Difference between revisions of "Modules:VMTKSlicerModule"
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| − | [[Documentation-3. | + | [[Documentation-3.6|Return to Slicer 3.6 Documentation]] |
| − | [[Announcements:Slicer3. | + | [[Announcements:Slicer3.6#Highlights|Gallery of New Features]] |
__NOTOC__ | __NOTOC__ | ||
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VmtkSlicerModule | VmtkSlicerModule | ||
| + | {| | ||
| + | |[[Image:Slicervmtk_logo.png|thumb|280px|Part of the VMTK in 3D Slicer collection]] | ||
| + | |} | ||
== General Information == | == General Information == | ||
| Line 17: | Line 20: | ||
===Authors, Collaborators & Contact=== | ===Authors, Collaborators & Contact=== | ||
* Author: Daniel Haehn, University of Heidelberg | * Author: Daniel Haehn, University of Heidelberg | ||
| − | * | + | * Acknowledgments: Luca Antiga, Mario Negri Institute; Steve Pieper, Isomics Inc. |
| − | |||
* Contact: Daniel Haehn, haehn@bwh.harvard.edu | * Contact: Daniel Haehn, haehn@bwh.harvard.edu | ||
===Module Description=== | ===Module Description=== | ||
| − | This GUI-less loadable module provides the libraries of the Vascular Modeling Toolkit (http://www.vmtk.org/) in 3D Slicer. | + | 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]. | 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 == | |
| + | ===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. | ||
| + | |||
| + | *[[Modules:VMTKCenterlines|VMTKCenterlines]] providing centerline computation of surface models | ||
| − | + | *[[Modules:VMTKEasyLevelSetSegmentation|VMTKEasyLevelSetSegmentation]] providing level-set segmentation of vessels, aneurysms and tubular structures using an easy interface | |
| − | |||
| − | [[Modules:VMTKLevelSetSegmentation|VMTKLevelSetSegmentation]] | + | *[[Modules:VMTKLevelSetSegmentation|VMTKLevelSetSegmentation]] providing level-set segmentation of vessels, aneurysms and tubular structures using different algorithms for initialization and evolution |
| − | [[Modules:VMTKVesselEnhancement|VMTKVesselEnhancement]] | + | *[[Modules:VMTKVesselEnhancement|VMTKVesselEnhancement]] providing vessel enhancement filters to highlight vascular 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=== | ||
| + | |||
| + | 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/ | + | * [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 |
| − | + | 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/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=== | ||
| Line 61: | Line 79: | ||
===Acknowledgment=== | ===Acknowledgment=== | ||
| − | + | 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. | ||
Latest revision as of 12:38, 27 November 2019
Home < Modules:VMTKSlicerModuleReturn to Slicer 3.6 Documentation
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 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.
- VMTKCenterlines providing centerline computation of surface models
- 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 for initialization and evolution
- VMTKVesselEnhancement providing vessel enhancement filters to highlight vascular or tubular structures
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:
- 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
- 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.
