Jon-Fredrik Nielsen, PhD

 Jon-Fredrik Nielsen, PhD
Research Associate Professor, UMOR Functional MRI Laboratory, Medical School
Research Associate Professor, Biomedical Engineering
Associate Research Scientist, Electrical Engineering and Computer Science, College of Engineering
[email protected]
Available to mentor
Jon-Fredrik Nielsen, PhD
Jon-Fredrik Nielsen, PhD
Research Associate Professor
  • About
  • Qualifications
  • Research Overview
  • Recent Publications

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    • About

    I am an MRI physicist in the functional MRI laboratory (now part of UM Radiology), specializing in developing, implementing, and disseminating new MRI pulse sequences. I collaborate with researchers in UM Neurology, Radiology, and Engineering, to improve functional and structural MRI. My works mostly involves brain imaging, but the techniques I have helped develop can also be used in other contexts.

    Qualifications
    • PhD
      Ohio State University, Columbus, United States
      1995 - 2001
    • BS
      University of Georgia, Athens, United States
      1992 - 1995

    Research Overview

    My main areas of research and development are: (1) making MRI measurements more robust across sites and scanner vendor platforms, (2) designing 'shaped' radiofrequency (RF) pulses that select a 2D/3D region to be imaged (as opposed to conventional 1D slice-selective RF pulses), and (3) quantitative MRI with a focus on brain tissue characterization in, e.g., neurodegenerative disease.

    Recent Publications

     See All Publications
    • Preprint
      Phantom- and simulation-based validation of combined diffusion relaxometry in ex vivo ADRD white matter
      Jacobson A, Murguia AM, Swanson SD, Nielsen J-F, Fessler JA, Seraji-Bozorgzad N. 2026 May 2; bioRxiv, DOI:10.64898/2026.04.27.721146
    • Preprint
      OpenMRF: A Modular, Vendor-Neutral Open-Source Framework for Reproducible Magnetic Resonance Fingerprinting using Pulseq
      Griesler T, Stebani J, Kaplan S, Angelov I, Albert P, Blaimer M, Wech T, Wang X, Chen Q, Zaitsev M, Zhu Z, Liu Q, Martin P, Nielsen J-F, Hamilton JI, Nordbeck P, Seiberlich N, Gram M. 2026 Apr 28; arXiv, DOI:10.48550/arxiv.2604.22713
    • Preprint
      OpenMRF: A Modular, Vendor-Neutral Open-Source Framework for Reproducible Magnetic Resonance Fingerprinting using Pulseq.
      Griesler T, Stebani J, Kaplan S, Angelov I, Albert P, Blaimer M, Wech T, Wang X, Chen Q, Zaitsev M, Zhu Z, Liu Q, Martin P, Nielsen J-F, Hamilton JI, Nordbeck P, Seiberlich N, Gram M. 2026 Apr 24;
      PMID: 42078496
    • Journal Article
      Correction: Naming convention for gradient system transfer function and gradient system frequency response for magnetic resonance imaging encoding field characterization.
      Wehkamp N, Hucker P, Fischer J, Greiner A, Nielsen J-F, Zaitsev M, Dehnert R. MAGMA, 2026 Mar 26; DOI:10.1007/s10334-026-01336-9
      PMID: 41886015
    • Journal Article
      A vendor-neutral functional MRI acquisition protocol for multi-site studies
      Nielsen J-F, Egan MK, Chen Q, Shafiekhani M, Wang JH, Hurley SA, Soldate JS, Lisinski J, LaConte SM, Sutton BP, Waggoner RA, Stirnberg R, Stöcker T, Fessler JA, Noll DC, Zaitsev M, Peltier SJ. Aperture Neuro, 2026 Feb 15; 6 (SI 1): DOI:10.52294/001c.155279
    • Journal Article
      Comment: naming convention for gradient system transfer function and gradient system frequency response for magnetic resonance imaging encoding field characterization.
      Wehkamp N, Hucker P, Fischer J, Greiner A, Nielsen J-F, Zaitsev M, Dehnert R. MAGMA, 2026 Jan 30; DOI:10.1007/s10334-025-01314-7
      PMID: 41615567
    • Proceeding / Abstract / Poster
      Multi-site use of a vendor-agnostic, open-source protocol (VOP) framework to validate and share open-source pulse sequences
      Geethanath S, Artiges A, Block T, Chen Q, Fernandes T, Ganji S, Grissom W, Hoinkiss D, Vaughan J, Konar A, Konstandin S, Mascarenhas V, Nagtegaal M, Nielsen J, Nunes R, Shafiekhani M, Zaitsev M. Proceedings of the International Society for Magnetic Resonance in Medicine ... Scientific Meeting and Exhibition., 2025 Sep 18; DOI:10.58530/2025/1971
    • Proceeding / Abstract / Poster
      Pulserver: an open-source Pulseq-based client-server framework for vendor agnostic, interactive MR sequence design
      Cencini M, Wang K, Huang S, Schulte R, Sprenger T, Noll D, Tosetti M, Nielsen J-F. Proceedings of the International Society for Magnetic Resonance in Medicine ... Scientific Meeting and Exhibition., 2025 Sep 18; DOI:10.58530/2025/1275