(MATLAB) 3D CT image reconstruction by 2D slices

Question

I have 2D slices of a 3D CT image. They are in DICOM format and there are 250 of them. I want to reconstruct the 3D image with MATLAB. How can I do this in a loop?

• I am using MATLAB R2010b on my Ubuntu system.
• Images' location is: /home/amadeus/Desktop/images

• Images are named:

   IM-0001-0001.dcm IM-0001-0002.dcm IM-0001-0003.dcm ... IM-0001-0250.dcm 

Answer 1

Apparantly there is a function just for reading DICOM files: dicomread , I suggest using that to load the images and then store them in a 3D matrix. sprintf can be used to construct the filenames of the images (use %04d to generate four-digit number with leading zeros).

Assuming all images are aligned and have same size:

N = 250;
img_dir = '/home/amadeus/Desktop/images'

% read the first image separately just to get the size
strfile = 'IM-0001-0001.dcm';
img = dicomread(fullfile(img_dir, strfile));
siz_img = size(img);

% create result matrix:
ct3d = NaN([siz_img N]);
ct3d(:,:,1) = img;    

% load all the remaining images and put them in the matrix
for ii=2:N
    strfile = sprintf('IM-0001-%04d.dcm',ii);
    ct3d(:,:,ii)= dicomread(fullfile(img_dir, strfile));
end

edit: This assumes image are grayscale (2d). In case they're full colour (width x height x 3), you should add another colon operator in the assignment to ct3d .