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

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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.  
 
**'''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:''' 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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**'''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 (default set at 75%).
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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 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 (default set at 0.2).
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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.
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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 (default set at -0.2).
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*'''Apply OpenCAD Segmentation:''' Perform Segmentation.
 
* '''OpenCAD Label Statistics'''
 
* '''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).
 
**'''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).
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*Select the pre-contrast volume
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*Select the first post-contrast volume
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*Select the second post-contrast volume
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*Select the third post-contrast volume
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*Select the fourth post-contrast volume
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*Create or select a label map volume node to represent the output of the segmentation
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*Click "Apply OpenCAD Segmentation"
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Revision as of 22:22, 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 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

Module Description

The OpenCAD is designed to segment tumors from DCE-MRI datasets which include pre-contrast image and post-contrast images at different time points. OpenCAD 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.


Methods

  • Only Voxels with a percent increase from pre-contrast to the first post-contrast time point greater than the Minimum Threshold of Increase (default = 75.00%) are considered for segmentation and classification.
  • Slope of delayed curve for each voxel is calculated as (Intensity at 4th time point - Intensity at 1st time point) / (Intensity at 1st time point).
  • Segmented voxels are individually classified by color according to slope of delayed curve:
    • Blue for Persistent curve
      • Slope of delayed curve > 0.2 (default) (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 (default) (Type III)
Classification based on Delayed Curve

Features

  • Segmentation - Generate Label Map delineating the regions of enhanced perfusion corresponding to the tumor with color representing the Type of Curve.
  • Interactive Charting - Calculates and displays 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 time points. The Y-axis represents percentage change from baseline/pre-contrast intensity.
  • Volume Rendering - A 3D Volume Rendering of the output Label Map is displayed in the 3D viewer after segmentation.
  • Label Statistics - Tabular display of statistics of all First Post-contrast time point voxels highlighted in the output Label Map and grouped according to curve type (Type I, II, and III). These statistics include: Voxel Count, Volume mm^3, Volume cc, Minimum Intensity, Maximum Intensity, Mean Intensity, Standard Deviation.

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)‎


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: Select the Post-contrast Image at the Second time point. This will only be used for the Interactive Charting feature.
    • Third Post-contrast Volume: 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 (default set at 75%).
    • 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 (default set at 0.2).
    • 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 (default set at -0.2).
  • Apply OpenCAD Segmentation: Perform Segmentation.
  • 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).
    • 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


Quick Instructions for Use

  • 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"

Module Output

OpenCAD Module Output

Similar Modules

N/A

References

N/A

Information for Developers

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


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