How do I save a series of dicom-files (slices from a CT scan) to one single dicom file?

As the title says, how do I save a series of dicom-files (slices from a CT scan) to one single dicom file? It would also work if it's saved as a nrrd-file.

Thanks!

[Abir AFFANE]

Hi i need this too if you have find the anser plz!!

thanks

Answer 1

[Gautam]

Hello, Jesper

You can follow these steps to combine a series of individual DICOM files

1. Use "dicomread" to load each DICOM slice into MATLAB.
2. Combine the individual slices into a 3D volume.
3. Use "dicominfo" from one of the slices to obtain metadata, which will help in writing the stacked file.
4. Use "dicomwrite" to save the 3D volume as a single DICOM file.

dicomFiles = dir(fullfile(dicomDir, '*.dcm')); 

% Read the first DICOM file to get the dimensions and metadata
firstFile = fullfile(dicomDir, dicomFiles(1).name);
firstSlice = dicomread(firstFile);
info = dicominfo(firstFile);

% Preallocate a 3D array to store the volume
numSlices = length(dicomFiles);
volumeData = zeros([size(firstSlice), numSlices], class(firstSlice));

% Read each slice and store it in the volume
for sliceIdx = 1:numSlices
    sliceFile = fullfile(dicomDir, dicomFiles(sliceIdx).name);
    volumeData(:, :, sliceIdx) = dicomread(sliceFile);
end

% Update metadata for the stacked DICOM file
info.NumberOfFrames = numSlices; % Set the number of frames to the number of slices

% Specify the output filename for the stacked DICOM file
stackedFileName = 'stacked_dicom.dcm';

% Write the 3D volume to a single DICOM file
dicomwrite(volumeData, stackedFileName, info, 'CreateMode', 'Copy');