Documentation/Nightly/Extensions/OpenCAD

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Introduction and Acknowledgements

This work is supported by NA-MIC, NCIGT, and the Slicer Community. Author: Vivek Narayan, Jayender Jagadeesan Contact: Jayender Jagadeesan <email> jayender@bwh.harvard.edu</email>

NA-MIC   NCIGT   SPL   This project is supported by P41 RR019703/RR/NCRR NIH HHS/United States, P01 CA067165/CA/NCI NIH HHS/United States and P41 EB015898/EB/NIBIB NIH HHS/United States

Modules

• SegmentCAD: Tumor Segmentation from DCE-MRI
• HeterogeneityCAD: Analyze Heterogeneity of Tumor Images and their Parameter Maps using various metrics)

Extension Description

• The SegmentCAD module is designed to segment tumors from DCE-MRI datasets which include a pre-contrast image and post-contrast images at different time points.
  • SegmentCAD uses blackbox methods to calculate the wash-in and wash-out slopes from the time-intensity curves.
  • The segmentation output is a Label Map with red, yellow, and blue colors respectively identifying washout (Type III), plateau (Type II), and persistent (Type I) voxels.
• The HeterogeneityCAD module is an extensible, image feature extraction toolbox primarily to quantify the heterogeneity of tumor images and their label maps. Metrics have been implemented from a variety of feature classes including:
  • First-Order/Histogram statistics
  • Morphology/Shape measures and Geometrical (4D Extrusion) measures
  • Renyi/Fractal dimensions
  • Texture features computed from Gray-Level Co-occurrence Matrices (GLCM) and from Gray-Level Run Length matrices (GLRL)

Tutorials

• SegmentCAD
  • SegmentCAD Tutorial (pptx)‎

Data sets

• SegmentCAD
  • Breast DCE-MRI Data Set 1 (zip file containing the nrrd volumes for the tutorial)‎
  • Breast DCE-MRI Data Set 2 (zip file containing additional test set of nrrd volumes)‎

Quick Instructions for Use

• SegmentCAD (Click link for detailed description)
  • Select the pre-contrast volume
  • Select the first post-contrast volume
  • Select the second post-contrast volume
  • Select the third post-contrast volume
  • Select the fourth post-contrast volume
  • Create or select a label map volume node to represent the output of the segmentation
  • Click "Apply OpenCAD Segmentation"

Similar Modules

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References

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Information for Developers

Source code: https://github.com/vnarayan13/Slicer-OpenCAD