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

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{{documentation/{{documentation/version}}/module-introduction-end}}
 
{{documentation/{{documentation/version}}/module-introduction-end}}
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{{documentation/{{documentation/version}}/module-section|Module Description}}
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{{documentation/{{documentation/version}}/extension-section|Modules}}
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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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*[[Documentation/{{documentation/version}}/Modules/SegmentCAD|SegmentCAD: Tumor Segmentation from DCE-MRI]]
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*[[Documentation/{{documentation/version}}/Modules/HeterogeneityCAD|HeterogeneityCAD: Feature Extraction toolbox for image heterogeneity analysis]]
  
  
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{{documentation/{{documentation/version}}/module-section|Methods}}
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{{documentation/{{documentation/version}}/extension-section|Extension Description}}
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{|
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*The SegmentCAD module is designed to segment tumors from DCE-MRI datasets which include a pre-contrast image and post-contrast images at different time points.
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|
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**SegmentCAD uses blackbox methods to calculate the wash-in and wash-out slopes from the time-intensity curves.  
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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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**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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*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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*The HeterogeneityCAD module is an extensible, image feature extraction toolbox primarily to quantify the heterogeneity of tumor images and their label maps.
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*Segmented voxels are individually classified by color according to slope of delayed curve:
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**Metrics have been implemented from a variety of feature classes including:
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**Blue for Persistent curve
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***First-Order/Histogram statistics
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***Slope of delayed curve > 0.2 (default) (Type I)
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***Morphology/Shape measures and Geometrical (4D Extrusion) measures
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**Yellow for Plateau curve
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***Renyi/Fractal dimensions
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***-0.2 < Slope of delayed curve < 0.2 (Type II)
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***Texture features computed from Gray-Level Co-occurrence Matrices (GLCM) and from Gray-Level Run Length matrices (GLRL)
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**Red for Washout curve
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***Slope of delayed curve < -0.2 (default) (Type III)
 
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|[[Image:Graph.png|thumb|280px|Classification based on Delayed Curve]]
 
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|}
 
  
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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.
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-->
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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 Final Post-contrast time points. The Y-axis represents percentage change from baseline/pre-contrast intensity.
 
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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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*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.
 
  
 
<!-- ---------------------------- -->
 
<!-- ---------------------------- -->
 
{{documentation/{{documentation/version}}/module-section|Tutorials}}
 
{{documentation/{{documentation/version}}/module-section|Tutorials}}
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[[Media:OpenCADTutorial.pptx|{{documentation/modulename}} Tutorial (pptx)]]‎  
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*SegmentCAD
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**[[Media:SegmentCADTutorial.pptx|SegmentCAD Tutorial (pptx)]]‎
  
 
<!-- ---------------------------- -->
 
<!-- ---------------------------- -->
 
{{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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*SegmentCAD
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**[[Media:Breast-data1.zip|Breast DCE-MRI Data Set 1 (zip file containing the nrrd volumes for the 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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**[[Media:Breast-data2.zip|Breast DCE-MRI Data Set 2 (zip file containing additional test set of nrrd volumes)]]‎
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*HeterogeneityCAD
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**[[Media:BreastHeteroCADData.zip|Breast DCE-MRI Data Set (zip file containing the nrrd volumes for the tutorial)]]‎
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<!-- ---------------------------- -->
 
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{{documentation/{{documentation/version}}/module-section|Panels and their use}}
 
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{|
 
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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 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 | |:''' 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 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.
 
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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 OpenCAD Segmentation:''' Perform Segmentation.
 
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* '''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).
 
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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 Final Post-contrast. Y-axis represents percentage change from baseline intensity.
 
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|[[Image:OpenCAD-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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*[[Documentation/{{documentation/version}}/Modules/SegmentCAD|SegmentCAD (Click link for detailed description)]]
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*Select the first post-contrast volume
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**Select the pre-contrast volume
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*Select the second post-contrast volume
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**Select the first post-contrast volume
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*Select the third post-contrast volume
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**Select the second post-contrast volume
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*Select the fourth 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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**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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*Click "Apply OpenCAD Segmentation"
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*[[Documentation/{{documentation/version}}/Modules/HeterogeneityCAD|HeterogeneityCAD (Click link for detailed description)]]
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**Add an image or parameter map (.nrrd file) to the Nodes List
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<!-- ---------------------------- -->
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**Select a corresponding segmentation label map to use as ROI
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{{documentation/{{documentation/version}}/module-section|Module Output}}
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**Click "Apply HeterogeneityCAD"
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[[Image:OpenCAD-Output.png|thumb|center|500px|{{documentation/modulename}} Module Output ]]
 
  
 
<!-- ---------------------------- -->
 
<!-- ---------------------------- -->
 
{{documentation/{{documentation/version}}/module-section|Similar Modules}}
 
{{documentation/{{documentation/version}}/module-section|Similar Modules}}
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N/A
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*SegmentCAD:
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*HeterogeneityCAD:
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**LabelStatistics
  
 
<!-- ---------------------------- -->
 
<!-- ---------------------------- -->
 
{{documentation/{{documentation/version}}/module-section|References}}
 
{{documentation/{{documentation/version}}/module-section|References}}
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N/A
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* J. Jayender, E. Gombos, S. Chikarmane, D. Dabydeen, F. A. Jolesz, and K. G. Vosburgh, “Statistical Learning Algorithm for In-situ and Invasive Breast Carcinoma Segmentation”, Journal of Computerized Medical Imaging and Graphics, vol. 37, no. 4, pp. 281-292, 2013
 +
* J. Jayender, S. A. Chikarmane, F. A. Jolesz and E. Gombos, “Automatic Segmentation of Invasive Breast Carcinomas from DCE-MRI using Time Series Analysis”, Journal of MRI, Article first published online 23 September 2013, doi: 10.1002/jmri.24394
 +
* J. Jayender, K.G. Vosburgh, E. Gombos, A. Ashraf, D. Kontos, S.C. Gavenonis, F. A. Jolesz and K. Pohl , “Automatic Segmentation of Breast Carcinomas from DCE-MRI using a Statistical Learning Algorithm”, IEEE International Symposium on Biomedical Imaging, pp. 122-125, 2012.
 +
* J. Jayender, D.T. Ruan, V. Narayan, N. Agrawal, F. A. Jolesz and H. Mamata, “Segmentation of Parathyroid Tumors from DCE-MRI using Linear Dynamic System Analysis”, IEEE International Symposium on Biomedical Imaging, 2013.
 +
* J. Jayender, J. Jagannathan, S.Chikarmane, C.P.Raut and F.A. Jolesz, “Computer-Aided Diagnosis of Breast Angiosarcoma: Results in 14 cases”, Quantitative Medical Imaging Symposium, 2013 (invited paper).
 +
* HJWL Aerts, ER Velazquez, RTH Leijenaar, et al., "Decoding tumour phenotype by noninvasive imaging using a quantitative radiomics approach", vol. 5, Nat Communication, 2014.
 +
 
  
 
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{{documentation/{{documentation/version}}/module-section|Information for Developers}}
 
{{documentation/{{documentation/version}}/module-section|Information for Developers}}
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−
 
  
 
Source code: https://github.com/vnarayan13/Slicer-OpenCAD
 
Source code: https://github.com/vnarayan13/Slicer-OpenCAD

Latest revision as of 03:46, 2 August 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


Modules


Extension Description

  • The SegmentCAD module is designed to segment tumors from DCE-MRI datasets which include a pre-contrast image and post-contrast images at different time points.
    • SegmentCAD 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.
  • The HeterogeneityCAD module is an extensible, image feature extraction toolbox primarily to quantify the heterogeneity of tumor images and their label maps.
    • Metrics have been implemented from a variety of feature classes including:
      • First-Order/Histogram statistics
      • Morphology/Shape measures and Geometrical (4D Extrusion) measures
      • Renyi/Fractal dimensions
      • Texture features computed from Gray-Level Co-occurrence Matrices (GLCM) and from Gray-Level Run Length matrices (GLRL)


Tutorials

Data sets


Quick Instructions for Use

  • SegmentCAD (Click link for detailed description)
    • 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"
  • HeterogeneityCAD (Click link for detailed description)
    • Add an image or parameter map (.nrrd file) to the Nodes List
    • Select a corresponding segmentation label map to use as ROI
    • Click "Apply HeterogeneityCAD"

Similar Modules

  • SegmentCAD:
  • HeterogeneityCAD:
    • LabelStatistics

References

  • J. Jayender, E. Gombos, S. Chikarmane, D. Dabydeen, F. A. Jolesz, and K. G. Vosburgh, “Statistical Learning Algorithm for In-situ and Invasive Breast Carcinoma Segmentation”, Journal of Computerized Medical Imaging and Graphics, vol. 37, no. 4, pp. 281-292, 2013
  • J. Jayender, S. A. Chikarmane, F. A. Jolesz and E. Gombos, “Automatic Segmentation of Invasive Breast Carcinomas from DCE-MRI using Time Series Analysis”, Journal of MRI, Article first published online 23 September 2013, doi: 10.1002/jmri.24394
  • J. Jayender, K.G. Vosburgh, E. Gombos, A. Ashraf, D. Kontos, S.C. Gavenonis, F. A. Jolesz and K. Pohl , “Automatic Segmentation of Breast Carcinomas from DCE-MRI using a Statistical Learning Algorithm”, IEEE International Symposium on Biomedical Imaging, pp. 122-125, 2012.
  • J. Jayender, D.T. Ruan, V. Narayan, N. Agrawal, F. A. Jolesz and H. Mamata, “Segmentation of Parathyroid Tumors from DCE-MRI using Linear Dynamic System Analysis”, IEEE International Symposium on Biomedical Imaging, 2013.
  • J. Jayender, J. Jagannathan, S.Chikarmane, C.P.Raut and F.A. Jolesz, “Computer-Aided Diagnosis of Breast Angiosarcoma: Results in 14 cases”, Quantitative Medical Imaging Symposium, 2013 (invited paper).
  • HJWL Aerts, ER Velazquez, RTH Leijenaar, et al., "Decoding tumour phenotype by noninvasive imaging using a quantitative radiomics approach", vol. 5, Nat Communication, 2014.


Information for Developers

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

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