How to use imregister

Hi lovely members of Mathworks. I am so grateful for your help so far. Need more help since I am kind new to image processing with Matlab. I want to use imregister to properly align misaligned dicom images. I have 15 dicom images with differences on their y coordinator. I need to imregister them to a proper reference x,y value. The differences of the y coordinator occur are mm +-.

Any idea? Can I have a txt file to determine for each image the difference on its y value and have Matlab read this txt?

Answer 1

[Jaynik]

Hi Stelios,

To align your DICOM images using imregister in MATLAB, you can follow these steps:

1. Use dicomread to load each of your DICOM images into MATLAB.
2. Decide on a reference image or a set of reference coordinates that all other images will align to.
3. 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.
4. 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!