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

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{{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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Red for washout curve
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(Sd < -0.2 | Type III)
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Yellow for plateau curve
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(-0.2 < Sd < 0.2 | Type II)
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Blue for persistent curve
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(Sd > 0.2 | Type I)   
 
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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 -  
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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 -
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*Label Statistics -  
  
 
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{{documentation/{{documentation/version}}/module-section|Tutorials}}
 
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[[Media:OpenCADTutorial.pptx|OpenCAD Tutorial (pptx)]]‎  
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[[Media:OpenCADTutorial.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 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)]]‎  
  
 
[[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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The GUI of the {{documentation/modulename}} module contains 5 sections:
 
The GUI of the {{documentation/modulename}} module contains 5 sections:
 
* '''Select DCE-MRI Volumes for Segmentation'''
 
* '''Select DCE-MRI Volumes for Segmentation'''
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** '''Pre-contrast Volume:'''
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** '''First Post-contrast Volume:'''
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** '''Second Post-contrast Volume:'''
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** '''Third Post-contrast Volume:'''
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** '''Fourth Post-contrast Volume:'''
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** '''Use Label Map as ROI:'''
 
* '''Select or Create Output OpenCAD Label Map'''
 
* '''Select or Create Output OpenCAD Label Map'''
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**'''Output OpenCAD Label Map:'''
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**'''Legend | |:'''
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**'''Display Volume Rendering:'''
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**'''Calculate OpenCAD Label statistics:'''
 
* '''Set Advanced Segmentation Parameters'''
 
* '''Set Advanced Segmentation Parameters'''
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**'''Minimum Threshold of Increase:'''
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**'''Type I (Persistent) Curve Minimum Slope:'''
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**'''Type 3 (Washout) Curve Maximum Slope:'''
 
* '''OpenCAD Label Statistics'''
 
* '''OpenCAD Label Statistics'''
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**'''Statistics Table:'''
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**'''Chart Statistics:'''
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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:'''
 
* '''Interactive Charting Settings'''
 
* '''Interactive Charting Settings'''
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|[[Image:Slicer-OpenCAD-GUI.png|thumb|400px|{{documentation/modulename}} GUI ]]
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**'''Enable/Disable Interactive Charting:'''
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|[[Image:OpenCAD-GUI.png|thumb|280px|{{documentation/modulename}} GUI ]]
 
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Revision as of 19:14, 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...

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.


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:
    • First Post-contrast Volume:
    • Second Post-contrast Volume:
    • Third Post-contrast Volume:
    • Fourth Post-contrast Volume:
    • Use Label Map as ROI:
  • Select or Create Output OpenCAD Label Map
    • Output OpenCAD Label Map:
    • Legend | |:
    • Display Volume Rendering:
    • Calculate OpenCAD Label statistics:
  • Set Advanced Segmentation Parameters
    • Minimum Threshold of Increase:
    • Type I (Persistent) Curve Minimum Slope:
    • Type 3 (Washout) Curve Maximum Slope:
  • OpenCAD Label Statistics
    • Statistics Table:
    • Chart Statistics:
      • Menu Items: Volume, Curve Type, Voxel Count, Volume mm^3, Volume cc, Minimum Intensity, Maximum Intensity, Mean Intensity, Standard Deviation
      • Ignore Zero label:
  • Interactive Charting Settings
    • Enable/Disable Interactive Charting:
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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