Cameron-Harris asked . 2021-06-03

How can I label DICOM images for classification based on folder name

I want to carry out transfer learning using AlexNet for a set of 128x128 DICOM images. It looks like on of the most efficient methods of storing and labeling images is using imageDatastore, however I don't think this supports DICOM formats, I can create the store with no errors using:

 images = imageDatastore(fullfile(pwd,'Project_Segmentations'),...
    'IncludeSubfolders',true,'FileExtensions','.dcm',...
    'LabelSource','foldernames');

This correctly labels the DICOMs based on the name of the folder they are in, however, when I try to use this data for training I'm met with the error:

Error using matlab.io.datastore.ImageDatastore/readimage (line 32)
Error using ReadFcn @readDatastoreImage function handle for file

Which makes sense given imread doesn't support DICOM images.

Ideally I want to keep the DICOM file format, is there anyway I can achieve this data labeling for DICOM images?

deep learning , matlab , programming , simulink

Expert Answer

Kshitij Singh answered . 2024-12-21 02:05:00

Perhaps write a utility that reads in all the images and stores them out in PNG format.

for k = 1 : numImages
    thisImage = dicomread(....
    outputFileName = strrep(lower(inputFileName), '.dcm', '.png');
    imwrite(thisImage, outputFileName);
end

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