Drawing a single ROI and then using it on multiple images in 3D matrix

Hello everyone,

I am relatively new to matlab, and I am currently working on a medical image segmentation of a multiple images stored in a 3D matrix. I was trying to draw a ROI on a first slice and then use that ROI for all other slices to implement segmentation algorithm on them. But, after multiple tries I did not come up with a solution. The best what I was able to do is to draw ROI on EVERY single slice but that is taking to much time. Is there any easier way I could do this? Perhaps there's a way to automate or semi-automate this process so I don't have to draw ROI at each slice? Somehow I think that there is a simple solution to this, but I just can not find it.

CT is my 3D matrix that contains images. My code for drawing ROI is:

for i = 1:size(CT,3)
  figure; imshow(CT (:,:,i), []);
  hFH = imfreehand();
  binaryImage(:,:,i) = hFH.createMask;
  xy = hFH.getPosition();
  blackMaskedImage =CT;
  blackMaskedImage(~binaryImage) = 1;
  setPositionConstraintFcn(hFH,xy);
  close ();
end

Thanks in advance.

Answer 1

[Image Analyst]

Maybe something like this (untested):

hFig = figure;  % Bring up a new figure.
for k = 1 : size(CT, 3)
  subplot(1, 3, 1);
  cla;
  imshow(CT(:,:,i), []);
  drawnow;
  if k == 1
    hFH = imfreehand();
    binaryImage = hFH.createMask;
    subplot(1, 3, 2);
    cla;
    imshow(binaryImage);
    % Enlarge figure to full screen.
    set(gcf, 'Units', 'Normalized', 'OuterPosition', [0 0 1 1]);
    drawnow;
    % xy = hFH.getPosition();  % Unused
  end
  blackMaskedImage = CT(:,:,i) .* uint8(binaryImage);
  subplot(1, 3, 3);
  cla;
  imshow(blackMaskedImage);
  drawnow;
end

Answer 2

[Mario]

I tested it and it is displays this error:

Error using .*

Integers can only be combined with integers of the same class, or scalar doubles.

Error in segmentation (line 51)

blackMaskedImage = CT(:,:,i) .* uint8(binaryImage); %when I put here binaryImage(:,:,i) it is doing something

When I put "binaryImage(:,:,i)" it's doing something on all images, but I do not know what is it doing. And also I need binaryImage and blackMaskedImage to be also 3D matrix since that is where I need those ROIs to be stored because I will be using that ROI to segment my images.

I hope I explained it for you to understand.

Thanks!