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BioPARR
- Biomechanics based Prediction
of Aneurysm Rupture Risk |
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Developed
by Grand Roman Joldes, Senior Research Fellow
Intelligent
Systems for Medicine Laboratory and Vascular Engineering Laboratory
The University of Western
Australia.
BioPARR (Biomechanics
based Prediction of Aneurysm Rupture Risk) is a software system that facilitates
the analysis of abdominal aortic aneurisms (AAA) and evaluation of rupture risk
using a finite element analysis based approach. Except semi-automatic
segmentation of the AAA and intraluminal thrombus (ILT) from medical images,
the entire analysis is performed automatically. The system is modular and
easily expandable, allows the extraction of information from images of
different modalities (CT, MRI) and the simulation of different modelling
scenarios.
The software
system will allow researchers to perform comparative evaluation of AAA using a
standardised approach and will help work towards a translational tool for the
clinic. It is free to use, you can download it
from here (Note: The software requires the installation of 3D Slicer and Paraview. Installers for the supported versions of these
programs are available in this archive.)
The software
system consists of a collection of programs and scripts which perform the
required steps in the AAA workflow, from image segmentation to geometry
creation, meshing, finite element analysis and rupture potential index (RPI)
computation (Figure 1). The software is divided into several modules which
perform specific tasks and are being run in sequence from a master script
(batch) file. Data communication between these modules is performed using files
in standard formats; this allows the user flexibility in changing or extending
the functionality of the software, by replacing or adding additional modules.
The software runs on 64Bit Windows operating systems and has been tested on
Windows 7 and 8.
I have created
a series of tutorial training videos for each step of the analysis - available
at the bottom of this page: Tutorials.
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Figure 1. Example of RPI computation results. a) Intra-luminal thrombus (ILT) thickness [mm]. b) Normalized
diameter. c) Wall strength for a female with family history of AAA [MPa]. d)
Rupture Potential Index (RPI) for a female with family history of AAA.
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Figure 2. a) Example of
geometry. AAA exterior surface in blue, interior surface in yellow and ILT surface
in red. b) Example of generated mesh. The AAA wall is meshed using 2 layers of
elements (configurable). The ILT is meshed using a minimum of 2 layers of
elements (configurable); the element size is increased in the middle of the ILT
layer to reduce the number of elements in the mesh. c) Example of generated Abaqus model.
BioPARR was developed
through funding by the National Health and Medical Research Council (NHMRC),
Grant APP1063986 (Dr. B. J. Doyle, Prof. D. Newby, Prof. P. R.
Hoskins, Prof. K. Miller and Prof.
A. Lu).
AAA tutorials
Tutorial 1: Slicer 3D usage and volume cropping
Tutorial 2: Segmentation of blood channel
Tutorial 3: Segmentation of AAA
Tutorial 4: AAA wall extraction (including ILT)
Sample data and results for Tutorials 2-4
AAA wall extraction - one click scripted version
Tutorial 5: Separate AAA surfaces
Software required for Tutorial 5
Separate AAA surfaces - one click scripted version
Tutorial 6: Measure wall thickness from MRI and CT
Register MRI to CT - one click scripted version
Tutorial 7: Volumes creation and meshing
Software required for Tutorial 7
Tutorial 8: Generate Abaqus input files
Software required for Tutorial 8
Tutorial 9: Abaqus analysis and stress extraction
Software required for Tutorial 9