2010 Summer Project Week/The Vascular Modeling Toolkit in 3D Slicer

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  Projects List

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  VMTK in 3D Slicer

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  Example network extraction of a vascular tree using stand-alone VMTK

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  The GUI of the new VMTKNetworkExtraction module in 3D Slicer

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  A surface model of brain arteries and veins

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  The extracted network as an overlay on the surface model - Runtime about 10 seconds

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  The extracted network can be colored by topology or vessel diameter

Key Investigators

• UPENN: Daniel Haehn, Kilian Pohl
• Mario Negri Institute, Italy: Luca Antiga
• SPL: Steve Pieper, Ron Kikinis, Johannes Schick

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.

Parts of VMTK exist as 3D Slicer extensions and f.e. can be combined to a pipeline for centerline extraction of vascular trees. This pipeline consisting of Vessel Enhancement filtering, level set segmentation and the actual centerline extraction was tested on different cases.

The official project page: http://www.vmtk.org/Main/VmtkIn3DSlicer

Approach, Plan

The plan for the project week is to create a new VMTK based module for network extraction of vascular trees. Network extraction is comparable to vessel centerlines with a little bit less accuracy but faster. The algorithm works on a triangulated surface of segmented vessels and would fit in the pipeline of existing VMTK modules.

Progress

The following VMTK in 3D Slicer extensions already exist:

• VmtkSlicerModule prerequisite install for all VMTK plug-ins
• VMTKCenterlines providing centerline computation of surface models
• VMTKEasyLevelSetSegmentation providing level-set segmentation of vessels, aneurysms and tubular structures using an easy interface
• VMTKVesselEnhancement providing vessel enhancement filters to highlight vascular or tubular structures

Project Week Update: A new extension called VMTKNetworkExtraction is now available for parameter-free centerline extraction of surface models. It attaches the vessel diameter to the generated network and is quick - but not as accurate as VMTKCenterlines.

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. Slicer Module
   1. Extension -- loadable YES

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.