With an indexed image, how do you make a specific color to be brighter by editing the colormap itself.

4 Jul 2022
1 Answer
Answer Accepted
Updated 5 Jul 2022
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With this line of code
% Load Atlas
% Relies on https://www.fieldtriptoolbox.org/template/atlas/ and
% https://github.com/fieldtrip/fieldtrip/tree/master/template/atlas and
% https://www.gin.cnrs.fr/en/tools/aal/
aalAtlas = ft_read_atlas('ROI_MNI_V4.nii');
BrainImage = ones(91, 109,'int8')
%help Image;
BrainImage(:,:) = aalAtlas.tissue(:, :, 50) %the tissue is part of the 3D BrainImage of the Atlas that looks at tissue
%BrainImage
%put it in a for loop to display each sect ion
for slice = 1:91
BrainImage(:,:) = aalAtlas.tissue(:, :, slice);
regions = ismember(BrainImage, [50,46,64]);
ColorBrainImage = ind2rgb(BrainImage, colorcube);
% Make those 3 regions a value brighter.
ColorBrainImage(regions) = uint8(5 * double(ColorBrainImage(regions))); %double allows to multipy with decimals and uint brings it back to whole number
BBrainImage = imresize(ColorBrainImage,10);
imshow(BBrainImage)
end
I am able to load a brain atlas that goes through the slices of the brain with the labelled respective regions. I have been able to highlight portions of the brain that I want, such as 50, 46, and 64. I can see these regions highlighted when I use different colormaps such as "copper," which is very easy to see the difference because it is in red compared to the rest of the image being shades of green. My issue is that I want to use the colorcube colormap because it is very easy to tell the portions of the brain labelled on the brain atlas I have apart, but since all the colors are already so bright, I can never tell which region is highlighted. Is there a way where I can possilbe make the colorcube colormap dimmer itself and then be able to see the highlighted regions I choose to be brighter?

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 Accepted Answer

Image Analyst
Image Analyst on 4 Jul 2022

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To replace your colors for 50, 46, and 64 with the colors from the copper colormap, do this, where cmap is your main colormap
% Create a copper colormap with same size as main existing colormap.
copperMap = copper(size(cmap, 1));
% Replace color for gray level 50, which happens at row 51 of the colormap, with the color from copper.
cmap(51, :) = copperMap(51, :);
% Replace color for gray level 46, which happens at row 47 of the colormap, with the color from copper.
cmap(47, :) = copperMap(47, :);
% Replace color for gray level 64, which happens at row 65 of the colormap, with the color from copper.
cmap(65, :) = copperMap(65, :);
I think this should also work
rows = [51, 47, 65];
cmap(rows, :) = copperMap(rows, :);

4 Comments
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Alexandar
Alexandar on 4 Jul 2022
Apologies, I am trying to change indeices that are labelled 50,46, and 64. I an not trying to change specific rows. Do you know what I can do for this?
Image Analyst
Image Analyst on 4 Jul 2022
Then I don't know what you mean. A colormap can have, say, 256 values mapping each gray level from 0-255 into a color. The way you do that is to create a colormap and apply it. So if you want pixels with gray levels of 50 to appear with some color, you have to set row 51 of the colormap to the desired color and apply the new colormap. Then all pixels with that gray level of 50 will appear with the new color.
So that's how it works.
I don't know what you mean when you say "I am trying to change indeices that are labelled 50,46, and 64". If you're not trying to change the color of pixels with those 3 gray levels by setting the coreresponding row of the colormap, then what are you trying to change?
Alexandar
Alexandar on 4 Jul 2022
For example, I have regions like this on my command window that show the image of the atlas I load up:
Columns 64 through 84
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
58 2 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2 2 2 2 2 2 2 12 12 12 0 0 0 0 0 0 0 0 0 0 0
2 2 2 2 2 2 12 12 12 12 12 12 0 0 0 0 0 0 0 0 0
2 2 2 2 2 12 12 12 12 12 12 12 14 14 14 14 0 0 0 0 0
2 2 2 2 2 12 12 12 12 12 12 12 14 14 14 14 14 0 0 0 0
2 2 2 2 12 12 12 12 12 12 12 14 14 14 14 14 14 14 0 0 0
2 2 2 2 12 12 12 12 12 12 12 14 14 14 14 14 14 14 14 14 0
2 2 2 12 12 12 12 12 12 12 12 14 14 14 14 14 14 14 14 14 0
2 2 2 12 12 12 12 12 12 12 14 14 14 14 14 14 14 14 14 14 8
2 2 12 12 12 12 12 12 12 12 14 14 14 14 14 14 14 14 14 14 8
0 2 2 12 12 12 12 12 12 12 14 14 14 14 14 14 14 14 14 14 8
0 2 12 12 12 12 12 12 12 14 14 14 14 14 14 14 14 14 14 14 8
0 12 12 12 12 12 12 12 14 14 14 14 14 14 14 14 14 14 14 8 8
0 12 12 12 12 12 12 12 14 14 14 14 14 14 14 14 14 14 8 8 8
0 12 12 12 12 12 12 12 14 14 14 14 14 14 14 14 14 14 8 8 8
0 0 0 0 0 0 0 12 14 14 14 14 14 14 14 14 14 8 8 8 8
0 0 0 0 0 0 0 14 14 14 14 14 14 14 14 14 14 8 8 8 8
0 0 0 0 0 0 0 14 14 14 14 14 14 14 14 14 8 8 8 8 8
0 0 0 0 0 0 0 14 14 0 0 0 0 14 14 0 8 8 8 8 8
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 8 8
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 8
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4
0 0 0 0 0 0 0 0 0 0 0 0 0 0 32 32 32 32 32 0 4
0 0 0 0 0 0 0 0 0 0 0 32 32 32 32 32 32 32 32 32 4
0 0 0 0 0 0 0 0 0 0 0 32 32 32 32 32 32 32 32 32 4
0 0 0 0 0 0 0 0 0 32 32 32 32 32 32 32 32 32 32 32 32
0 0 0 0 0 0 0 32 32 32 32 32 32 32 32 32 32 32 32 32 32
0 0 0 0 0 0 32 32 32 32 32 32 32 32 32 32 32 32 32 32 32
0 0 0 0 0 32 32 32 32 32 32 32 32 32 32 32 32 32 32 32 32
0 0 0 0 32 32 32 32 32 32 32 32 32 32 32 32 31 31 31 31 31
0 0 0 31 31 31 31 31 31 31 31 31 31 31 31 31 31 31 31 31 31
0 0 0 31 31 31 31 31 31 31 31 31 31 31 31 31 31 31 31 31 31
0 0 0 0 31 31 31 31 31 31 31 31 31 31 31 31 31 31 31 31 31
0 0 0 0 0 31 31 31 31 31 31 31 31 31 31 31 31 31 31 31 23
0 0 0 0 0 0 0 31 31 31 31 31 31 31 31 31 31 31 31 31 23
0 0 0 0 0 0 0 0 0 0 0 0 0 31 31 31 31 31 31 23 23
0 0 0 0 0 0 0 0 0 0 0 0 0 0 31 31 31 31 23 23 23
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 31 23 23 23 23
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 7 7
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 7 7
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 7 7
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 7 7 7 7
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 7 7 7 7
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 7 7 7 7
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 7 7 7 7 7
0 0 0 0 0 0 0 0 0 0 0 0 0 7 13 13 7 7 7 7 7
0 0 11 11 11 13 13 11 11 0 0 13 13 13 13 13 13 13 7 7 7
0 11 11 11 11 13 13 13 13 13 13 13 13 13 13 13 13 13 13 7 7
1 11 11 11 11 13 13 13 13 13 13 13 13 13 13 13 13 13 13 7 7
1 11 11 11 11 13 13 13 13 13 13 13 13 13 13 13 13 13 13 7 7
1 1 11 11 11 13 13 13 13 13 13 13 13 13 13 13 13 13 13 7 7
1 1 11 11 11 11 13 13 13 13 13 13 13 13 13 13 13 13 13 7 7
1 1 11 11 11 11 13 13 13 13 13 13 13 13 13 13 13 13 13 7 7
1 1 1 11 11 11 13 13 13 13 13 13 13 13 13 13 13 13 13 0 0
1 1 1 1 11 11 11 13 13 13 13 13 13 13 13 13 13 13 13 0 0
1 1 1 1 11 11 11 13 13 13 13 13 13 13 13 13 13 13 13 0 0
1 1 1 1 1 11 11 11 13 13 13 13 13 13 13 13 13 0 0 0 0
1 1 1 1 1 11 11 11 11 13 13 13 13 13 13 0 0 0 0 0 0
1 1 1 1 1 11 11 11 11 13 13 13 13 13 0 0 0 0 0 0 0
1 1 1 1 1 11 11 11 11 13 13 0 0 0 0 0 0 0 0 0 0
57 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
57 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Each region corresponds to a location of the brain. So for that region, I want to make it brighter than the rest. But it is hard to see when I use the colorcube colormap.
Stephen23
Stephen23 on 5 Jul 2022
Edited: Image Analyst on 5 Jul 2022
@Alexandar: then change those rows of the colormap, just as Image Analyst showed you.
You might also like to try this: https://www.mathworks.com/help/matlab/ref/colormapeditor.html
or label2rgb

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