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NA-MIC Project Weeks

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Updates to Batch Anonymizer

SlicerBatchAnonymize is a Slicer Extension that strips off metadata from dicom files, and converts them to various file formats. The work during project week will involve investigating and creating prototypes for defacing in medical images, support and single file dicom export.

Key Investigators

Project Description

The very first step to make any medical data available to research community is it’s anonymization. SlicerBatchAnonymize is a 3D Slicer extension to anonymize a batch of DICOM images by stripping most of metadata (image information stays intact). The tool currently provies a user-friendly UI, supports export to several popular research formats including DICOM series, and also generates a crosswalk files for future uses.


  1. Support export to a single DICOM file.
  2. Investiage existing defacing methods
  3. Come up with a prototype for defacing of CBCT images.

Approach and Plan

  1. Use either DICOMlib or pydicom for export to DICOM as a single file.
  2. Get guidance from community on existing defacing methods, and lookup existing tools/literature available for defacing
  3. Decide and implement a prototype for defacing of CBCT images

Progress and Next Steps

  1. During this project week we implemented a functionality that will call AMASS extension. This CBCT segmentation extension will return a mask for the skin ROI. Using this mask we zero out those voxels from the CBCT scan and save the resulting dicom without metadata and defaced.


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Background and References

  1. Source code in Github repository
  2. AMASS extension