Difference between revisions of "Modules:VMTKSlicerModule"

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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__
 
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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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* Supervisor1: Luca Antiga, Mario Negri Institute
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* Acknowledgments: Luca Antiga, Mario Negri Institute; Steve Pieper, Isomics Inc.
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* Supervisor2: Steve Pieper, Isomics Inc.
 
 
* Contact: Daniel Haehn, haehn@bwh.harvard.edu
 
* Contact: Daniel Haehn, haehn@bwh.harvard.edu
  
 
===Module Description===
 
===Module Description===
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This GUI-less loadable module provides the libraries of the Vascular Modeling Toolkit (http://www.vmtk.org/) in 3D Slicer.
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This GUI-less loadable module provides the libraries of '''the Vascular Modeling Toolkit''' (http://www.vmtk.org/) in 3D Slicer.
  
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== Usage and Installation ==
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It is part of the [http://wiki.na-mic.org/Wiki/index.php/NA-MIC_VMTK_Collaboration NA-MIC VMTK Collaboration].
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TODO manual install
 
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TODO extension
 
  
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'''Official project page:''' http://www.vmtk.org/Main/VmtkIn3DSlicer
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== 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===
 
===Examples, Use Cases & Tutorials===
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TODO link to python modules
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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.
 +
 
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*[[Modules:VMTKCenterlines|VMTKCenterlines]] providing centerline computation of surface models
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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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*[[Modules:VMTKVesselEnhancement|VMTKVesselEnhancement]] providing vessel enhancement filters to highlight vascular or tubular structures
  
 
== Development ==
 
== Development ==
  
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===Dependencies===
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===Notes from the Developer(s)===
 +
The algorithms provided by VMTK and by this module are C++ classes implemented using VTK and ITK.
  
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Other modules or packages that are required for this module's use.
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===Source code & Documentation===
  
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===Known bugs===
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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:
  
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Follow this [http://www.nitrc.org/tracker/?func=browse&group_id=196&atid=821 link] to the VMTK in 3D Slicer bug tracker.
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* [http://www.nitrc.org/plugins/scmsvn/viewcvs.php/VmtkSlicerModule/CMakeLists.txt?root=slicervmtklvlst&view=markup CMakeLists.txt] to include the vtkVmtk libraries during compilation
  
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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
  
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===Usability issues===
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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.
  
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Follow this [http://www.nitrc.org/tracker/?func=browse&group_id=196&atid=821 link] to the VMTK in 3D Slicer bug tracker. Please select the '''usability issue category''' when browsing or contributing.
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Since the Tcl initialization is performed, the vtkVmtk library can also be accessed from Python in 3D Slicer.
  
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===Source code & documentation===
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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].
  
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Customize following [http://viewvc.slicer.org/viewcvs.cgi/ links] for your module.
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Documentation of the VMTK libraries is available [http://www.vmtk.org/doxygen/html/annotated.html here].
  
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[http://www.na-mic.org/Slicer/Documentation/Slicer3/html/ Links] to documentation generated by doxygen.
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===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 ==  
 
== More Information ==  
  
 
===Acknowledgment===
 
===Acknowledgment===
−
Include funding and other support here.
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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===
−
Publications related to this module go here. Links to pdfs would be useful.
+
* 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.

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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