Difference between revisions of "Documentation/Nightly/Modules/HeterogeneityCAD"

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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}} module 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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The {{documentation/modulename}} module is an image feature extraction toolbox primarily to quantify the heterogeneity of tumor images and their label maps.
  
  
 
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{{documentation/{{documentation/version}}/module-section|Methods}}
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{{documentation/{{documentation/version}}/module-section|Image Features and Metrics}}
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{|
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*First-Order and Distribution Statistics
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|
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**Data Node
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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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**Voxel Count
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*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).
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**Energy
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*Segmented voxels are individually classified by color according to slope of delayed curve:
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**Entropy 
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**Blue for Persistent curve
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**Minimum Intensity
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***Slope of delayed curve > 0.2 (default) (Type I)
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**Maximum Intensity  
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**Yellow for Plateau curve
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**Mean Intensity  
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***-0.2 < Slope of delayed curve < 0.2 (Type II)
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**Median Intensity  
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**Red for Washout curve
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**Range
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***Slope of delayed curve < -0.2 (default) (Type III)
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**Mean Deviation
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|[[Image:Graph.png|thumb|280px|Classification based on Delayed Curve]]
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**Root Mean Square
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|}
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**Standard Deviation
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**Skewness
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**Kurtosis
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**Variance
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**Uniformity
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*Shape and Morphology Metrics
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**Volume mm^3
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**Volume cc
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**Surface Area mm^2
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**Surface:Volume Ratio
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**Compactness 1
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**Compactness 2
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**Maximum 3D Diameter
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**Spherical Disproportion
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**Sphericity
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*Renyi Dimensions   
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**Box-Counting Dimension
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**Information Dimension
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**Correlation Dimension
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*Geometrical Measures
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**Extruded Surface Area
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**Extruded Volume
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**Extruded Surface:Volume Ratio
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**Extruded Box-Dimension
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*Texture: Gray-Level Co-occurrence Matrix (GLCM)
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**Autocorrelation
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**Cluster Prominence
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**Cluster Shade
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**Cluster Tendency
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**Contrast
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**Correlation
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**Difference Entropy
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**Dissimilarity
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**Energy (GLCM)  
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**Entropy(H)
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**Homogeneity 1
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**Homogeneity 2  
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**Informational Measure of Correlation 1 (IMC1)  
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**Informational Measure of Correlation 2 (IMC2)
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**Inverse Difference Moment Normalized (IDMN)  
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**Inverse Difference Normalized (IDN)  
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**Inverse Variance
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**Maximum Probability
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**Sum Average
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**Sum Entropy
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**Sum Variance
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**Variance (GLCM)
  
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*Texture: Gray-Level Run Length Matrix (GLRL)
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{{documentation/{{documentation/version}}/module-section|Features}}
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**Short Run Emphasis (SRE)
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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.
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**Long Run Emphasis (LRE)
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*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 the Final Post-contrast time point. The Y-axis represents percentage change from baseline/pre-contrast intensity.
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**Gray Level Non-Uniformity (GLN)
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*Volume Rendering - A 3D Volume Rendering of the output Label Map is displayed in the 3D viewer after segmentation.
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**Run Length Non-Uniformity (RLN)
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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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**Run Percentage (RP)
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**Low Gray Level Run Emphasis (LGLRE)
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**High Gray Level Run Emphasis (HGLRE)
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**Short Run Low Gray Level Emphasis (SRLGLE)
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**Short Run High Gray Level Emphasis (SRHGLE)  
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**Long Run Low Gray Level Emphasis (LRLGLE)
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**Long Run High Gray Level Emphasis (LRHGLE)  
  
 
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{{documentation/{{documentation/version}}/module-section|Tutorials}}
 
{{documentation/{{documentation/version}}/module-section|Tutorials}}
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[[Media:SegmentCADTutorial.pptx|{{documentation/modulename}} Tutorial (pptx)]]‎
 
  
 
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{{documentation/{{documentation/version}}/module-section|Data sets}}
 
{{documentation/{{documentation/version}}/module-section|Data sets}}
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[[Media:Breast-data1.zip|Breast DCE-MRI Data Set 1 (zip file containing the nrrd volumes for the {{documentation/modulename}} tutorial)]]‎
 
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[[Media:Breast-data2.zip|Breast DCE-MRI Data Set 2 (zip file containing additional test set of nrrd volumes)]]‎
 
  
  
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{|
 
{|
 
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The GUI of the {{documentation/modulename}} module contains 5 sections:
 
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* '''Select DCE-MRI Volumes for Segmentation'''
 
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** '''Pre-contrast Volume:''' Select the Pre-contrast Image
 
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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:''' 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:'''  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:''' Select the Post-contrast Image at the Fourth or Final time point.
 
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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.
 
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* '''Select or Create Output SegmentCAD Label Map'''
 
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**'''Output SegmentCAD Label Map:''' Create or select a label map volume node to represent the output of the segmentation.
 
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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:''' Enable this to display a 3D Volume Rendering of the Label Map output in the 3D viewer after segmentation.
 
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**'''Calculate SegmentCAD Label statistics:''' Enable this to calculate and display statistics of all the First Post-contrast time point voxels highlighted in the output Label Map.
 
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* '''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 (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 (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 (default set at -0.2).
 
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*'''Apply SegmentCAD:''' Perform Segmentation.
 
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* '''SegmentCAD 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).
 
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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.
 
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***'''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:''' Ignore the unsegmented region of the First Post-contrast image when displaying bar graph.
 
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* '''Interactive Charting Settings'''
 
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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 the Final Post-contrast. Y-axis represents percentage change from baseline intensity.
 
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|[[Image:SegmentCAD-GUI.png|thumb|340px|{{documentation/modulename}} GUI ]]
 
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|}
 
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{{documentation/{{documentation/version}}/module-section|Quick Instructions for Use}}
 
{{documentation/{{documentation/version}}/module-section|Quick Instructions for Use}}
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*Select the pre-contrast volume
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*Select a nrrd volume
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*Select the first post-contrast volume
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*Select a segmentation label map to use as ROI
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*Select the second post-contrast volume
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*Click "Apply HeterogeneityCAD"
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*Select the third post-contrast volume
 
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*Select the fourth post-contrast volume
 
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*Uncheck 'Use Label Map as ROI'
 
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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 SegmentCAD"
 
  
 
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{{documentation/{{documentation/version}}/module-section|Module Output}}
 
{{documentation/{{documentation/version}}/module-section|Module Output}}
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[[Image:SegmentCAD-Output.png|thumb|center|500px|{{documentation/modulename}} Module Output ]]
 
  
 
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{{documentation/{{documentation/version}}/module-footer}}
 
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[[Category:Documentation/{{documentation/version}}/Modules/Segmentation]]
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[[Category:Documentation/{{documentation/version}}/Modules/Quantification]]
 
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Revision as of 19:18, 2 July 2014

Home < Documentation < Nightly < Modules < HeterogeneityCAD


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


OpenCAD.PNG

Introduction and Acknowledgements

Extension: OpenCAD
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 HeterogeneityCAD module is an image feature extraction toolbox primarily to quantify the heterogeneity of tumor images and their label maps.


Image Features and Metrics

  • First-Order and Distribution Statistics
    • Data Node
    • Voxel Count
    • Energy
    • Entropy
    • Minimum Intensity
    • Maximum Intensity
    • Mean Intensity
    • Median Intensity
    • Range
    • Mean Deviation
    • Root Mean Square
    • Standard Deviation
    • Skewness
    • Kurtosis
    • Variance
    • Uniformity
  • Shape and Morphology Metrics
    • Volume mm^3
    • Volume cc
    • Surface Area mm^2
    • Surface:Volume Ratio
    • Compactness 1
    • Compactness 2
    • Maximum 3D Diameter
    • Spherical Disproportion
    • Sphericity
  • Renyi Dimensions
    • Box-Counting Dimension
    • Information Dimension
    • Correlation Dimension
  • Geometrical Measures
    • Extruded Surface Area
    • Extruded Volume
    • Extruded Surface:Volume Ratio
    • Extruded Box-Dimension
  • Texture: Gray-Level Co-occurrence Matrix (GLCM)
    • Autocorrelation
    • Cluster Prominence
    • Cluster Shade
    • Cluster Tendency
    • Contrast
    • Correlation
    • Difference Entropy
    • Dissimilarity
    • Energy (GLCM)
    • Entropy(H)
    • Homogeneity 1
    • Homogeneity 2
    • Informational Measure of Correlation 1 (IMC1)
    • Informational Measure of Correlation 2 (IMC2)
    • Inverse Difference Moment Normalized (IDMN)
    • Inverse Difference Normalized (IDN)
    • Inverse Variance
    • Maximum Probability
    • Sum Average
    • Sum Entropy
    • Sum Variance
    • Variance (GLCM)
  • Texture: Gray-Level Run Length Matrix (GLRL)
    • Short Run Emphasis (SRE)
    • Long Run Emphasis (LRE)
    • Gray Level Non-Uniformity (GLN)
    • Run Length Non-Uniformity (RLN)
    • Run Percentage (RP)
    • Low Gray Level Run Emphasis (LGLRE)
    • High Gray Level Run Emphasis (HGLRE)
    • Short Run Low Gray Level Emphasis (SRLGLE)
    • Short Run High Gray Level Emphasis (SRHGLE)
    • Long Run Low Gray Level Emphasis (LRLGLE)
    • Long Run High Gray Level Emphasis (LRHGLE)

Tutorials

Data sets

Panels and their use


Quick Instructions for Use

  • Select a nrrd volume
  • Select a segmentation label map to use as ROI
  • Click "Apply HeterogeneityCAD"

Module Output

Similar Modules

N/A

References

N/A

Information for Developers

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

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