asta project patient-specific modeling of abdominal aortic ... · reviewed poster presentation). 2)...

© 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


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


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


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


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


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.


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


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


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


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


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


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


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

asta project patient-specific modeling of abdominal aortic ... · reviewed poster presentation). 2)...

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