ASTA
ASTA project
j
Patient‐Specific Modeling of Abdominal Aortic Aneurysms(AAAs)
Anirban Jana, PhD
Anirban
Jana, PhD
Prof Ender Finol
O t b 17 2011
October 17, 2011
© 2011 Pittsburgh Supercomputing Center
Motivation and broad objectives
 Increase in diameter of more than 50% (normal healthy diameter of ~2 cm)
 Present in as many as 8.8% of the population over the age of 65
the age of 65
 AAA rupture 10th leading cause of death for men above the age of 50
 Current protocol –
l surgical repair if maximum AAA l
f
diameter > 5 ‐ 6 cm or growth rate > 1 cm/yr. But often smaller AAAs rupture, while larger ones do not
Aorta
Renal Arteries
Right common iliac artery
 Risk of rupture vs
Risk of rupture vs Risk of surgical intervention
Risk of surgical intervention
 Biomechanical assessment for rupture potential
p
p
 Influence of variations in individual biomechanical variables
Left common iliac artery
© 2011 Pittsburgh Supercomputing Center
Anirban Jana, Ender Finol
AAA research
Biomechanics
Computational modeling techniques
• Fillinger, M.F., Raghavan, M.L., Marra S.P., Cronenwett, J.L., Kennedy, F.E., Journal of Vascular Surgery 33(3):589‐597 (2002). • Di Martino E.S., Gudagni, G., Fumero, A., Ballerini, G. Spirito R., Biglioli, P., Redaeilli A., Medical Engineering Physics 23(9):647‐655 (2001).
• Scotti C.M., Shkolnik, A.D., Muluk, S., Finol, E.A., Biomed Engineering Online 4:64 (2005).
Boundary conditions
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•
•
•
•
Di Martino E.S., Gudagni, G., Fumero, A., Ballerini, G. Spirito R., Biglioli, P., Redaeilli A., Medical Engineering Physics 23(9):647‐655 (2001).
Olufsen, M.S., Peskin, C.S., Kim, W.Y., Pedersen, E.M., Nadim, A., Larse, J., Annals of Biomedical Engineering, 28:1281‐1299 (2000). Steele, B.N., Taylor, C.A., Proceedings of the 2003 ASME Summer Bioengineering Meeting (2003). Vi
Vignon‐Clementel
Cl
t l , I.E., Figueroa C.A., Jansen K.E., Taylor, C.A, Computer methods Appl. Mech. Eng. 195:3776‐3796 (2006).
I E Fi
CA J
KE T l CA C
t
th d A l M h E 195 3776 3796 (2006)
Scotti, C.M., Jimenez, J., Muluk, S.C., Finol, E.A., Computer methods in Biomechanics and Biomedical Engineering 11(3):301‐322 (2008). Material models/properties
• Di Martino, E., Mantero, S., Inzoli, F., Melissano, G., Astore, D., Chiesa, R., Fumero, R, European Journal of Vascular Endovascular Surgery 15:290‐299 (1998).
• Raghavan, M.L., Webster, M.W., Vorp, D.A., Journal of Biomechanics, 33:475‐482 (2000). • Vande Geest , J.P.,Sacks, M.S., Vorp, D.A., Journal of Biomechanics, 39(7):1324‐1334 (2006).
• Vande Geest, J.P. ,Sacks, M., Vorp, D.A., Journal of Biomechanics, 39, 2347‐2354 (2006)
Mesh generation
Mesh generation
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•
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Wolters, B. J., Rutten, M. C., Schurink, G. W., Kose, U., de Hart, J., and van de Vosse, F. N., 2005, Med Eng Phys, 27(10), pp. 871‐883.
Auer M, G. T., 2010, IEEE Trans Med Imaging, pp. 1022‐1028.
Zhang,Y., Wang,W., Liang, X., Bazilevs,Y., Hsu,M.‐C.,Kvamsdal,T.,Brekken,R., Isaksen, J., 2009, CMES Comp Mod in Eng and Sc, 42(2), pp. 1‐18.
Shim, M.‐B., Gunay, M., and Shimada, K., 2009, Computer‐Aided Design, 41(8), pp. 555 ‐ 565.
Sh
Shum, J., Xu, A., Chatnuntawech, I., Finol, E. A., 2011, Annals of Biomedical Engineering, 39(1), pp. 249‐259.
J X A Ch t
t
h I Fi l E A 2011 A
l f Bi
di l E i
i 39(1)
249 259
Pathogenesis
© 2011 Pittsburgh Supercomputing Center
Genetics
Molecular biology
Anirban Jana, Ender Finol
Medical imaging
Model construction
M di l i
Medical image based patient specific modeling
b d ti t
ifi
d li
CT/MRI
image
Segmentation in
VESSEG
2D masks
3D reconstructed Volume mesh
geometry/surface mesh
Wall
Thrombus
Lumen
© 2011 Pittsburgh Supercomputing Center
Anirban Jana, Ender Finol
Computational predictions
predictions (stress, strain etc)
Software
Preprocessing (model construction, boundary conditions)
Preprocessing
(model construction boundary conditions)
MATLAB
www.mathworks.com
Biomechanics simulations (CFD, CSS and FSI)
Biomechanics
simulations (CFD CSS and FSI)
ADINA (a commercial finite‐element multiphysics package;
developed by Prof K.J.Bathe, Mech Eng, MIT)
www.adina.com
Post processing
Post‐processing
ENSIGHT, MATLAB
www.ensight.com
© 2011 Pittsburgh Supercomputing Center
Anirban Jana, Ender Finol
My contributions
Help improve TeraGrid/XSEDE research proposals (benchmarking, Help
improve TeraGrid/XSEDE research proposals (benchmarking
scaling, SU justification)
Provide guidance and troubleshooting advice for ADINA (choosing Provide
guidance and troubleshooting advice for ADINA (choosing
best ADINA simulation options and element types, output control)
Provide expert advice on efficient MATLAB coding
Develop patient specific boundary conditions (MATLAB codes)
Provide expertise in computational fluid dynamics and computational solid mechanics on a reg lar basis to enhance science o tp t
solid mechanics on a regular basis to enhance science output
Co‐author
Co
author papers, critique manuscripts and presentation slides
papers, critique manuscripts and presentation slides
© 2011 Pittsburgh Supercomputing Center
Anirban Jana, Ender Finol
Publications
1)
2)
3)
4)
5)
My contributions
S. Raut, S. Chandra, A. Jana and E. Finol, Individual Anisotropic FSI Modeling of Aortic Aneurysms: Phase Contrast and Dynamic MRI validation, 2009 Biomedical Engineering Society Annual Fall Meeting, Pittsburgh, PA, October 2009 (Peer reviewed poster presentation). S. Raut, S. Chandra, A. Jana, S. Muluk and E. Finol, The Effect of Local Infrarenal Flow Conditions on Intra‐aneurysmal
Flow Dynamics, 2009 Biomedical Engineering Society Annual Fall Meeting, Pittsburgh, PA, October 2009 (Peer reviewed poster presentation).
Samarth S. Raut, Anirban Jana, Ender A. Finol, Effects Of Shape Versus Material Model Variations On AAA Wall Mechanics, Sixth M.I.T. Conference on Computational Fluid and Solid Mechanics, Boston, MA, June 2011 (Peer‐reviewed abstract and presentation)
abstract and presentation).
Samarth Raut, Peng Liu, Anirban Jana, Ender Finol, Aortic Wall Mechanics: A Geometry‐Driven Problem, ASME 2011 Summer Bioengineering Conference, Farmington, PA, June 2011 (Peer‐reviewed abstract and poster).
Samarth Raut, Judy Shum, Santanu Chandra, Anirban Jana, Peng Liu, Kibaek Lee, Elena Di Martino, Todd Doehring, Ender Finol, AAAVASC: A novel Integrated Approach for Image Based Modeling Toward Individualized AAA Rupture Risk
Ender Finol, AAAVASC: A novel Integrated Approach for Image Based Modeling Toward Individualized AAA Rupture Risk Assessment,2011 Biomedical Engineering Society Annual Meeting, Hartford, CT, October 2011 (Peer‐reviewed abstract and presentation).
Mentoring
Advisory Committee and Co‐advisor, Samarth Raut, PhD candidate, Mechanical Engineering, Carnegie Mellon University, Biomechanics of Abdominal Aortic Aneurysms.
© 2011 Pittsburgh Supercomputing Center
Anirban Jana, Ender Finol
AAA parallel simulation benchmarks
14000
 Performed previously on PSC’s Pople, currently on PSC’s Blacklight
 Computational Solid Stress (CSS) simulation of a patient AAA wall
 2,889,837 degrees of freedom
 Memory required ~13 GB
 ADINA SMP version
 8 cores optimal for this problem, up to 32 cores if fastest time to solution desired (for this problem size)
desired (for this problem size)
12000
Computtational time,s
10000
8000
6000
4000
2000
0
0
10
20
30
40
50
60
#cores
© 2011 Pittsburgh Supercomputing Center
Anirban Jana, Ender Finol
CSS validation for hyperelastic materials
% errror in max principall stress
0
8
9
10
Analytical solution1
12
13
14
‐2
Element type
Element type
Hex20
Hex8
‐4
Pri15
Tet11
6
‐6
Hex27
‐8
Straight tube section, plain strain,
i
incompressible Mooney‐Rivlin
ibl M
Ri li material
t i l
11
ln( # of Equations )
8
6
Hex27
4
ln
n(Time)
Hex20
Hex8
2
P i15
Pri15
0
0
2
4
6
8
10
12
14Tet11
‐2
‐4
ln(#Eqns)
 Tet11 most efficient, followed by Hex27, but Pri15 also not too bad
 ILT ‐> Tet11, wall‐> Hex27 or Pri15
1
Batra R. C. , ‘Finite plane strain deformation of rubberlike materials’ , Int. J Num Method in Eng, vol.15, 145‐160,1980
© 2011 Pittsburgh Supercomputing Center
Anirban Jana, Ender Finol
CSS validation for hyperelastic materials
Additional observations
Additional observations
 3D iterative solver fails to converge for all element types except Tet11. Sparse solver converges for almost all cases. However, sparse solver consumes more memory and time converges for almost all cases. However, sparse solver
consumes more memory and time
compared to 3D iterative solver (up to 2x, especially for large models).
 ADINA cannot simulate perfectly incompressible (Poisson’s ratio =0.5)Mooney‐Rivlin
materials, but can model almost incompressible Mooney‐Rivlin materials (Poisson’s ratio =0.49, 0.499, …). We tested the sensitivity of the results as the Poisson’s ratio is made to ,
, )
y
approach the limiting value of 0.5.
© 2011 Pittsburgh Supercomputing Center
Anirban Jana, Ender Finol
Geometry reconstruction and meshing  AAAVASC : A unified framework for multi‐domain mesh generation from medical images
 Written in MATLAB
Written in MATLAB
 Surface meshes generated first, followed by volume meshes
 Completely unstructured meshes for ILT and lumen, extruded mesh for wall (based on prescribed uniform/non‐uniform thickness)
 Smoothing operations performed to reduce mesh irregularities and improve element quality
 Computes some geometric parameters of the final model, e.g., volume, surface area, curvatures
© 2011 Pittsburgh Supercomputing Center
Anirban Jana, Ender Finol
Boundary conditions
Plug profile
• Circle fit to convex hull of inlet surface mesh
Flow rate waveform
Parabolic profile
• Circle fit to convex hull of inlet surface mesh
• Hagen‐Poiseuille
Hagen Poiseuille eqn for velocity profile (u
for velocity profile (umax(t)=2 u
(t)=2 uavg(t) )
(t) )
Womersley profile
• Circle fit to convex hull of inlet surface mesh
Ci l fi
h ll f i l
f
h
• Fourier decomposition of flow rate waveform
• Womersley eqn of velocity profile at specific frequencies
Patient specific profile
• Schwarz‐Christoffel mapping of phase‐contrast MR image to inlet mesh
© 2011 Pittsburgh Supercomputing Center
Anirban Jana, Ender Finol
Boundary conditions
• Differences between computationally predicted average velocity and pressure at midsection and MR measured flow rate at midsection was recorded to be the greatest for the inlet plug profile
• Comparison of FSI predicted stress was also performed with patient specific vs Womersley profile prescribed at inlet
• Both amplitude and phase errors were observed for the Womersley
Both amplitude and phase errors were observed for the Womersley
profile
© 2011 Pittsburgh Supercomputing Center
Anirban Jana, Ender Finol
Concluding remarks
 Broad research goal: Medical image based simulation of B d
h
l M di l i
b d i l i
f
biomechanical response of AAAs, towards AAA rupture risk prediction
My activities: Proposal writing, parallel benchmarking, simulation y
p
g, p
g,
software (ADINA) options and troubleshooting, MATLAB coding, advising student research, publications/presentations
 Research areas to which I contributed: boundary conditions, mesh R
h
t hi h I
t ib t d b
d
diti
h
generation, AAA biomechanics simulation strategies and algorithms © 2011 Pittsburgh Supercomputing Center
Anirban Jana, Ender Finol