Hemodynamic Modeling of Intracranial Aneurysms Using Open Source Computational Fluid Dynamics Software
Mathew Bligh (MD) , Allan Demtrio Sales de Lima Dias (B.Eng) , Rodrigo Del Rio (B.Eng) , Julio Militzer (Ph.D) , Jai Shankar (MD)
1
Department of Diagnostic Radiology, Dalhousie University, Halifax, Nova Scotia, Canada; Universidade Estadual Paulista, Ilha Solteira, So Paulo, Brazil; Department of Mechanical Engineering, Dalhousie University, Halifax, Nova Scotia, Canada
INTRODUCTION
Background
Intracranial aneurysm rupture causes 80-85% of non-traumatic subarachnoid hemorrhage (SAH).1
Unruptured intracranial aneurysms (UIAs) have a general population prevalence of at least 2-5%.
Morbidity and mortality remain high despite improvements in diagnosis and therapy.2
Computed tomography angiography (CTA) and magnetic resonance angiography (MRA) have largely
supplanted catheter angiography in the initial acute diagnostic setting, but the latter remains important
for subsequent management.2
Current treatment options in both the acute and elective settings include surgical clipping and
endovascular coiling or flow diverter placement.3
Incidental detection of UIAs is becoming more common due to prevalent use of CTA and MRA.
While the decision to treat or simply observe a UIA may be clear if the aneurysm is either large or small,
it can be very difficult for mid-sized aneurysms (such as in the 5-8 mm range) when the risk to benefit
ratio is less clear.1-3
Improving rupture risk models is of great interest and high importance due to the high stakes involved in
therapeutic decision-making.3
Geometric factors such as size ratio and aspect ratio may improve prediction, but likely do not tell the
whole story.4-5
Adding hemodynamic data to rupture risk models may improve prediction, and is a primary goal of
computational modeling.
Computational Fluid Dynamics (CFD)
CFD is a numerical method of solving fluid mechanics problems using the Navier-Stokes (NS)
equations (a series of time-dependent partial differential equations describing conservation of mass,
momentum and energy for a viscous fluid).
Mainly applied to engineering problems until early 2000s when the spatial resolution of CT
and MRI could provide adequate spatial resolution high-fidelity vascular modeling.
CFD provides hemodynamic data with superior spatial and temporal resolution to any
current in-vivo medical imaging technique, and has been validated against phase contrast
MRI and physical vascular phantoms.6-7
In this guide, we describe the basic approach to computational aneurysm modeling using
exclusively open source software. More detailed instruction is provided in referenced
material.
For additional background information, please see our other poster at ASNR 2015:
Computational Flow Modeling of Intracranial Aneurysms for Rupture Prediction
SOFTWARE
All software packages described in this guide are available for free download. Please see the available documentation
for details on download, installation and use.
OPERATING SYSTEM (OS)
The chosen CFD package (OpenFOAM, see below) is native to Linux, an open source OS that
supports many other engineering and multiphysics software packages.
Ubuntu (Canonical, Lexington, MA, USA) is a popular Linux build and is used by our group.
An alternative option is CAE (Computer Aided Engineering) Linux (NRCTech, Lausanne,
Switzerland), which comes with a wide variety of computer aided design (CAD) and CFD software
pre-installed. This includes OpenFOAM and modeling/meshing applications such as Salome and
Netgen. However, user support for CAE Linux is limited.
Linux can be installed alongside other operating systems. Alternatively, Linux can be run on a
virtual machine within another OS environment using a tool such as VirtualBox (Oracle, Redwood
Shores, CA, USA). However, this is less desirable due to reduced system resources.
ANEURYSM/VESSEL SEGMENTATION & MODEL
CREATION
Vascular Modeling Toolkit (VMTK, Orobix, Bergamo, Italy) is an open source package of scripts
for visualization, volume of interest (VOI) selection, aneurysm and vessel segmentation, model
pre-processing and mesh generation.8
Accepts DICOM files from CTA, MRA and three-dimensional rotational angiography (3DRA)
studies and provides a wealth of image and model processing tools.
Intuitive viewer application allows easy manipulation of image sets and model files.
Exports to proprietary mesh formats for use with various commercial packages.
MESH GENERATION
VMTK can be used for mesh generation and allows incorportation of boundary layers,
radius adaptive cell cell size and inlet/outlet extensions.8
Netgen (developed by Joachim Schberl at Johannes Kepler University, Linz, Austria) is
another open source meshing tool that integrates well with VMTK. It provides a graphical
user interface (GUI) and allows easy manipulation of mesh cell density and boundary
conditions.9
COMPUTATIONAL SIMULATIONS
OpenFOAM (OpenCFD, ESI Group, Paris, France) is a well-established C++-based open
source CFD software package with numerous applications capable of solving a multitude
of computational fluid problems.10
Incorporates pre- and post-processing capabilities.
Large online community with many tutorials and in-person courses available for
researchers.11
Results have been shown to compare well with other available commercial packages for
vascular CFD.12
POST-PROCESSING
Paraview (Kitware, Clifton Park, New York, USA) is an open source data analysis and
visualization application that comes packaged with OpenFOAM.13
Hemodynamic data easily displayed and analyzed using a variety of techniques, including
surface and volume mapping as well as graphical analysis of probe points placed within the
flow environment.
1 2 2 3 1
2 3
SOURCE DATA MESH GENERATION POST-PROCESSING
Imaging Modality Meshing with VMTK Data Visualization and Analysis
Vascular CFD is most often performed using meshes with edge length 0.1-
Accurate surface model and mesh generation rely on cross-sectional Simulation results are visualized in Paraview, opened from the terminal
imaging with high spatial and contrast resolution. This can be 0.2 mm.16-17 Further increases in cell density produce diminishing returns in precision within the simulation folder using the command paraFoam.
accomplished with CTA, MRA or 3DRA. (model accuracy is limited largely by the spatial resolution of the source data) and significantly Velocity data can be visualized in a variety of ways using spatial mapping
3DRA provides the highest spatial resolution and allows easier increase computation time. over a defined volume or plane of interest.
Ruptured middle cerebral artery vessel segmentation due to lack of interfering non-vascular Some researchers use uniform meshes, where all cells are equally sized, which is the simplest case to Streamlines and directional arrow glyphs can also be plotted to define
aneurysm with active hemorrhage. anatomy. This is the preferred source imaging of many CFD studies. produce. This can be done using vmtkmeshgenerator using a defined edge length. paths of flow. This is a useful way to communicate data and to visually
Ostium
However, it requires an invasive procedure and is not typically the A boundary layer (BL) can be defined to incorporate smaller cells near the vessel/aneurysm wall, assess complexity of flow.
Parent vessel
Dome
modality of initial detection. Ultimately, valid CFD simulations providing increased spatial resolution where accuracy is critical while not significantly inreasing Pressure and wall shear stress (WSS) data can similarly be mapped over
derived from non-invasive imaging hold the most potential utility. the computational load.17-18 This is done within the vmtkmeshgenerator script. Boundary layers the model surface or within the flow field.
MRA can be performed using time-of-flight imaging without are not typically used at the inlet and outlet faces as this would not significantly alter the solution.
C
administration of intravenous gadolinium contrast, which may be It is critical to scale the mesh to the units used by the CFD solver prior to the simulation.
B the only feasible modality in patients with renal failure or other For example, if the units of the source data are millimetres while the solver uses metres,
contraindications. the mesh should be scaled by a factor of 0.001. This can be accomplished with the
A = vessel diameter For this example, a CTA of the brain demonstrating an incidental CTA of the circle of willis showing an unruptured 8 mm basilar tip vmtkmeshscaling script.
A
B = aneurysm height
C = aneurysm diameter non-ruptured 8 mm basilar tip aneurysm was used. aneurysm (arrow). This is the demonstration case. The BL provides higher near-wall
B/A = size ratio
resolution normal to the surface, where the
Source images
B/C = aspect ratio
flow gradient produces wall shear stress.
Uniform mesh with 0.15 mm cell edge length
CTA studies are typically acquired using mutidetector CT with isotropic voxel
The number of divisions and relative cell
heights of the BL are user-defined.
and a three-level BL produced in VMTK.
This mesh contains 1.9 million cells.
size and include axial reconstructions with 0.625-1 mm slice thickness.
These images are ideal for vessel segmentation. Thicker reconstructions such
at 3 or 5 mm should not be used as these do not provide adequate spatial A) Sagittal cutplane displaying the inflow jet at select timepoints in the cardiac cycle; B) Normalized
resolution for accurate modeling. time-dependent VFR; C) Surface map of WSS at corresponding time points. Note that WSS is
CTA studies with suboptimal contrast opacification, extensive atherosclerotic normalized to density in OpenFOAM by default
calcification or beam hardening artifact may also be inadequate for model
extraction.
Meshing with Netgen Select cutplanes can be assessed within the model volume. This is useful to define the inflow/
Models can be exported to the .stl format and processed using Netgen. outflow profile at the aneurysm neck. Derived data can be used to calculate changes in kinetic
Note 3 mm anterior energy among other quantities.
communicating artery
This program includes a graphical user interface (GUI) with easier
aneurysm manipulation and mesh refinement capabilities. Netgen allows local
Probes can be placed at any desired location and data can be plotted over time in
manipulation of imperfections in the mesh and increased cell density at
graphical format.
locations of interest.9
Using the velocity and pressure solution, derived quantities such as WSS can be
Rotational acquisition with 3D reconstruction from a right Netgen produces a radius-adaptive mesh by
default, assigning high cell density to regions
retrospectively calculated in OpenFOAM for the entire flow environment.
internal carotid artery (ICA) contrast injection at catheter Time-of-flight MRA axial maximal intensity projection (MIP) of higher surface curvature. This can also be
angiography. showing a 1.5 cm basilar tip aneurysm (arrow). accomplished with VMTK using the terminal.
Streamlines can be color-mapped
to velocity
Many
ANEURYSM SEGMENTATION CFD SIMULATION
& MODEL PROCESSING
Velocity streamlines are a useful visual tool to communicate flow
Setting Up the Simulation Folder WSS and other calculated data can be plotted
vs time at a selected cell surface. This allows
patterns, but do not necessarily represent the entire flow field. They
can help define the number of vortices within the aneurysm.
focused investigation of a point of interest
OpenFOAM is operated via command line entry at the terminal. All required input files must be
such as a known rupture point.
present in the active folder, defining boundary conditions, mesh geometry, timestep information and
solver variables.10
Volume of Interest (VOI) extraction Many solvers are included in OpenFOAM, and it is possible to users to generate their own. Of key
CONCLUSIONS
importance is whether or not turbulance modeling is needed. This depends on the Reynolds number,
Digital Imaging and Communications in Medicine (DICOM) images are exported
which relates inertial to viscous forces and predicts the likelihood of turbulent flow:
from the Picture Archiving and Communication System (PACS) for processing
in VMTK. These contain Hounsfield unit density information needed for vessel
segmentation.8
Using the vmtkimagevoiselector script, a VOI containing the aneurysm and parent
vessel(s) is selected for subsequent processing. The included parent vessel should
where v=velocity, d
h
=hydraulic diameter (simply diameter for a round pipe), =kinematic viscosity CFD can be used to assess the hemodynamic environment within intracranial aneurysms. Many studies
have been conducted aiming to identify hemodynamic risk factors for aneurysm rupture with some success.
ideally consist of at least a 10:1 length-to-diameter ratio for subsequent flow modeling, Typical vascular simulations fall in the laminar flow range (Re < 2300) and turbulence modeling is not
One of two outlet boundaries displayed in VMTK
using vmtkmeshboundaryinspector Flow complexity, inflow jet impingement, WSS and hydrostatic pressure all likely play a role but the exact
but this may not be feasible depending on anatomy. required. contribution of these factors has not been fully determined.
Volumetric CT DICOM data are reviewed in The pimpleFoam solver is an efficient, robust algorithm for transient incompressible flows that has the
three planes and a VOI is selected advantage of an adjustable timestep. This can operate with or without turbulence modeling. Further study is required to elucidate high-risk hemodynamic factors before CFD can be incorporated routinely
into rupture prediction for UIAs.
Aneurysm & Vessel Segmentation Boundary Conditions Because many commercial CFD packages are expensive and not available to all interested researchers, we used
exclusively open source software to demonstrate the ability to produce CFD simulations without committing to
Vascular structures are extracted from the VOI using the vmtklevelsetsegmentation The flow must be defined in relation to velocity or pressure at the inlet, outlet
script. This can be accomplished using one or more of several supported region-growing additional financial cost.
and vessel wall. Pulsatile flow at the inlet approximating that expected in the
algorithms. ICA or vertebral artery (VA) distribution is typically employed. This is usually This guide provides a basic overview of the key components of CFD simulation for intracranial aneurysms, with
For this example, the fast marching algorithm was used, which requires user selection of derived from studies of normal subjects as it is unfeasible to obtain reliable data the goal of introducing interested researchers to the process. More detailed instruction for each step can be
seed and target points. The region covered by an advancing front between seed and target from each patient for simulation purposes. found in the documentation for the respective software packages, which can be accessed through the provided
points is included in the initial model. The aneurysm-vessel complex can be segmented in Ford et al. (2005) measured ICA and VA volume flow rates (VFR) for 17 young, matrix barcodes. For additional information, check out CFD Online, an extensive free resource with an active
The region-growing algorithm propagates a front multiple steps using this algorithm. online community.
healthy subjects using phase contrast MRI, reported as mean normalized VFR
between seed and target nodes to define a volume. The raw segmented volume is then deformed to create a regular, smooth surface for at 17 feature points over the cardiac cycle. This data can be interpolated using Downloadable cubic
subsequent processing. This is accomplished by defining degrees of propagation, the cubic spline method to estimate VFR across the cardiac cycle with desired splines spreadsheet Disclosure statement: None of the authors have any commercial interest
regularization and attenuation within the vmtklevelsetsegmentation program. This may program with examples
temporal resolution. Absolute VFRs are also reported by Ford et al. and can be Post-coiling digital subtraction angiogram (DSA) in any of the software discussed in this exhibit.
result in loss of aneurysm features and difficult with poor quality source data.8 demonstrating the treated unruptured basilar tip aneurysm.
multiplied by the normalized waveform and inlet cross section to determine
velocity.19 Example file located in
Surface Smoothing and Clipping Alternatively, inlet velocities between simulations can be normalized to acheive the simulation directory
defining the velocity
REFERENCES
Irregularities in the surface model are reduced using the a defined WSS at the parent vessel wall shortly beyond the boundary.16 boundary conditions.
Where multiple inlets exist, relative contribution can be estimated in proportion
vmtksurfacesmoothing script. This further refines the surface to
allow high quality mesh generation. Smoothing parameters can be to boundary area but accuracy may be limited as the aneurysm inflow/outflow
Further instruction is
found in the OpenFOAM
profile can be significantly affected by variation in this balance20. documentation and
adjusted to avoid loss of true surface features.
The outlet boundary can be defined by zero pressure as the flow is driven by the example cases.
To define inlet and outlet boundary surfaces, the ends of the parent vessels are
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Courant number as needed.