# How can I display the parametric map from multivolume analysis as a colormap?

**URL:** <https://discourse.slicer.org/t/how-can-i-display-the-parametric-map-from-multivolume-analysis-as-a-colormap/3589>\
**Category:** Development\
**Tags:** visualization\
**Created:** [July 27, 2018, 12:36am UTC](https://discourse.slicer.org/t/how-can-i-display-the-parametric-map-from-multivolume-analysis-as-a-colormap/3589 "2018-07-27T00:36:45Z")\
**Posts on this page:** 13\
**Page:** 1

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**Author:** ![Kyu\_Sung\_Choi](https://avatars.discourse-cdn.com/v4/letter/k/b77776/32.png) [@Kyu\_Sung\_Choi](https://discourse.slicer.org/u/Kyu_Sung_Choi)\
**Post date:** [July 27, 2018, 12:36am UTC](https://discourse.slicer.org/t/how-can-i-display-the-parametric-map-from-multivolume-analysis-as-a-colormap/3589/1 "2018-07-27T00:36:45Z")

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Dear Dr.Fedorov,

Thank you for your awesome work and kind comments.  
However, I have another question using DSCMRIAnalysis module.  
How can I display the grayscale rCBV map acquired by DSCMRIAnalysis as a colormap?  
I obtained the grayscale rCBV map (attached below, upper) but want to display this rCBV map as a colormap.  
I think technicians usually upload the rCBV map as a colormap on PACS.  
Moreover, most papers upload their rCBV map as a colormap.  
Actually I use fslview, but it returns a colormap like the one I attached below (middle), which is a bit different from the ones in most papers (attached below, lower).  
 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/f/a/fa90431dedc7ae7a5f9b6420007eeae5bfa544b0.png)  
 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/3/d/3d23f10a777765389296de717956a456922cb373.png)  
 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/0/0/006160e1dbf94a86d81e877bf1fe92cef01962fc.jpeg)  
Is there any recommendation or appropriate functions in DSCMRIAnalysis module?  
Thank you in advance!

All the best,  
Kyu Sung

> [@How can I convert DICOM series to NRRD files in batch mode?](https://discourse.slicer.org/t/how-can-i-convert-dicom-series-to-nrrd-files-in-batch-mode/3421/8):
>
> It could be that the extensions were not yet built/packaged at the time you tried. Looking at the dashboard [here](http://slicer.cdash.org/index.php?project=SlicerPreview), the package of DSCAnalysis extension is now ready, so you should try again.

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**Author:** ![fedorov](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/fedorov/32/14_2.png) [@fedorov](https://discourse.slicer.org/u/fedorov)\
**Post date:** [July 27, 2018, 2:26pm UTC](https://discourse.slicer.org/t/how-can-i-display-the-parametric-map-from-multivolume-analysis-as-a-colormap/3589/2 "2018-07-27T14:26:05Z")

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**Author:** ![fedorov](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/fedorov/32/14_2.png) [@fedorov](https://discourse.slicer.org/u/fedorov)\
**Post date:** [July 27, 2018, 2:28pm UTC](https://discourse.slicer.org/t/how-can-i-display-the-parametric-map-from-multivolume-analysis-as-a-colormap/3589/3 "2018-07-27T14:28:46Z")

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@Kyu_Sung_Choi I made the topic public, since I do not see anything sensitive in the content, and I think other users might benefit from the answer.

The mapping from the image voxel values to the color is handled via a lookup table that every volume in Slicer has assigned. By default, scalar volumes are assigned grayscale color map. To change that, you should select “Volumes” module, and you can change the assigned lookup table. You can try the one “ColdToHotRainbow”.

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**Author:** ![Kyu\_Sung\_Choi](https://avatars.discourse-cdn.com/v4/letter/k/b77776/32.png) [@Kyu\_Sung\_Choi](https://discourse.slicer.org/u/Kyu_Sung_Choi)\
**Post date:** [July 30, 2018, 4:08am UTC](https://discourse.slicer.org/t/how-can-i-display-the-parametric-map-from-multivolume-analysis-as-a-colormap/3589/4 "2018-07-30T04:08:51Z")

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Okay, it works perfect.  
Thanks!

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**Author:** ![tigerhu7](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/tigerhu7/32/67201_2.png) [@tigerhu7](https://discourse.slicer.org/u/tigerhu7)\
**Post date:** [August 10, 2018, 10:45am UTC](https://discourse.slicer.org/t/how-can-i-display-the-parametric-map-from-multivolume-analysis-as-a-colormap/3589/5 "2018-08-10T10:45:58Z")

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Hello speled,  
I got similar picture, I can get Ktrans in grey but not in color.  
Could you tell me how you managed that?  
Thank you so much!

-Tiger

 ![aaa](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/b/9/b987748383ccaa9177737b30de453fbc46837ac1.png)

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**Author:** ![fedorov](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/fedorov/32/14_2.png) [@fedorov](https://discourse.slicer.org/u/fedorov)\
**Post date:** [August 10, 2018, 2:45pm UTC](https://discourse.slicer.org/t/how-can-i-display-the-parametric-map-from-multivolume-analysis-as-a-colormap/3589/6 "2018-08-10T14:45:00Z")

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@tigerhu7 I moved your question to the topic where this was answered earlier - please go to the topic on discourse, read above this post, and let us know if you have further questions.

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**Author:** ![tigerhu7](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/tigerhu7/32/67201_2.png) [@tigerhu7](https://discourse.slicer.org/u/tigerhu7)\
**Post date:** [August 13, 2018, 12:58am UTC](https://discourse.slicer.org/t/how-can-i-display-the-parametric-map-from-multivolume-analysis-as-a-colormap/3589/7 "2018-08-13T00:58:19Z")

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Thank you so much !!

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**Author:** ![tigerhu7](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/tigerhu7/32/67201_2.png) [@tigerhu7](https://discourse.slicer.org/u/tigerhu7)\
**Post date:** [August 13, 2018, 2:01am UTC](https://discourse.slicer.org/t/how-can-i-display-the-parametric-map-from-multivolume-analysis-as-a-colormap/3589/8 "2018-08-13T02:01:08Z")

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Dear Dr Fedorov,  
It worked, thank you!

 ![ppp](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/b/6/b6a12253010e63914a1f84637f32d940a54fdbfd.png)

May I ask you some additional questions?  
(1) on the volume module, I set the output ktrans image display-\>lookup table-\>ColdToHotRainbow, and illustrate image of a certain frame and Ktrans image together, the blue dim background (as is on the pic) is bit annoying. Is there a way to clear blue background?  
(2) for the ktrans map, I would like to get the exact value of each pixel (voxel), is there a way to extract the data?  
I read your previous conversation with [kirezgik](https://discourse.slicer.org/u/kirezgik), are those values Ktrans map, ve map values? If so, how could I extract them?

> [@How to analyze DCE-MRI data](https://discourse.slicer.org/t/how-to-analyze-dce-mri-data/622/3):
>
> Thank you! I installed the extension and analyzed the data. This is the chart I got: And it autogenerates a DoubleArray file with an extension .mcsv and it includes this result: nolabels 0,5813.11,0 6.94764e+006,4719.33,0 1.38953e+007,4900.67,0 2.08429e+007,5255.11,0 2.77906e+007,5131.78,0 3.47382e+007,5241.11,0 4.16859e+007,5384.22,0 4.86335e+007,4986.33,0 5.55811e+007,5158.11,0 6.25288e+007,5173.11,0 6.94764e+007,5138.44,0 7.64241e+007,5346.67,0 8.33717e+007,6408.22,0 …

Sorry for my maybe silly questions, I am a newbie in 3DSlicer. I find this community is very nice and kind. And most of all, I am very grateful to all the contributors!!!

-Tiger Hu

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**Author:** ![tigerhu7](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/tigerhu7/32/67201_2.png) [@tigerhu7](https://discourse.slicer.org/u/tigerhu7)\
**Post date:** [August 13, 2018, 6:48am UTC](https://discourse.slicer.org/t/how-can-i-display-the-parametric-map-from-multivolume-analysis-as-a-colormap/3589/9 "2018-08-13T06:48:43Z")

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[fedorov](https://discourse.slicer.org/u/fedorov)

Dr Fedorov,  
To clear blue background, I figured out. Adjusting threshold makes it work.

 ![threshold](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/7/f/7f683eb4d815b6f9fa65bf5c6505389ba3509626.png)

But I still do not understand the values in .mcsv file.

-Tiger Hu

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**Author:** ![fedorov](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/fedorov/32/14_2.png) [@fedorov](https://discourse.slicer.org/u/fedorov)\
**Post date:** [August 13, 2018, 1:53pm UTC](https://discourse.slicer.org/t/how-can-i-display-the-parametric-map-from-multivolume-analysis-as-a-colormap/3589/10 "2018-08-13T13:53:27Z")

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> [@tigerhu7](#):
>
> I would like to get the exact value of each pixel (voxel)

When you save the Ktrans/ve map into a file (eg NRRD), it will contain values for each voxel arranged in a 3d array. You can use any software that supports specific format to get values at the individual voxels (e.g., Matlab, SimpleITK, itk-python). Where do you want to use that map?

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**Author:** ![tigerhu7](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/tigerhu7/32/67201_2.png) [@tigerhu7](https://discourse.slicer.org/u/tigerhu7)\
**Post date:** [August 13, 2018, 2:16pm UTC](https://discourse.slicer.org/t/how-can-i-display-the-parametric-map-from-multivolume-analysis-as-a-colormap/3589/12 "2018-08-13T14:16:03Z")

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Dr Fedorov,  
I would like to use this map in Matlab.  
Do I need special code to open it?  
Thanks,

-Tiger Hu

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**Author:** ![fedorov](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/fedorov/32/14_2.png) [@fedorov](https://discourse.slicer.org/u/fedorov)\
**Post date:** [August 13, 2018, 2:19pm UTC](https://discourse.slicer.org/t/how-can-i-display-the-parametric-map-from-multivolume-analysis-as-a-colormap/3589/13 "2018-08-13T14:19:40Z")

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Excellent, thank you for the details! In this case, you should look into the MatlabBridge extension. You can send the output of PkModeling directly into Matlab with minimum effort. I personally do not use Matlab and do not have a lot of experience, but everyone I know who tried it could figure out the usage from documentation.

Please see documentation here: [https://www.slicer.org/wiki/Documentation/Nightly/Extensions/MatlabBridge](https://www.slicer.org/wiki/Documentation/Nightly/Extensions/MatlabBridge)

I copy Andras who developed that module, and Sharon who is working with me and used it specifically with the DCE analysis functionality in Slicer: @lassoan @speled.

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**Author:** ![tigerhu7](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/tigerhu7/32/67201_2.png) [@tigerhu7](https://discourse.slicer.org/u/tigerhu7)\
**Post date:** [August 13, 2018, 2:22pm UTC](https://discourse.slicer.org/t/how-can-i-display-the-parametric-map-from-multivolume-analysis-as-a-colormap/3589/14 "2018-08-13T14:22:48Z")

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Dr Fedorov,  
Thank you so so much for your quick reply.  
I will read this document and give it a try.

-Tiger Hu