Difference between revisions of "Modules:VMTKSlicerModule"

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[[Documentation-3.4|Return to Slicer 3.4 Documentation]]
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[[Documentation-3.6|Return to Slicer 3.6 Documentation]]
  
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[[Announcements:Slicer3.4#Highlights|Gallery of New Features]]
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[[Announcements:Slicer3.6#Highlights|Gallery of New Features]]
  
 
__NOTOC__
 
__NOTOC__
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VmtkSlicerModule
 
VmtkSlicerModule
  
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{|
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|[[Image:Slicervmtk_logo.png|thumb|280px|Part of the VMTK in 3D Slicer collection]]
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|}
  
 
== General Information ==
 
== General Information ==
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===Authors, Collaborators & Contact===
 
===Authors, Collaborators & Contact===
 
* Author: Daniel Haehn, University of Heidelberg
 
* Author: Daniel Haehn, University of Heidelberg
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* Supervisor: Luca Antiga, Mario Negri Institute
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* Acknowledgments: Luca Antiga, Mario Negri Institute; Steve Pieper, Isomics Inc.
 
* Contact: Daniel Haehn, haehn@bwh.harvard.edu
 
* Contact: Daniel Haehn, haehn@bwh.harvard.edu
  
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'''Official project page:''' http://www.vmtk.org/Main/VmtkIn3DSlicer
 
'''Official project page:''' http://www.vmtk.org/Main/VmtkIn3DSlicer
  
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== Usage and Installation ==
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== Usage ==
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This module can be installed using the 3D Slicer Extension Build System or by a manual installation. Either way will automatically include the latest version of the VMTK libraries by accessing the official VMTK SVN repository.
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===Installation===
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This module can be installed using the '''3D Slicer extension wizard'''. The extension is called ''VmtkSlicerModule''.
  
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* Installation using the 3D Slicer Extension Build System
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When the module was successfully installed, all VMTK extensions can be used.
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Inside the 3D Slicer extension system, the module is called ''VmtkSlicerModule''.
 
  
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* Manual Installation and Compilation
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===Examples, Use Cases & Tutorials===
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1. To get the latest source code, perform the following SVN checkout command:
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The actual VMTK functions for end users are provided as Python scripted modules.
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<pre>svn checkout https://www.nitrc.org/svn/slicervmtklvlst</pre>
 
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2. A directory named ''VmtkSlicerModule'' is downloaded and the latest VMTK libraries get checked out as well.
 
  
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3. Copy this directory to ''Slicer3/Modules/'' of your local Slicer installation.
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After installing this module, the following extensions can be installed and used.
  
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4. Edit the ''Slicer3/Modules/CMakeLists.txt'' file and add ''VmtkSlicerModule'' to the Subdirs directive.
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*[[Modules:VMTKCenterlines|VMTKCenterlines]] providing centerline computation of surface models
  
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5. Change directory to ''Slicer3-build/'' and issue a ''make -j2'' command to start the compilation.
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*[[Modules:VMTKEasyLevelSetSegmentation|VMTKEasyLevelSetSegmentation]] providing level-set segmentation of vessels, aneurysms and tubular structures using an easy interface
  
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*[[Modules:VMTKLevelSetSegmentation|VMTKLevelSetSegmentation]] providing level-set segmentation of vessels, aneurysms and tubular structures using different algorithms for initialization and evolution
  
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When the module was successfully installed, all VMTK methods are available for developer access within 3D Slicer.
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*[[Modules:VMTKVesselEnhancement|VMTKVesselEnhancement]] providing vessel enhancement filters to highlight vascular or tubular structures
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===Examples, Use Cases & Tutorials===
 
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After installing this module, the following Python scripted modules can be installed and used.
 
−
 
 
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[[Modules:VMTKLevelSetSegmentation|VMTKLevelSetSegmentation]] - providing level-set segmentation of vessels, aneurysms and tubular structures using different algorithms
 
−
 
 
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[[Modules:VMTKVesselEnhancement|VMTKVesselEnhancement]] - providing vessel enhancement filters to highlight vasculature or tubular structures
 
  
 
== Development ==
 
== Development ==
  
 +
===Notes from the Developer(s)===
 +
The algorithms provided by VMTK and by this module are C++ classes implemented using VTK and ITK.
  
 
===Source code & Documentation===
 
===Source code & Documentation===
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* [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
 
* [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
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 +
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.
 
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].
+
Information and documentation concerning the integration of VMTK can be found in this [http://www.slicer.org/w/img_auth.php/4/42/Slicer_VMTK_student_research_project.pdf student research project write-up].
 +
 
 +
Documentation of the VMTK libraries is available [http://www.vmtk.org/doxygen/html/annotated.html here].
  
 
===Known bugs===
 
===Known bugs===
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===Acknowledgment===
 
===Acknowledgment===
−
This work was funded by a charitable grant of the Thomas­-Gessmann Foundation part of the Founder Federation for German Science.
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This work was funded by a grant of the Thomas­-Gessmann Foundation part of the Founder Federation for German Science.
  
 
===References===
 
===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.
 
* 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.
 
* 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.
 

Latest revision as of 12:38, 27 November 2019

Home < Modules:VMTKSlicerModule

Return to Slicer 3.6 Documentation

Gallery of New Features


Module Name

VmtkSlicerModule

Part of the VMTK in 3D Slicer collection

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 using the 3D Slicer extension wizard. The extension is called VmtkSlicerModule.

When the module was successfully installed, all VMTK extensions can be used.

Examples, Use Cases & Tutorials

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

After installing this module, the following extensions can be installed and used.

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

Development

Notes from the Developer(s)

The algorithms provided by VMTK and by this module are C++ classes implemented using VTK and ITK.

Source code & Documentation

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

The most important files are the following:

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

  • 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.
  • 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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