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

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{{documentation/{{documentation/version}}/module-section|Module Description}}
 
{{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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{{documentation/{{documentation/version}}/module-section|Methods}}
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{|
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|
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*Blue for Persistent curve
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**Slope of delayed curve > 0.2 | Type I|
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*Yellow for Plateau curve
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**-0.2 < Slope of delayed curve < 0.2 | Type II
 
*Red for Washout curve
 
*Red for Washout curve
 
**Slope of delayed curve < -0.2 | Type III
 
**Slope of delayed curve < -0.2 | Type III
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*Yellow for Plateau curve
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|[[Image:Graph.png|thumb|280px|Classification based on Delayed Curve]]
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**-0.2 < Slope of delayed curve < 0.2 | Type II
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|}
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*Blue for Persistent curve
 
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**Slope of delayed curve > 0.2 | Type I
 
  
 
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The GUI of the {{documentation/modulename}} module contains 5 sections:
 
The GUI of the {{documentation/modulename}} module contains 5 sections:
 
* '''Select DCE-MRI Volumes for Segmentation'''
 
* '''Select DCE-MRI Volumes for Segmentation'''
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** '''Pre-contrast Volume:'''
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** '''Pre-contrast Volume:''' Select the Pre-contrast Image
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** '''First Post-contrast Volume:'''
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** '''First Post-contrast Volume:''' Select the Post-contrast Image at the First time point
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** '''Second Post-contrast Volume:'''
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** '''Second Post-contrast Volume:''' (optional) Select the Post-contrast Image at the Second time point. This will only be used for the Interactive Charting feature.
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** '''Third Post-contrast Volume:'''
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** '''Third Post-contrast Volume:''' (optional) Select the Post-contrast Image at the Third time point. This will only be used for the Interactive Charting feature.
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** '''Fourth Post-contrast Volume:'''
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** '''Fourth Post-contrast Volume:''' Select the Post-contrast Image at the Fourth or Final time point.
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** '''Use Label Map as ROI:'''
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** '''Use Label Map as ROI:''' Enable this to select a custom label map input to restrict the segmentation analysis to a specific ROI.
 
* '''Select or Create Output OpenCAD Label Map'''
 
* '''Select or Create Output OpenCAD Label Map'''
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**'''Output OpenCAD Label Map:'''
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**'''Output OpenCAD Label Map:''' Create or select a label map volume node to represent the output of the segmentation.
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**'''Legend | |:'''
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**'''Legend | |:''' A reference for what type of curves are represented by the colors of the label map.
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**'''Display Volume Rendering:'''
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**'''Display Volume Rendering:''' Enable this to display a 3D Volume Rendering of the Label Map output in the 3D viewer after segmentation.
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**'''Calculate OpenCAD Label statistics:'''
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**'''Calculate OpenCAD Label statistics:''' Enable this to calculate and display statistics of all the First Post-contrast time point voxels highlighted in the output Label Map.
 
* '''Set Advanced Segmentation Parameters'''
 
* '''Set Advanced Segmentation Parameters'''
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**'''Minimum Threshold of Increase:'''
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**'''Minimum Threshold of Increase:''' The minimum percentage increase from pre-contrast to the first post-contrast time point for a voxel to be included in the segmentation output and classified.
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**'''Type I (Persistent) Curve Minimum Slope:'''
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**'''Type I (Persistent) Curve Minimum Slope:''' The minimum slope of the delayed curve for a voxel to be classified as having a Type I Persistent Curve.
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**'''Type 3 (Washout) Curve Maximum Slope:'''
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**'''Type 3 (Washout) Curve Maximum Slope:''' The maximum slope of the delayed curve for a voxel to be classified as having a Type III Washout Curve.
 
* '''OpenCAD Label Statistics'''
 
* '''OpenCAD Label Statistics'''
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**'''Statistics Table:'''
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**'''Statistics Table:''' Table displaying statistics of all First Post-contrast time point voxels highlighted by the Label Map and grouped according to curve type (Type I, II, and III). Logic is derived from the Label Statistics Module.
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**'''Chart Statistics:'''
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**'''Chart Statistics:''' Generates bar graph comparing all labels in the label map based on the statistical criterion specified in the menu.
 
***'''Menu Items:''' Volume, Curve Type, Voxel Count, Volume mm^3, Volume cc, Minimum Intensity, Maximum Intensity, Mean Intensity, Standard Deviation  
 
***'''Menu Items:''' Volume, Curve Type, Voxel Count, Volume mm^3, Volume cc, Minimum Intensity, Maximum Intensity, Mean Intensity, Standard Deviation  
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***'''Ignore Zero label:'''
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***'''Ignore Zero label:''' Ignore the unsegmented region of the First Post-contrast image when displaying bar graph.
 
* '''Interactive Charting Settings'''
 
* '''Interactive Charting Settings'''
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**'''Enable/Disable Interactive Charting:'''
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**'''Enable/Disable Interactive Charting:''' Toggle the calculation and display of the percent increase from baseline(pre-contrast intensity) of the voxel under the current mouse pointer location, at each time point. On the X-axis, 0.0 is Pre-contrast, 1.0 is First Post-contrast, ..., 4.0 is Final Post-contrast. Y-axis represents percentage change from baseline intensity.
−
|[[Image:OpenCAD-GUI.png|thumb|280px|{{documentation/modulename}} GUI ]]
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|[[Image:OpenCAD-GUI.png|thumb|340px|{{documentation/modulename}} GUI ]]
 
|}
 
|}
  

Revision as of 20:37, 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.


Methods

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

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: Select the Pre-contrast Image
    • First Post-contrast Volume: Select the Post-contrast Image at the First time point
    • Second Post-contrast Volume: (optional) Select the Post-contrast Image at the Second time point. This will only be used for the Interactive Charting feature.
    • Third Post-contrast Volume: (optional) Select the Post-contrast Image at the Third time point. This will only be used for the Interactive Charting feature.
    • Fourth Post-contrast Volume: Select the Post-contrast Image at the Fourth or Final time point.
    • Use Label Map as ROI: Enable this to select a custom label map input to restrict the segmentation analysis to a specific ROI.
  • Select or Create Output OpenCAD Label Map
    • Output OpenCAD Label Map: Create or select a label map volume node to represent the output of the segmentation.
    • Legend | |: A reference for what type of curves are represented by the colors of the label map.
    • Display Volume Rendering: Enable this to display a 3D Volume Rendering of the Label Map output in the 3D viewer after segmentation.
    • Calculate OpenCAD Label statistics: Enable this to calculate and display statistics of all the First Post-contrast time point voxels highlighted in the output Label Map.
  • Set Advanced Segmentation Parameters
    • Minimum Threshold of Increase: The minimum percentage increase from pre-contrast to the first post-contrast time point for a voxel to be included in the segmentation output and classified.
    • Type I (Persistent) Curve Minimum Slope: The minimum slope of the delayed curve for a voxel to be classified as having a Type I Persistent Curve.
    • Type 3 (Washout) Curve Maximum Slope: The maximum slope of the delayed curve for a voxel to be classified as having a Type III Washout Curve.
  • OpenCAD Label Statistics
    • Statistics Table: Table displaying statistics of all First Post-contrast time point voxels highlighted by the Label Map and grouped according to curve type (Type I, II, and III). Logic is derived from the Label Statistics Module.
    • Chart Statistics: Generates bar graph comparing all labels in the label map based on the statistical criterion specified in the menu.
      • Menu Items: Volume, Curve Type, Voxel Count, Volume mm^3, Volume cc, Minimum Intensity, Maximum Intensity, Mean Intensity, Standard Deviation
      • Ignore Zero label: Ignore the unsegmented region of the First Post-contrast image when displaying bar graph.
  • Interactive Charting Settings
    • Enable/Disable Interactive Charting: Toggle the calculation and display of the percent increase from baseline(pre-contrast intensity) of the voxel under the current mouse pointer location, at each time point. On the X-axis, 0.0 is Pre-contrast, 1.0 is First Post-contrast, ..., 4.0 is Final Post-contrast. Y-axis represents percentage change from baseline intensity.
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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