Altering CT Volume voxel values in Matlab

I am trying to alter some voxel values in Matlab.

I am using the following code:

for p=1:100
    Vol(Vol(:,:,p) > 0) = 65535; %altering voxel values in the volume to 65535 if value > 0. 
end

Unfortunately, I find all the values being altered, as if the condition is not working, although if i write Vol(Vol(:,:,1)>0)= 65535 immediately in the command line it works perfectly.

Any clue where the error is??

Answer 1

[Ben11]

It looks like when you use this line:

    Vol(Vol(:,:,p) > 0) = 65535

you are in fact referring to a 2D matrix corresponding to a single channel from an image instead of a 3-channel image from your volume. I think it would save you trouble if you used this:

Vol(Vol > 0) = 65535;

instead of your for-loop, since you would then replace all the pixel values greater than 0 with 65535.

EDIT:

I just saw that you asked this question on Stack Overflow, good idea by the way, and that Ray provided a very thorough explanation! Anyhow I hope it is clearer for you now :)

[Noha Asas]

Ohhh...it worked :). Many thanks :).

But still what I should do if I want to use same syntax for thresholding image by image in a volume ?? It will still give the same false response.

and still I don't understand why it worked when I write the index explicitly: Vol(Vol(:,:,1)>0)=65535; outside the loop and it doesn't work inside the loop.

Thanks for the help, appreciate it :).

[Ben11]

Great! If the answer helped you please mark it as accepted :)

If you need to threshold every image individually you can create a matrix containing an 'extra' dimension, so that you can access both the channel AND the image of your choice while looping in the volume. For instance:

% First you might want to initialize the array. Here I declare 'uint16' as the type of data.

Vol = zeros(ImageHeight,ImageWidth,NumberChannels,NumberImages,'uint16') % NumberChannels is probably 3.

for p = 1:100

% Add you code
Vol(Vol(:,:,ChannelofInterest,p) > 0) = 65535; 

end

Note that if you want to threshold on all channels you can use rgb2gray(YourImage).

Hope that helps! If not please ask for more details.

[Noha Asas]

Many thanks again....that's very helpful :). Sorry for late response....was away from internet connection.

[Ben11]

No problem! Glad I could help :)