© 2011 Pittsburgh Supercomputing Center
Patient-Specific Modeling of Abdominal Aortic Aneurysms(AAAs)
Anirban Jana, PhD Prof Ender Finol
October 17, 2011
ASTA project
© 2011 Pittsburgh Supercomputing Center Anirban Jana, Ender Finol
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
AAA rupture 10th leading cause of death for men above the age of 50
Current protocol – surgical repair if maximum AAA diameter > 5 - 6 cm or growth rate > 1 cm/yr. But often smaller AAAs rupture, while larger ones do not
Risk of rupture vs Risk of surgical intervention
Biomechanical assessment for rupture potential
Influence of variations in individual biomechanical variables
Aorta
Renal Arteries
Right common iliac artery Left common iliac artery
© 2011 Pittsburgh Supercomputing Center Anirban Jana, Ender Finol
AAA research
• 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). • Vignon-Clementel , I.E., Figueroa C.A., Jansen K.E., Taylor, C.A, Computer methods Appl. Mech. Eng. 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).
Computational modeling techniques
Boundary conditions
Material models/properties
Mesh generation
Pathogenesis Genetics Molecular biology Medical imaging
• 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)
• 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).
• 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. • Shum, J., Xu, A., Chatnuntawech, I., Finol, E. A., 2011, Annals of Biomedical Engineering, 39(1), pp. 249-259.
Biomechanics
© 2011 Pittsburgh Supercomputing Center Anirban Jana, Ender Finol
Model construction
Thrombus
Wall
Lumen
Computational predictions
(stress, strain etc)
CT/MRI image
Segmentation in VESSEG
2D masks 3D reconstructed geometry/surface mesh
Volume mesh
Medical image based patient specific modeling
© 2011 Pittsburgh Supercomputing Center Anirban Jana, Ender Finol
Software Preprocessing (model construction, boundary conditions)
MATLAB
Biomechanics simulations (CFD, CSS and FSI) ADINA (a commercial finite-element multiphysics package; developed by Prof K.J.Bathe, Mech Eng, MIT)
ENSIGHT, MATLAB Post-processing
www.mathworks.com
www.adina.com
www.ensight.com
© 2011 Pittsburgh Supercomputing Center Anirban Jana, Ender Finol
My contributions Help improve TeraGrid/XSEDE research proposals (benchmarking,
scaling, SU justification)
Provide guidance and troubleshooting advice for ADINA (choosing best ADINA simulation options and element types, output control)
Provide expert advice on efficient MATLAB coding
Provide expertise in computational fluid dynamics and computational solid mechanics on a regular basis to enhance science output
Develop patient specific boundary conditions (MATLAB codes)
Co-author papers, critique manuscripts and presentation slides
© 2011 Pittsburgh Supercomputing Center Anirban Jana, Ender Finol
My contributions 1) 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).
2) 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).
3) 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).
4) 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).
5) 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 Assessment,2011 Biomedical Engineering Society Annual Meeting, Hartford, CT, October 2011 (Peer-reviewed abstract and presentation).
Publications
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 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)
0
2000
4000
6000
8000
10000
12000
14000
0 10 20 30 40 50 60
Com
puta
tiona
l tim
e,s
#cores
© 2011 Pittsburgh Supercomputing Center Anirban Jana, Ender Finol
CSS validation for hyperelastic materials
Straight tube section, plain strain, incompressible Mooney-Rivlin material
Analytical solution1
1 Batra R. C. , ‘Finite plane strain deformation of rubberlike materials’ , Int. J Num Method in Eng, vol.15, 145-160,1980
-8
-6
-4
-2
0 8 9 10 11 12 13 14
% e
rror
in m
ax p
rinci
pal
stre
ss
ln( # of Equations )
Hex20
Hex8
Pri15
Tet11
Hex27
Element type
-4
-2
0
2
4
6
8
0 2 4 6 8 10 12 14
ln(T
ime)
ln(#Eqns)
Hex27
Hex20
Hex8
Pri15
Tet11
Tet11 most efficient, followed by Hex27, but Pri15 also not too bad ILT -> Tet11, wall-> Hex27 or Pri15
© 2011 Pittsburgh Supercomputing Center Anirban Jana, Ender Finol
CSS validation for hyperelastic materials
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 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 approach the limiting value of 0.5.
Additional observations
© 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
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
Parabolic profile • Circle fit to convex hull of inlet surface mesh • Hagen-Poiseuille eqn for velocity profile (umax(t)=2 uavg(t) )
Womersley profile • Circle fit to convex hull of inlet surface mesh • 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
Flow rate waveform
© 2011 Pittsburgh Supercomputing Center Anirban Jana, Ender Finol
Boundary conditions
• Difference is between computationally predicted average velocity and pressure at midsection and MR measured flow rate at midsection
• Comparison of FSI predicted stress with patient specific vs Womersley profile prescribed at inlet
• Amplitude and phase errors
© 2011 Pittsburgh Supercomputing Center Anirban Jana, Ender Finol
Concluding remarks
My activities: Proposal writing, parallel benchmarking, simulation software (ADINA) options and troubleshooting, MATLAB coding, advising student research, publications/presentations
Research areas to which I contributed: boundary conditions, mesh generation, AAA biomechanics simulation strategies and algorithms
Broad research goal: Medical image based simulation of biomechanical response of AAAs, towards AAA rupture risk prediction
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