Modules:VMTK in 3D Slicer Tutorial: Coronary Artery Centerline Extraction

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Segmentation of the Right Coronary Artery using VMTK in 3D Slicer
Close-Up of the segmented Vessel
The Voronoi Diagram and the corresponding Centerline

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]).

Even if this documentation shows how to establish a work flow between three VMTK in 3D Slicer tools, each of the three documented segmentation steps can be considered as a guide for the individual module.

Human heart with Coronary Arteries

VMTK in 3D Slicer Installation

Before using VMTK in 3D Slicer a set of modules has to be installed. Since the 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 cogwheel icon starts the 3D Slicer 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.

  • STEP ONE: Select Find & Install and click next.
  • STEP TWO: Choose the desired modules and click Download & Install. In this tutorial we use the following extensions:
    • VmtkSlicerModule to get the VMTK libraries (see also this page for further documentation)
    • VMTKVesselEnhancement to generate a vessel enhanced image (see also this page for further documentation)
    • VMTKEasyLevelSetSegmentation to perform level-set initialization and evolution (see also this page for further documentation)
    • VMTKCenterlines to compute the centerlines (see also this page for further documentation)
  • STEP THREE: Restart 3D Slicer
After restarting 3D Slicer, the VMTK tools are available in the module selector inside the category Vascular Modeling Toolkit.
Step one: Find & Install
Step two: Selection of the modules
Step three: Restart 3D Slicer
The VMTK tools appear 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.

A flow-chart of the VMTK in 3D Slicer tools involved in this tutorial and their connection as a pipeline.

Due to time-consuming calculations, it is highly recommended to extract a subvolume of the region of interest prior to the segmentation process. This can be done by using Converters -> Extract Subvolume or Converters -> Extract Subvolume ROI in the 3D Slicer module selector.

The original CTA volume.
The extracted subvolume.

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.