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PyRadiomics Models

Key Investigators

1 Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA.
2 Department of Radiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA.
3 Department of Radiology, Netherlands Cancer Institute, Amsterdam, The Netherlands.
4GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands.
5 Kitware, Inc.
6 Isomics, Inc.

Project Description

Objective

  1. Develop framework to easily apply and share radiomic models using PyRadiomics and it’s 3D slicer extension SlicerRadiomics.
  2. In addition to the current lesion-based extraction, add a voxel-based extraction.
  3. Update the SlicerRadiomics extension to accept the PyRadiomics parameter files.

Approach and Plan

Objective #1

  1. Develop configuration file to store a radiomic model.
  2. Add a pyradiomics module or a separate github python repository that can read/write the config file and use radiomics to apply it.
  3. Add commandline interface to use new functionality.
  4. Develop new Slicer module to interface with this new pyradiomics module to make this new functionality directly available in slicer.

Objective #2

  1. Update radiomics base module to allow voxel-based extraction
  2. Add new feature extractor module to provide interface for voxel-based extraction
  3. Add Commandline interface for voxel based extraction
  4. Add examples (settings, usage) to show new functionality

Objective #3

  1. Update the SlicerRadiomics widget to have a toggle button for manual customization (UI elements in Slicer) or parameter file customization (path line edit to select file)
  2. Update the SlicerRadiomics logic to allow an extraction using the parameter file customization
  3. Add a test to SlicerRadiomicsTest to test this new functionality

Progress and Next Steps

Objective #1

Related PR

TODO:

Objective #2

Related PR

TODO:

Objective #3

Related PR

Illustrations

Objective #2

The input for the voxel based extraction

The result of the voxel based extraction (Original GLCM Entropy)

Objective #3

Slicer Radiomics new layout 1 (manual customization)

Slicer Radiomics new layout 2 (parameter file customization)

Background and References

Other related references: