Hi Stelios,
To align your DICOM images using imregister in MATLAB, you can follow these steps:
- Use dicomread to load each of your DICOM images into MATLAB.
- Decide on a reference image or a set of reference coordinates that all other images will align to.
- If you have the differences in the y-coordinates for each image, you can store them in a text file. Then use fopen and fscanf to read the file.
- Apply imregister to each image using the reference image and the y-coordinate differences to align them. You might need to use an affine transformation to account for translation in the y-direction.
Below is a sample code to implement this in MATLAB:
% Assuming 'refImage' is your reference image loaded using dicomread
% 'yDifferences.txt' is a text file with y-coordinate differences for each image
fileID = fopen('yDifferences.txt', 'r');
yDiffs = fscanf(fileID, '%f');
fclose(fileID);
% Cell array to hold the aligned images
alignedImages = cell(1, 15);
for i = 1:15
movingImage = dicomread(sprintf('image%d.dcm', i));
yOffset = yDiffs(i);
% Define the transformation matrix including the y-coordinate difference
transform = [1 0 0; 0 1 yOffset; 0 0 1];
% Create the affine transformation object
tform = affinetform2d(transform);
% Use imregister to align the moving image to the reference image
% Specify the transformation type as 'translation'
alignedImages{i} = imregister(movingImage, refImage, 'translation', tform, 'OutputView', imref2d(size(refImage)));
end
Refer to the following documentation to learn more about these functions: fopen, fscanf, fclose, dicomread
- imregister: https://www.mathworks.com/help/images/ref/imregister.html
- imref2d: https://www.mathworks.com/help/images/ref/imref2d.html
- affinetform2d: https://www.mathworks.com/help/images/ref/affinetform2d.html
- dicomread: https://www.mathworks.com/help/images/ref/dicomread.html
- fopen: https://www.mathworks.com/help/matlab/ref/fopen.html
- fscanf: https://www.mathworks.com/help/matlab/ref/fscanf.html
- fclose: https://www.mathworks.com/help/matlab/ref/fclose.html
Hope this helps!