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 (Tba).

  • Staff
    • 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

  • 2015-2017 Marie Curie Postdoctoral Fellowship EU Horizon 2020.
    Grant: 658589 – MWMI. Starting date: 12/2015.

    2015 -2016 Postdoctoral Fellowship to Isabel Ellerbrock. Supervisor.
    Awarded by the University Medical Center Hamburg-Eppendorf. Starting date: 11/2015.

    2015-2018 Co-PI on “International Foundation for Research in Paraplegia” grant for a PhD position in collaboration with Patrick Freund in Zürich (Grant: P158 MRI).

    Upcoming projects:

    Emmy Noether Project : „ Validating MRI-based in-vivo histology“
    Emerging job vacancies: 1 Postdoc and 2 PhD Students positions

    UKE Pressemitteilung zum Emmy Noether Grant

    International ERANET Neuron Network Project : „Understanding the mechanisms of atrophy associated with spinal cord injury: “The application of MRI-based in vivo histology and ex vivo histology
    Emerging job vacancies: 1 Postdoc position

    For more information please contact: s.mohammadi@uke.de

  • 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

    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