NA-MIC/Projects/External Collaboration/Slicer3-vmtk Integration

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Home < NA-MIC < Projects < External Collaboration < Slicer3-vmtk Integration
Vmtk working inside Slicer3.

Key Investigators

  • Mario Negri Institute, University of Verona: Luca Antiga
  • Dan Blezek
  • Mike Halle
  • Steve Piper


To create a Slicer-based platform for segmentation of vascular segments from angiographic images (CTA, MRA, ...), analysis of vascular geometry, mesh generation, computational hemodynamics (CFD) and visualization.

Approach, Plan

To integrate vmtk scripts within Slicer as command-line modules for the non-interactive tasks, and to create ad-hoc GUI modules for the more interactive tasks (i.e. segmentation).

The plan for the project week is to finalize the implementation of an interactive LevelSetSegment module that replicates (and improves) the interactive segmentation tool currently in vmtk. Tentatively, LevelSetSegment will be a Python Scripted Module.


During project weeks last year (see 2007 Project Week at MIT), automated conversion of vmtk script pipes to Slicer command-line modules has been implemented.

During June 2008 project week, the architecture of the new LevelSetSegment module has been finalized. A new vtkMRMLLevelSetNode, subclass of vtkMRMLScalarVolumeNode, has been introduced. The corresponding display node directly displays the poly data corresponding to the level set surface. The final implementation of the module (except the new MRML nodes) will be converted to a Python scripted module.


  • Lee SW, Antiga L, Spence JD and Steinman DA. Geometry of the carotid bifurcation predicts its exposure to disturbed flow. Stroke. Accepted.
  • Thomas JB, Antiga L, Che S, Milner JS, Hangan Steinman DA, Spence JD, Rutt BK and Steinman DA. Variation in the carotid bifurcation geometry of young vs. older adults: Implications for "geometric risk" of atherosclerosis. Stroke, 36(11): 2450-2456, Nov 2005.
  • Antiga L, Steinman DA. Robust and objective decomposition and mapping of bifurcating vessels. IEEE Transactions on Medical Imaging, 23(6): 704-713, June 2004.
  • Antiga L, Ene-Iordache B and Remuzzi A. Computational geometry for patient-specific reconstruction and meshing of blood vessels from MR and CT angiography. IEEE Transactions on Medical Imaging, 22(5): 674-684, May 2003.