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Awaiting Approval

Materials and Equipment

  • Python 3.x and Pydicom package (need installation)
  • RSNA CTP software (included in the package)
  • Lookup tables: image_map.csv, personal_map.csv, see /pydicom/lookup_table/ for templates

Procedures

STEP 1: De-Identification using Pydicom Script

Preparation

  • Ensure lookup tables (image_map.csv, personal_map.csv) are available in the lookup directory.
  • Install dependencies: pip install pydicom

Execution

Run the de-identification script:

python pydicom_deid.py --map_table_dir <lookup_table_dir> --input_dir
<DICOM_input_root_dir> --output_dir <DICOM_output_root_dir> 2>&1 | tee logs.txt

Input Parameters

  • <lookup_table_dir>: Path to lookup CSVs
  • <DICOM_input_root_dir>: Input DICOM directory, organized by patient
  • <DICOM_output_root_dir>: Output directory for processed files

Output Subfolders:

  • dicom_processed/: De-identified files
  • dicom_unprocessed/: Files skipped due to missing PatientID/AccessionNumber or improper tag type

Metadata Shift Tags:

Refer to the manual for the complete list of DICOM data tags that will be shifted by a ptient-specific offset.

STEP 2: De-Identification using RSNA CTP Software

Installation

Launch the installer to Install RSNA CTP in the desired directory.

CTP-installer.jar

Configuration

  • Modify config.xml:
    • Update root and treeRoot paths
    • Adjust server settings (port, maxThreads) if needed
  • Copy scripts into/scripts directory:
    • DicomAnonymizer_chorus.scipt
    • DicomFilter.script

Pipeline Overview

  • ArchiveImportService: Reads and imports DICOM files
  • DicomFilter: Filters modalities (CR, DX, MG, CT, MR)
  • IDMap: Maps UID elements
  • DicomAnonymizer: De-identifies metadata
  • DirectoryStorageService: Saves output in organized folder structure

Execution

  • Launch CTP using Launcher.jar
  • In the UI, under the "General" tab, click Start to begin processing
  • Click Stop to halt the pipeline when needed

Output Folder Structure:

  • roots/: De-identified DICOM files and mapping files
  • quarantines/: Problematic files

Reference Materials

Can reference manual here