Difference between revisions of "Documentation/4.3/Extensions/OpenCAD"

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{{documentation/{{documentation/version}}/module-section|Module Description}}
 
{{documentation/{{documentation/version}}/module-section|Module Description}}
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{{documentation/modulename}} module allows to output a filtered transform node based on an tracker input (transform node). Tracking sensors are particularly usefull to track surgical tools, robots, patient motion, etc... . However, data imported in 3D Slicer from these devices are often noisy. To reduce the noise and smoothly control objects, such as 3D Slicer camera, the {{documentation/modulename}} module will apply a low-pass filter on input data. The cut-off frequency (i.e. the smoothing parameter) is adjustable by the user.
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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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It is important to notice that filters induce delay, and the smoother the motion is, the bigger the delay between the raw data and the filtered position will be. -->
 
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Here comes a description what the module is good for. Explain briefly how it works and point to the [[documentation/{{documentation/version}}/Modules/{{documentation/modulename}}#References|references]] giving more details on the algorithm.
 
  
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If you are documenting a CLI, the description should be extracted from the corresponding XML description. This could be done automatically using the following wiki template:<pre>{{documentation/{{documentation/version}}/module-description}}
 
  
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{{documentation/{{documentation/version}}/module-section|Methods}}
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{|
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|
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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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*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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*Segmented voxels are individually classified by color according to slope of delayed curve:
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**Blue for Persistent curve
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***Slope of delayed curve > 0.2 (default) | Type I|
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**Yellow for Plateau curve
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***-0.2 < Slope of delayed curve < 0.2 | Type II
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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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{{documentation/{{documentation/version}}/module-section|Features}}
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The {{documentation/modulename}} module could be used in any situation requiring stable tracking data and not requiring a "real-time" information. Indeed, applying a filter on raw data will induce a delay (depending on choosen parameters) on the filtered position/orientation.
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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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An example could be to drive Slicer's virtual camera. Having some noise on the transformation driving the camera will cause the camera to "shake" which could be really distracting and uncomfortable to look at. By filtering this raw data, camera motion is smoothed. -->
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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. Logic is derived from the Label Statistics Module.  
  
 
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[[media:OpenCAD.pptx|Tutorial for OpenCAD (pptx)]]‎  
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[[Media:OpenCADTutorial.pptx|{{documentation/modulename}} Tutorial (pptx)]]‎  
  
 
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[[media:Breast-data1.zip|Breast DCE-MRI Data Set 1 (zip file containing the nrrd volumes for the OpenCAD tutorial)]]‎  
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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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[[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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[[Media:Liver-data1.zip|Liver DCE-MRI Data Set 1 (zip file containing additional test set of nrrd volumes)]]‎
  
 
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{{documentation/{{documentation/version}}/module-section|Panels and their use}}
 
{{documentation/{{documentation/version}}/module-section|Panels and their use}}
 
{|
 
{|
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The GUI of the {{documentation/modulename}} module contains 4 sections:
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|
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* Select DCE-MRI Volumes for Segmentation
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The GUI of the {{documentation/modulename}} module contains 5 sections:
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* Select or Create Output OpenCAD Label Map
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* '''Select DCE-MRI Volumes for Segmentation'''
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* Set Advanced Segmentation Parameters
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** '''Pre-contrast Volume:''' Select the Pre-contrast Image
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* OpenCAD Label Statistics  
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** '''First Post-contrast Volume:''' Select the Post-contrast Image at the First time point
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* Interactive Charting Settings
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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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|}
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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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{|
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** '''Fourth Post-contrast Volume:''' Select the Post-contrast Image at the Fourth or Final time point.
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|[[Image:Slicer-OpenCAD-GUI.png|thumb|400px|{{documentation/modulename}} GUI ]]
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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.
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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:''' The maximum slope of the delayed curve for a voxel to be classified as having a Type III Washout Curve.
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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). Logic is derived from the Label Statistics Module.
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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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Revision as of 21:01, 25 April 2014

Home < Documentation < 4.3 < 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

  • 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

  • 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. Logic is derived from the Label Statistics Module.

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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