Modules:VMTKCenterlines - Revision history

Haehn: /* Examples, Use Cases */

2010-04-20T14:54:36Z

Examples, Use Cases

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

2010-04-20T14:53:42Z

Quick Tour of Features and Use

Haehn: /* Dependencies */

2010-04-20T14:46:26Z

Dependencies

Haehn: /* Examples, Use Cases */

2010-04-20T14:45:35Z

Examples, Use Cases

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

2010-04-20T14:41:40Z

Notes from the Developer(s)

Haehn: /* Examples, Use Cases */

2010-04-20T14:39:23Z

Examples, Use Cases

Haehn: /* Module Name */

2010-04-20T14:15:40Z

Module Name

Haehn: /* Module Description */

2010-04-20T14:01:33Z

Module Description

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

2010-04-20T14:00:01Z

Notes from the Developer(s)

Haehn: /* Module Description */

2010-04-20T13:59:36Z

Module Description

@@ Line 57: / Line 57: @@
 |}
-Now source and target fiducials have to be placed on the model in the 3D rendering window to specify the centerline routes. The fiducial positioning does not have to be exact because the module calculates the nearest position on the surface model to the input fiducials. After placing the fiducials, the centerline computation can be started.
+Now source and target fiducials have to be placed on the model in the 3D rendering window to specify the centerline routes. The fiducial positioning does not have to be exact because the module calculates the nearest position on the surface model to the input fiducials. After placing the fiducials, the centerline computation can be started. Depending on the surface model size the process can take a couple of minutes.
 On completion of the calculation, the inner Voronoi diagram and the corresponding centerlines are visible as polydata models in the 3D rendering window.

@@ Line 83: / Line 83: @@
 ===Quick Tour of Features and Use===
-The graphical user interface of the VMTKEasyLevelSetSegmentation module consists of four panels.
+The graphical user interface of the VMTKCenterlines module consists of five panels.
 [[Image:Centerlinesgui.png|thumb|500x500px|The GUI of VMTKCenterlines. Click to enlarge.]]
-* Main module panel:
+* Input panel:
-Parameter presets exist for different use-cases. These get loaded from the MRML file ''presets.xml'' inside the module directory and can be edited.
+The input surface model can be selected using this panel.
-* I/O panel:
+* Preparation Step panel:
-The input volume and the output volumes for the initialization and evolution stage can be selected using this panel.
+The preparation step includes surface capping and removing unneeded traingles of the input model.
-* Initialization panel:
+* Centerline Computation panel:
-The threshold slider is used as a parameter for the Fast Marching Upwind Gradient Image Filter and updates the slice viewers during change for visualization.
+This step includes the actual centerline extraction. Source and target points can be specified as fiducial lists. At least one source and one target point have to exist but it is possible to use f.e. only one source point and several target points. The centerlines run between these points.
-* Evolution panel:
+Additionally the output models for the centerlines and the Voronoi diagram can be specified.
-Different weights are available to configure the inflation of the initial level-set. Is is possible to adjust the importance of inflation, curvature shape and attraction to the gradient ridges.
+* Export panel:
-The number of iterations defines how many steps of evolution are performed.
+The module supports the export of the extracted centerlines as cloud of points to the filesystem. It is possible to add a header to these files or additional details like the radii. Inverting the coordinates multiplies the X,Y coordinates by -1.
 == Development ==

@@ Line 112: / Line 112: @@
 ===Dependencies===
-This module depends on the VMTK libraries which are provided in the [[Modules:VMTKSlicerModule|VmtkSlicerModule]]. Therefore the [[Modules:VMTKSlicerModule|VmtkSlicerModule]] has to be installed before the VMTKEasyLevelSetSegmentation module can be used.
+This module depends on the VMTK libraries which are provided in the [[Modules:VMTKSlicerModule|VmtkSlicerModule]]. Therefore the [[Modules:VMTKSlicerModule|VmtkSlicerModule]] has to be installed before the VMTKCenterlines module can be used.
 ===Known bugs & Usability issues===

@@ Line 69: / Line 69: @@
 {|
-|[[Image:Avf_3d_voronoi_big.png|thumb|460x460px|A close-up of the Voronoi diagram colored by the maximal inscribed sphere radius [vx].]]
+|[[Image:Avf_3d_voronoi_big.png|thumb|460x460px|A close-up of the Voronoi diagram colored by the maximal inscribed sphere radius [mm].]]
 |}

@@ Line 108: / Line 108: @@
 ===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. More information on Voronoi diagrams can be found on Wikipedia (http://en.wikipedia.org/wiki/Voronoi_diagram). The algorithm using the minimal path on this diagram is described in Luca Antiga's PhD thesis (http://villacamozzi.marionegri.it/~luca/files/AntigaPhDThesis.pdf).
 ===Dependencies===

← Older revision		Revision as of 14:39, 20 April 2010
Line 45:		Line 45:

	===Examples, Use Cases===		===Examples, Use Cases===
		+	* '''Example centerline extraction'''
		+	The centerline computation requires an existing 3D surface model. This can be obtained using the [[Modules:VMTKEasyLevelSetSegmentation\|VMTKEasyLevelSetSegmentation]] module.
		+
		+	After selecting the existing surface model as input, the second step is to prepare this model. This includes capping holes in the surface and removing unneeded triangles. The surface model color changes to green.
		+
		+	{\|
		+	\|-valign="top"
		+	\|[[Image:Avf_orig_axial.png\|thumb\|260x260px\|Axial view of a contrast-enhanced three-dimensional image acquired from a MR scanner, showing an AV fistula in an arm. (Courtesy of L. Antiga, Bioengineering Department, Mario Negri Institute, Ranica (BG), Italy and N.R. Planken, Academisch Ziekenhuis Maastricht, the Netherlands.)]]
		+	\|[[Image:Avf_3d_evolution_new.png\|thumb\|260x260px\|A surface model of a segmentation of the original image obtained with the [[Modules:VMTKEasyLevelSetSegmentation\|VMTKEasyLevelSetSegmentation]] module.]]
		+	\|[[Image:Avf_3d_preparation.png\|thumb\|260x260px\|This surface model after the preparation stage. Holes in the surface were closed.]]
		+	\|}
		+
		+	Now source and target fiducials have to be placed on the model in the 3D rendering window to specify the centerline routes. The fiducial positioning does not have to be exact because the module calculates the nearest position on the surface model to the input fiducials. After placing the fiducials, the centerline computation can be started.
		+
		+	On completion of the calculation, the inner Voronoi diagram and the corresponding centerlines are visible as polydata models in the 3D rendering window.
		+	{\|
		+	\|-valign="top"
		+	\|[[Image:Avf_3d_eikonal.png\|thumb\|260x260px\|The inner Voronoi diagram colored by the solutions of the Eikonal equation obtained by Fast Marching back-tracking along the minimal path. The legend can be displayed using the [[Modules:Colors-Documentation-3.6\| Colors module]].]]
		+	\|[[Image:Avf_3d_centerlines.png\|thumb\|260x260px\|The centerline representation of the vessel's topology.]]
		+	\|}
		+
		+	A close-up of the Voronoi diagram shows the tiles separating the Voronoi regions. The modules also calculates the radius of the lumen for each point along the centerlines.
		+
		+	{\|
		+	\|[[Image:Avf_3d_voronoi_big.png\|thumb\|460x460px\|A close-up of the Voronoi diagram colored by the maximal inscribed sphere radius [vx].]]
		+	\|}
		+
		+	The extracted centerlines as well as the calculated radii along the centerlines can be exported and imported as a cloud of points to the filesystem.

	===Tutorials===		===Tutorials===

@@ Line 11: / Line 11: @@
 |[[Image:Centerlinesgui.png|thumb|280x280px|Main GUI of VMTKCenterlines.]]
 |[[Image:Avf_orig_axial.png|thumb|260x260px|Axial view of a contrast-enhanced three-dimensional image acquired from a MR scanner, showing an AV fistula in an arm. (Courtesy of L. Antiga, Bioengineering Department, Mario Negri Institute, Ranica (BG), Italy and N.R. Planken, Academisch Ziekenhuis Maastricht, the Netherlands.)]]
-|[[Image:Avf_3d_preparation.png|thumb|260x260px|A surface model representation of an already existing segmentation.]]
+|[[Image:Avf_3d_preparation.png|thumb|260x260px|A surface model representation of an already existing segmentation after preparation stage.]]
 |[[Image:Avf_3d_centerlines.png|thumb|260x260px|Resulting centerline representation of the vessel topology.]]
 |}

@@ Line 28: / Line 28: @@
 ===Module Description===
-This module provides centerline computation of surface models in 3D Slicer using methods of the '''geometric analysis functionality of the Vascular Modeling Toolkit''' (http://www.vmtk.org). Centerlines are the central lumen lines in tubular structures and f.e. can be powerful descriptors of the vessel's topology. The module targets easy-to-use centerline extraction using seed and target points.
+This module provides centerline computation of surface models in 3D Slicer using methods of the '''geometric analysis functionality of the Vascular Modeling Toolkit''' (http://www.vmtk.org). Centerlines are the central lumen lines in tubular structures and f.e. can be powerful descriptors of the vessel's topology. The module targets easy-to-use centerline extraction using seed and target points and also enables import and export functionality.
 The actual centerline extraction is based on calculating an inner Voronoi diagram by computing the Delaunay tessellation.