer will create a colour table from the information in that file. You can change the color table that's used to display it in the Models module, Display, Scalars, Color Table drop down. To make a new one, you can create a text file using the format described here:
Save it to disk and then you can load the color table and assign it to your model's scalar overlay.
Or you can copy and modify a current color table (for example the one that was created on reading in your overlay), in the Colors module.

Nicole

On Mon, Feb 6, 2017 at 3:52 PM, Gregory Book <[hidden email]> wrote:
Is there a way in Slicer to view a freesurfer surface (*.pial) and assign a different colors to each of the parcellations instead of the default random colors?

I'm able to load a surface and view that, but how do I
a) create a custom parcellation color lookup table
b) view it on a surface

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[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ



--
Nicole Aucoin
Harmonus Inc.
Harvard Launch Lab
114 Western Ave, Allston, MA 02134

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Re: freesurfer parcellation lookup table

lasso2
In reply to this post by Gregory Book

You can set a color map in the Models module, Display / Scalars section. You can create and edit color maps in the Colors module.

 

Andras

 

From: slicer-devel [mailto:[hidden email]] On Behalf Of Gregory Book
Sent: February 6, 2017 15:52
To: SPL Slicer Devel <[hidden email]>
Subject: [slicer-devel] freesurfer parcellation lookup table

 

Is there a way in Slicer to view a freesurfer surface (*.pial) and assign a different colors to each of the parcellations instead of the default random colors?

 

I'm able to load a surface and view that, but how do I

a) create a custom parcellation color lookup table

b) view it on a surface


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Re: freesurfer parcellation lookup table

Gregory Book
In reply to this post by Gregory Book
Thanks. I tried that after you posted the reply, and it worked. However, I'm trying to do it again, and I can't seem to replicate the results. I'm doing the following:

1) Load lh.pial
2) Go into the Models->Scalars section
3) Click Visible, and change the color table

Changing the color table or scalar range type does nothing. I still only see the gray pial surface. If I change the Active Scalar to "Normals", I see the color, but that's not the type of overlay I'm looking for.

On Tue, Feb 7, 2017 at 9:09 AM, Andras Lasso <[hidden email]> wrote:

You can set a color map in the Models module, Display / Scalars section. You can create and edit color maps in the Colors module.

 

Andras

 

From: slicer-devel [mailto:[hidden email]] On Behalf Of Gregory Book
Sent: February 6, 2017 15:52
To: SPL Slicer Devel <[hidden email]>
Subject: [slicer-devel] freesurfer parcellation lookup table

 

Is there a way in Slicer to view a freesurfer surface (*.pial) and assign a different colors to each of the parcellations instead of the default random colors?

 

I'm able to load a surface and view that, but how do I

a) create a custom parcellation color lookup table

b) view it on a surface



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[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ
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Re: freesurfer parcellation lookup table

Nicole Aucoin
Hi,

Did you load the overlay? In the Add Data pop up if you click Show Options it will let you add the overlay to lh.pial.

Nicole

On Thu, Mar 9, 2017 at 9:27 AM, Gregory Book <[hidden email]> wrote:
Thanks. I tried that after you posted the reply, and it worked. However, I'm trying to do it again, and I can't seem to replicate the results. I'm doing the following:

1) Load lh.pial
2) Go into the Models->Scalars section
3) Click Visible, and change the color table

Changing the color table or scalar range type does nothing. I still only see the gray pial surface. If I change the Active Scalar to "Normals", I see the color, but that's not the type of overlay I'm looking for.

On Tue, Feb 7, 2017 at 9:09 AM, Andras Lasso <[hidden email]> wrote:

You can set a color map in the Models module, Display / Scalars section. You can create and edit color maps in the Colors module.

 

Andras

 

From: slicer-devel [mailto:[hidden email]] On Behalf Of Gregory Book
Sent: February 6, 2017 15:52
To: SPL Slicer Devel <[hidden email]>
Subject: [slicer-devel] freesurfer parcellation lookup table

 

Is there a way in Slicer to view a freesurfer surface (*.pial) and assign a different colors to each of the parcellations instead of the default random colors?

 

I'm able to load a surface and view that, but how do I

a) create a custom parcellation color lookup table

b) view it on a surface



_______________________________________________
slicer-devel mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ



--
Nicole Aucoin
Harmonus Inc.
Harvard Launch Lab
114 Western Ave, Allston, MA 02134

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Re: freesurfer parcellation lookup table

Gregory Book
In reply to this post by Gregory Book
Now, that worked. Thanks!

If I wanted to create a custom lookup table, how would I do that? I've tried creating a LUT, which has the following format:

integer_label label color
14 3rd-Ventricle rgb(61,61,255)
15 4th-Ventricle rgb(209,209,255)
72 5th-Ventricle rgb(188,188,255)
410 BA1 rgb(255,107,107)
407 BA2 rgb(255,132,132)
412 BA3a rgb(255,188,188)
...

and i see the LUT as "File..." in the list of color tables. When I select that, I see no coloration though. I have tried the Scalar Range Type of "Data" and "LUT", but neither changes anything. Still a gray pial surface.

Then I loaded the *.annot file from the freesurfer directory, and using the "ColorTable" color table, it displayed with colors as before. If I select the "File..." color table, it doesn't display anything.

Do I need to change the *.annot file to include a different color table?


On Thu, Mar 9, 2017 at 9:38 AM, Nicole Aucoin <[hidden email]> wrote:
Hi,

Did you load the overlay? In the Add Data pop up if you click Show Options it will let you add the overlay to lh.pial.

Nicole

On Thu, Mar 9, 2017 at 9:27 AM, Gregory Book <[hidden email]> wrote:
Thanks. I tried that after you posted the reply, and it worked. However, I'm trying to do it again, and I can't seem to replicate the results. I'm doing the following:

1) Load lh.pial
2) Go into the Models->Scalars section
3) Click Visible, and change the color table

Changing the color table or scalar range type does nothing. I still only see the gray pial surface. If I change the Active Scalar to "Normals", I see the color, but that's not the type of overlay I'm looking for.

On Tue, Feb 7, 2017 at 9:09 AM, Andras Lasso <[hidden email]> wrote:

You can set a color map in the Models module, Display / Scalars section. You can create and edit color maps in the Colors module.

 

Andras

 

From: slicer-devel [mailto:[hidden email]] On Behalf Of Gregory Book
Sent: February 6, 2017 15:52
To: SPL Slicer Devel <[hidden email]>
Subject: [slicer-devel] freesurfer parcellation lookup table

 

Is there a way in Slicer to view a freesurfer surface (*.pial) and assign a different colors to each of the parcellations instead of the default random colors?

 

I'm able to load a surface and view that, but how do I

a) create a custom parcellation color lookup table

b) view it on a surface



_______________________________________________
slicer-devel mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ



--
Nicole Aucoin
Harmonus Inc.
Harvard Launch Lab
114 Western Ave, Allston, MA 02134


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Re: freesurfer parcellation lookup table

Nicole Aucoin
In reply to this post by Gregory Book
The above format will most likely generate an error if you try to load it as a Slicer color node. If you go to the Colors module and select your custom one, does it display properly in the table? 

The Color node file format is specified here and includes instructions for making a new LUT:
You should have a 0, background entry with an opacity of 0.

Nicole

On Thu, Mar 9, 2017 at 1:51 PM, Gregory Book <[hidden email]> wrote:
Now, that worked. Thanks!

If I wanted to create a custom lookup table, how would I do that? I've tried creating a LUT, which has the following format:

integer_label label color
14 3rd-Ventricle rgb(61,61,255)
15 4th-Ventricle rgb(209,209,255)
72 5th-Ventricle rgb(188,188,255)
410 BA1 rgb(255,107,107)
407 BA2 rgb(255,132,132)
412 BA3a rgb(255,188,188)
...

and i see the LUT as "File..." in the list of color tables. When I select that, I see no coloration though. I have tried the Scalar Range Type of "Data" and "LUT", but neither changes anything. Still a gray pial surface.

Then I loaded the *.annot file from the freesurfer directory, and using the "ColorTable" color table, it displayed with colors as before. If I select the "File..." color table, it doesn't display anything.

Do I need to change the *.annot file to include a different color table?


On Thu, Mar 9, 2017 at 9:38 AM, Nicole Aucoin <[hidden email]> wrote:
Hi,

Did you load the overlay? In the Add Data pop up if you click Show Options it will let you add the overlay to lh.pial.

Nicole

On Thu, Mar 9, 2017 at 9:27 AM, Gregory Book <[hidden email]> wrote:
Thanks. I tried that after you posted the reply, and it worked. However, I'm trying to do it again, and I can't seem to replicate the results. I'm doing the following:

1) Load lh.pial
2) Go into the Models->Scalars section
3) Click Visible, and change the color table

Changing the color table or scalar range type does nothing. I still only see the gray pial surface. If I change the Active Scalar to "Normals", I see the color, but that's not the type of overlay I'm looking for.

On Tue, Feb 7, 2017 at 9:09 AM, Andras Lasso <[hidden email]> wrote:

You can set a color map in the Models module, Display / Scalars section. You can create and edit color maps in the Colors module.

 

Andras

 

From: slicer-devel [mailto:[hidden email]] On Behalf Of Gregory Book
Sent: February 6, 2017 15:52
To: SPL Slicer Devel <[hidden email]>
Subject: [slicer-devel] freesurfer parcellation lookup table

 

Is there a way in Slicer to view a freesurfer surface (*.pial) and assign a different colors to each of the parcellations instead of the default random colors?

 

I'm able to load a surface and view that, but how do I

a) create a custom parcellation color lookup table

b) view it on a surface



_______________________________________________
slicer-devel mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ



--
Nicole Aucoin
Harmonus Inc.
Harvard Launch Lab
114 Western Ave, Allston, MA 02134




--
Nicole Aucoin
Harmonus Inc.
Harvard Launch Lab
114 Western Ave, Allston, MA 02134

_______________________________________________
slicer-devel mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ
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Re: freesurfer parcellation lookup table

Gregory Book
In reply to this post by Gregory Book
Thanks, using the correct format worked. I'm getting closer. I'm not able to see my color LUT, but not all of the freesurfer parcellations are visible. Some are blank but some have the correct color.

my LUT now looks like this. But i'm wondering if those IDs and labels are correct? And if not, where to find the correct labels.
...
1003 ctx-lh-caudalmiddlefrontal 255 198 198 255
2003 ctx-rh-caudalmiddlefrontal 255 198 198 255
255 CC_Anterior 255 163 163 255
253 CC_Central 234 234 255 255
254 CC_Mid_Anterior 249 249 255 255
252 CC_Mid_Posterior 255 224 224 255
251 CC_Posterior 255 91 91 255
24 CSF 112 112 255 255
1005 ctx-lh-cuneus 255 168 168 255
2005 ctx-rh-cuneus 255 204 204 255
1006 ctx-lh-entorhinal 255 229 229 255
2006 ctx-rh-entorhinal 249 249 255 255
1032 ctx-lh-frontalpole 255 163 163 255
2032 ctx-rh-frontalpole 255 153 153 255
1007 ctx-lh-fusiform 255 198 198 255
2007 ctx-rh-fusiform 239 239 255 255
11106 ctx_lh_G_and_S_cingul-Ant 214 214 255 255
12106 ctx_rh_G_and_S_cingul-Ant 204 204 255 255
11107 ctx_lh_G_and_S_cingul-Mid-Ant 255 229 229 255
12107 ctx_rh_G_and_S_cingul-Mid-Ant 255 178 178 255
11108 ctx_lh_G_and_S_cingul-Mid-Post 255 255 255 255
12108 ctx_rh_G_and_S_cingul-Mid-Post 255 229 229 255
...

On Thu, Mar 9, 2017 at 2:04 PM, Nicole Aucoin <[hidden email]> wrote:
The above format will most likely generate an error if you try to load it as a Slicer color node. If you go to the Colors module and select your custom one, does it display properly in the table? 

The Color node file format is specified here and includes instructions for making a new LUT:
You should have a 0, background entry with an opacity of 0.

Nicole

On Thu, Mar 9, 2017 at 1:51 PM, Gregory Book <[hidden email]> wrote:
Now, that worked. Thanks!

If I wanted to create a custom lookup table, how would I do that? I've tried creating a LUT, which has the following format:

integer_label label color
14 3rd-Ventricle rgb(61,61,255)
15 4th-Ventricle rgb(209,209,255)
72 5th-Ventricle rgb(188,188,255)
410 BA1 rgb(255,107,107)
407 BA2 rgb(255,132,132)
412 BA3a rgb(255,188,188)
...

and i see the LUT as "File..." in the list of color tables. When I select that, I see no coloration though. I have tried the Scalar Range Type of "Data" and "LUT", but neither changes anything. Still a gray pial surface.

Then I loaded the *.annot file from the freesurfer directory, and using the "ColorTable" color table, it displayed with colors as before. If I select the "File..." color table, it doesn't display anything.

Do I need to change the *.annot file to include a different color table?


On Thu, Mar 9, 2017 at 9:38 AM, Nicole Aucoin <[hidden email]> wrote:
Hi,

Did you load the overlay? In the Add Data pop up if you click Show Options it will let you add the overlay to lh.pial.

Nicole

On Thu, Mar 9, 2017 at 9:27 AM, Gregory Book <[hidden email]> wrote:
Thanks. I tried that after you posted the reply, and it worked. However, I'm trying to do it again, and I can't seem to replicate the results. I'm doing the following:

1) Load lh.pial
2) Go into the Models->Scalars section
3) Click Visible, and change the color table

Changing the color table or scalar range type does nothing. I still only see the gray pial surface. If I change the Active Scalar to "Normals", I see the color, but that's not the type of overlay I'm looking for.

On Tue, Feb 7, 2017 at 9:09 AM, Andras Lasso <[hidden email]> wrote:

You can set a color map in the Models module, Display / Scalars section. You can create and edit color maps in the Colors module.

 

Andras

 

From: slicer-devel [mailto:[hidden email]] On Behalf Of Gregory Book
Sent: February 6, 2017 15:52
To: SPL Slicer Devel <[hidden email]>
Subject: [slicer-devel] freesurfer parcellation lookup table

 

Is there a way in Slicer to view a freesurfer surface (*.pial) and assign a different colors to each of the parcellations instead of the default random colors?

 

I'm able to load a surface and view that, but how do I

a) create a custom parcellation color lookup table

b) view it on a surface



_______________________________________________
slicer-devel mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ



--
Nicole Aucoin
Harmonus Inc.
Harvard Launch Lab
114 Western Ave, Allston, MA 02134




--
Nicole Aucoin
Harmonus Inc.
Harvard Launch Lab
114 Western Ave, Allston, MA 02134


_______________________________________________
slicer-devel mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-devel
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/FAQ