Modules:VMTKVesselEnhancement - Revision history

Kikinis: /* Quick Tour of Features and Use */

2010-05-24T12:03:32Z

Quick Tour of Features and Use

Haehn: /* Notes from the Developer(s) */

2010-04-20T13:04:06Z

Notes from the Developer(s)

Haehn: /* Quick Tour of Features and Use */

2010-04-20T13:03:20Z

Quick Tour of Features and Use

Haehn: /* Development */

2010-04-20T11:19:16Z

Development

Haehn: /* Quick Tour of Features and Use */

2010-04-06T10:57:47Z

Quick Tour of Features and Use

Haehn: /* References */

2010-04-06T10:52:06Z

References

Haehn: /* Source code & documentation */

2010-04-06T10:49:21Z

Source code & documentation

Haehn: /* Known bugs & Usability issues */

2010-04-06T10:45:31Z

Known bugs & Usability issues

Haehn: /* Tutorials */

2010-04-06T10:44:52Z

Tutorials

Haehn: /* Quick Tour of Features and Use */

2010-04-06T10:20:37Z

Quick Tour of Features and Use

@@ Line 75: / Line 75: @@
 ===Quick Tour of Features and Use===
 The graphical user interface of the VMTKVesselEnhancement module consists of two panels.
 [[Image:Vesselenhancementgui.png|thumb|500x500px|The GUI of VMTKVesselEnhancement showing the interface to Frangi's method. Click to enlarge.]]

@@ Line 95: / Line 95: @@
 ===Notes from the Developer(s)===
-The algorithms provided by VMTK and used by this module are C++ classes implemented using VTK and ITK.
+The algorithms provided by VMTK and used by this module are C++ classes implemented using VTK and ITK. The module using the following algorithms: ''FrangiVesselness'' based on Multiscale Vessel Enhancement Filtering by Frangi A. et al. (http://www.tecn.upf.es/~afrangi/articles/miccai1998.pdf), ''SatoVesselness'' based on Three-dimensional multi-scale line filter for segmentation and visualization of curvilinear structures in medical images by Sato Y. et al. (http://www.spl.harvard.edu/publications/bitstream/download/2732) and ''VesselEnhancingDiffusion'' based on Vessel Enhancing Diffusion Filter by Enquobahrie A. et al. (http://hdl.handle.net/1926/558).
 ===Dependencies===

@@ Line 81: / Line 81: @@
 The MRML volume nodes to use as input and output can be specified at this panel.
 * Vessel Enhancement panel:
-Different filtering methods are available to highlight or enhance tubular structures. These are:
+Different filtering methods are available to highlight or enhance tubular structures. These can be chosen by using the tabs.
-- ''FrangiVesselness'' based on Multiscale Vessel Enhancement Filtering by Frangi A. et al. (http://www.tecn.upf.es/~afrangi/articles/miccai1998.pdf)
+The range of tube diameters to be highlighted can be specified in voxels or millimeters. The steps between the minimal and maximal diameters regulate the accuracy of the vessel detection process.
-- ''SatoVesselness'' based on Three-dimensional multi-scale line filter for segmentation and visualization of curvilinear structures in medical images by Sato Y. et al. (http://www.spl.harvard.edu/publications/bitstream/download/2732)
+Sensitivity thresholds can be specified to control the filtering for different types of structures. The lower a threshold is, the more sensitive is the detection of this structure type. A common approach is to set this value to 0.25*Max_Intensity.
 '''For example to enhance line-like structures''' rather than plate-like or blob-like structures, set the sensitivity thresholds for Frangi's method to the following:

← Older revision		Revision as of 11:19, 20 April 2010
Line 99:		Line 99:

	== Development ==		== Development ==
		+
		+	===Notes from the Developer(s)===
		+	The algorithms provided by VMTK and used by this module are C++ classes implemented using VTK and ITK.

	===Dependencies===		===Dependencies===

@@ Line 76: / Line 76: @@
 ===Quick Tour of Features and Use===
 The graphical user interface of the VMTKVesselEnhancement module consists of two panels.
-[[Image:Vesselenhancementgui.png|thumb|400x400px|The GUI of VMTKVesselEnhancement showing the interface to Frangi's method. Click to enlarge.]]
+[[Image:Vesselenhancementgui.png|thumb|500x500px|The GUI of VMTKVesselEnhancement showing the interface to Frangi's method. Click to enlarge.]]
 * I/O panel:

← Older revision		Revision as of 10:52, 6 April 2010
Line 126:		Line 126:

	===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.
		+	* D. Hähn. Centerline Extraction of Coronary Arteries in 3D Slicer using VMTK based Tools. Master's Thesis. Department of Medical Informatics, University of Heidelberg, Germany. Feb 2010.
	* 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.

@@ Line 109: / Line 109: @@
 ===Source code & documentation===
 VMTKVesselEnhancement is a Python Scripted Module. It follows the conventions of the Model View Controller pattern of slicer modules. This implies the separation of logic and GUI.
 The class ''SlicerVMTKVesselEnhancementGUI'' derives from ''ScriptedModuleGUI'' and saves the current user interface state to its own MRML node. The MRML nodes of the used volume and model data are additionally attached. This allows different instances of the vessel enhancement module to be run at the same time. The actual calls to the VMTK libraries are only performed in the class ''SlicerVMTKVesselEnhancementLogic''.
 Separate classes derived from the interface ''SlicerVMTKAdvancedPageSkeleton'' were created for each filtering method in order to ensure the possibility of maintenance and extension. The calls to the required methods like UpdateGUI() or UpdateMRML() get forwarded to each individual sub-class to support the modular design and enable code encapsulation.

← Older revision		Revision as of 10:45, 6 April 2010
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	===Known bugs & Usability issues===		===Known bugs & Usability issues===
−
−	~~'''Fix when you installed old versions of the module and it does not work or the buttons on the interface look strange:'''~~
−
−	~~Manually delete lib/Slicer3/Modules/@SVN@/VMTK* or where ever the extensions were installed (replace @SVN@ with the revision of your Slicer installation).~~

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

← Older revision		Revision as of 10:44, 6 April 2010
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	===Tutorials===		===Tutorials===
		+	The following tutorials demonstrate the use of VMTKVesselEnhancement as a processing step in a pipeline of VMTK modules to extract the centerlines of coronary arteries.
		+
		+	{\|
		+	\|[[Image:Vmtkaftercenterline.png\|thumb\|260x260px\|Step-by-step online tutorial: Segmentation of the Right Coronary Artery using VMTK in 3D Slicer. View online [[Modules:VMTK_in_3D_Slicer_Tutorial:_Coronary_Artery_Centerline_Extraction\|here]].]]
		+	\|[[Image:VMTKCenterlines_Tutorial_first_slide.png\|thumb\|280x280px\|Step-by-step tutorial including example dataset: The first slide of the Centerline Extraction tutorial. Download [http://www.na-mic.org/Wiki/images/4/40/TutorialVMTKCoronariesCenterlinesMRI_Winter2010AHM.pdf here].]]
		+	\|}

	===Quick Tour of Features and Use===		===Quick Tour of Features and Use===

@@ Line 85: / Line 85: @@
 The range of tube diameters to be highlighted can be specified in voxels. The steps between the minimal and maximal diameters regulate the accuracy of the vessel detection process.
-Sensitivity thresholds can be specified to control the filtering for different types of structures. The lower a threshold is, the more sensitive is the detection of this structure type. '''For example to enhance line-like structures''' rather than plate-like or blob-like structures, set the sensitivity thresholds for Frangi's method to the following:
+Sensitivity thresholds can be specified to control the filtering for different types of structures. The lower a threshold is, the more sensitive is the detection of this structure type.
 * Plate-like and line-like structures: 0.3
 * Blob-like structures: 500