How can I label DICOM images for classification based on folder name
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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.
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Image Analyst
2018-3-10
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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ahmed adam
2018-5-14
I have the same problem now , did you change the format to PNG or continue as dicom images ?
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Khalid
2019-1-19
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
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Khalid Babutain
2020-3-26
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
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