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

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
image
image
Is there any recommendation or appropriate functions in DSCMRIAnalysis module?
Thank you in advance!

All the best,
Kyu Sung

@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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Okay, it works perfect.
Thanks!

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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

@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.

Thank you so much !!

Dear Dr Fedorov,
It worked, thank you!
ppp

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, are those values Ktrans map, ve map values? If so, how could I extract them?
https://discourse.slicer.org/t/how-to-analyze-dce-mri-data/622/3?u=tigerhu7

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

fedorov

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

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

-Tiger Hu

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?

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

-Tiger Hu

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

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.

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

-Tiger Hu