The problem you have is that when you have a greyscale image, each pixel has one intensity value. When you want RGB, you need a value for each of red, green and blue. So an image that in greyscale is 256x256x1 becomes 256x256x3. Or a stack of 10 slices which would be 256x256x10 needs to become 256x256x3x10.
I'm not intimately familiar with the functions you mention but whenever I've thresholded medical images, I do it 'manually'. Something like this:
input=imread('cameraman.tif'); % load example image to be your 'slice'
segmented=zeros(size(N)); % Initiates segmented copy of slice
segmented(input>128)=1; % if the input > 128, marks as 1
segmented(input>168)=2; % Second threshold level
imagesc(segmented)
That code should be translatable to 3D arrays too (except imagesc won't display them).
If you must use label2rgb then it would be fairly simple to write a for loop to iterate through the slices one at a time:
newimage=flipud(segmented); % make another slice as an example
img_stack=segmented;
img_stack(:,:,2)=newimage; % Stacks the slices
img_stackRGB=zeros(256, 256, 3, 2); % the 'RGB' stack is the same size as the original but adds an extra dimension for each RGB value
for i=1:size(img_stack,3)
img_stackRGB(:,:,:,i)=label2rgb(img_stack(:,:,i));
end
implay(img_stackRGB)
Caveat: I'm not familiar with label2rgb though and it's possible it would treat each slice differently. Looks OK at first glance.
implay appears to like a 4D array input in the format 256 x 256 x 3 x nSlices.
