Difference between revisions of "Modules:VMTK in 3D Slicer Tutorial: Coronary Artery Centerline Extraction"
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== Segmentation == | == Segmentation == | ||
+ | The centerline extraction using VMTK in 3D Slicer consists of a processing sequence using three different modules. The flow-chart shows their connection. Required user inputs are shown in blue and optional user inputs are labeled | ||
+ | [[File:Vmtkcenterlinepipeline.png|thumb|800x800px|A flow-chart of the VMTK in 3D Slicer tools involved in this tutorial and their connection as a pipeline.]] | ||
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+ | {| | ||
+ | |[[File:Vmtkoriginal.png|thumb|280x280px|The original CTA volume.]] | ||
+ | |[[File:Vmtkroi.png|thumb|280x280px|The extracted subvolume.]] | ||
+ | |} | ||
+ | |||
=== Generating Vesselness using VMTKVesselEnhancement === | === Generating Vesselness using VMTKVesselEnhancement === | ||
=== Lumen Segmentation using VMTKEasyLevelSetSegmentation === | === Lumen Segmentation using VMTKEasyLevelSetSegmentation === | ||
=== Centerline Computation using VMTKCenterlines === | === Centerline Computation using VMTKCenterlines === | ||
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== Evaluation == | == Evaluation == | ||
== References == | == References == |
Revision as of 02:19, 15 November 2009
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Contents
Background
Coronary heart disease (CHD) is the leading cause of death in high-income countries and one of the main causes of death worldwide [WHO2008]. The primary cause for CHD is atherosclerosis of the coronary arteries and is called coronary artery disease (CAD). Plaque within the walls of the coronaries narrows the lumen of the affected vessels (so-called stenosis) and disturbs the regularization abilities of the vessel walls. Consequently this reduces the blood flow inside the affected vessels and constrains the supply of oxygen and nutrients to the myocardium. Beside of heart pain, symptoms of the CHD can appear as heart-rhythm-disturbances, cardiac insufficiency, angina-pectoris-attacks, cardiac infarcts or sudden cardiac deaths [HJ07, pp307].
Medical imaging is used for the diagnosis of CAD and for the quantification and grading of stenosis. The extraction of the central lumen line (centerline) of coronary arteries is helpful for visualization purposes, stenosis quantification or further processing steps (e.g. reformatting) [Schaap2009]. This tutorial shows how to use tools based on the Vascular Modeling Toolkit (VMTK) ([Antiga2008]) in 3D Slicer to segment the right coronary artery (A. coronaria dextra, RCA) in a computed tomography angiography (CTA) volume and extract the associated centerline. In particular the segmentation is performed on a CTA dataset which was obtained through the Rotterdam Coronary Artery Algorithm Evaluation Framework ([Schaap2009]). |
VMTK in 3D Slicer Installation
Before using VMTK in 3D Slicer a set of modules has to be installed. Since 3D Slicer version 3.5 the modules are available as extensions and can be downloaded into an existing Slicer installation by using the extension wizard.The 3D Slicer extension build system provides VMTK in 3D Slicer packages for different OS platforms. At the moment Linux 64bit and Darwin are supported.
Using the extension wizard, the VMTK in 3D Slicer modules can be installed following three steps.
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After restarting 3D Slicer, the VMTK tools are available in the module selector inside the category Vascular Modeling Toolkit. |
If the extension wizard does not work for you or if you want to use VMTK in 3D Slicer on unsupported OS platforms, you should give the manual installation a shot.
Segmentation
The centerline extraction using VMTK in 3D Slicer consists of a processing sequence using three different modules. The flow-chart shows their connection. Required user inputs are shown in blue and optional user inputs are labeled
Generating Vesselness using VMTKVesselEnhancement
Lumen Segmentation using VMTKEasyLevelSetSegmentation
Centerline Computation using VMTKCenterlines
Evaluation
References
[Antiga2008] | Antiga, L.; Piccinelli, M.; Botti, L.; Ene-Iordache, B.; Remuzzi, A. & Steinman, D. A. An image-based modeling framework for patient-specific computational hemodynamics. Med Biol Eng Comput, Biomedical Engineering Department, Mario Negri Institute for Pharmacological Research, Villa Camozzi, Ranica, BG, Italy. 2008, 46, 1097-1112 | |
[HJ07] | Huch, R. & Jürgens, K. D. Mensch, Körper, Krankheit. Urban & Fischer Verlag, 2007 | |
[Schaap2009] | Schaap, M.; Metz, C.; van Walsum, T.; van der Giessen, A.; Weustink, A.; Mollet, N.; Bauer, C.; Bogunović, H.; Castro, C.; Deng, X.; Dikici, E.; O'Donnell, T.; Frenay, M.; Friman, O.; Hoyos, M. H.; Kitslaar, P.; Krissian, K.; Kühnel, C.; Luengo-Oroz, M. A.; Orkisz, M.; Smedby, Ö.; Styner, M.; Szymczak, A.; Tek, H.; Wang, C.; Warfield, S. K.; Zambal, S.; Zhang, Y.; Krestin, G. P. & Niessen, W. Standardized Evaluation Methodology and Reference Database for Evaluating Coronary Artery Centerline Extraction Algorithms. Medical Image Analysis, 2009, 13/5, 701-714 | |
[WHO08] | World Health Organization WHO. The top ten causes of death. Fact sheet N310, 10 2008. |