NA-MIC Project Weeks

Upper airway segmentation and airflow simulation

Key Investigators

Kitti Farkas (University of Szeged)
Attila Nagy (University of Szeged)
Bence Horváth (University of Szeged)
Endre Vecsernyés (University of Szeged)
Andras Lasso (Queen’s University, Canada)
Jean-Christophe Fillion-Robin (Kitware Inc.)

Project Description

We want to do some airflow simulations in a finite element software but we didn’t managed to import the 3D upper airway models which we made in the Slicer.

Objective

Smooth the 3D models
Import the models successfully to the finite element software and mesh them
Do some airflow simulations

Approach and Plan

Describe specific steps of what you plan to do to achieve the above described objectives.
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Progress and Next Steps

Potential solutions identified:

A. Fix up STL

Fix data in Slicer: Smooth segmentation before export (using Segment Editor module), clean up surface using SurfaceToolbox module
Inspect incorrect element reported by Comsol using Paraview
Use mesh cleanup functions in MeshLab and MeshMixer

B. Create volumetric mesh directly in Slicer, from segmentation - using SegmentMesher module. Cleaver works directly from labelmap, therefore it is robust and guaranteed to always generate valid mesh. We can save .vtk or .vtu that is note directly readable in Comsol. Convert FE mesh to compatible format:

Paraview: can read VTK and write few formats, none of them directly readable in Comsol, could write a compatible format (xdf) but Comsol could not read it
FreeCAD: can read some VTK formats and could write a compatible format but the exported file was invalid
MeshIO: support several file formats, VTK input, but no directly usable output. No binary available, so we would need to build from source.

C. Use FeBIO solver

Open-source. Free for research use. Pre/post view available with nice GUI. Can directly read FE mesh saved in Slicer.

It supports airflow analysis and fluid-structure interactions. See overview and applications in upper airway mechanics:

Luo, H., Mittal, R., Zheng, X., Bielamowicz, S. A., Walsh, R. J., and Hahn, J. K., 2008, “An Immersed-Boundary Method for Flow–Structure Interaction in Biological Systems With Application to Phonation,” J. Comput. Phys., 227(22), pp. 9303–9332.
Malve, M., Peerez del Palomar, A., Chandra, S., Loopez-Villalobos, J. L., Mena, A., Finol, E. A., Ginel, A., and Doblare, M., 2011, “FSI Analysis of a Healthy and a Stenotic Human Trachea Under Impedance-Based Boundary Conditions,” ASME J. Biomech. Eng., 133(2), p. 021001.