View source for Modules:VMTKSlicerModule

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__NOTOC__
===Module Name===
VmtkSlicerModule


== General Information ==
===Module Type & Category===

Type: GUI-less loadable module

Category: Extension

===Authors, Collaborators & Contact===
* Author: Daniel Haehn, University of Heidelberg
* Supervisor: Luca Antiga, Mario Negri Institute
* 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 [http://wiki.na-mic.org/Wiki/index.php/NA-MIC_VMTK_Collaboration NA-MIC VMTK Collaboration].

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

== Usage and Installation ==
This module can be installed using the 3D Slicer Extension Build System or manually. Either way will automatically include the latest version of the VMTK libraries by accessing the official VMTK SVN repository.

* Installation using the 3D Slicer Extension Build System
Inside the 3D Slicer extension system, the module is called ''VmtkSlicerModule''.

* Manual Installation and Compilation
1. To get the latest source code, perform the following SVN checkout command:
<pre>svn checkout https://www.nitrc.org/svn/slicervmtklvlst</pre>
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===
After installing this module, the following Python scripted modules can be installed and used.

[[Modules:VMTKLevelSetSegmentation|VMTKLevelSetSegmentation]] - providing level-set segmentation of vessels, aneurysms and tubular structures using different algorithms

[[Modules:VMTKVesselEnhancement|VMTKVesselEnhancement]] - providing vessel enhancement filters to highlight vasculature or tubular structures

== Development ==


===Source code & Documentation===

The complete source code is available at a [http://www.nitrc.org/plugins/scmsvn/viewcvs.php/VmtkSlicerModule/?root=slicervmtklvlst NITRC SVN repository].

The most important files are the following:

* [http://www.nitrc.org/plugins/scmsvn/viewcvs.php/VmtkSlicerModule/CMakeLists.txt?root=slicervmtklvlst&view=markup CMakeLists.txt] to include the vtkVmtk libraries during compilation

* [http://www.nitrc.org/plugins/scmsvn/viewcvs.php/VmtkSlicerModule/vtkVmtkSlicerModuleLogic.cxx?root=slicervmtklvlst&view=markup vtkVmtkSlicerModuleLogic.cxx] to initialize the generated Tcl wrapper classes of the vtkVmtk libraries

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 [http://www.slicer.org/slicerWiki/images/4/42/Slicer_VMTK_student_research_project.pdf student research project write-up].

===Known bugs===

Follow this [http://www.nitrc.org/tracker/?func=browse&group_id=196&atid=821 link] to the VMTK in 3D Slicer bug tracker.

== More Information == 

===Acknowledgment===
This work was funded by a charitable 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.