How to show the image slice from the below example?

Hello, I want to show the image slice from the below example, where CT and SPECT both are image array with the same width, size and spacing.

% This is a part of the code
% Visualize the CT and SPECT together
for m = 1:199                      
    CT_img = new_CT(:,:,m);
    SPECT_img = SPECT(:,:,m);
    final_img = imfuse(CT_img, SPECT_img);
    % Visualize CT and SPECT together
    imshow(final_img, [-800 1000]);
end
% Now, I want to see the overlapped slices one by one, so I want somethig like:
show_20th_slice =  imshow(final_img(:,:,20)) %...>> but this says: "Index in position 3 exceeds array bounds (must not exceed 3)."

How can I do this?

Answer 1

[Walter Roberson]

% This is a part of the code
% Visualize the CT and SPECT together
for m = 1:199                      
    CT_img = new_CT(:,:,m);
    SPECT_img = SPECT(:,:,m);
    final_img(:,:,:,m) = imfuse(CT_img, SPECT_img);
    % Visualize CT and SPECT together
    imshow(final_img(:,:,:,m), [-800 1000]);
end
% Now, I want to see the overlapped slices one by one, so I want somethig like:
show_20th_slice =  imshow(final_img(:,:,:,20))

I am not sure at the moment why you are getting back color images instead of grayscale, but your error message would have been different if you were getting back grayscale.

[blues]

Thank you for the reply but I am not yet sure why I am getting the following:

Index in position 3 exceeds array bounds (must not exceed 3).

Error in method (line 64)
show_20th_slice = imshow(final_img(:,:,20));

Any help will be appreciated.

[Walter Roberson]

You are getting it because you did not copy my code properly. Notice I had

show_20th_slice =  imshow(final_img(:,:,:,20))
                                    1 2 3

but you are using

show_20th_slice = imshow(final_img(:,:,20));
                                   1 2

For reasons I do not know at the moment, each of your imfuse() calls is returning a 3D (RGB) image -- an array that is something by something by 3. The code I wrote pushes all of those 3D (RGB) images together along the 4th dimension, giving you something x something x 3 x 199. You then tried to index that third dimension at 20 instead of indexing the 4th dimension at 20.

[blues]

One additional thing: When I use imfuse the colormap of CT image becomes green and SPECT becomes pink. Is there a way to change the colormap to grey and hot or jet? See attached.

Thank you, Walter, for your help. Have a great weekened.

[Walter Roberson]

im1 = imread('cameraman.tif');
im2 = rgb2gray(imread('flamingos.jpg'));
im2 = imresize(im2, size(im1));
fused_by_function = imfuse(im1, im2);
fused_manually = cat(3, im2, im1, im2);
subplot(2,1,1);
imshow(fused_by_function);
title('imfuse()')
subplot(2,1,2)
imshow(fused_manually);
title('manual fuse')

max(abs(double(fused_by_function(:)) - double(fused_manually(:))))

ans = 12

We can see from this that imfuse(A,B) is effectively the same as putting B into the red and blue panes and A into the green pane.

And that in turn tells us that using a different colormap would not be easy, because it is not really "calculating" a color for each pixel, and is more "just letting it happen". So you would need a quite different approach.

Perhaps something like:

alpha = 0.7;
cmap1 = gray(256);
cmap2 = jet(256);
im1rgb = ind2rgb(im1, cmap1);
im2rgb = ind2rgb(im2, cmap2);
blended = alpha * im1rgb + (1-alpha) * im2rgb;
figure()
subplot(3,1,1)
imshow(im1rgb); title('image1 recolored');
subplot(3,1,2);
imshow(im2rgb); title('image2 recolored');
subplot(3,1,3);
imshow(blended); title('blended')