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?

Many Thanks.

Answer 1

[Image Analyst]

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

[Cameron Harris]

Thanks for this, I had figured I could just write them out to a new format if needed. Ideally I wanted to keep the DICOM format in my network, but to be entirely honest I am not sure how much changing the format would really affect my transfer learning results, provided lossless/minimal compression in the conversion.

Happy to accept this answer for now though as PNG seems to be an easier format to work with for transfer learning for a beginner.

[ahmed adam]

I have the same problem now , did you change the format to PNG or continue as dicom images ?

[Cameron Harris]

I continued using PNGs as I also wanted to use imagedatastore's built in image augmentation.

Answer 2

[Khalid]

I have faced a similar issue in wich I had to create another readDatastoreImage function. You might solved it this way:

Create a copy of the readDatastoreImage function within the imageDatastore function and give it a different name, for example: readDicomDatastoreImage

Then change the imread(filename) function wihin the one you copyed to dicomread(filename)

finaly, use it with the imageDatastore function this way:

imds = imageDatastore(imageDir, 'FileExtensions','.dcm','ReadFcn',@readDicomDatastoreImage);

Hope this can help

Khalid

[shivan artosh]

hello sir

could you please write complete the code for reading a .dicom files

thanks

[Khalid Babutain]

1. write in your main code:

imds = imageDatastore('DataSet', ...
    'IncludeSubfolders',true, 'LabelSource','foldernames', ... % this for labeling by folder names
    'FileExtensions','.dcm','ReadFcn',@readDicomDatastoreImage);

2. create (readDicomDatastoreImage) function that include:

function I = readDicomDatastoreImage(filename)

    onState = warning('off', 'backtrace');
    c = onCleanup(@() warning(onState));
    I = dicomread(filename);

in this way, each time you read an image from your (imds) it will be read using (readDicomDatastoreImage) function

Hope this is clear

Khalid

[shivan artosh]

thank you so much sir it is really helpful