Stephen F. Cauley

Assistant Professor in Radiology, Harvard Medical School

Assistant in Biomedical Engineering, Massachusetts General Hospital

My research interests lie in the development of high performance computing techniques for MRI applications. I examine how cutting edge numerical techniques can be applied for the development and optimization of data acquisition and image reconstruction methodologies. This requires detailed knowledge of software algorithm development, MR physics, and the underlying neuroscience. It is my aim to develop new accelerated imaging technologies and tools that will allow for high patient throughput imaging. Some of my current research topics are listed below:

• Joint optimization; Auto-calibrated mitigation of encoding errors and patient motion in MRI reconstruction
• Machine Learning for MRI reconstruction
• Wave-CAIPI rapid anatomical imaging
• Simultaneous Multi-slice (SMS) imaging
• MR Fingerprinting (MRF)
• Magnetic Particle Imaging (MPI)
• Hierarchically Semiseparable Matrices (HSS): modeling, optimization, and simulation with HSS matrices. Collaboration with Profs. Ragu Balakrishnan and Jianlin Xia at Purdue University

Information: Curriculum Vitae, Publications.

Contact Information

Email: stcauley@nmr.mgh.harvard.edu
Phone: +1 (765) 490-7606

Education

• Purdue University, West Lafayette, IN
  School of Electrical and Computer Engineering [August 2003-May 2009]
  Ph.D. Electrical & Computer Engineering
• Purdue University, West Lafayette, IN
  School of Electrical and Computer Engineering [August 1999-May 2003]
  B.S. Electrical & Computer Engineering

Professional Appointments

• Instructor
  Athinoula A. Martinos Center for Biomedical Imaging
  MGH / Harvard-MIT [June 2014-February 2017]
  
• Research Engineer
  Athinoula A. Martinos Center for Biomedical Imaging
  MGH / Harvard-MIT [July 2011-May 2014]
  
• Senior Engineer
  Computational Lithography Group
  Intel Corporation [July 2010-June 2011]
  
• Visiting Assistant Professor
  Purdue University, West Lafayette, IN
  School of Electrical and Computer Engineering [August 2009-May 2010]
  

Fellowships

• Awarded GAANN Fellowship, providing three years of funding for the pursuit of Direct Ph.D. in Electrical Engineering, Purdue University, IN. (August 2005 - 2008)
• Awarded Ross Fellowship for pursuit of Direct Ph.D. in Electrical Engineering, Purdue University, IN. (August 2003 - 2004)

Teaching

• Course Instructor, January 2010 - May 2010
  ECE 602: Lumped System Theory
  Graduate level core course for electrical engineering students.
• Course Instructor, September 2009 - December 2009
  ECE 301: Signals and Systems
  Junior level undergraduate course for electrical and computer engineering students.
• Co-Instructor, July 13-16, 2009, Trinity College Dublin, Ireland
  Applied Optimization
  Graduate level short course, lectures can be viewed at:
  http://www.networkmaths.ie/courses/
• Course Instructor, January 2009 - May 2009
  ECE 602: Lumped System Theory
  Graduate level core course for electrical engineering students.
• Teaching Fellow, January 2008 - May 2008
  ECE 602: Lumped System Theory
  Graduate level core course for electrical engineering students.
• Course Instructor, June 2007 - August 2007
  ECE 369: Discrete Mathematics for Computer Engineers
  Junior level undergraduate course for electrical and computer engineering students.
• Teaching Fellow, January 2007 - May 2007
  ECE 580: Optimization Methods for System and Control
  Graduate level course for electrical engineering students.

Publications

JOURNAL ARTICLES

• F. Cauley, S. Cauley, K. Lee, Y. Xie, and N. Wang, Standing Wave Annealing Technique: For the Design and Optimization of Nonlinear Simulated Moving Bed Systems with Significant Mass-Transfer Effects; Industrial & Engineering Chemistry Research, 45 (25), 8697-8712 (2006). [10.1021/ie060300a]
• S. Cauley, J. Jain, C. Koh, and V. Balakrishnan, A scalable distributed method for quantum-scale device simulation; Journal of Applied Physics, 101, 123715 (2007). [10.1063/1.2748621]
• F. Cauley, S. Cauley, N. Wang, Standing Wave Optimization of SMB using a Hybrid Simulated Annealing and Genetic Algorithm (SAGA); International Journal of Adsorption, 14, 665-678 (2008). [10.1007/s10450-008-9119-8]
• S. Cauley, C. Koh, and V. Balakrishnan, A Parallel Direct Solver for Large-scale Power/Ground Networks; IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems, Vol. 29, No. 4 (2010). [10.1109/TCAD.2010.2042901]
• S. Cauley, V. Balakrishnan, Y. Hu, and C. Koh, A Parallel Branch-and-Cut Approach for Detailed Placement; ACM Transactions on Design and Automation, Vol. 16, No. 2 (2011). [10.1145/1929943.1929950]
• S. Cauley, V. Balakrishnan, G. Klimeck, and C. Koh, A Two-Dimensional Domain Decomposition Technique for the Simulation of Quantum-Scale Devices; Journal of Computational Physics, Vol. 231, 1293-1313 (2011). [10.1016/j.jcp.2011.10.006]
• S. Cauley, M. Luisier, V. Balakrishnan, G. Klimeck, and C. Koh, Distributed Non-Equilibruim Green's Function Algorithms for the Simulation of Nanoelectronic Devices with Scattering; Journal of Applied Physics, Vol. 110, 043713 (2011). [10.1063/1.3624612]
• B. Guerin, M. Gebhardt, S. Cauley, E. Adalsteinsson, and L. Wald, Local SAR, global SAR, transmitter power and pulse fidelity trade-offs in low flip angle parallel transmit pulse design; Mag Res Med, Apr; 71(4):1446-1457 (2014) [PMC3871989]
• K. Setsompop, R. Kimmlingen, E. Eberlein, T. Witzel, J. Cohen-Adad, J. McNab, B. Keil, D. Tisdall, P. Hoecht, P. Dietz, S. Cauley, V. Tountcheva, V. Matschl, V. Lenz, K. Heberlein, A. Potthast, H. Thein, J. Van Horn, A. Toga, F. Schmitt, D. Lehne, B. Rosen, V. Wedeen, and L. Wald, Pushing the limits of in vivo diffusion MRI for the Human Connectome Project; Neuroimage, Vol 80, 220-233 (2013). [PMC3725309]
• S. Cauley, J. Polimeni, H. Bhat, D. Wang, L.L. Wald, K. Setsompop; Inter-slice Leakage Artifact Reduction Technique for Simultaneous Multi-Slice Acquisitions; Magn Reson Med; Jul;72(1):93-102 (2014). [PMC4364522]
• B. Bilgic, I. Chatnuntawech, A.P. Fan, K. Setsompop, S.F. Cauley, L.L. Wald, E. Adalsteinsson; Fast Image Reconstruction with L2-Regularization; Journal of Magnetic Resonance Imaging; Jul; 40(1): 181-191 (2014). [PMC4106040]
• B. Bilgic, I. Chatnuntawech, K. Setsompop, S.F. Cauley, L.L. Wald, E. Adalsteinsson; Fast Diffusion Spectrum Imaging Reconstruction with Trained Dictionaries; IEEE Transactions on Medical Imaging; Nov; 32(11):2022-33 (2013); [PMC4689148]
• B. Bilgic, A.P. Fan, J.R. Polimeni, S.F. Cauley, M. Bianciardi, E. Adalsteinsson, L.L. Wald, K. Setsompop; Fast Quantitative Susceptibility Mapping with L1-Regularization and Automatic Parameter Selection; Magn Reson Med; Nov; 72(5):1444-59 (2014). [PMC4111791]
• C. Eichner, K. Jafari-Khouzani, S. Cauley, H. Bhat, P. Polaskova, O. Rapalino, R.F. Turner, L.L. Wald, S. Stufflebeam, K. Setsompop; Slice Accelerated Gradient-Echo Spin-Echo Dynamic Susceptibility Contrast Imaging with blipped CAIPI for Increased Slice Coverage; Magn Reson Med; Sep 72(3):770-778 (2014). [PMC4002660]
• Y. Xi, J. Xia, S. Cauley, V. Balakrishnan; Superfast and Stable Structured Solvers for Toeplitz Least Squares Via Randomized Sampling; accepted SIAM Journal on Matrix Analysis and Applications. [10.1137/120895755]
• S. Cauley, Y. Xi, B. Bilgic, J. Xia, E. Adalsteinsson, V. Balakrishnan, L. Wald, and K. Setsompop; Fast Reconstruction for Multichannel Compressed Sensing Using a Hierarchically Semiseparable Solver; Magn Reson Med; Mar; 73(3):1034-1040 (2015). [PMC4167172]
• B. Bilgic, B. Gagoski, S. Cauley, A. Fan, J. Polimeni, P. Ellen Grant, L. Wald, and K. Setsompop; Wave-CAIPI for Highly Accelerated 3D Imaging, Magn Reson Med; Jun; 73(6):2151-62 (2015). [PMC4281518]
• I. Chatnuntawech, B. Gagoski, B. Bilgic, S. Cauley, K. Setsompop, and E. Adalsteinsson; Accelerated 1H MRSI Using Randomly Undersampled Spiral-based k-space Trajectories; Magn Reson Med 2014; early view. [PMC: in process]
• S. Cauley, K. Setsompop, D. Ma, Y. Jiang, H. Ye, E. Adalsteinsson, M. Griswold, and L. Wald; Fast Group Matching for MR Fingerprinting Reconstruction; Magn Reson Med; Aug; 74(2):523-9 (2015). [PMC4700821]
• C. Eichner, S. Cauley, J. Cohen-Adad, HE. Möller, R. Turner, K. Setsompop, LL. Wald; Real Diffusion Weighted MRI Enabling True Signal Averaging and Increased Diffusion Contrast; Neuroimage, 122:373-384 (2015). [PMC4651971]
• J. Xia, Y. Xi, S. Cauley, and V. Balakrishnan, Fast sparse selected inversion, SIAM J. Matrix Anal. Appl., 36 (2015), pp. 1283-1314. [10.1137/14095755X]
• B. Zhao, K. Setsompop, H. Ye, S. Cauley, L. Wald; Maximum Likelihood Reconstruction for Magnetic Resonance Fingerprinting; IEEE Transactions on Medical Imaging; Aug; 35(8):1812-23 (2016). [PMC: in process]
• H. Ye, D. Ma, Y. Jiang, S. Cauley, Y. Du, LL. Wald, M.A. Griswold, K. Setsompop; Accelerating magnetic resonance fingerprinting (MRF) using t-blipped simultaneous multislice (SMS) acquisition; Mag Res Med, May; 75(5):2078-85 (2016). [PMC4673043]
• J. Vogel, J. Xia, S. Cauley, and V. Balakrishnan, Superfast divide-and-conquer method and perturbation analysis for structured eigenvalue solutions, SIAM J. Sci. Comput., 38(3):1358-1382 (2016). [10.1137/15M1018812]
• H. Ye, S. Cauley, B. Gagoski, B. Bilgic, D. Ma, Y. Jiang, YP. Du, M. Griswold, L. Wald, and K. Setsompop; Simultaneous multislice magnetic resonance fingerprinting (SMS-MRF) with direct-spiral slice-GRAPPA (ds-SG) reconstruction; Mag Res Med, 2016; [PMC5123982]
• I. Chatnuntawech, P. McDaniel, S. Cauley, B. Gagoski, C. Langkammer, A. Martin, PE. Grant, L. Wald, K. Setsompop, E. Adalsteinsson, and B. Bilgic; Single-Step Quantitative Susceptibility Mapping with Variational Penalties; NMR Biomed, 2016; [PMC5179325]
• C. Mekkaoui, T.G. Reese, S. Cauley, K. Setsompop, M.P. Jackowski, D. E. Sosnovik; Diffusion Tractography of the Entire Left Ventricle Using Free-Breathing Accelerated Simultaneous Multislice Imaging; Radiology, 2016; [PMC: in process]
• S. Cauley, K. Setsompop, B. Bilgic, H. Bhat, B. Gagoski, and L. Wald; Auto-calibrated Wave-CAIPI Reconstruction; Joint Optimization of K-space Trajectory and Parallel Imaging Reconstruction; Mag Res Med, 2016; [PMC5400736]
• EE. Mason, CZ. Cooley, S. Cauley, M. Griswold, S. Conolly, L. Wald. Design analysis of an MPI human functional brain scanner. Int J Magn Part Imaging. 2017;3(1) PMID: 28752130 PMCID: PMC5526464
• D. Polak, K. Setsompop, S. Cauley, B. Gagoski, H. Bhat, F. Maier, P. Bachert, LL. Wald, B. Bilgic. Wave-CAIPI for highly accelerated MP-RAGE imaging. Magn Reson Med. 2017 ePub PMID:28220617
• K. Setsompop K, Q. Fan, J. Stockman, B. Bilgic, S. Huang, S. Cauley, A. Nummenmaa, F. Wang, Y. Rathi, T. Witzel, LL. Wald. High-resolution in vivo diffusion imaging of the human brain with generalized slice dithered enhanced resolution: Simultaneous multislice (gSlider-SMS). Magn. Reson. Med. 2017 Epub. PMID:28261904
• C. Cooley, M. Haskell, S. Cauley, C. Sappo, C. Lapierre, C. Ha, J. Stockmann, L. Wald. Design of Sparse Halbach Magnet Arrays for Portable MRI Using a Genetic Algorithm. IEEE Transactions on Magnetics, vol. 54, no. 1, pp. 1-12, Jan. 2018. doi: 10.1109/TMAG.2017.2751001
• X Ye, J Xia, RH Chan, S Cauley, V Balakrishnan. A fast contour-integral eigensolver for non-Hermitian matrices. SIAM Journal on Matrix Analysis and Applications 38 (4), 1268-1297
• Y. Jiang, D. Ma, H. Bhat, H. Ye, S. Cauley, L. Wald, K. Setsompop, M. Griswold. Use of pattern recognition for unaliasing simultaneously acquired slices in simultaneous multislice MR fingerprinting. Magn Reson Med 78 (5), 1870-1876
• Z Xin, J Xia, MV de Hoop, S Cauley, V Balakrishnan. A distributed-memory randomized structured multifrontal method for sparse direct solutions. SIAM Journal on Scientific Computing 39 (4), C292-C318
• EE Mason, CZ Cooley, SF Cauley, MA Griswold, SM Conolly, LL Wald. Design analysis of an MPI human functional brain scanner. International Journal on Magnetic Particle Imaging 3 (1)
• M. Haskell, S. Cauley, L. Wald, TArgeted Motion Estimation and Reduction (TAMER): Data Consistency Based Motion Mitigation for MRI using a Reduced Model Joint Optimization. Accepted IEEE Transactions on Medical Imaging
• B Zhu, J Z Liu, S F Cauley, B R Rosen, and M S Rosen, Image Reconstruction by Domain Transform Manifold Learning. Accepted Nature

BOOK CHAPTERS

• Jiun-Lang Huang, Cheng-Kok Koh, and Stephen F Cauley, Electronic Design Automation: Synthesis, Verification, and Test, Chapter 8: Logic and Circuit Simulation, Elsevier Science & Technology 2009.
• Cheng-Kok Koh, Jitesh Jain, and Stephen F Cauley, Electronic Design Automation: Synthesis, Verification, and Test, Chapter 13: Synthesis of Clock and Power/Ground Networks, Elsevier Science & Technology 2009.

Patent Applications

• Stephen F. Cauley, Jitesh Jain, Cheng-Kok Koh, and Venkataramanan Balakrishnan, Parallel Algorithms for Sparse Matrix Simulations, Purdue Research Foundation.
• Nien-Hwa Linda Wang, Yi Xie, and Stephen F. Cauley, VErsatile Reaction SEparation (VERSE) - A Dynamic Simulation Package for Batch and Simulated Moving Bed (SMB) Chromatography, Purdue Research Foundation.
• JR Polimeni, H Bhat, KA Heberlein, K Setsompop, T Witzel, SF Cauley Methods, systems and apparatuses for rapid segmented, accelerated, and simultaneous multi-slice echo planar imaging US Patent 9,588,208
• S Cauley, K Setsompop, LL Wald Systems and methods for joint trajectory and parallel magnetic resonance imaging optimization for auto-calibrated image reconstruction US Patent App. 15/281,457
• H Bhat, K Heberlein, S Cauley, M Tisdall, K Setsompop, A Van Der Kouwe Fast Prospective Motion Correction For MR Imaging US Patent App. 14/797,784
• C Eichner, K Setsompop, L Wald, S Cauley Systems and methods for preserving phase information in diffusion-weighted magnetic resonance imaging US Patent App. 15/314,210
• S Cauley, M Griswold, K Setsompop, L Wald Fast Group Matching For Magnetic Resonance Fingerprinting Reconstruction US Patent 20150346301A1
• S Cauley, B Bilgic, K Setsompop, L Wald Systems and methods for fast magnetic resonance image reconstruction using a heirarchically semiseparable solver US Patent 20150323633A1
• S Cauley, J Polimeni, K Setsompop, L Wald Hierrarchical mapping framework for coil compression in magnetic resonance image reconstruction US Patent App. 15/305,436