View source for Summer2009:The Vascular Modeling Toolkit in 3D Slicer

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Image:PW2009-v3.png|[[2009_Summer_Project_Week#Projects|Project Week Main Page]]
File:Screenshot-VMTK in 3D Slicer.png|Example segmentation of cerebral vessels and a tumor using VMTK in 3D Slicer
File:Screenshot-VMTK_in_3D_Slicer2.png|Example segmentation of vessels in an arm bearing a vascular access for hemodialysis 
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==Key Investigators==
* [[User:haehn |Daniel Haehn]] (Student of Medical Informatics, University of Heidelberg) 

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<h3>Objective</h3>
The Vascular Modeling Toolkit ([http://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. It should be very interesting to offer such techniques in 3D Slicer.


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<h3>Approach, Plan</h3>
To provide VMTK tools in 3D Slicer the ''vtkVmtk'' library has to be available as an add-on.
With the connection of VMTK and 3D Slicer processing pipelines 
between VMTK code and other algorithms can be established. <br><br>
The plan is to clean-up existing ''VMTK in 3D Slicer'' code, provide additional VMTK functionality in 3D Slicer as well as to optimize the work-flow between the existing VMTK modules. This includes more level set evolution methods and variable calculation of feature images during level set segmentation.

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<h3>Progress</h3>
The library of VMTK was made available in 3D Slicer using a GUI-less loadable module approach in order to 
provide a flexible way of distributing and including it. Therefore all VMTK functions are available to 3D Slicer developers. <br><br>Python scripted modules offering VMTK level set segmentation methods and VMTK vessel enhancement filters within 3D Slicer were created. These include the following algorithms:
* Colliding Fronts and Fast Marching Upwind Gradient initialization
* Geodesic Active Contour and Curves evolution
* FrangiVesselness, SatoVesselness and VesselEnhancingDiffusion filters
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The created modules are available at the VMTK in 3D Slicer NITRC page:
http://www.nitrc.org/projects/slicervmtklvlst/

'''Summer Project Week Update:'''
* Fast Marching Upwind Gradient initialization: target points were made optional and the algorithm can run with one or more source points (seeds).
* The initialization can now be performed on an enhanced vesselness image. During evolution stage this initial level set can be inflated within a feature image based on the original volume to avoid the loss of information.
* For using the gui-less VMTK library module as a Slicer3 extension, necessary updates to the CMake files of VMTK were performed to remove deprecated INSTALL_FILES and INSTALL_TARGET calls. These changes make vtkVmtk Slicer3 compliant by using CMake 2.6, will be send to Luca Antiga and hopefully be in the official VMTK release soon.

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==References==
*Antiga L, Piccinelli M, Botti L, EneIordache B, Remuzzi A, Steinmann DA. (2008) An imagebased modeling framework for patientspecific computational hemodynamics. Med Biol Eng Comput 46(11):10971112
*Antiga L, Steinman DA (2008) The Vascular Modeling Toolkit. http://www.vmtk.org/
*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.