DICOM Patcher

This module fixes common errors in DICOM files to make them possible to import them into Slicer.

DICOM is a large and complex standard and device manufacturers and third-party software deveopers often make mistakes in their implementation. DICOM patcher module can recognize some common mistakes and certain known device-specific mistakes and create a modified copy of the DICOM files.

Panels and their use

  • Input DICOM directory: folder containing the original, invalid DICOM files
  • Output DICOM directory: folder that will contain the new, corrected DICOM files, typically this is a new, empty folder that is not a subfolder of the input DICOM directory
  • Normalize file names: Replace file and folder names with automatically generated names. Fixes errors caused by file path containing special characters or being too long.
  • Force same patient name and ID in each directory: Generate patient name and ID from the first file in a directory and force all other files in the same directory to have the same patient name and ID. Enable this option if a separate patient directory is created for each patched file.
  • Generate missing patient/study/series IDs: Generate missing patient, study, series IDs. It is assumed that all files in a directory belong to the same series. Fixes error caused by too aggressive anonymization or incorrect DICOM image converters.
  • Generate slice position for multi-frame volumes: Generate ‘image position sequence’ for multi-frame files that only have ‘SliceThickness’ field. Fixes error in Dolphin 3D CBCT scanners.
  • Partially anonymize: If checked, then some patient identifiable information will be removed from the patched DICOM files. There are many fields that can identify a patient, this function does not remove all of them.
  • Patch: create a fixed up copy of input files in the output folder
  • Import: import fixed up files into Slicer DICOM database
  • Go to DICOM module: switches to DICOM module, to see the imported DICOM files in the DICOM browser

Tutorial

  • If you have already attempted to import files from the input folder then delete that from the Slicer DICOM database: go to DICOM module, right-click on the imported patient, and click Delete.
  • Go to DICOM Patcher module (in Utilities category)
  • Select input DICOM directory
  • Select a new, empty folder as Output DICOM directory
  • Click checkboxes of each fix operations that must be performed
  • Click Patch button to create a fixed up copy of input files in the output folder
  • Click Import button to import fixed up files into Slicer DICOM database
  • Click Go to DICOM module to see the imported DICOM files in the DICOM browser

Information for Developers

This is a Python scripted module. Source code is available at https://github.com/Slicer/Slicer/blob/master/Modules/Scripted/DICOMPatcher/DICOMPatcher.py.

Contributors

  • Contributors: Andras Lasso (PerkLab, Queen’s University)

Acknowledgements

This module is partly funded by an Applied Cancer Research Unit of Cancer Care Ontario with funds provided by the Ministry of Health and Long-Term Care and the Ontario Consortium for Adaptive Interventions in Radiation Oncology (OCAIRO) to provide free, open-source toolset for radiotherapy and related image-guided interventions.

Laboratory for Percutaneous Surgery, Queen's University