Convert a cell array containing binary images to a 3D array and build 3D volume from the 3D array

I have 20 DICOM images, from these images I have extracted region of interest using Activecontour function. The extracted ROI of all 20 images(binary images) are stored in a cell array and I need to stack these images to build a 3D volume.

    clc
    close all
    imtool close all

    %%Read N images
    % Read images
    [filename, pathname, filterindex] = uigetfile( ...
    {  '*.dcm','DICOM IMages (*.dcm)'; ...
    '*.*',  'All Files (*.*)'}, ...
    'Pick a file', ...
    'MultiSelect', 'on');
    % Get number of images
    files_length = length(filename);
    % figure,montage(filename,'displayRange',[]);
    for q = 1:files_length
     I = dicomread(filename{q});

     if q == 1
       imshow(I,[]);
       [x,y]=(ginput(1)); 
       mask = zeros(size(I));
       mask(y-50:y+50,x-50:x+50)=1;
     end

     % Region growing using acclc

     seg = activecontour(I,mask,'chan-vese');
     seg_gray{q} = ind2rgb(seg, lines(20));
    end
    save('newmatFile.mat','seg_gray');

   %%Reconstruction:

   load newmatFile
   seg_gray = squeeze(seg_gray);
   [a,b,z,seg_gray] = subvolume(seg_gray,[nan,nan,nan,nan,nan,nan]);
   p1 = patch(isosurface(a,b,z,seg_gray, 5),...
     'FaceColor','red','EdgeColor','none');
   isonormals(a,b,z,seg_gray,p1);
   p2 = patch(isocaps(a,b,z,seg_gray, 5),...
     'FaceColor','interp','EdgeColor','none');
   view(3); axis tight; daspect([1,1,.4])
   colormap(gray(100))
   camlight right; camlight left; lighting gouraud

[Amith Kamath]

Nitin: I see that you've submitted another related question here http://www.mathworks.com/matlabcentral/answers/221954-build-a-3d-volume-using-using-processed-roi-extracted-slices-but-i-am-unable-to-do-it-can-anybody, and you mention that you encounter an error. It would be nice if you could share the error message you see as well. Also, from a quick glance through your code here, it seems like you are creating a cell array

seg_gray

Is there a particular reason why this is a cell array? Why not create a 3D matrix, like

seg_gray(:,:,q)

?

[NITIN V P]

Images may be of different size

Answer 1

[Image Analyst]

Don't use a cell array. Get the gray image by masking then insert into a 3D array

seg_gray(:, :, q) = uint8(seg) .* I;

[NITIN V P]

There is an error Error using .* Integers can only be combined with integers of the same class, or scalar doubles.

[Image Analyst]

Nitin V P's "Answer" moved here:

Convert all the extracted images to same class(int)

seg{q} = im2int16(seg1);

[Image Analyst]

I and seg have to be the same type of integer. Cast one of them to match the other and it should be okay. Maybe you have to use uint16 instead of uint8.