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ASTA jPatient‐Specific Modeling of
ASTA project
Abdominal Aortic Aneurysms(AAAs)Anirban Jana, PhDAnirban Jana, PhDProf Ender FinolO t b 17 2011
© 2011 Pittsburgh Supercomputing Center
October 17, 2011
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 65the age of 65
AAA rupture 10th leading cause of death for men above the age of 50
l l f 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 Risk of rupture vs Risk of surgical intervention
Biomechanical assessment for rupture potential
Aorta
Renal Arteries p p
Influence of variations in individual biomechanical variablesRight common
iliac artery
© 2011 Pittsburgh Supercomputing Center Anirban Jana, Ender Finol
Left common iliac artery
AAA researchBiomechanicsComputational 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).
• 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 Cl t l I E Fi C A J K E T l C A C t th d A l M h E 195 3776 3796 (2006)
Boundary conditions
• 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).
Material models/properties• Di Martino, E., Mantero, S., Inzoli, F., Melissano, G., Astore, D., Chiesa, R., Fumero, R, European Journal of Vascular Endovascular Surgery
Mesh generation
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• 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 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
© 2011 Pittsburgh Supercomputing Center Anirban Jana, Ender Finol
Pathogenesis Genetics Molecular biology Medical imaging• Shum, J., Xu, A., Chatnuntawech, I., Finol, E. A., 2011, Annals of Biomedical Engineering, 39(1), pp. 249‐259.
Model constructionM di l i b d ti t ifi d liMedical image based patient specific modeling
CT/MRIimage
Segmentation inVESSEG
2D masks 3D reconstructed geometry/surface mesh
Volume mesh
Wall Computational predictions
Thrombus
Lumen
predictions (stress, strain etc)
© 2011 Pittsburgh Supercomputing Center Anirban Jana, Ender Finol
SoftwarePreprocessing (model construction boundary conditions)Preprocessing (model construction, boundary conditions)
MATLABwww.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)
Post‐processing
www.adina.com
ENSIGHT, MATLABPost processing
www.ensight.com
© 2011 Pittsburgh Supercomputing Center Anirban Jana, Ender Finol
www.ensight.com
My contributionsHelp improve TeraGrid/XSEDE research proposals (benchmarkingHelp improve TeraGrid/XSEDE research proposals (benchmarking, scaling, SU justification)
Provide guidance and troubleshooting advice for ADINA (choosingProvide 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 tsolid mechanics on a regular basis to enhance science output
Co‐author papers, critique manuscripts and presentation slides
© 2011 Pittsburgh Supercomputing Center Anirban Jana, Ender Finol
Co author papers, critique manuscripts and presentation slides
My contributionsPublications1) 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‐aneurysmalFlow 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)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 RiskEnder 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).
MentoringAdvisory 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 benchmarks14000
Performed previously on PSC’s Pople, currently on PSC’s Blacklight
Computational Solid Stress (CSS) 12000
14000
simulation of a patient AAA wall 2,889,837 degrees of freedom Memory required ~13 GB
8000
10000
tatio
nal tim
e,s
ADINA SMP version 8 cores optimal for this problem, up to
32 cores if fastest time to solution desired (for this problem size)
4000
6000
Compu
t
desired (for this problem size)
0
2000
0 10 20 30 40 50 60##cores
© 2011 Pittsburgh Supercomputing Center Anirban Jana, Ender Finol
CSS validation for hyperelastic materials0
8 9 10 11 12 13 14l Element type
6
‐4
‐2
8 9 10 11 12 13 14
ror in max prin
cipa
lstress
Hex20
Hex8
Pri15
Tet11
Element type
Straight tube section, plain strain,i ibl M Ri li t i l
‐8
‐6
% err
ln( # of Equations )
Tet11
Hex27
8incompressible Mooney‐Rivlin material
Analytical solution12
4
6
n(Time)
Hex27
Hex20
Hex8
P i15
‐4
‐2
00 2 4 6 8 10 12 14
ln
ln(#Eqns)
Pri15
Tet11
Tet11most efficient, followed by Hex27, but Pri15 also not too bad ILT ‐> Tet11, wall‐> Hex27 or Pri15
© 2011 Pittsburgh Supercomputing Center Anirban Jana, Ender Finol
1 Batra R. C. , ‘Finite plane strain deformation of rubberlike materials’ , Int. J Num Method in Eng, vol.15, 145‐160,1980
CSS validation for hyperelastic materialsAdditional 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
Additional observations
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‐Rivlinmaterials, 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 , , ) yapproach 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 MATLABWritten 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 conditionsPlug 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 (u (t)=2 u (t) )
Flow rate waveform
• Hagen‐Poiseuille eqn for velocity profile (umax(t)=2 uavg(t) )
Womersley profileCi l fi h ll f i l f h• 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
© 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 WomersleyBoth amplitude and phase errors were observed for the Womersleyprofile
© 2011 Pittsburgh Supercomputing Center Anirban Jana, Ender Finol
Concluding remarks B d h l M di l i b d i l i f Broad research goal: Medical image based simulation of 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
R h t hi h I t ib t d b d diti h Research areas to which I contributed: boundary conditions, mesh generation, AAA biomechanics simulation strategies and algorithms
© 2011 Pittsburgh Supercomputing Center Anirban Jana, Ender Finol