Modules:VMTKSlicerModule

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Module Name

VmtkSlicerModule

General Information

Module Type & Category

Type: GUI-less loadable module

Category: Extension

Authors, Collaborators & Contact

• Author: Daniel Haehn, University of Heidelberg
• Acknowledgments: Luca Antiga, Mario Negri Institute; Steve Pieper, Isomics Inc.
• Contact: Daniel Haehn, haehn@bwh.harvard.edu

Module Description

This GUI-less loadable module provides the libraries of the Vascular Modeling Toolkit (http://www.vmtk.org/) in 3D Slicer.

It is part of the NA-MIC VMTK Collaboration.

Official project page: http://www.vmtk.org/Main/VmtkIn3DSlicer

Usage

Installation

This module can be installed as a 3D Slicer Extension or manually. Either way will automatically include the latest version of the VMTK libraries by accessing the official VMTK SVN repository.

• Installation as a 3D Slicer Extension

Inside the 3D Slicer extension system, the module is called VmtkSlicerModule.

• Manual Installation

1. To get the latest source code, perform the following SVN checkout command:

svn checkout https://www.nitrc.org/svn/slicervmtklvlst

2. A directory named VmtkSlicerModule is downloaded and the latest VMTK libraries get checked out as well.

3. Copy this directory to Slicer3/Modules/ of your local Slicer installation.

4. Edit the Slicer3/Modules/CMakeLists.txt file and add VmtkSlicerModule to the Subdirs directive.

5. Change directory to Slicer3-build/ and issue a make -j2 command to start the compilation.

When the module was successfully installed, all VMTK methods are available for developer access within 3D Slicer.

Examples, Use Cases & Tutorials

The actual VMTK functions for end users are provided as Python scripted modules.

After installing this module, these can be installed and used.

• VMTKEasyLevelSetSegmentation - providing level-set segmentation of vessels, aneurysms and tubular structures using an easy interface

• VMTKLevelSetSegmentation - providing level-set segmentation of vessels, aneurysms and tubular structures using different algorithms

• VMTKVesselEnhancement - providing vessel enhancement filters to highlight vasculature or tubular structures

Development

Source code & Documentation

The complete source code is available at a NITRC SVN repository.

The most important files are the following:

• CMakeLists.txt to include the vtkVmtk libraries during compilation

• vtkVmtkSlicerModuleLogic.cxx to initialize the generated Tcl wrapper classes of the vtkVmtk libraries

During a SVN check out, the actual VMTK libraries are automatically checked out using a svn:external repository. Therefore always the latest version of VMTK is included as a subdirectory.

Since the Tcl initialization is performed, the vtkVmtk library can also be accessed from Python in 3D Slicer.

Information and documentation concerning the integration of VMTK can be found in this student research project write-up.

Documentation of the VMTK libraries is available here.

Known bugs

Follow this link to the VMTK in 3D Slicer bug tracker.

More Information

Acknowledgment

This work was funded by a grant of the Thomas­-Gessmann Foundation part of the Founder Federation for German Science.

References

• 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.
• 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.