Quantitative MRI and in vivo histology
Research group


Understanding basic mechanisms underlying normal and diseased human brain developments crucially depends on reliable knowledge of its anatomical microstructure and connectivity. Our long-term goal is to estimate microstructural properties non-invasively in living subjects using biophysical models of the MRI signal.

We are developing novel methods for fusion of high-resolution quantitative MRI (qMRI) to enable MRI-based in vivo histology (hMRI) in the brain and spinal cord. The main focus is to develop valid MRI metrics that characterize key white matter microstructure properties as known from ex vivo histology (e.g. myelin density, fiber density, and the g-ratio – i.e. the ratio between inner and outer fiber diameter).

To achieve these goals, we are currently working on three projects:

Basic science: Validating MRI-based in vivo histology by comparison with ex vivo histology (Funded by the DFG Emmy Noether Program )

Clinical research: Understanding the microstructural mechanisms of spinal cord injury (Funded by EU ERA-NET Neuron)

Connectomics: In vivo and ex vivo characterization of the human microstructural connectome (Funded by DFG SPP 2041).

  • Staff
  • Staff

    Principal Investigator

    Siawoosh Mohammadi
    Siawoosh Mohammadi


    Phd Students

    Gergely Dávid is developing novel tools for robust spinal cord DTI and optimizing their sensitivity to detect microstructural correlates of spinal cord injury. This project is done in collaboration with Patrick Freund at the UZH in Zürich ( http://www.sci-research.uzh.ch/en/aboutus/Freund.html ).

    Tobias Streubel

    In his PhD project, Tobias will work on establishing an MRI pipeline for validation of biophysical models. He will be engaged in the Emmy Noether and Microstructural Connectome projects .

    Behnam Ashtarayeh

    In his PhD project, Behnam will continue the work of Joshua Engels on Inpanting. Moreover, he will be engaged in the Microstructural Connectome project .

    Bachelor, Master and Student assistants

    Christoph Nicolai is working in his MSc project on a novel segmentation method for high-resolution data. This project is done in collaboration with Marko Lindner at the TUHH in Hamburg-Harburg.

    Annkristin Lange is working in her MSc project on a method for registration of 2D histology data to 3D volumes. This project is done in collaboration with Jan Modersitzki at the MIC Institute at the University of Lübeck.


    Dr. Isabel Ellerbrock

    Dr. Mohammad Hassan Farsbaf Shaker

    Joshua Engels

    Sara Holm

    Hatice-Kübra Ögreten

    • High-resolution quantitative MRI (qMRI) and in vivo histology (hMRI)

    • Artifact correction and robust measurement of qMRI and hMRI metrics ( ACID toolbox )

    • Neuroscience: structural and microstructural mechanisms of long-term nociception and pain

    • Clinical research: robust biomarkers for spinal cord injury

  • Secured Funding (last 5 years)

    2017-2022 Emmy Noether Grant, German Research Foundation (DFG). Grant: MO 2397/4-1 .

    2018-2020 Priority Programme „Computational Connectomics” (SPP 2041), German Research Foundation (DFG). Grant: MO 2397/5-1 ).

    2017-2020 ERA-Net NEURON Cofund, European Union’s Horizon 2020, Grant: No.88: hMRIofSCI

    2015-2019 Co-PI on “International Foundation for Research in Paraplegia” grant (~€185k) for a PhD position (Gergely David) for investigation of trauma induced structural spinal changes in collaboration with Patrick Freund in Zürich (Grant: P158 MRI).

    2015-2017 Marie Curie Postdoctoral Fellowship, European Union’s Horizon 2020, Grant: 658589 - MWMI.

    2012-2014 DFG Postdoctoral Fellowship, Deutsche Forschungsgemeinschaft (DFG), Grant: MO 2397/1-1.

    2013 “UCL-ZNZ collaboration” grant for laying the foundation of a larger multi-center grant between UCL and “Zentrum für Neurowissenschaften Zürich” (ZNZ).

  • MR Physics

    Nikolaus Weiskopf
    Department of Neurophysics, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany

    Martina Callaghan
    Wellcome Trust Centre for Neuroimaging, UCL Institute of Neurology,
    University College London, UK

    Mathematics and Computer Science

    Lars Ruthotto
    Department of Mathematics and Computer Science,
    Emory University, Atlanta, USA

    Karsten Tabelow and Joerg Polzehl
    Stochastic Algorithms and Nonparametric Statistics,
    Weierstrass Institute for Applied Analysis and Stochastics, Berlin, Germany

    Patrick Freund
    Spinal Cord Injury Center Balgrist, University Hospital Zurich,
    University of Zurich, Switzerland

    Marko Lindner
    Institut für Mathematik,
    Technische Universität Hamburg

    Jan Modersitzki
    Institute of Mathematics and Image Computing,
    University of Lübeck

    Histology and Clinics

    Patrick Freund
    Spinal Cord Injury Center Balgrist, University Hospital Zurich,
    University of Zurich, Switzerland

    Markus Morawski
    Paul Flechsig Institute for Brain Research,
    University of Leipzig

    Gabriele Rune and Lars Fester
    Institute of Neuroanatomy,
    Medical Center Hamburg-Eppendorf

    Klaus Püschel
    Department of Legal Medicine,
    Medical Center Hamburg-Eppendorf

  • There are ongoing employment opportunities for doctoral students and post-docs. On a speculative application with motivation letter and CV to s.mohammadi@uke.de we look forward.”