Dicom Processing Tool

• This builds ontop of the original Niffler toool the group used
• Code is reduced/modified so that extraction of PNGS/Tomo/CT/MRI are in a single interface with up todate dependenceis

Installation

• Have an enviroment with python 3.10 installed

    cd /path/To/Repo
    python3 -m pip install -r ./reqs.txt 
    python3 -m pip install -e .     

Running Extraction

    python3 -m A3IDicomTools.DicomExtract --ConfigPath ./YourConfig.json

{
 "DICOMHome": "PathToDicomFolders",
 "OutputDirectory":"DirectoryToSaveOutputs",
 "SaveBatchSize": 20,
 "SavePNGs": true,
 "PublicHeadersOnly": true,
 "SpecificHeadersOnly": false,
 "NumProcesses": 10,
 "ApplyVOILUT": true,
 "Extractor":"TOMO"
}

Parameters Explained

• SaveBatchSize: Sometimes dicom tags are excessively large. As a workaround we save batches of metadata with sizes (100-200) if using privateTages
• SavePngs: Save the images. If set to False no images are saved
• PublicHeadersOnly: If set to false we will also output Private dicom tags. 99.9% of the time private tags are not used
• SpecificHeadersOnly: DONOT modify
• NumProcesses: Number of processes to use for parallel extraction. Warning more does not always mean better.
• ApplyVoiLut: Apply Windowing operation only used for mammograms and x-ray images
• Extractor: Type of extractor to use Currently support
  • "PNG" for Mammograms,X-ray,RetinalFundus any Modality that is stored as 2D
  • "TOMO" Process multiframe Tomography images. Only processes images with specific SOPClassUIDs.