Difference between revisions of "2011 Winter Project Week:The Vascular Modeling Toolkit in 3D Slicer"

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(Created page with '__NOTOC__ <gallery> Image:3D_Segmentation_LA.png | 3D View of the Segmentation of Endocardial Wall Image:2d_axial_LA.png | 2D View </gallery> ==Key Investigators== * Georgia Tec…')
 
 
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__NOTOC__
 
__NOTOC__
 
<gallery>
 
<gallery>
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Image:3D_Segmentation_LA.png | 3D View of the Segmentation of Endocardial Wall
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Image:PW-SLC2011.png|[[2011_Winter_Project_Week#Projects|Projects List]]
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Image:2d_axial_LA.png | 2D View
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Image:Slicervmtk logo.png|VMTK in 3D Slicer
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Image:Vesselenhancement.png|Enhancing vasculature structures
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Image:Easylevelsetsegmentation.png|Level-Set segmentation
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Image:Centerlines.png|Computation of Centerlines
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Image:Networkextraction.png|Network extraction of vessel trees
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Image:Branchsplitting.png|Branchsplitting
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Image:Anim.gif|The new parameter widget for VMTKVesselness4
 
</gallery>
 
</gallery>
  
 
==Key Investigators==
 
==Key Investigators==
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* Georgia Tech: Behnood Gholami, Yi Gao, and Allen Tannenbaum
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* UPenn: Daniel Haehn, Kilian Pohl
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* Rutgers: M. Gokhan Uzunbas
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* [http://www.orobix.com Orobix], Italy: Luca Antiga
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* SPL: Steve Pieper, Ron Kikinis
  
 
<div style="margin: 20px;">
 
<div style="margin: 20px;">
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<h3>Objective</h3>
 
<h3>Objective</h3>
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The Vascular Modeling Toolkit ([http://www.vmtk.org VMTK]) is a collection of libraries and tools for 3D reconstruction, geometric analysis, mesh generation and surface data analysis for image-based modeling of blood vessels.
  
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Atrial fibrillation, a cardiac arrhythmia characterized by unsynchronized electrical activity in the atrial chambers of the heart, is a rapidly growing problem in modern societies. Electrical cardioversion and antiarrhythmic drugs are used to manage this condition, but suffer from low success rates and involve major side effects. In an alternative treatment, known as catheter ablation, specific parts of the left atrium are targeted for radio frequency ablation using an intracardiac catheter. Application of radio frequency energy to the cardiac tissue causes thermal injury (lesions), which in turn results into scar tissue. Successful ablation can eliminate, or isolate, the problematic sources of electrical activity and effectively cure atrial fibrillation.
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Several 3D Slicer extensions already exist and provide VMTK functionality in Slicer3.  
  
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Magnetic resonance imaging (MRI) has been used for both pre- and and post-ablation assessment of the atrial wall. MRI can aid in selecting the right candidate for the ablation procedure and assessing post-ablation scar formations. Image processing techniques can be used for automatic segmentation of the atrial wall, which facilitates an accurate statistical assessment of the region. As a first step towards the general solution to the computer-assisted segmentation of the left atrial wall, in this research we propose a shape-based image segmentation framework to segment the endocardial wall of the left atrium.
 
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We are developing methods to segment the left atrial wall in delayed-enhanced MR imagery.
 
 
</div>
 
</div>
  
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<h3>Approach, Plan</h3>
 
<h3>Approach, Plan</h3>
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We want to investigate how to include the VMTK in 3D Slicer functionality in the upcoming Slicer4 application. This should include several enhancements to the existing user interfaces.
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We plan to finalize a fully-automatic segmentation approach to identify the blood pool in MRAs. The approach uses the robust statistics segmentation framework developed earlier at Georgia Tech.
 
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</div>
 
</div>
  
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<h3>Progress</h3>
 
<h3>Progress</h3>
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'''Project Week Update:'''
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Unfortunately, we did not have as much time as we liked to spend on this project. Nevertheless, we created a QT widget to optimize the selection of user-defined parameters for vessel enhancement. The new widget will be part of the upcoming first VMTK module for Slicer4 called VMTKVesselness4.
  
 +
We plan to investigate if the integration of the new widget in CTK makes sense.
  
 
</div>
 
</div>
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<div style="width: 97%; float: left;">
 
<div style="width: 97%; float: left;">
  
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==Delivery Mechanism==
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 +
This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)
 +
 +
#ITK Module
 +
#Slicer Module
 +
##Built-in
 +
##Extension -- commandline
 +
##Extension -- loadable [X]
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#Other (Please specify)
  
 
==References==
 
==References==
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* Y. Gao, B. Gholami, R. MacLeod, J. Blauer, W. M. Haddad, and A. R. Tannenbaum, "Segmentation of the Endocardial Wall of the Left Atrium using Localized Region-Based Active Contours and Statistical Shape Learning," Proc. SPIE Med. Imag., San Diego, CA, vol. 7623, 76234Z-1, 2010.
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* Antiga L, Piccinelli M, Botti L, Ene-Iordache B, Remuzzi A and Steinman DA. An image-based modeling framework for patient-specific computational hemodynamics. Medical and Biological Engineering and Computing, 46: 1097-1112, Nov 2008.
 +
* D. Hähn. Integration of the vascular modeling toolkit in 3d slicer. SPL, 04 2009. Available online at http://www.spl.harvard.edu/publications/item/view/1728.
 +
* D. Hähn. Centerline Extraction of Coronary Arteries in 3D Slicer using VMTK based Tools. Master's Thesis. Department of Medical Informatics, University of Heidelberg, Germany. Feb 2010.
 +
* Piccinelli M, Veneziani A, Steinman DA, Remuzzi A, Antiga L (2009) A framework for geometric analysis of vascular structures: applications to cerebral aneurysms. IEEE Trans Med Imaging. In press.
  
 
</div>
 
</div>

Latest revision as of 15:37, 14 January 2011

Home < 2011 Winter Project Week:The Vascular Modeling Toolkit in 3D Slicer

  • VMTK in 3D Slicer

  • Enhancing vasculature structures

  • Level-Set segmentation

  • Computation of Centerlines

  • Network extraction of vessel trees

  • Branchsplitting

  • The new parameter widget for VMTKVesselness4

Key Investigators

  • UPenn: Daniel Haehn, Kilian Pohl
  • Rutgers: M. Gokhan Uzunbas
  • Orobix, Italy: Luca Antiga
  • SPL: Steve Pieper, Ron Kikinis

Objective

The Vascular Modeling Toolkit (VMTK) is a collection of libraries and tools for 3D reconstruction, geometric analysis, mesh generation and surface data analysis for image-based modeling of blood vessels.

Several 3D Slicer extensions already exist and provide VMTK functionality in Slicer3.

Approach, Plan

We want to investigate how to include the VMTK in 3D Slicer functionality in the upcoming Slicer4 application. This should include several enhancements to the existing user interfaces.

Progress

Project Week Update: Unfortunately, we did not have as much time as we liked to spend on this project. Nevertheless, we created a QT widget to optimize the selection of user-defined parameters for vessel enhancement. The new widget will be part of the upcoming first VMTK module for Slicer4 called VMTKVesselness4.

We plan to investigate if the integration of the new widget in CTK makes sense.

Delivery Mechanism

This work will be delivered to the NA-MIC Kit as a (please select the appropriate options by noting YES against them below)

  1. ITK Module
  2. Slicer Module
    1. Built-in
    2. Extension -- commandline
    3. Extension -- loadable [X]
  3. Other (Please specify)

References

  • Antiga L, Piccinelli M, Botti L, Ene-Iordache B, Remuzzi A and Steinman DA. An image-based modeling framework for patient-specific computational hemodynamics. Medical and Biological Engineering and Computing, 46: 1097-1112, Nov 2008.
  • D. Hähn. Integration of the vascular modeling toolkit in 3d slicer. SPL, 04 2009. Available online at http://www.spl.harvard.edu/publications/item/view/1728.
  • D. Hähn. Centerline Extraction of Coronary Arteries in 3D Slicer using VMTK based Tools. Master's Thesis. Department of Medical Informatics, University of Heidelberg, Germany. Feb 2010.
  • Piccinelli M, Veneziani A, Steinman DA, Remuzzi A, Antiga L (2009) A framework for geometric analysis of vascular structures: applications to cerebral aneurysms. IEEE Trans Med Imaging. In press.
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