Staff Collaborate Conference Room

Andrew Nencka, PhD

Andrew S. Nencka, PhD

Andrew S. Nencka, PhD

Associate Director

Contact Information


PhD, Biophysics, Medical College of Wisconsin, Milwaukee, WI, 2009
BS, Physics & Mathematics, Marquette University, Milwaukee, WI, 2004

Research Experience

  • Data Interpretation, Statistical
  • Echo-Planar Imaging
  • Image Enhancement
  • Image Processing, Computer-Assisted
  • Magnetic Resonance Imaging
  • Models, Statistical
  • Monte Carlo Method
  • Regression Analysis

Leadership Positions

  • Associate Director, Center for Imaging Research, 2016-Present
  • Chair, Faculty IT Committee, 2014-2016
  • Chair, Research MRI Safety Committee, 2012-Present
  • Secretary, Faculty IT Committee, 2016-Present

Research Interests

Image Acquisition Acceleration

One aspect of my research work has been to leverage the phase of acquired images, along with varying receive coil sensitivities, to further spatially encode the acquired data. With the assumption of real-valued images—an assumption often made for partial Fourier image reconstruction—this insight theoretically enables acceleration factors of 2N for an array of N coils. We have used this technology to implement a parallel slice acquisition method that simultaneously excites an array of slices with varying magnetization phase such that the magnetization phase and receive coil sensitivity profiles can be used to unalias the acquired slices. We have also used this technology to acquire and unalias accelerated single-slice images acquired with a single-channel body receiver coil.

Fast MR Relaxometry

Image acceleration techniques have enabled the development of a fast relaxometry pulse sequence, which we have named the gradient-recalled echo, asymmetric spin echo (GREASE) pulse sequence. The pulse sequence, including six echo-planar imaging readouts, two 90-degree excitation pulses, and two 180-degree refocusing pulses in each repetition, allows the computation of T1, T2, and T2* with each repetition. The acceleration techniques of GRAPPA and partial Fourier acquisition in the echo-planar imaging readouts reduce the duration of the imaging readout train so that signal decay does not eliminate the needed signal in later echoes. Thus, the relaxivity values for a single slice of 2 mm isotropic resolution can be acquired in less than 300 ms with this sequence. Further, the nearly simultaneous acquisition of the six images, the identical echo-planar imaging readouts, and the usage of the six images from each repetition for the estimation of relaxivity parameters allow the perfect coregistration of the computed maps.             


  • Resting-State fMRI Metrics in Acute Sport-Related Concussion and Their Association with Clinical Recovery: A Study from the NCAA-DOD CARE Consortium.

    (Meier TB, Giraldo-Chica M, España LY, Mayer AR, Harezlak J, Nencka AS, Wang Y, Koch KM, Wu YC, Saykin AJ, Giza CC, Goldman J, DiFiori JP, Guskiewicz KM, Mihalik JP, Brooks A, Broglio SP, McAllister T, McCrea MA.) J Neurotrauma. 2020 Jan 01;37(1):152-162 PMID: 31407610 PMCID: PMC6921290 SCOPUS ID: 2-s2.0-85076896953 08/14/2019

  • Image processing and analysis methods for the Adolescent Brain Cognitive Development Study.

    (Hagler DJ Jr, Hatton S, Cornejo MD, Makowski C, Fair DA, Dick AS, Sutherland MT, Casey BJ, Barch DM, Harms MP, Watts R, Bjork JM, Garavan HP, Hilmer L, Pung CJ, Sicat CS, Kuperman J, Bartsch H, Xue F, Heitzeg MM, Laird AR, Trinh TT, Gonzalez R, Tapert SF, Riedel MC, Squeglia LM, Hyde LW, Rosenberg MD, Earl EA, Howlett KD, Baker FC, Soules M, Diaz J, de Leon OR, Thompson WK, Neale MC, Herting M, Sowell ER, Alvarez RP, Hawes SW, Sanchez M, Bodurka J, Breslin FJ, Morris AS, Paulus MP, Simmons WK, Polimeni JR, van der Kouwe A, Nencka AS, Gray KM, Pierpaoli C, Matochik JA, Noronha A, Aklin WM, Conway K, Glantz M, Hoffman E, Little R, Lopez M, Pariyadath V, Weiss SR, Wolff-Hughes DL, DelCarmen-Wiggins R, Feldstein Ewing SW, Miranda-Dominguez O, Nagel BJ, Perrone AJ, Sturgeon DT, Goldstone A, Pfefferbaum A, Pohl KM, Prouty D, Uban K, Bookheimer SY, Dapretto M, Galvan A, Bagot K, Giedd J, Infante MA, Jacobus J, Patrick K, Shilling PD, Desikan R, Li Y, Sugrue L, Banich MT, Friedman N, Hewitt JK, Hopfer C, Sakai J, Tanabe J, Cottler LB, Nixon SJ, Chang L, Cloak C, Ernst T, Reeves G, Kennedy DN, Heeringa S, Peltier S, Schulenberg J, Sripada C, Zucker RA, Iacono WG, Luciana M, Calabro FJ, Clark DB, Lewis DA, Luna B, Schirda C, Brima T, Foxe JJ, Freedman EG, Mruzek DW, Mason MJ, Huber R, McGlade E, Prescot A, Renshaw PF, Yurgelun-Todd DA, Allgaier NA, Dumas JA, Ivanova M, Potter A, Florsheim P, Larson C, Lisdahl K, Charness ME, Fuemmeler B, Hettema JM, Maes HH, Steinberg J, Anokhin AP, Glaser P, Heath AC, Madden PA, Baskin-Sommers A, Constable RT, Grant SJ, Dowling GJ, Brown SA, Jernigan TL, Dale AM.) Neuroimage. 2019 11 15;202:116091 PMID: 31415884 PMCID: PMC6981278 08/16/2019

  • Analysis of errors in diffusion kurtosis imaging caused by slice crosstalk in simultaneous multi-slice imaging.

    (Olson DV, Nencka AS, Arpinar VE, Muftuler LT.) NMR Biomed. 2019 11;32(11):e4162 PMID: 31385637 08/07/2019

  • Prevalence of Potentially Clinically Significant Magnetic Resonance Imaging Findings in Athletes with and without Sport-Related Concussion.

    (Klein AP, Tetzlaff JE, Bonis JM, Nelson LD, Mayer AR, Huber DL, Harezlak J, Mathews VP, Ulmer JL, Sinson GP, Nencka AS, Koch KM, Wu YC, Saykin AJ, DiFiori JP, Giza CC, Goldman J, Guskiewicz KM, Mihalik JP, Duma SM, Rowson S, Brooks A, Broglio SP, McAllister T, McCrea MA, Meier TB.) J Neurotrauma. 2019 Jun;36(11):1776-1785 PMID: 30618331 PMCID: PMC6551984 SCOPUS ID: 2-s2.0-85066742597 01/09/2019

  • Resting-state functional connectivity after concussion is associated with clinical recovery.

    (Kaushal M, España LY, Nencka AS, Wang Y, Nelson LD, McCrea MA, Meier TB.) Hum Brain Mapp. 2019 03;40(4):1211-1220 PMID: 30451340 PMCID: PMC6365215 SCOPUS ID: 2-s2.0-85056732323 11/20/2018

  • Effective Connectivity Within the Default Mode Network in Left Temporal Lobe Epilepsy: Findings from the Epilepsy Connectome Project.

    (Cook CJ, Hwang G, Mathis J, Nair VA, Conant LL, Allen L, Almane DN, Birn R, DeYoe EA, Felton E, Forseth C, Humphries CJ, Kraegel P, Nencka A, Nwoke O, Raghavan M, Rivera-Bonet C, Rozman M, Tellapragada N, Ustine C, Ward BD, Struck A, Maganti R, Hermann B, Prabhakaran V, Binder JR, Meyerand ME.) Brain Connect. 2019 03;9(2):174-183 PMID: 30398367 PMCID: PMC6444922 SCOPUS ID: 2-s2.0-85063100708 11/07/2018

  • Editorial for Top 10 Reviewer Critiques of Radiology Artificial Intelligence (AI) Articles: Qualitative Thematic Analysis of Reviewer Critiques of Machine Learning / Deep Learning Manuscripts Submitted to JMRI.

    (Nencka AS.) J Magn Reson Imaging. 2020 Jan 10 PMID: 31922318 01/11/2020

  • Generalized simultaneous multi-orientation 2D imaging.

    (Mickevicius NJ, Nencka AS, Paulson ES.) Magn Reson Med. 2019 Dec 24 PMID: 31872496 12/25/2019

  • Multispectral diffusion-weighted MRI of the instrumented cervical spinal cord: a preliminary study of 5 cases.

    (Koch KM, Bhave S, Kaushik SS, Nencka AS, Budde MD.) Eur Spine J. 2019 Dec 12 PMID: 31832875 SCOPUS ID: 2-s2.0-85076835282 12/14/2019

  • Longitudinal Reproducibility of MR Perfusion Using 3D Pseudocontinuous Arterial Spin Labeling With Hadamard-Encoded Multiple Postlabeling Delays.

    (Cohen AD, Agarwal M, Jagra AS, Nencka AS, Meier TB, Lebel RM, McCrea MA, Wang Y.) J Magn Reson Imaging. 2019 Nov 30 PMID: 31785062 12/01/2019

  • Image processing and analysis methods for the Adolescent Brain Cognitive Development Study

    (Donald J Hagler Jr., Sean N. Hatton, Carolina Makowski, M. Daniela Cornejo, Damien A. Fair, Anthony Steven Dick, Matthew T. Sutherland, B.J. Casey, Deanna M. Barch, Michael P. Harms, Richard Watts, James M. Bjork, Hugh P. Garavan, Laura Hilmer, Christopher J. Pung, Chelsea S. Sicat, Joshua Kuperman, Hauke Bartsch, Feng Xue, Mary M. Heitzeg, Angela R. Laird, Thanh T. Trinh, Raul Gonzalez, Susan F. Tapert, Michael C. Riedel, Lindsay M. Squeglia, Luke W. Hyde, Monica D. Rosenberg, Eric A. Earl, Katia D. Howlett, Fiona C. Baker, Mary Soules, Jazmin Diaz, Octavio Ruiz de Leon, Wesley K. Thompson, Michael C. Neale, Megan Herting, Elizabeth R. Sowell, Ruben P. Alvarez, Samuel W. Hawes, Mariana Sanchez, Jerzy Bodurka, Florence J. Breslin, Amanda Sheffield Morris, Martin P. Paulus, W. Kyle Simmons, Jonathan R. Polimeni, Andre van der Kouwe, Andrew S. Nencka, Kevin M. Gray, Carlo Pierpaoli, John A. Matochik, Antonio Noronha, Will M. Aklin, Kevin Conway, Meyer Glantz, Elizabeth Hoffman, Roger Little, Marsha Lopez, Vani Pariyadath, Susan R.B. Weiss, Dana L. Wolff-Hughes, Rebecca DelCarmen-Wiggins, Sarah W. Feldstein Ewing, Oscar Miranda-Dominguez, Bonnie J. Nagel, Anders J. Perrone, Darrick T. Sturgeon, Aimee Goldstone, Adolf Pfefferbaum, Kilian M. Pohl, Devin Prouty, Kristina Uban, Susan Y. Bookheimer, Mirella Dapretto, Adriana Galvan, Kara Bagot, Jay Giedd, M. Alejandra Infante, Joanna Jacobus, Kevin Patrick, Paul D. Shilling, Rahul Desikan, Yi Li, Leo Sugrue, Marie T. Banich, Naomi Friedman, John K. Hewitt, Christian Hopfer, Joseph Sakai, Jody Tanabe, Linda B. Cottler, Sara Jo Nixon, Linda Chang, Christine Cloak, Thomas Ernst, Gloria Reeves, David N. Kennedy, Steve Heeringa, Scott Peltier, John Schulenberg, Chandra Sripada, Robert A. Zucker, William G. Iacono, Monica Luciana, Finnegan J. Calabro, Duncan B. Clark, David A. Lewis, Beatriz Luna, Claudiu Schirda, Tufikameni Brima, John J. Foxe, Edward G. Freedman, Daniel W. Mruzek, Michael J. Mason, Rebekah Huber, Erin McGlade, Andrew Prescot, Perry F. Renshaw, Deborah A. Yurgelun-Todd, Nicholas A Allgaier, Julie A. Dumas, Masha Ivanova, Alexandra Potter, Paul Florsheim, Christine Larson, Krista Lisdahl, Michael E. Charness, Bernard Fuemmeler, John M. Hettema, Joel Steinberg, Andrey P. Anokhin, Paul Glaser, Andrew C. Heath, Pamela A. Madden, Arielle Baskin-Sommers, R. Todd Constable, Steven J. Grant, Gayathri J. Dowling, Sandra A. Brown, Terry L. Jernigan, Anders M. Dale.) biorxiv (preprint). 03/18/2019

  • Build-A-FLAIR: Synthetic T2-FLAIR Contrast Generation through Physics Informed Deep Learning

    (Andrew S. Nencka, Andrew Klein, Kevin M. Koch, Sean D. McGarry, Peter S. LaViolette, Eric S. Paulson, Nikolai J. Mickevicius, L. Tugan Muftuler, Brad Swearingen, Michael A. McCrea.) Nencka AS, Klein A, Koch KM, McGarry SD, LaViolette PS, Paulson ES, Mickevicius NJ, Muftuler LT, Swearingen B, McCrea MA. Build-A-FLAIR: Synthetic T2 Contrast Generation through Physics Informed Deep Learning. (2019): 1901.04871. 01/15/2019