Difference between revisions of "Documentation/Nightly/Extensions/OpenCAD"

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{{documentation/{{documentation/version}}/module-section|Module Description}}
 
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The {{documentation/modulename}} is designed to segment tumors from DCE-MRI datasets which include 1 pre-contrast image and 2-4 post-contrast images at different time points. {{documentation/modulename}} uses blackbox methods to calculate the wash-in and wash-out slopes of the contrast dye based on voxel intensity values. The segmentation output is a Label Map with red, yellow, and blue colors respectively identifying washout, plateau, and persistent voxels.
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The {{documentation/modulename}} is designed to segment tumors from DCE-MRI datasets which include 1 pre-contrast image and 2-4 post-contrast images at different time points. {{documentation/modulename}} uses blackbox methods to calculate the wash-in and wash-out slopes of the contrast dye based on voxel intensity values. The segmentation output is a Label Map with red, yellow, and blue colors respectively identifying washout, plateau, and persistent voxels:
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*Red for Washout curve
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**Slope of delayed curve < -0.2 | Type III
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*Yellow for Plateau curve
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**-0.2 < Slope of delayed curve < 0.2 | Type II
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*Blue for Persistent curve
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**Slope of delayed curve > 0.2 | Type I
  
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Red for washout curve
 
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(Sd < -0.2 | Type III)
 
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Yellow for plateau curve
 
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(-0.2 < Sd < 0.2 | Type II)
 
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Blue for persistent curve
 
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(Sd > 0.2 | Type I)   
 
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{{documentation/{{documentation/version}}/module-section|Features}}
 
{{documentation/{{documentation/version}}/module-section|Features}}
 
*Interactive Charting -  
 
*Interactive Charting -  

Revision as of 19:20, 25 April 2014

Home < Documentation < Nightly < Extensions < OpenCAD


For the latest Slicer documentation, visit the read-the-docs.


OpenCAD.PNG

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...

Module Description

The OpenCAD is designed to segment tumors from DCE-MRI datasets which include 1 pre-contrast image and 2-4 post-contrast images at different time points. OpenCAD uses blackbox methods to calculate the wash-in and wash-out slopes of the contrast dye based on voxel intensity values. The segmentation output is a Label Map with red, yellow, and blue colors respectively identifying washout, plateau, and persistent voxels:

  • Red for Washout curve
    • Slope of delayed curve < -0.2 | Type III
  • Yellow for Plateau curve
    • -0.2 < Slope of delayed curve < 0.2 | Type II
  • Blue for Persistent curve
    • Slope of delayed curve > 0.2 | Type I

Features

  • Interactive Charting -
  • Volume Rendering -
  • Label Statistics -

Tutorials

OpenCAD Tutorial (pptx)‎

Data sets

Breast DCE-MRI Data Set 1 (zip file containing the nrrd volumes for the OpenCAD tutorial)‎

Breast DCE-MRI Data Set 2 (zip file containing additional test set of nrrd volumes)‎

Liver DCE-MRI Data Set 1 (zip file containing additional test set of nrrd volumes)‎

Panels and their use

The GUI of the OpenCAD module contains 5 sections:

  • Select DCE-MRI Volumes for Segmentation
    • Pre-contrast Volume:
    • First Post-contrast Volume:
    • Second Post-contrast Volume:
    • Third Post-contrast Volume:
    • Fourth Post-contrast Volume:
    • Use Label Map as ROI:
  • Select or Create Output OpenCAD Label Map
    • Output OpenCAD Label Map:
    • Legend | |:
    • Display Volume Rendering:
    • Calculate OpenCAD Label statistics:
  • Set Advanced Segmentation Parameters
    • Minimum Threshold of Increase:
    • Type I (Persistent) Curve Minimum Slope:
    • Type 3 (Washout) Curve Maximum Slope:
  • OpenCAD Label Statistics
    • Statistics Table:
    • Chart Statistics:
      • Menu Items: Volume, Curve Type, Voxel Count, Volume mm^3, Volume cc, Minimum Intensity, Maximum Intensity, Mean Intensity, Standard Deviation
      • Ignore Zero label:
  • Interactive Charting Settings
    • Enable/Disable Interactive Charting:
OpenCAD GUI


Similar Modules

N/A

References

N/A

Information for Developers

Work in progress
 Section under construction.



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


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