Image Processing trouble and masking. Is there a way to mask multiple images with a new mask every time in a loop?

I have a stack of dicom images(about 600) in a 4-D array and based on the image I want to create a mask and apply it to that image for segmentation of the image. I want to have this done in a loop so I dont have to manually do it for each image.Can this be done? I have converted all the images to bw so to create a mask. I have tried but I am getting a error. Below Is part of the code that I have been using and the error. I get the error at qline1 = imline(gca, [x1(i,3) y1(i,3) ; x1(i,2) y1(i,2)]);

Code:

     % Drawing of lines for quadrants

for i = prim:fin;
    BW4(:,:,:,i) = imshow(BW3(:,:,:,i));
    qline1(i,1) = imline(gca, [x1(3,1,i) y1(3,1,i) ; x1(2,1,i) y1(2,1,i)]);
    M1(i,1) = createMask(qline1(i,1), BW4(:,:,:,i));
    qline2(i,1) = imline(gca, [x2(3,1,i) y2(3,1,i) ; x2(2,1,i) y2(2,1,i)]);
    M2(i,1) = createMask(qline2(i,1), BW4(:,:,:,i));
end

BW3(M1) = 0;
BW3(M2) = 0;

% Defining Ellipse 

r{i} = {tot,1};
h{i} = {tot,1};

ratio = 0.8;
for i = prim:fin;
    r{i} = regionprops(BW3(:,:,:,i), 'MajorAxisLength');
    h{i} = regionprops(BW3(:,:,:,i), 'MinorAxisLength');
    R(i,1) = ((extractfield(r{i}, 'MajorAxisLength'))*ratio);
    H(i,1) = ((extractfield(h{i}, 'MinorAxisLength'))*ratio);
end

% Drawing of Ellipse

loc1 = zeros(tot,1);
loc2 = zeros(tot,1);

for i = prim:fin;
   loc1(i,1) = cent(i,1);
   loc2(i,1) = cent(i,2); 
end

lc1 = loc1 - (R/2);
lc2 = loc2 - (H/2);

for i = prim:fin;
    vbEllipse(i) =  imellipse(gca, [lc1(i,1) lc2(i,1) R(i,1) H(i,1)]);
    xy(i) = vbEllipse(i).getVertices();
    axesHandlesToChildObjects = findobj(gca, 'Type', 'line');
    if ~isempty(axesHandlesToChildObjects);
        delete(axesHandlesToChildObjects);
    end
    hold on;
    x(i,:) = xy(:,1,i);
    y(i,:) = xy(:,2,i);
    xCenter(i) = mean(x(i,:));
    yCenter(i) = mean(y(i,:));
    x(i,:) = x(i,:) - xCenter(i);
    y(i,:) = y(i,:) - yCenter(i);
    xy(:,:,i) = [x(i,:) y(i,:)];
    theta =  -rot(mid);
    rotationArray = [cosd(theta) -sind(theta); sind(theta) cosd(theta)];
    rotated_xy(:,:,i) = xy(:,:,i) * rotationArray;
    x(:,:,i) = rotated_xy(:,1,i) + xCenter(i);
    y(:,:,i) = rotated_xy(:,2,i) + yCenter(i);
    VBEllipse(:,:,i) = [x(:,:,i) y(:,:,i)];
    ellip(:,:,i) = impoly(gca, VBEllipse(:,:,i));
    M3(i) = ellip(:,:,i).createMask();
    BW3(M3) = 0;
    montage(BW3(:,:,:,i));
end

BW5(M3) = 1;
BW5(~M3) = 0;
BW5(M1) = 0;
BW5(M2) = 0;

Error:

Error using iptSetPointerBehavior>parseInputs (line 135)
First input argument, h, contains one or more invalid handles.

Error in iptSetPointerBehavior (line 119)
[h, pointerBehavior] = parseInputs(varargin{:});

Error in manageInteractivePlacement/resetChildPointerManagement (line
155)
              iptSetPointerBehavior(cached_pointer_behavior{k,1},...

Error in manageInteractivePlacement (line 106)
      resetChildPointerManagement();

Error in imline>imlineAPI (line 258)
    placement_aborted =
    manageInteractivePlacement(h_axes,h_group,@placeLine);

Error in imline (line 89)
            [h_group,draw_api] = imlineAPI(varargin{:});

Error in im_seg2 (line 155)
    qline1(i,1) = imline(gca, [x1(3,1,i) y1(3,1,i) ; x1(2,1,i)
    y1(2,1,i)]);

Thanks for the help

Matt

Answer 1

[Sean de Wolski]

Make sure you use the:

imshow(I,'parent',ax)

syntax to draw the image on the existing axes. Otherwise, a new axes is created which is why your imroi disappears (I believe).

[Matt]

ax is supposed to be the array of axes correct? But I'm not exactly sure how to create that array of axes from my array of images. Any advice?

Thank you for your time.

Matt

[Sean de Wolski]

ax is supposed to be the handle to the axes you want to plot to.