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[EXPIRED] The Capital Region of Copenhagen is looking for a Postdoc in mapping brain microstructure and its functional correlates

Postdoc in mapping brain microstructure and its functional correlates

Are you fascinated by modeling tissue microstructure from high quality diffusion MRI acquisitions, exploring its morphological validity against novel 3D histology imaging technologies and investigating its correlates to the communication speed of brain pathways? How does disease impact the microstructure, and can you predict the impact on saltatory conduction velocity along white matter axons? Are you curious if biophysical models or machine learning are the best modeling approaches? Try it out!

Join our diverse research group headed by Professor Tim B. Dyrby at the Danish Research Centre for MR (DRCMR) at Copenhagen University Hospital - Amager and Hvidovre in the Copenhagen area of Denmark. We have all the expertise to leverage your scientific curiosity and develop you as a researcher. Take part to make a difference in predicting how brain diseases impact patients for establishing future diagnostic tools. The research is supported by the European Research Council (ERC) consolidator project “Non-invasive Conduction Velocity Mapping in Brain Networks” - CoM-BraiN. The research will also be carried out at the Department of Applied Mathematics and Computer Science at the Technical University of Denmark (DTU Compute) with access to large scale computing facilities.

Your responsibilities:

  • To establish machine learning and/or biophysical models for mapping axon morphology and cells in health and disease from diffusion MRI and quantitative MRI acquisitions.
  • To explore diffusion MRI parameters for obtaining the best model fits using a powerful preclinical MRI scanner or a clinical MRI scanner.
  • To verify your models via diffusion MRI simulations, validate your models against 3D histology data, and correlate them with functional data.
  • To actively collaborate and create synergies with group members, i.e., taking part in image analysis and participating in the collection of 3D histology data. We use nanoscopic 3D imaging using large-scale x-ray synchrotron imaging facilities, microscopic imaging using Light-sheet fluorescence Microscopy experiments, and Electron Microscopy. Animal models or tissue samples will be made for you by team members.

Your profile:

You should be a highly motivated open-minded team player with the following qualifications:

  • Ph.D. degree in MRI physics, computer science or relevant field with a foundation in MRI data modelling.
  • Interest in experimental MRI techniques. It is a plus if you have experience with preclinical scanner systems but is not a requirement as we will train you.
  • Proven expertise in biophysical modelling or machine learning models and working with Monte Carlo simulations.
  • Experience in 3D histology techniques such x-ray synchrotron imaging and Light-Sheet Fluorescence Microscopy (LSFM) is a plus but not a requirement as you will be introduced to this. 
  • Fluency in English writing and scientific communication.
  • Demonstrated ability to work independently and think critically, while also effectively collaborating and contributing to the research team.

About us:

The project will be carried out at the Danish Research Centre for Magnetic Resonance (DRCMR) which is a leading research centre for biomedical MRI in Europe (www.drcmr.dk). Our mission is to triangulate MR physics and basic physiology from preclinical to clinical research. Approximately 75 researchers from a diverse range of disciplines are currently pursuing basic and clinically applied MR research and its validation with a focus on structural, functional, and metabolic MRI of the human brain and its disorders. The DRCMR is embedded in the Department of Radiology and Nuclear Medicine, a large diagnostic imaging department that houses all biomedical imaging modalities at the Copenhagen University Hospital - Amager and Hvidovre. The hospital has strong collaborative links with the Technical University of Denmark and is part of the newly established organisational framework, The Technical University Hospital of Greater Copenhagen.

The DRCMR has a state-of-the-art MR research infrastructure enabling translational research, which includes a pre-clinical 7T Bruker MR scanner, and six whole-body MR scanners (one 7T, four 3T, and one 1.5T scanners). The DRCMR has high performance computing cluster facilities, pre-clinical labs, a neuropsychology laboratory, an EEG laboratory, and two laboratories for non-invasive brain stimulation.

Our preclinical labs perform basic research in functional, microstructure, and plasticity imaging centred around the 7T Bruker BioSpec MRI system. The preclinical labs include a GMO2-classified virus lab fully equipped with stereotaxic surgery equipment, and electrophysiology facilities. Our cross-disciplinary research team is designing and validating new types of diffusion MRI and quantitative MRI imaging technologies for non-invasively disentangling the microstructure of brain networks and their function. Here, it is key to have a true interest in how the microanatomy and saltatory conduction velocity are related in the normal, and how it impacts brain function in the diseased brain. Our vision is translating our research to clinics to improve future non-invasive imaging technologies for better patient diagnosis.

Your position:

The candidate will be employed for a period of 24 months with the possibility for an extension at the Danish Research Centre for Magnetic Resonance where he/she will be an active part of the Microstructure and Plasticity Group (drcmr.dk/map) and the Preclinical Method group, both led by Professor Tim B. Dyrby.

 

Selected Publications

Gregersen, F., Eroğlu, H. H., Göksu, C., Puonti, O., Zuo, Z., Thielscher, A. & Hanson, L. G.
MR imaging of the magnetic fields induced by injected currents can guide improvements of individualized head volume conductor models.
Imaging Neuroscience. 2, p. 1-15, https://doi.org/10.1162/imag_a_00176 (2024).

Göksu, C., Gregersen, F., Scheffler, K., Eroğlu, H. H., Heule, R., Siebner, H. R., Hanson, L. G. & Thielscher, A. Volumetric measurements of weak current-induced magnetic fields in the human brain at high resolution. Magn Reson Med.  DOI: 10.1002/mrm.29780 (2023).

Hosseini, S., Puonti, O., Treeby, B., Hanson, L. G. & Thielscher, A.
A Head Template for Computational Dose Modelling for Transcranial Focused Ultrasound Stimulation. NeuroImage. p. 120227. DOI: 0.1016/j.neuroimage.2023.120227 (2023).

Rahbek, S., Mahmood, F., Tomaszewski, M. R., Hanson, L. G. & Madsen, K. H. Decomposition-based framework for tumor classification and prediction of treatment response from longitudinal MRI, Phys in Med and Biol. DOI: 10.1088/1361-6560/acaa85, 2023.

Rahbek, S., Schakel, T., Mahmood, F., Madsen, K. H., Philippens, M. E. P. & Hanson, L. G. Optimized flip angle schemes for the split acquisition of fast spin-echo signals (SPLICE) sequence and application to diffusion-weighted imaging. Magn Reson Med, DOI: 10.1002/mrm.29545, 2023.

Laustsen, M., Andersen M., Xue, R., Madsen, K. H., & Hanson, L. G.Tracking of rigid head motion during MRI using an EEG system, Magn Reson Med, DOI: 10.1002/mrm.29251, 2022.

Gregersen, F., Göksu, C., Schaefers, G., Xue, R., Thielscher A., & Hanson L. G., Safety evaluation of a new setup for Transcranial Electric Stimulation during Magnetic Resonance Imaging, Brain Stimulation. 14, 3, p. 488-497, 2021.

Göksu, C., Scheffler, K., Gregersen, F., Eroğlu, H. H., Heule, R., Siebner, H. R., Hanson, L. G. & Thielscher, A. Sensitivity and resolution improvement for in vivo magnetic resonance current-density imaging of the human brain. Magn. Reson. Med. 86, p. 3131-3146, 2021.

Rahbek, S., Madsen, K. H., Lundell, H., Mahmood, F. & Hanson, L. G. Data-driven separation of MRI signal components for tissue characterization. J. Mag. Res. 333, p. 1-11. 2021.

Busoni, S., Bock, M., Chmelik, M., Colgan, N., De Bondt, T., Hanson, L. G., Israel, M., Kugel, H., Maieron, M., Mazzoni, L. N., Seimenis, I. & Vestergaard, P. ADDENDUM to EFOMP Policy statement No.14 "The role of the Medical Physicist in the management of safety within the magnetic resonance imaging environment: EFOMP recommendations". Physica Medica. 89, p. 303-305, 2021.

Sánchez-Heredia, J. D., Olin, R. B., McLean, M. A., Laustsen, C., Hansen A., Hanson, L.G., & Ardenkjaer-Larsen, J. H., Multi-Site Benchmarking of Clinical 13C RF Coils at 3 T, J Magn Reson, 318:106798, 2020.

Olin, R. B., Sánchez-Heredia, J. D., Schulte, R. F., Bøgh, N., Hansen, E. S. S., Laustsen, C., Hanson, L. G. & Ardenkjaer-Larsen, J. H. Three-dimensional accelerated acquisition for hyperpolarized 13 C MR  with blipped stack-of-spirals and conjugate-gradient  SENSE. Magn Reson Med 84, p. 519-34, 2020.

Pedersen, J. O., Hanson, C. G., Xue, R. & Hanson, L. G. Inductive measurement and encoding of k-space trajectories in MR raw data. MAGMA 32, p. 655-667, 2019.

Göksu, C., Scheffler K., Siebner H. R., Thielscher, A., & Hanson, L. G. The stray magnetic fields in Magnetic Resonance Current Density Imaging (MRCDI), Phys Med 59, p. 142-150, 2019.

Pedersen, J. O., Hanson, C. G., Xue, R. & Hanson, L. G. Regularization of Digitally Integrated, Inductive k-Space Trajectory Measures.
ISMRM 27th Annual Meeting & Exhibition 2019.

Pasquinelli, C., Hanson, L. G., Siebner, H. R., Lee, H. J. & Thielscher, A. Safety of transcranial focused ultrasound stimulation: A systematic review of the state of knowledge from both human and animal studies. Brain Stimulation. 12, 6, p. 1367-13802019.

Hansen, R. B., Sánchez-Heredia, J. D., Bøgh, N., Hansen, E. S. S., Laustsen C., L. G. Hanson & Ardenkjær-Larsen,  J. H. Coil profile estimation strategies for parallel imaging with hyperpolarized 13 C MRI, Magn Reson Med 82, p. 2104-17, 2019.

Göksu, C., Scheffler K., Siebner H. R., Thielscher, A., & Hanson, L.G. The stray magnetic fields in Magnetic Resonance Current Density Imaging (MRCDI), Phys Med 59, 142-150, 2019.

Magnusson, P., Boer, V., Marsman, A., Paulson, O. B., Hanson, L. G. & Petersen, E. T. Gamma-aminobutyric acid edited echo-planar spectroscopic imaging (EPSI) with MEGA-sLASER at 7T, Magn Reson Med, 81(2), p. 773-780, 2019.

Pedersen, J. O. Encoding of non-MR signals in Magnetic Resonance Imaging data. PhD thesis, Technical University of Denmark, Electrical Engineering, 2018.

Pedersen, J. O., Hanson, C. G., Xue, R.  & Hanson, L. G. General Purpose Electronics for Real-Time Processing and encoding of non-MR Data in MR Acquisitions, Concepts in Magn Reson B, 48B(2), e21385, 2018.

Eldirdiri, A., Posse, S., Hanson, L. G., Hansen, R. B., Holst, P., Schøier, C., Kristensen, A. T., Johannesen, H. H., Kjaer, A., Hansen, A. E.  & Ardenkjær-Larsen, J. H. Development of a Symmetric Echo Planar Spectroscopic Imaging Framework for Hyperpolarized 13C Imaging in a Clinical PET/MR Scanner, Tomography, 4(3), p. 110-22, 20184(3), p. 110-22, 2018.

Wilhjelm J. E., Duun-Henriksen J. & Hanson L. G., A virtual scanner for teaching fundamental magnetic resonance in biomedical engineering, Comput Appl Eng Educ, 26(6), p. 2197-2209, 2018

Göksu, C., Hanson, L. G., Siebner, H. R., Ehses, P., Scheffler, K. & Thielscher, A. Human in-vivo brain magnetic resonance current density imaging (MRCDI). NeuroImage. 171, p. 26-39, 2018.

Göksu C, Scheffler K, Ehses P, Hanson L.G & Thielscher A. Sensitivity Analysis of Magnetic Field Measurements for Magnetic Resonance Electrical Impedance Tomography (MREIT), Magnetic Resonance in Medicine. 79, p. 748-760, 2018.

Laustsen, M., Andersen, M., Lehmann, P. M., Xue, R., Madsen, K. H. & Hanson, L. G. Slice-wise motion tracking during simultaneous EEG-fMRI. Joint Annual Meeting ISMRM-ESMRMB 2018.

Petersen, J. R., Pedersen, J. O., Zhurbenko, V., Ardenkjær-Larsen, J. H. & Hanson, L. G. Ultra-low power transmitter for encoding non-MR signals in Magnetic Resonance  recordings. Joint Annual Meeting ISMRM-ESMRMB 2018.

Göksu, C., Hanson, L. G., Siebner, H. R., Ehses, P., Scheffler, K. & Thielscher, A. Comparison of two alternative sequences for human in-vivo brain MR Current Density Imaging (MRCDI). Joint Annual Meeting ISMRM-ESMRMB 2018.

Göksu, C., Hanson, L. G., Siebner, H. R., Ehses, P., Scheffler, K. & Thielscher, A. Human In-vivo Brain MR Current Density Imaging (MRCDI) based on Steady-state Free Precession Free Induction Decay (SSFP-FID). Joint Annual Meeting ISMRM-ESMRMB 2018.

Andersen, M., Hanson, L. G., Madsen, K. H., Wezel, J., Boer, V., van der Velden, T., van Osch, M. J. P., Klomp, D., Webb, A. G. & Versluis, M. J. Measuring motion-induced B0 -fluctuations in the brain using field probes. Magnetic Resonance in Medicine, 75(5):2020-30, 2016.

Andersen, M., Towards Motion-Insensitive Magnetic Resonance Imaging Using Dynamic Field Measurements. PhD thesis, Technical University of Denmark, Electrical Engineering. 109 p., 2016.

Hanson, L. G. The Ups and Downs of Classical and Quantum Formulations of Magnetic Resonance. Book chapter in Anthropic Awareness: The Human Aspects of Scientific Thinking in NMR Spectroscopy and Mass Spectrometry. Edited by: C Szantay, Jr. Elsevier, Chap. 3, p. 141-171, 2015.

de Nijs, R., Miranda, MJ., Hansen, LK., Hanson, LG. Motion correction of single-voxel spectroscopy by independent component analysis applied to spectra from nonanesthetized pediatric subjects. Magn Reson Med 2009, 62(5), 1147-1154.

Hanson, LG. Is quantum mechanics necessary for understanding magnetic resonance? Concepts in Magnetic Resonance Part A 2008, 32A(5), 329-340.

Hanson, LG. A graphical simulator for teaching basic and advanced MR imaging techniques. Radiographics 2007, 27(6), e27.

Hanson, LG., Lund, TE., Hanson, CG. Encoding of electrophysiology and other signals in MR images. J. Magn Reson Imaging 2007, 25(5), 1059-1066. 

Hanson, LG., Lund, TE., Hanson, CG. Encoding and transmission of signals as RF signals for detection using an MR apparatus. WO/2005/116676, PCT/DK2005/000343 2005.

Andersen, IK., Szymkowiak, A., Rasmussen, CE., Hanson, LG., Marstrand, JR., Larsson, HB. & Hansen, LK. Perfusion quantification using Gaussian process deconvolution. Magn Reson Med 2002, 48(2), 351-361.

Hanson, LG., Adalsteinsson, E., Pfefferbaum, A., Spielman, DM. Optimal voxel size for measuring global gray and white matter proton metabolite concentrations using chemical shift imaging. Magn Reson Med 2000, 44(1), 10-18.

Hanson, LG., Schaumburg, K., Paulson, OB. Reconstruction strategy for echo planar spectroscopy and its application to partially undersampled imaging. Magn Reson Med 2000, 44(3), 412-417.

News & Events

Group Members

Lars G. Hanson

Group Leader

External Collaborators

Section for MR, DTU Health Tech

Technical University of Denmark, Lyngby


Institute of Biophysics

Chinese Academy of Sciences, Beijing, China


Max Planck Institute for Biological Cybernetics

Tübingen, Germany