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 pre-contrast image and post-contrast images at different time points. {{documentation/modulename}} 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.
  
  
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*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.
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*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).
 
*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:
 
*Segmented voxels are individually classified by color according to slope of delayed curve:
 
**Blue for Persistent curve
 
**Blue for Persistent curve
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***Slope of delayed curve > 0.2 (default) | Type I|
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***Slope of delayed curve > 0.2 (default) (Type I)
 
**Yellow for Plateau curve
 
**Yellow for Plateau curve
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***-0.2 < Slope of delayed curve < 0.2 | Type II
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***-0.2 < Slope of delayed curve < 0.2 (Type II)
 
**Red for Washout curve
 
**Red for Washout curve
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***Slope of delayed curve < -0.2 (default) | Type III
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***Slope of delayed curve < -0.2 (default) (Type III)
 
|[[Image:Graph.png|thumb|280px|Classification based on Delayed Curve]]
 
|[[Image:Graph.png|thumb|280px|Classification based on Delayed Curve]]
 
|}
 
|}
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{{documentation/{{documentation/version}}/module-section|Features}}
 
{{documentation/{{documentation/version}}/module-section|Features}}
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*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.  
 
*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.  
 
*Volume Rendering - A 3D Volume Rendering of the output Label Map is displayed in the 3D viewer after segmentation.  
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*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. Logic is derived from the Label Statistics Module.  
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*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.
  
 
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[[Media:Breast-data2.zip|Breast DCE-MRI Data Set 2 (zip file containing additional test set of nrrd volumes)]]‎
 
[[Media:Breast-data2.zip|Breast DCE-MRI Data Set 2 (zip file containing additional test set of nrrd volumes)]]‎
  
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[[Media:Liver-data1.zip|Liver DCE-MRI Data Set 1 (zip file containing additional test set of nrrd volumes)]]‎
 
  
 
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** '''Pre-contrast Volume:''' Select the Pre-contrast Image
 
** '''Pre-contrast Volume:''' Select the Pre-contrast Image
 
** '''First Post-contrast Volume:''' Select the Post-contrast Image at the First time point
 
** '''First Post-contrast Volume:''' Select the Post-contrast Image at the First time point
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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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** '''Second Post-contrast Volume:''' 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:''' (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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** '''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.
 
** '''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.
 
** '''Use Label Map as ROI:''' Enable this to select a custom label map input to restrict the segmentation analysis to a specific ROI.
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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.
 
**'''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:''' 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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**'''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.  
 
**'''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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{{documentation/{{documentation/version}}/module-section|Information for Developers}}
 
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{{documentation/{{documentation/version}}/module-developerinfo}}
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Revision as of 21:46, 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.
    • 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).
    • 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

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


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