CODEWITHSUNDEEP
imagematlabimage-processing
vigenere
vigenere

Reputation: 307

Coloring only specific pixels

I have a matrix representing an image of brain with each (i,j) position having a value between 0 and 1. I am applying a color map, so that those pixels with value 1 are red and 0 are yellow, those in between get intermediary values. Now, what i want is that those pixels having values above 0.8 get color according to colormap and rest become trasparent(that is they dont get any color), so that i can overlay this image with the another image of brain and identify high activity region. How do i do this ?

i have images like this fmri image

I want only the bright yellow part, so that i can overlay it with other image and get something like this. overlayed image
(source: psychcentral.com)

Edit:

I followed the method suggested by Jigg, but recently observed that the final image was rotated and inverted , any idea why ? final_image

Upvotes: 1

Views: 143

Answers (2)

Cape Code
Cape Code

Reputation: 3574

Here is another option, create a 3-layers array replicating your grayscale brain image (imagesc will scale each layer similarly resulting in equal r, g, and b values -> levels of gray).

GrayBckgnd = repmat(brain, [1, 1, 3]);
data = …

Then overlay it with the activity data:

imagesc(GrayBcknd);
hold on;
DataImg = imagesc(data);
set(DataImg, 'AlphaData', im2double(data>0.8));
colormap jet; % or any other colormap.

Upvotes: 3

Nicu Stiurca
Nicu Stiurca

Reputation: 8677

You can do this by plotting a surf(-ace) and passing in alpha values as follows.

brain = ... % background brain image
data = ...  % the data you are trying to overlay
imshow(brain);
hold on;
surf(zeros(size(data)), data, 'AlphaData', data > 0.8);
colormap(...); % whatever colormap you like

Have a look at the surface properties documentation for more options you can pass to surf.

Upvotes: 2

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