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

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

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

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.

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

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

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

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.

Associated Publications

2017

Bentz, M., Jepsen, J. R. M., Pedersen, T., Bulik, C. M., Pedersen, L., Pagsberg, A. K. & Plessen, K. J. Impairment of Social Function in Young Females With Recent-Onset Anorexia Nervosa and Recovered Individuals.
Journal of Adolescent Health. 60, 1, p. 23-32, 2017.

Bentz, M., Jepsen, J. R. M., Kjaersdam Telléus, G., Moslet, U., Pedersen, T., Bulik, C. M. & Plessen, K. J. Neurocognitive functions and social functioning in young females with recent-onset anorexia nervosa and recovered individuals. International Journal of Eating Disorders. 5, p. 1-10, 2017.

Bentz, M., Guldberg, J., Vangkilde, S., Pedersen, T., Plessen, K. J. & Jepsen, J. R. M. Heightened Olfactory Sensitivity in Young Females with Recent-Onset Anorexia Nervosa and Recovered Individuals. P L o S One. 12, 1, p. 1-17, e0169183 2017.

Kwon, S., Watanabe, M., Fischer, E. & Bartels, A. Attention reorganizes connectivity across networks in a frequency specific manner. NeuroImage. 144, p. 217-226, 2017.

2016
Reichenbach, A., Bresciani, J-P., Bülthoff, H. H. & Thielscher, A. Reaching with the sixth sense: Vestibular contributions to voluntary motor control in the human right parietal cortex. NeuroImage. 124, p. 869-875, 2016.

Angstmann, S., Madsen, K. S., Skimminge, A., Jernigan, T. L., Baaré, W. F. C. & Siebner, H. R. Microstructural asymmetry of the corticospinal tracts predicts right-left differences in circle drawing skill in right-handed adolescents. Brain structure & function.

Bergmann, T. O., Karabanov, A., Hartwigsen, G., Thielscher, A. & Siebner, H. R. Combining non-invasive transcranial brain stimulation with neuroimaging and electrophysiology: Current approaches and future perspectives. NeuroImage.

Gelskov, S. V., Madsen, K. H., Ramsøy, T. Z. & Siebner, H. R. Aberrant neural signatures of decision-making: Pathological gamblers display cortico-striatal hypersensitivity to extreme gambles. NeuroImage.

Hartwigsen, G. & Siebner, H. R. Joint Contribution of Left Dorsal Premotor Cortex and Supramarginal Gyrus to Rapid Action Reprogramming. Brain Stimulation. p. 1-8.

Hartwigsen, G., Weigel, A., Schuschan, P., Siebner, H. R., Weise, D., Classen, J. & Saur, D. Dissociating Parieto-Frontal Networks for Phonological and Semantic Word Decisions: A Condition-and-Perturb TMS Study. Cerebral cortex.

Herz, D., Haagensen, B. N., Nielsen, S. H., Madsen, K. H., Løkkegaard, A. & Siebner, H. R. Resting-state connectivity predicts levodopa-induced dyskinesias in Parkinson’s disease. Movement Disorders.

Hjortkjær, J. Sound objects – Auditory objects – Musical objects. Danish Musicology Online. p. 47-56.

Meder, D., Haagensen, B. N., Hulme, O., Morville, T., Gelskov, S., Herz, D. M., Diomsina, B., Madsen, K. H., Siebner, H. Tuning the Brake while Raising the Stake: Network Dynamics during Sequential Decision-Making. Journal of Neuroscience, 136.

Meder, D., Madsen, K. H., Hulme, O., Siebner, H. R. Chasing probabilities — Signaling negative and positive prediction errors across domains. Neuroimage, 134, 180-191.

2015
Chao, C-C., Karabanov, A. N., Paine, R., Carolina de Campos, A., Kukke, S. N., Wu, T., Wang, H. & Hallett, M. Induction of Motor Associative Plasticity in the Posterior Parietal Cortex-Primary Motor Network. Cerebral cortex. 25, 2, p. 365-373, 2015.

Cogliati Dezza, I., Zito, G., Tomasevic, L., Filippi, M. M., Ghazaryan, A., Porcaro, C., Squitti, R., Ventriglia, M., Lupoi, D. & Tecchio, F. Functional and structural balances of homologous sensorimotor regions in multiple sclerosis fatigue. Journal of Neurology. 262, 3, p. 614-622, 2015.

Gelskov, S. V., Henningsson, S., Madsen, K. H., Siebner, H. R. & Ramsøy, T. Z. Amygdala signals subjective appetitiveness and aversiveness of mixed gambles. Cortex. 66, p. 81-90, 2015.

Hartwigsen, G., Bergmann, T. O., Herz, D. M., Angstmann, S., Karabanov, A., Raffin, E., Thielscher, A. & Siebner, H. R. Modeling the effects of noninvasive transcranial brain stimulation at the biophysical, network, and cognitive Level. Progress in Brain Research. 222, p. 261-287, 2015.

Herz, D. M., Haagensen, B. N., Christensen, M. S., Madsen, K. H., Rowe, J. B., Løkkegaard, A. & Siebner, H. R. Abnormal dopaminergic modulation of striato-cortical networks underlies levodopa-induced dyskinesias in humans. Brain. 138, Pt 6, p. 1658-66, 2015.

Karabanov, A. N., Paine, R., Chao, C. C., Schulze, K., Scott, B., Hallett, M. & Mishkin, M. Participation of the classical speech areas in auditory long-term memory. P L o S One. 10, 3, s. e0119472 15 p., 2015.

Karabanov, A. N., Raffin, E. & Siebner, H. R. The Resting Motor Threshold - Restless or Resting?: A Repeated Threshold Hunting Technique to Track Dynamic Changes in Resting Motor Threshold. Brain Stimulation. 8, 6, p. 1191-1194, 2015.

Karabanov, A., Ziemann, U., Hamada, M., George, M. S., Quartarone, A., Classen, J., Massimini, M., Rothwell, J. & Siebner, H. R. Consensus Paper: Probing Homeostatic Plasticity of Human Cortex With Non-invasive Transcranial Brain Stimulation. Brain Stimulation. 8, 3, p. 442-454, 2015.

Lange, V. M., Perret, C. & Laganaro, M. Comparison of single-word and adjective-noun phrase production using event-related brain potentials. Cortex. 67, p. 15-29, 2015.

Leitão, J., Thielscher, A., Tünnerhoff, J. & Noppeney, U. Concurrent TMS-fMRI Reveals Interactions between Dorsal and Ventral Attentional Systems. The Journal of neuroscience. 35, 32, p. 11445-57, 2015.

Madsen, K. H., Ewald, L., Siebner, H. R. & Thielscher, A. Transcranial Magnetic Stimulation: An Automated Procedure to Obtain Coil-specific Models for Field Calculations. Brain Stimulation. 8, 6, p. 1205-1208, 2015.

Raffin, E., Pellegrino, G., Di Lazzaro, V., Thielscher, A. & Siebner, H. R. Bringing transcranial mapping into shape: Sulcus-aligned mapping captures motor somatotopy in human primary motor hand area. NeuroImage. 120, p. 164-175, 2015.

Rossini, P. M., Burke, D., Chen, R., Cohen, L. G., Daskalakis, Z., Di Iorio, R., Di Lazzaro, V., Ferreri, F., Fitzgerald, P. B., George, M. S., Hallett, M., Lefaucheur, J. P., Langguth, B., Matsumoto, H., Miniussi, C., Nitsche, M. A., Pascual-Leone, A., Paulus, W., Rossi, S., Rothwell, J. C., Siebner, H. R., Ugawa, Y., Walsh, V. & Ziemann, U. Non-invasive electrical and magnetic stimulation of the brain, spinal cord, roots and peripheral nerves: Basic principles and procedures for routine clinical and research application. An updated report from an I.F.C.N. Committee. Clinical neurophysiology. 126, 6, p. 1071-107, 2015.

Saturnino, G. B., Antunes, A. & Thielscher, A. On the importance of electrode parameters for shaping electric field patterns generated by tDCS. NeuroImage. 120, p. 25-35, 2015.

Schmock, H., Vangkilde, A., Larsen, K. M., Fischer, E., Birknow, M. R., Jepsen, J. R. M., Olesen, C., Skovby, F., Plessen, K. J., Mørup, M., Hulme, O., Baaré, W. F. C., Didriksen, M., Siebner, H. R., Werge, T. & Olsen, L. The Danish 22q11 research initiative. B M C Psychiatry. 15 2015.

Thielscher, A., Antunes, A. & Saturnino, G. B. Field modeling for transcranial magnetic stimulation: A useful tool to understand the physiological effects of TMS? Conference proceedings : .. Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference. 2015, p. 222-5, 2015.

Weier, K., Banwell, B., Cerasa, A., Collins, D. L., Dogonowski, A-M., Lassmann, H., Quattrone, A., Sahraian, M. A., Siebner, H. R. & Sprenger, T. The role of the cerebellum in multiple sclerosis. Cerebellum. 14, 3, p. 364-74, 2015.

Ziemann, U. & Siebner, H. R. Inter-subject and Inter-session Variability of Plasticity Induction by Non-invasive Brain Stimulation: Boon or Bane? Brain Stimulation. 8, 3, p. 662-3, 2015.

Zittel, S., Heinbokel, C., van der Vegt, J. P. M., Niessen, E., Buhmann, C., Gerloff, C., Siebner, H. R., Münchau, A. & Bäumer, T. Effects of dopaminergic treatment on functional cortico-cortical connectivity in Parkinson's disease. Experimental Brain Research. 233, 1, p. 329-37, 2015.

2014
Delvendahl, I., Gattinger, N., Berger, T., Gleich, B., Siebner, H. R. & Mall, V. The role of pulse shape in motor cortex transcranial magnetic stimulation using full-sine stimuli. P L o S One. 9, 12, s. e115247 2014.

Delvendahl, I., Lindemann, H., Jung, N. H., Pechmann, A., Siebner, H. R. & Mall, V. Influence of waveform and current direction on short-interval intracortical facilitation: a paired-pulse TMS study. Brain Stimulation. 7, 1, p. 49-58, 2014

Herz, D. M., Christensen, M. S., Bruggemann, N., Hulme, O. J., Ridderinkhof, K. R., Madsen, K. H. & Siebner, H. R. Motivational tuning of fronto-subthalamic connectivity facilitates control of action impulses. The Journal of neuroscience. 34, 9, p. 3210-7, 2014.

Herz, D. M., Eickhoff, S. B., Løkkegaard, A. & Siebner, H. R. Functional neuroimaging of motor control in parkinson's disease: A meta-analysis. Human brain mapping. 35, 7, p. 3227-37, 2014.

Herz, D. M., Florin, E., Christensen, M. S., Reck, C., Barbe, M. T., Tscheuschler, M. K., Tittgemeyer, M., Siebner, H. R. & Timmermann, L. Dopamine Replacement Modulates Oscillatory Coupling Between Premotor and Motor Cortical Areas in Parkinson's Disease. Cerebral cortex. 24, 11, p. 2873-83, 2014.

Herz, D. M., Haagensen, B. N., Christensen, M. S., Madsen, K. H., Rowe, J. B., Løkkegaard, A. & Siebner, H. R. The acute brain response to levodopa heralds dyskinesias in Parkinson disease. Annals of Neurology. 75, 6, p. 829-36, 2014.

Herz, D. M., Siebner, H. R., Hulme, O. J., Florin, E., Christensen, M. S. & Timmermann, L. Levodopa reinstates connectivity from prefrontal to premotor cortex during externally paced movement in Parkinson's disease. NeuroImage. 90, p. 15, 2014

Hjortkjær, J. & Walther-Hansen, M. Perceptual Effects of Dynamic Range Compression in Popular Music Recordings. Journal of the Audio Engineering Society . 62, 1/2, p. 37-41, 2014.

Hjortkjær, J. & Walther-Hansen, M. Perceptual effects of dynamic range compression in popular music recordings. Journal of the Audio Engineering Society . 62, 1, p. 37-41, 2014.

Hulme, O. J., Skov, M., Chadwick, M. J., Siebner, H. R. & Ramsøy, T. Z. Sparse encoding of automatic visual association in hippocampal networks. NeuroImage. 102 Pt 2, p. 458-64, 2014.

Kassuba, T., Klinge, C., Hölig, C., Röder, B. & Siebner, H. R. Short-term plasticity of visuo-haptic object recognition. Frontiers in Psychology. 5, p. 1-16, 274 2014.

Laursen, H. R., Siebner, H. R., Haren, T., Madsen, K., Grønlund, R., Hulme, O. & Henningsson, S. Variation in the oxytocin receptor gene is associated with behavioral and neural correlates of empathic accuracy. Frontiers in Behavioral Neuroscience. 8, p. 423, 2014.

Raffin, E. & Siebner, H. R. Transcranial brain stimulation to promote functional recovery after stroke. Current Opinion in Neurology. 27, 1, p. 54-60, 2014.

Reichenbach, A., Thielscher, A., Peer, A., Bülthoff, H. H. & Bresciani, J-P. A key region in the human parietal cortex for processing proprioceptive hand feedback during reaching movements. NeuroImage. 84, p. 615-25, 2014.

Ricci, R., Salatino, A., Siebner, H. R., Mazzeo, G. & Nobili, M. Normalizing biased spatial attention with parietal rTMS in a patient with focal hand dystonia. Brain Stimulation. 7, 6, p. 912-4, 2014.

Rosso, C., Valabregue, R., Arbizu, C., Ferrieux, S., Vargas, P., Humbert, F., Attal, Y., Messé, A., Zavanone, C., Meunier, S., Cohen, L., Delmaire, C., Thielscher, A., Herz, D., Siebner, H. R., Samson, Y. & Lehéricy, S. Connectivity between Right Inferior Frontal Gyrus and Supplementary Motor Area Predicts After-Effects of Right Frontal Cathodal tDCS on Picture Naming Speed. Brain Stimulation. 7, 1, p. 122-129, 2014.

Siebner, H. R. & Ziemann, U. What is the threshold for developing and applying optimized procedures to determine the corticomotor threshold? Clinical Neurophysiology. 125, 1, p. 1-2, 2014.

Thomalla, G., Jonas, M., Bäumer, T., Siebner, H. R., Biermann-Ruben, K., Ganos, C., Orth, M., Hummel, F. C., Gerloff, C., Müller-Vahl, K., Schnitzler, A. & Münchau, A. Costs of control: decreased motor cortex engagement during a Go/NoGo task in Tourette's syndrome. Brain. 137, Pt 1, p. 122-36, 2014.

2013
Baumgaertner, A., Hartwigsen, G. & Roman Siebner, H. Right-hemispheric processing of non-linguistic word features: Implications for mapping language recovery after stroke. Human Brain Mapping. 34, 6, p. 1293-1305, 2013.

Dogonowski, A-M., Andersen, K. W., Madsen, K. H., Sørensen, P. S., Paulson, O. B., Blinkenberg, M. & Siebner, H. R. Multiple sclerosis impairs regional functional connectivity in the cerebellum. NeuroImage. Clinical. 4, p. 130-8, 2013.

Dogonowski, A-M., Siebner, H. R., Sørensen, P. S., Paulson, O. B., Dyrby, T. B., Blinkenberg, M. & Madsen, K. H. Resting-state connectivity of pre-motor cortex reflects disability in multiple sclerosis. Acta Neurologica Scandinavica. 128, 5, p. 328,–335 2013.

Dogonowski, A-M., Siebner, H. R., Sørensen, P. S., Wu, X., Biswal, B., Paulson, O. B., Dyrby, T. B., Skimminge, A., Blinkenberg, M. & Madsen, K. H. Expanded functional coupling of subcortical nuclei with the motor resting-state network in multiple sclerosis. Multiple Sclerosis. 19, 5, p. 559-566, 2013.

Groppa, S., Muthuraman, M., Otto, B., Deuschl, G., Siebner, H. R. & Raethjen, J. Subcortical substrates of TMS induced modulation of the cortico-cortical connectivity. Brain Stimulation. 6, 2, p. 138-146, 2013.

Hartwigsen, G. & Siebner, H. R. Novel methods to study aphasia recovery after stroke. Frontiers of Neurology and Neuroscience. 32, p. 101-111, 2013.

Hartwigsen, G., Saur, D., Price, C. J., Baumgaertner, A., Ulmer, S. & Siebner, H. R. Increased facilitatory connectivity from the pre-SMA to the left dorsal premotor cortex during pseudoword repetition. Journal of Cognitive Neuroscience (Online). 25, 4, p. 580-94, 2013.

Hartwigsen, G., Saur, D., Price, C. J., Ulmer, S., Baumgaertner, A. & Siebner, H. R. Perturbation of the left inferior frontal gyrus triggers adaptive plasticity in the right homologous area during speech production. Proceedings of the National Academy of Sciences of the United States of America. 110, 41, p. 16402-7, 2013.

Havsteen, I., Madsen, K. H., Christensen, H. K., Christensen, A. F. & Siebner, H. R. Diagnostic approach to functional recovery: functional magnetic resonance imaging after stroke. Frontiers of Neurology and Neuroscience. 32, p. 9-25, 2013.

Karabanov, A. N., Chao, C-C., Paine, R. & Hallett, M. Mapping different intra-hemispheric parietal-motor networks using twin Coil TMS. Brain Stimulation. 6, 3, p. 384-9, 2013.

Kassuba, T., Klinge, C., Hölig, C., Röder, B. & Siebner, H. R. Vision holds a greater share in visuo-haptic object recognition than touch. NeuroImage. 65, p. 59-68, 2013.

Kassuba, T., Menz, M. M., Röder, B. & Siebner, H. R. Multisensory Interactions between Auditory and Haptic Object Recognition. Cerebral Cortex. 23, 5, p. 1097-107, 2013.

Kimberley, T. J., Borich, M. R., Arora, S. & Siebner, H. R. Multiple sessions of low-frequency repetitive transcranial magnetic stimulation in focal hand dystonia: clinical and physiological effects. Restorative Neurology and Neuroscience. 31, 5, p. 533-542, 2013.

Leitão, J., Thielscher, A., Werner, S., Pohmann, R. & Noppeney, U. Effects of parietal TMS on visual and auditory processing at the primary cortical level -- a concurrent TMS-fMRI study. Cerebral Cortex. 23, 4, p. 873-84, 2013.

Mastroeni, C., Bergmann, T. O., Rizzo, V., Ritter, C., Klein, C., Pohlmann, I., Brueggemann, N., Quartarone, A. & Siebner, H. R. Brain-derived neurotrophic factor--a major player in stimulation-induced homeostatic metaplasticity of human motor cortex? P L o S One. 8, 2, s. e57957 2013.

Raffin, E. & Dyrby, T. B. Diagnostic approach to functional recovery: diffusion-weighted imaging and tractography. Frontiers of Neurology and Neuroscience. 32, p. 26-35, 2013.

Windhoff, M., Opitz, A. & Thielscher, A. Electric field calculations in brain stimulation based on finite elements: an optimized processing pipeline for the generation and usage of accurate individual head models. Human brain mapping. 34, 4, p. 923-35, 2013.

Wolpe, N., Haggard, P., Siebner, H. R. & Rowe, J. B. Cue integration and the perception of action in intentional binding. Experimental Brain Research. 229, 3, p. 467-74, 2013.

van der Vegt, J. P. M., Hulme, O. J., Zittel, S., Madsen, K. H., Weiss, M. M., Buhmann, C., Bloem, B. R., Münchau, A. & Siebner, H. R. Attenuated neural response to gamble outcomes in drug-naive patients with Parkinson's disease. Brain. 136, Pt 4, p. 1192-203, 2013.

2012
Balslev, D., Siebner, H. R., Paulson, O. B. & Kassuba, T. The cortical eye proprioceptive signal modulates neural activity in higher-order visual cortex as predicted by the variation in visual sensitivity. NeuroImage. 61, 4, p. 950-6, 2012.

Bergmann, T. O., Mölle, M., Diedrichs, J., Born, J. & Siebner, H. R. Sleep spindle-related reactivation of category-specific cortical regions after learning face-scene associations. NeuroImage. 59, 3, p. 2733-42, 2012.

Bergmann, T. O., Mölle, M., Schmidt, M. A., Lindner, C., Marshall, L., Born, J. & Siebner, H. R. EEG-guided transcranial magnetic stimulation reveals rapid shifts in motor cortical excitability during the human sleep slow oscillation. Journal of Neuroscience. 32, 1, p. 243-53, 2012.

Gagnon, L., Schneider, F. C., Siebner, H. R., Paulson, O. B., Kupers, R. & Ptito, M. Activation of the hippocampal complex during tactile maze solving in congenitally blind subjects. Neuropsychologia. 50, 7, p. 1663-71, 2012.

Groppa, S., Oliviero, A., Eisen, A., Quartarone, A., Cohen, L. G., Mall, V., Kaelin-Lang, A., Mima, T., Rossi, S., Thickbroom, G. W., Rossini, P. M., Ziemann, U., Valls-Solé, J. & Siebner, H. R. A practical guide to diagnostic transcranial magnetic stimulation: report of an IFCN committee. Clinical Neurophysiology. 123, 5, p. 858-82, 2012.

Groppa, S., Schlaak, B. H., Münchau, A., Werner-Petroll, N., Dünnweber, J., Bäumer, T., van Nuenen, B. F. L. & Siebner, H. R. The human dorsal premotor cortex facilitates the excitability of ipsilateral primary motor cortex via a short latency cortico-cortical route. Human Brain Mapping. 33, 2, p. 419-30, 2012.

Hartwigsen, G., Bestmann, S., Ward, N. S., Woerbel, S., Mastroeni, C., Granert, O. & Siebner, H. R. Left Dorsal Premotor Cortex and Supramarginal Gyrus Complement Each Other during Rapid Action Reprogramming. Journal of Neuroscience. 32, 46, p. 16162-16171, 2012.

Hellriegel, H., Schulz, E. M., Siebner, H. R., Deuschl, G. & Raethjen, J. H. Continuous theta-burst stimulation of the primary motor cortex in essential tremor. Clinical Neurophysiology. 123, 5, p. 1010-5, 2012.

Herz, D. M., Christensen, M. S., Reck, C., Florin, E., Barbe, M. T., Stahlhut, C., Pauls, K. A. M., Tittgemeyer, M., Siebner, H. R. & Timmermann, L. Task-specific modulation of effective connectivity during two simple unimanual motor tasks: a 122-channel EEG study. NeuroImage. 59, 4, p. 3187-93, 2012.

Iftime-Nielsen, S. D., Christensen, M. S., Vingborg, R. J., Sinkjaer, T., Roepstorff, A. & Grey, M. J. Interaction of electrical stimulation and voluntary hand movement in SII and the cerebellum during simulated therapeutic functional electrical stimulation in healthy adults. Human Brain Mapping. 33, 1, p. 40-9, 2012.

Jung, N. H., Delvendahl, I., Pechmann, A., Gleich, B., Gattinger, N., Mall, V. & Siebner, H. R. Transcranial magnetic stimulation with a half-sine wave pulse elicits direction-specific effects in human motor cortex. B M C Neuroscience. 13, 1, p. 139, 2012.

Karabanov, A. & Siebner, H. R. Unravelling homeostatic interactions in inhibitory and excitatory networks in human motor cortex. Journal of Physiology. 590, Pt 22, p. 5557-8, 2012.

Karabanov, A., Jin, S-H., Joutsen, A., Poston, B., Aizen, J., Ellenstein, A. & Hallett, M. Timing-dependent modulation of the posterior parietal cortex-primary motor cortex pathway by sensorimotor training. Journal of Neurophysiology. 107, 11, p. 3190-9, 2012.

Kasten, M., Kertelge, L., Tadic, V., Brüggemann, N., Schmidt, A., van der Vegt, J., Siebner, H., Buhmann, C., Lencer, R., Kumar, K. R., Lohmann, K., Hagenah, J. & Klein, C. Depression and quality of life in monogenic compared to idiopathic, early-onset Parkinson's disease. Movement Disorders. 27, 6, p. 754-9, 2012.

Moisa, M., Siebner, H. R., Pohmann, R. & Thielscher, A. Uncovering a context-specific connectional fingerprint of human dorsal premotor cortex. Journal of Neuroscience. 32, 21, p. 7244-52, 2012.

Pechmann, A., Delvendahl, I., Bergmann, T. O., Ritter, C., Hartwigsen, G., Gleich, B., Gattinger, N., Mall, V. & Siebner, H. R. The number of full-sine cycles per pulse influences the efficacy of multicycle transcranial magnetic stimulation. Brain Stimulation. 5, 2, p. 148-154, 2012.

Ptito, M., Matteau, I., Zhi Wang, A., Paulson, O. B., Siebner, H. R. & Kupers, R. Crossmodal recruitment of the ventral visual stream in congenital blindness. Neural Plasticity. 2012, 9 p., 2012.

Ramsøy, T., Friis-Olivarius, M. D. F., Jacobsen, C., B. Jensen, S. & Skov, M. Ø. Effects of perceptual uncertainty on arousal and preference across different visual domains. Journal of Neuroscience, Psychology and Economics. 5, 4, p. 212-226, 2012.

Ramsøy, T., Liptrot, M. G., Skimminge, A., Lund, T. E., Sidaros, K., Christensen, M. S., Baaré, W., Paulson, O. B., Jernigan, T. L. & Siebner, H. R. Healthy aging attenuates task-related specialization in the human medial temporal lobe. Neurobiology of Aging. 33, 9, p. 1874-89, 2012.

Rowe, J. B. & Siebner, H. R. The motor system and its disorders. NeuroImage. 61, 2, p. 464-77, 2012.

Zittel, S., Kroeger, J., van der Vegt, J. P. M., Siebner, H. R., Brüggemann, N., Ramirez, A., Behrens, M. I., Gerloff, C., Bäumer, T., Klein, C. & Münchau, A. Motor pathway excitability in ATP13A2 mutation carriers: A transcranial magnetic stimulation study. Parkinsonism & Related Disorders. 18, 5, p. 590-94, 2012.

van Nuenen, B. F. L., Kuhtz-Buschbeck, J., Schulz, C., Bloem, B. R. & Siebner, H. R. Weight-specific anticipatory coding of grip force in human dorsal premotor cortex. Journal of Neuroscience. 32, 15, p. 5272-83, 2012.

2011
Balslev D;Albert N;Miall RC. Eye muscle proprioception represented bilaterally in the sensorimotor cortex. Hum Brain Mapp 2011, 32(4), 624-631.

Balslev D;Gowen E;Miall RC. Decreased Visual Attention Further from the Perceived Direction of Gaze for Equidistant Retinal Targets. J Cogn Neurosci 2011, 23(3), 661-669.

Granert O;Peller M;Gaser C;Groppa S;Hallett M;Knutzen A;Deuschl G;Zeuner KE;Siebner HR. Manual activity shapes structure and function in contralateral human motor hand area. Neuroimage 2011, 54(1), 32-41.

Granert O;Peller M;Jabusch HC;Altenmuller E;Siebner HR. Sensorimotor skills and focal dystonia are linked to putaminal grey-matter volume in pianists. J Neurol Neurosurg Psychiatry 2011, 82(11), 1225-1231.

Kassuba T;Klinge C;Holig C;Menz MM;Ptito M;Roder B;Siebner HR. The left fusiform gyrus hosts trisensory representations of manipulable objects. Neuroimage 2011, 56(3), 1566-1577.

Rizzo V;Bove M;Naro A;Tacchino A;Mastroeni C;Avanzino L;Crupi D;Morgante F;Siebner HR;Quartarone A. Associative cortico-cortical plasticity may affect ipsilateral finger opposition movements. Behav Brain Res 2011, 216(1), 433-439.