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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

2021

Albers KJ, Ambrosen KS, Liptrot MG, Dyrby TB, Schmidt MN, Mørup M. 2021. Using connectomics for predictive assessment of brain parcellations. NeuroImage. 238:1-18. https://doi.org/10.1016/j.neuroimage.2021.118170

He Y, Aznar S, Siebner HR, Dyrby TB. 2021. In vivo tensor-valued diffusion MRI of focal demyelination in white and deep grey matter of rodents. NeuroImage. Clinical. 30:1-9. https://doi.org/10.1016/j.nicl.2021.102675

Lundell H, Ingo C, Dyrby TB, Ronen I. 2021. Cytosolic diffusivity and microscopic anisotropy of N-acetyl aspartate in human white matter with diffusion-weighted MRS at 7 T. NMR in Biomedicine. 34(5):1-14. https://doi.org/10.1002/nbm.4304

Perens J, Salinas CG, Skytte JL, Roostalu U, Dahl AB, Dyrby TB, Wichern F, Barkholt P, Vrang N, Jelsing J, Hecksher-Sørensen J. 2021. An Optimized Mouse Brain Atlas for Automated Mapping and Quantification of Neuronal Activity Using iDISCO+ and Light Sheet Fluorescence Microscopy. Neuroinformatics. 19(3):433-446. https://doi.org/10.1007/s12021-020-09490-8

Skoven C, Tomasevic L, Kvitsiani D, Dyrby TB, Siebner HR. 2021. Profiling the transcallosal response of rat motor cortex evoked by contralateral optogenetic stimulation of glutamatergic cortical neurons. bioRxiv. 1-31. https://doi.org/10.1101/2021.04.15.439619

2020

Ambrosen, K. S., Eskildsen, S. F., Hinne, M., Krug, K., Lundell, H., Schmidt, M. N., van Gerven, M. A. J., Mørup, M. & Dyrby, T. B. (2020). Validation of structural brain connectivity networks: The impact of scanning parameters. NeuroImage. 204, p. 1-13, 116207.

Andreasen, S. H., Andersen, K. W., Conde, V., Dyrby, T. B., Puonti, O. T., Kammersgaard, L. P., Madsen, C. G., Madsen, K. H., Poulsen, I. & Siebner, H. R. (2020). Limited Colocalization of microbleeds and microstructural changes after severe traumatic brain injury. Journal of Neurotrauma. 37, 4, p. 581-592.

Cavaliere, C., Aiello, M., Soddu, A., Laureys, S., Reislev, N. L., Ptito, M. & Kupers, R. (2020).
Organization of the commissural fiber system in congenital and late-onset blindness.
NeuroImage. Clinical. 25, 102133.  

Nath, V., Schilling, K. G., Parvathaneni, P., Huo, Y., Blaber, J. A., Hainline, A. E., Barakovic, M., Rafael-Patino, J., Frigo, M., Girard, G., Thiran, J-P., Daducci, A., Rowe, M., Rodrigues, P., Prčkovska, V., Aydogan, D. B., Sun, W., Shi, Y., Parker, W. A., Ould Ismail, A. A., Verma, R., Cabeen, R. P., Toga, A. W., Newton, A. T., Wasserthal, J., Neher, P., Maier-Hein, K., Savini, G., Palesi, F., Kaden, E., Wu, Y., He, J., Feng, Y., Paquette, M., Rheault, F., Sidhu, J., Lebel, C., Leemans, A., Descoteaux, M., Dyrby, T. B., Kang, H. & Landman, B. A. (2020). Tractography reproducibility challenge with empirical data (TraCED): The 2017 ISMRM diffusion study group challenge. Journal of magnetic resonance imaging: JMRI. 51, 1, p. 234-249.

Barrett, R. L. C., Dawson, M., Dyrby, T. B., Krug, K., Ptito, M., D'Arceuil, H., Croxson, P. L., Johnson, P., Howells, H., Forkel, S. J., Dell'Acqua, F. & Catani, M. (2020). Differences in frontal network anatomy across primate species. The Journal of Neuroscience. 25 p., 1650-18.

Benavides, F. D., Jin Jo, H., Lundell, H., Edgerton, V. R., Gerasimenko, Y. & Perez, M. A. (2020).
Cortical and Subcortical Effects of Transcutaneous Spinal Cord Stimulation in Humans with Tetraplegia. The Journal of Neuroscience.

Postans, M., Parker, G. D., Lundell, H., Ptito, M., Hamandi, K., Gray, W. P., Aggleton, J. P., Dyrby, T. B., Jones, D. K. & Winter, M. (2020). Uncovering a Role for the Dorsal Hippocampal Commissure in Recognition Memory. Cerebral Cortex. 15 p., bhz143.

Romascano, D., Barakovic, M., Rafael-Patino, J., Dyrby, T. B., Thiran, J-P. & Daducci, A. (2020).
ActiveAxADD: Toward non-parametric and orientationally invariant axon diameter distribution mapping using PGSE. Magnetic Resonance in Medicine.

2019

Bauer, C. (2019). Structural correlates of fatigue in multiple sclerosis assessed with magnetic resonance imaging (MRI). Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.

Alexander, D. C., Dyrby, T. B., Nilsson, M. & Zhang, H. (2019). Imaging brain microstructure with diffusion MRI: practicality and applications. N M R in Biomedicine. 32, 4, p. 1-26, e3841.

Borg, L., Sporring, J., Dam, E. B., Dahl, V. A., Dyrby, T. B., Feidenhans'l, R., Dahl, A. B. & Pingel, J. (2019). Muscle fibre morphology and microarchitecture in cerebral palsy patients obtained by 3D synchrotron X-ray computed tomography. Computers in Biology and Medicine. 107, p. 265-269.

Innocenti, G. M., Caminiti, R., Rouiller, E. M., Knott, G., Dyrby, T. B., Descoteaux, M. & Thiran, J-P. (2019). Diversity of Cortico-descending Projections: Histological and Diffusion MRI Characterization in the Monkey. Cerebral Cortex. 29, 2, p. 788-801.

Innocenti, G. M., Dyrby, T. B., Girard, G., St-Onge, E., Thiran, J-P., Daducci, A. & Descoteaux, M. (2019). Topological principles and developmental algorithms might refine diffusion tractography. Brain structure & function. 224, 1, p. 1-8.

Lundell, H., Nilsson, M., Dyrby, T. B., Parker, G. J. M., Cristinacce, P. L. H., Zhou, F-L., Topgaard, D. & Lasič, S. (2019). Multidimensional diffusion MRI with spectrally modulated gradients reveals unprecedented microstructural detail. Scientific Reports. 9, 1, p. 1-12, 9026.

Sangari, S., Lundell, H., Kirshblum, S. & Perez, M. A. (2019). Residual Descending Motor Pathways Influence Spasticity after Spinal Cord Injury. Annals of Neurology. 86, 1, p. 28-41.

Schilling, K. G., Nath, V., Hansen, C., Parvathaneni, P., Blaber, J., Gao, Y., Neher, P., Aydogan, D. B., Shi, Y., Ocampo-Pineda, M., Schiavi, S., Daducci, A., Girard, G., Barakovic, M., Rafael-Patino, J., Romascano, D., Rensonnet, G., Pizzolato, M., Bates, A., Fischi, E., Thiran, J-P., Canales-Rodríguez, E. J., Huang, C., Zhu, H., Zhong, L., Cabeen, R., Toga, A. W., Rheault, F., Theaud, G., Houde, J-C., Sidhu, J., Chamberland, M., Westin, C-F., Dyrby, T. B., Verma, R., Rathi, Y., Irfanoglu, M. O., Thomas, C., Pierpaoli, C., Descoteaux, M., Anderson, A. W. & Landman, B. A. (2019). Limits to anatomical accuracy of diffusion tractography using modern approaches.
NeuroImage. 185, p. 1-11.

Lasič, S., Topgaard, D., Nilsson, M. & Lundell, H. (2019). A method of performing diffusion weighted magnetic resonance measurements on a sample. IPC nr. G01R33/56341, G01R33/4835, G01R33/543, G01R33/5608, A61B5/055, Patentnr. 16348580, 9 nov. 2017, Prioritetsdato 9 nov. 2016, Prioritetsnr. SE1651469-7 2019.

Lindhøj, M. B., Henriksen, T., Pedersen, L. & Sporring, J. (2019). Using a high-level parallel programming language for GPU-accelerated tomographic reconstruction. (Accepteret/In press) Using a high-level parallel programming language for GPU-accelerated tomographic reconstruction. p. 27-32.

2018

Lasič, S., Lundell, H., Topgaard, D. & Dyrby, T. B. (2018). Effects of imaging gradients in sequences with varying longitudinal storage time-Case of diffusion exchange imaging. Magnetic Resonance in Medicine. 79, p. 2228-2235.

Nielsen, J. S., Dyrby, T. B. & Lundell, H. (2018). Magnetic resonance temporal diffusion tensor spectroscopy of disordered anisotropic tissue. Scientific Reports. 8, 2930.

Sickmann, H. M., Skoven, C., Bastlund, J. F., Dyrby, T. B., Plath, N., Kohlmeier, K. A. & Kristensen, M. P. (2018). Sleep patterning changes in a prenatal stress model of depression.
Journal of Developmental Origins of Health and Disease. 9, 1, p. 102-111.

Alexander, D. C., Dyrby, T. B., Nilsson, M. & Zhang, H. (2018). Imaging brain microstructure with diffusion MRI: practicality and applications. N M R in Biomedicine.

Dogonowski, A. M., Andersen, K. W., Sellebjerg, F., Schreiber, K., Madsen, K. H. & Siebner, H. R. (2018). Functional neuroimaging of recovery from motor conversion disorder: A case report. NeuroImage.

Dyrby, T. B., Innocenti, G., Bech, M. & Lundell, H. (2018). Validation strategies for the interpretation of microstructure imaging using diffusion MRI. NeuroImage.

Innocenti, G. M., Caminiti, R., Rouiller, E. M., Knott, G., Dyrby, T. B., Descoteaux, M. & Thiran, J-P. (2018). Diversity of Cortico-descending Projections: Histological and Diffusion MRI Characterization in the Monkey. Cerebral Cortex.

2017

Røge, R., Sandø Ambrosen, K. M., Albers, K. J., Eriksen, C. T., Liptrot, M. G., Schmidt, M. N., Madsen, K. H. & Mørup, M. (2017). Whole Brain Functional Connectivity Predicted by Indirect Structural Connections.

Lundell, H. M. H., Ingo, C., Dyrby, T. B. & Ronen, I. (2017). Accurate estimation of intra-axonal diffusivity and anisotropy of NAA in humans at 7T.

Lundell, H. M. H., Nilsson, M., Dyrby, T. B., Parker, G. J. M., Cristinacce, P. L. H., Zhou, F., Topgaard, D. & Lasic, S. (2017). Microscopic anisotropy with spectrally modulated q-space trajectory encoding.

2016

Large I, Bridge H, Ahmed B, Clare S, Kolasinski J, Lam WW, Miller KL, Dyrby TB, Parker AJ, Smith JET, Daubney G, Sallet J Bell AH, Krug K, (2016). Individual differences in the alignment of structural and functional markers of the V5/MT complex in primates, Cerebral Cortex, Accepted.

Donahue C, Sotiropoulos S, Jbabdi S, Hernandez-Fernandez M, Beherens T, Dyrby TB, Kennedy H, Knoblauch K, Coalson T, Glasser M, Van Essen D, (2016). Using Diffusion Tractography to Predict Cortical Connection Strength and Distance: A Quantitative Comparison with Tracers in the Monkey, Journal Neuroscience, 36(25): 6758-6770

Innocenti GM, Dyrby TB, Winther Andersen K, Rouillier EM, Caminiti R (2016). The crossed projection to the striatum in two species of monkey and in humans: Behavioral and evolutionary significance, Cerebral Cortex,  doi: 10.1093/cercor/bhw161

2015

Reislev NL, Dyrby TB, Siebner HR, Kupers R, (2015). Simultaneous assessment of white matter changes in microstructure and connectedness in the blind brain, Neural Plasticity, Article ID 795865.

Ratzer R, Iversen P, Börnsen L, Dyrby TB, Christensen JR, Ammitzbøll C, Madsen CG, Garde E, Andersen B, Hyldstrup L, Sørensen PS, Siebner HR, Sellebjerg F, (2015). Monthly oral methylprednisolone pulse treatment in progressive multiple sclerosis, Multiple Sclerosis Journal (accepted).

Shemesh N, Jespersen SN, Alexander DC, Cohen Y, Drobnjak I, Dyrby TB, Finsterbusch J, Koch MA, Kuder T, Laun F, Lawrenz M, Lundell H, Mitra PP, Nilsson M, Özarslan E, Topgaard D, Westin CF, Conventions and nomenclature for double diffusion encoding NMR and MRI, Magn Reson Med, 2015 (accepted)

Barthélemy D, Willerslev-Olsen M, Lundell H, Biering-Sørensen F, Nielsen JB. (2015). Assessment of transmission in specific descending pathways in relation to gait and balance following spinal cord injury, Prog Brain Res. 218:79-101.

Knösche TR, Anwander A, Liptrot MG, Dyrby TB, (2015). Validation of Tractography – Comparison with Manganese Tracing, Human Brain Mapping, Human Brain Mapping, DOI: 10.1002/hbm.22902.

Reislev NL, Kupers R, Siebner HR, Ptito M, Dyrby TB, (2015). Blindness alters the microstructure of the ventral but not the dorsal visual stream. Brain Structure and Function, DOI: 10.1007/s00429-015-1078-8.

Sickmann HM, Arentzen TS, Dyrby TB, PlathN, Kristensen MP, (2015). Prenatal Stress Produces Sex Specific Changes in Depression-like Behavior in Rats: Implications for increased vulnerability in females, Journal of Developmental Origins of Health and Disease, (Accepted).

Lundell H, Sønderby CK, Dyrby TB, (2015). Diffusion weighted imaging with circularly polarized oscillating gradients,Magn Reson Med., 73(3), 171:1176.

Daducci A, Canales-Rodriguez EJ, Zhang H, Dyrby TB, Alexander DC, Thiran JP, (2015). Accelerated Microstructure Imaging via Convex Optimization (AMICO) from diffusion MRI data, Neuroimage, 35, 32-44.

2014

Dyrby TB, Lundell H, Burke MW, Reislev NL, Paulson OB, Ptito M, Siebner HR, (2014). Interpolation of diffusion weighted imaging datasets, NeuroImage, 103, 202–213.

Jespersen SN, Lundel H, Sønderby C, Dyrby TB, (2014). Commentary on ”Microanisotropy imaging: quantification of microscopic diffusion anisotropy and orientation of order parameter by diffusion MRI with magic-angle spinning of the q-vector”, Frontiers in Physics, doi: 10.3389/fphy.2014.00028.

Lundell HM, Alexander DC, Dyrby TB, (2014). High angular resolution diffusion imaging with stimulated echoes: compensation and correction in experiment design and analysis, NMR in Biomedicine.

Liptrot GM, Sidaros K, Dyrby TB, (2014). Addressing The Path-Length-Dependency Confound In White Matter Tract Segmentation, PLOS ONE, 9 (5), e96247.

Lyksborg M, Siebner HR, Sørensen PS, Blinkenberg M, Parker GJM, Dogonowski A, Garde E, Larsen R, Dyrby TB, (2014). Secondary progressive and relapsing remitting multiple sclerosis leads to motor-related decreased anatomical connectivity,  PLOS ONE 9 (4), e95540.

Lundell HM, Sønderby CK, Dyrby TB, (2014). Diffusion weighted imaging with circularly polarized oscillating gradients,Magn Reson Med. (accepted).

Christensen JR, Ratzer R, Börnsen L, Lyksborg M, Garde E, Dyrby TB, Siebner HR, Sørensen PS, Sellebjerg F, (2014). Natalizumab in progressive MS – results of an open-label phase 2A proof-of- concept trial. Neurology (accepted). 

Sønderby, C. K., Lundell, H. M., Søgaard, L. V. and Dyrby, T. B. (2014). Apparent exchange rate imaging in anisotropic systems. Magn Reson Med., 72(3), 756-762.

2013

Jespersen SN, Lundell H, Sønderby KS, Dyrby TB, (2013). Rotationally invariant sampling of double pulsed field gradient diffusion: estimating apparent compartment eccentricity, NMR in biomedicine, (in press).

Assaf Y, Alexander DC, Jones DK, Bizzi A, Behrens T, Clark C, Cohen Y, Dyrby TB, Huppi P, Knoesche T, LeBihan D, Parker GJM, (2013). CONNECT Consortium, The CONNECT project: Combining Macro- and Micro-structure, NeuroImage, 80, 273-282.

Dyrby TB, Søgaard LV, Hall MG, Ptito M, Alexander DC, (2013). Contrast and stability of the axon diameter index from microstructure imaging with diffusion MRI, Magnetic Resonance in Medicine. 70(3), 711:721.

2012

Lundell H, Barthelemy D, Biering-Sørensen F, Cohen-Adad J, Nielsen JB, Dyrby TB. (2012). Fast diffusion tensor imaging and tractography of the whole cervical spinal cord using point spread function corrected echo planar imaging., Magn Reson Med. 2012 Mar 6. doi: 10.1002/mrm.24235. [Epub ahead of print].

2011

Zhang H, Dyrby TB, Alexander DC., (2011) Axon diameter mapping in crossing fibers with diffusion MRI, Med Image Comput Comput Assist Interv.;14(Pt 2):82-9.

Lundell H, Nielsen J  B, Ptito M, Dyrby T B. (2011). Distribution of collateral fibers in the monkey cervical spinal cord detected with diffusion weighted magnetic resonance imaging. NeuroImage, 56(3):923-9.

Dyrby TB, Baaré WFC, Alexander DC, Jelsing J, Garde E, Søgaard LV, (2011). An ex vivo imaging pipeline for producing high-quality and high-resolution diffusion weighted imaging datasets. Hum Brain Mapp. 2011 Apr;32(4):544-63.

2010

Alexander DC, Hubbard PL, Hall MG, Moore EA, Ptito M, Parker GJ, Dyrby TB. Orientationally invariant indices of axon diameter and density from diffusion MRI. Neuroimage. 2010, 52(4):1374-89.

2009

Stavngaard T, Søgaard LV, Batz M, Schreiber LM, Dirksen A. Progression of emphysema evaluated by MRI using hyperpolarized 3He (HP 3He) measurements in patients with alpha-1 antitrypsin deficiency (A1AT), compared with CT and lung function tests. Acta Radiol. 2009, 50(9):1019-26.

2008

Sidaros A, Engberg AW, Sidaros K, Liptrot MG, Herning M, Petersen P, Paulson OB, Jernigan TL, Rostrup E. Diffusion tensor imaging during recovery from severe traumatic brain injury and relation to clinical outcome: a longitudinal study. Brain 2008, 131(Pt 2), 559-572.

2007

Dyrby TB, Sogaard LV, Parker GJ, Alexander DC, Lind NM, Baare WF, Hay-Schmidt A, Eriksen N, Pakkenberg B, Paulson OB, Jelsing J. Validation of in vitro probabilistic tractography. Neuroimage 2007, 37(4), 1267

News & Events

Group Members

Tim Dyrby

Group Leader

Samo Lasic

Mariam Andersson

Show all group members (10)

External Collaborators

Associate Prof. Sune Jespersen

CFIN, AArhus University, Denmark

Prof. Jean-Philippe Thiran

EPFL, Lausanne, Switzerland

Associate Prof. Itamar Ronen

Leiden University Medical Center, Leiden, The Netherlands

Prof. Giorgio Innocenti

Karolinska Institut, Stockhom, Sweden

Prof. Daniel C. Alexander

University London College (UCL), London, United Kingdom

Dr. Ivana Drobnajk

UCL, United Kingdom

Prof. Geoff JM Parker

Manchester University, Manchester, United Kingdom

Prof. Bente Pakkenberg

Copenhagen University Hospital Bispebjerg, Copenhagen, Denmark

Associate Prof. Morten Mørup

Technical University of Deamark (DTU), Lyngby, Denmark