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Quick start guide to the Bloch Simulator

This page provides step-by-step examples to practical use of the Bloch Simulator made for visualizing basic and advanced Magnetic Resonance techniques. The examples are spin-echo formation and the excitation process, which are also demonstrated in corresponding YouTube videos. The basic MR knowledge needed to understand the text below is described in an MRI tutorial targeted at a broad audience.

  • It is easiest to run the simulator directly in an internet browser. If you have not already started it, please do so by following this link starting the software in a new browser window: http://www.drcmr.dk/BlochSimulator
  • If you have Flash installed on your computer, you should now see the magnetization vector of an imaginary sample precessing in a magnetic field, B0, pointing upwards. You can always get back to this situation by choosing "Scene: Precession" in the pull-down menu on the lower left.
  • First try to adjust the B0 field strength by moving the slider named "B0". Notice how the precession frequency changes with the field. Think of the units as tesla, for example.

Spin-echo demonstration, step by step:

The spin echo sequence
The spin echo sequence
  • Now, let's introduce field inhomogeneity so that all nuclei do not precess at the same frequency. This can be done by choosing "Scene: Weak inhomogeneity" in the pull-down menu on the lower left. You now see the magnetization in thermal equilibrium. The floor rotates since you see this in the rotating frame of resonance which is only needed later. Therefore, shift back to the stationary frame by pressing the  "Change frame"-button.
  • Since weak inhomogeneity was selected above, the nuclei precess at different frequencies, but it does not show until the magnetization is rotated into the transversal plane. Do this by pressing the "90x hard" button (initiates 90 degree RF pulse rotating the magnetization quickly around the x-axis in the transversal plane). You should now see different components of the magnetization precessing at slightly different frequencies. Gradual dephasing leads to a loss of signal seen in the lower right graph. Press the "v" key on keyboard a few times - it toggles the viewing angle.
  • You may want to repeat the last few steps by pressing the "Scene: Weak inhomogeneity" button again and doing a new excitation. Proceed when you understand what you are seeing so far. Let's add a short 180 degree refocusing pulse to our sequence after some dephasing has occurred (press the "180y hard"-button). This will lead to the formation of a spin-echo after a period equal to the dephasing period. Notice how the nuclei get back in phase and how the lost signal is recovered.
  • This finishes the spin-echo demonstration, but you can continue experimenting with it, e.g. by playing out extra refocusing pulses or by adding a bit of relaxation using the T2-slider for example (choose a large value for T2 initially, e.g. 20 seconds). You can also watch the events in the rotating frame of resonance.

Off- and on-resonance excitation, step by step:

  • Go back to the initial situation by  choosing "Scene: Precession" in the pull-down menu on the lower left.
  • Adjust the B0 field strength by moving the slider named "B0". Notice how the precession frequency changes with the field. Set the value of B0 back to 3 by typing the value in the text field above the slider, followed by "enter". Think of the units as tesla, for example.
  • Radio waves applied off-resonance
    Radio waves applied off-resonance
    Now turn on a radio wave field. Do this by setting the RF amplitude to 0.1 using the appropriate slider or by typing the value in the corresponding text field, followed by "enter". The units are the same as for the B0 field. The red bar shows the push of the radio waves on the magnetization (the torque). Notice how the push is orthogonal to the magnetization, and how it rotates.
  • The push does not seem to have much of an effect on the magnetization. This is because the frequency of the radio waves is not matched to the Larmor frequency (the radiowaves are off-resonance). The reason for the missing effect may be easier to see in the rotating frame of reference. Press "Change frame" to toggle between viewing in the stationary and the rotating frames of reference as you wish. Notice how the magnetization is not pushed consistently by off-resonance radiowaves (in synchony with the precession). Therefore it just wiggles slightly in the radio wave field. Switch back to the stationary frame of reference.
  • Adjust the radio frequency to match the Larmor frequency simply by setting the RF frequency equal to B0 (3 in this case). This is valid since the gyromagnetic ratio in the simulator is set to 1 Hz/T (approximately). Hence the resonance frequency for a field of value 3 is simply 3. Notice how the magnetization is now gradually changed by the RF field. Watching this in the rotating frame makes it appear much simpler -- switch back and forth a few times, and notice how resonance radiowaves induces rotations in the rotating frame of reference.
  • Radio waves applied on resonance
    Radio waves applied on resonance
    Now you have seen how resonant radiowaves change the magnetization, and how off-resonant waves does not, lets start from equilibrium and do an excitation. Choose "Scene: Equilibrium". Add an RF field by setting the RF amplitude equal to 0.1. Notice how little happens since the RF frequency is not adjusted to the Larmor frequency. Adjust it as described above and see how the magnetization is rotated away from equilibirum, e.g. so it after a while points in the exact opposite directions. Similarly, on-resonance rotations away from equilibrium can be triggered by pressing the buttons labelled "90x hard", "90x selective", "180y hard" and "30x hard" that send bursts of radiowaves sufficiently long to cause the specified rotations.


The simulator can do much more. A few examples are given in YouTube videos and on the project homepage but you really need to experiment yourself to get full benefit. The "Challenges" section in the "Help" menu may also be of inspiration.

 

This page provides step-by-step examples to practical use of the Bloch Simulator made for visualizing basic and advanced Magnetic Resonance techniques. The examples are spin-echo formation and the excitation process, which are also demonstrated in corresponding YouTube videos. The basic MR knowledge needed to understand the text below is described in an MRI tutorial targeted at a broad audience.

  • It is easiest to run the simulator directly in an internet browser. If you have not already started it, please do so by following this link starting the software in a new browser window: http://www.drcmr.dk/BlochSimulator
  • If you have Flash installed on your computer, you should now see the magnetization vector of an imaginary sample precessing in a magnetic field, B0, pointing upwards. You can always get back to this situation by choosing "Scene: Precession" in the pull-down menu on the lower left.
  • First try to adjust the B0 field strength by moving the slider named "B0". Notice how the precession frequency changes with the field. Think of the units as tesla, for example.

Spin-echo demonstration, step by step:

The spin echo sequence
The spin echo sequence
  • Now, let's introduce field inhomogeneity so that all nuclei do not precess at the same frequency. This can be done by choosing "Scene: Weak inhomogeneity" in the pull-down menu on the lower left. You now see the magnetization in thermal equilibrium. The floor rotates since you see this in the rotating frame of resonance which is only needed later. Therefore, shift back to the stationary frame by pressing the  "Change frame"-button.
  • Since weak inhomogeneity was selected above, the nuclei precess at different frequencies, but it does not show until the magnetization is rotated into the transversal plane. Do this by pressing the "90x hard" button (initiates 90 degree RF pulse rotating the magnetization quickly around the x-axis in the transversal plane). You should now see different components of the magnetization precessing at slightly different frequencies. Gradual dephasing leads to a loss of signal seen in the lower right graph. Press the "v" key on keyboard a few times - it toggles the viewing angle.
  • You may want to repeat the last few steps by pressing the "Scene: Weak inhomogeneity" button again and doing a new excitation. Proceed when you understand what you are seeing so far. Let's add a short 180 degree refocusing pulse to our sequence after some dephasing has occurred (press the "180y hard"-button). This will lead to the formation of a spin-echo after a period equal to the dephasing period. Notice how the nuclei get back in phase and how the lost signal is recovered.
  • This finishes the spin-echo demonstration, but you can continue experimenting with it, e.g. by playing out extra refocusing pulses or by adding a bit of relaxation using the T2-slider for example (choose a large value for T2 initially, e.g. 20 seconds). You can also watch the events in the rotating frame of resonance.

Off- and on-resonance excitation, step by step:

  • Go back to the initial situation by  choosing "Scene: Precession" in the pull-down menu on the lower left.
  • Adjust the B0 field strength by moving the slider named "B0". Notice how the precession frequency changes with the field. Set the value of B0 back to 3 by typing the value in the text field above the slider, followed by "enter". Think of the units as tesla, for example.
  • Radio waves applied off-resonance
    Radio waves applied off-resonance
    Now turn on a radio wave field. Do this by setting the RF amplitude to 0.1 using the appropriate slider or by typing the value in the corresponding text field, followed by "enter". The units are the same as for the B0 field. The red bar shows the push of the radio waves on the magnetization (the torque). Notice how the push is orthogonal to the magnetization, and how it rotates.
  • The push does not seem to have much of an effect on the magnetization. This is because the frequency of the radio waves is not matched to the Larmor frequency (the radiowaves are off-resonance). The reason for the missing effect may be easier to see in the rotating frame of reference. Press "Change frame" to toggle between viewing in the stationary and the rotating frames of reference as you wish. Notice how the magnetization is not pushed consistently by off-resonance radiowaves (in synchony with the precession). Therefore it just wiggles slightly in the radio wave field. Switch back to the stationary frame of reference.
  • Adjust the radio frequency to match the Larmor frequency simply by setting the RF frequency equal to B0 (3 in this case). This is valid since the gyromagnetic ratio in the simulator is set to 1 Hz/T (approximately). Hence the resonance frequency for a field of value 3 is simply 3. Notice how the magnetization is now gradually changed by the RF field. Watching this in the rotating frame makes it appear much simpler -- switch back and forth a few times, and notice how resonance radiowaves induces rotations in the rotating frame of reference.
  • Radio waves applied on resonance
    Radio waves applied on resonance
    Now you have seen how resonant radiowaves change the magnetization, and how off-resonant waves does not, lets start from equilibrium and do an excitation. Choose "Scene: Equilibrium". Add an RF field by setting the RF amplitude equal to 0.1. Notice how little happens since the RF frequency is not adjusted to the Larmor frequency. Adjust it as described above and see how the magnetization is rotated away from equilibirum, e.g. so it after a while points in the exact opposite directions. Similarly, on-resonance rotations away from equilibrium can be triggered by pressing the buttons labelled "90x hard", "90x selective", "180y hard" and "30x hard" that send bursts of radiowaves sufficiently long to cause the specified rotations.


The simulator can do much more. A few examples are given in YouTube videos and on the project homepage but you really need to experiment yourself to get full benefit. The "Challenges" section in the "Help" menu may also be of inspiration.

 

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