MRI acquisition and analysis course 2010

Course title: Magnetic Resonance Imaging Techniques and Analysis

Content and format: The course covers introductory MRI acquisition and image processing methods. Analysis of functional imaging data will be covered in detail. The first half of the course is mainly lectures on MR-basics. It also includes data acquisition for the remaining part of the course that is focused on hands-on data analysis.

The course starts at a level requiring little or no MR experience. A technical background is not required. The target audience is employees and students at the MR department but the course is open and free for external participants.

DRCMR employees, students, new-comers and co-workers are given priority if we (against expectations) have to limit the number of participants due to space limitations.

The course covers the basics needed to follow the somewhat more technical course Medical Magnetic Resonance Imaging offered as part of the Medicine&Technology program at the Technical University of Denmark in the spring, and which is also available for non-DTU-students under "Open University".

Dates and time: Starting September 21st 2010, the course is given Tuesdays 14:00-16:00 in the conference room of the MR-department at Hvidovre Hospital (dept. 340).

Registration: Please register below.

Literature and software: Course notes and relevant articles are provided during the course. Before the first lecture, it is recommended to install the software freely available at http://www.drcmr.dk/bloch as this will play an important role in the acquisition part of the course (access to the software is not needed during lectures). The same applies to the SPM software available at http://www.fil.ion.ucl.ac.uk/spm/ which will be used during the analysis part. The latter software package requires a working installation of Matlab as described on the SPM home page.

Credit: The course has a workload corresponding to 2-5 ECTS points depending on exams/assignments taken (2 is 1/15 semester workload) but you do not automatically get credit for the course in any educational institution. You may apply for credit at your school, but be aware that no general evaluation is planned, which may be required for a credit bearing course. This can possibly be arranged on an individual basis upon request, and is required for the organizers to recommend more than 2 ECTS.

Language: The course is given in English, or in Danish if all participants are Danish speaking.

Lecturers: The acquisition part is coordinated by Lars G. Hanson , and the analysis part by Arnold Skimminge. Lectures are by the organizers, Lise Vejby Søgaard and Kristoffer H. Madsen.

Preliminary program:

September 21th, MRI acquisition, part 1:

Sections "Magnetic Resonance" until "Sequences" in MR notes are discussed during the coming few weeks (the English and Danish versions are similar).
Protons, spin, net magnetization, precession, radio waves, resonance, relaxation, rotating and stationary frames of reference, T1 and T2.

September 28th, MRI acquisition, part 2:

Relaxation time weighting. Dephasing, refocusing, T2*, spin echoes, and sequences.

October 5th, MRI acquisition, part 3:

Earlier subjects continued. Contrast overview, slice selection spectroscopy.

October 12th: Spectroscopy continued, dephasing/refocusing, flow/diffusion measurements.

October 19th: No lecture.

October 26th, MRI acquisition, part 4:

Saturation and inversion.
MR notes from "Imaging" and beyond are covered during the coming weeks.
Gradients, image-formation and k-space. Echo time revisited.

November 2nd, MRI acquisition, part 5:

Imaging continued, field strength issues, coils and safety.

November 9th: MRI acquisition, part 6:

Sequence elements, k-space trajectories, artifacts (distortions, ghosting and aliasing), noise and image quality quantification.

November 16th, MRI analysis, preprocessing

Introduction to analysis section of the course.

Introduction to SPM8.
fMRI preprocessing.
N-back hands-on preprocessing.

November 23rd, MRI analysis, first level analysis:

Introduction to fMRI statistics.
First level analysis.
N-back hands-on first level specification and estimation.

November 30th: MRI analysis, contrasts:

Introduction to statistical inference.
Contrasts, plotting and visualizations.
N-back hands-on statistical inference.

December 7th: MRI analysis, part 4:

Scripting and batching basics
N-back hands-on scripting

December 14th: MRI analysis, second level

Second level analysis

N-back hands-on group study

December 21st: MRI analysis, second level inference

Contrasts, plotting and visualizations.
N-back hands-on second level inference.

Course title: Magnetic Resonance Imaging Techniques and Analysis

DRCMR employees, students, new-comers and co-workers are given priority if we (against expectations) have to limit the number of participants due to space limitations.

Dates and time: Starting September 21st 2010, the course is given Tuesdays 14:00-16:00 in the conference room of the MR-department at Hvidovre Hospital (dept. 340).

Registration: Please register below.

September 21th, MRI acquisition, part 1:

Sections "Magnetic Resonance" until "Sequences" in MR notes are discussed during the coming few weeks (the English and Danish versions are similar).
Protons, spin, net magnetization, precession, radio waves, resonance, relaxation, rotating and stationary frames of reference, T1 and T2.

September 28th, MRI acquisition, part 2:

Relaxation time weighting. Dephasing, refocusing, T2*, spin echoes, and sequences.

October 5th, MRI acquisition, part 3:

Earlier subjects continued. Contrast overview, slice selection spectroscopy.

October 12th: Spectroscopy continued, dephasing/refocusing, flow/diffusion measurements.

October 19th: No lecture.

October 26th, MRI acquisition, part 4:

Saturation and inversion.
MR notes from "Imaging" and beyond are covered during the coming weeks.
Gradients, image-formation and k-space. Echo time revisited.

November 2nd, MRI acquisition, part 5:

Imaging continued, field strength issues, coils and safety.

November 9th: MRI acquisition, part 6:

Sequence elements, k-space trajectories, artifacts (distortions, ghosting and aliasing), noise and image quality quantification.

November 16th, MRI analysis, preprocessing

Introduction to analysis section of the course.

Introduction to SPM8.
fMRI preprocessing.
N-back hands-on preprocessing.

November 23rd, MRI analysis, first level analysis:

Introduction to fMRI statistics.
First level analysis.
N-back hands-on first level specification and estimation.

November 30th: MRI analysis, contrasts:

Introduction to statistical inference.
Contrasts, plotting and visualizations.
N-back hands-on statistical inference.

December 7th: MRI analysis, part 4:

Scripting and batching basics
N-back hands-on scripting

December 14th: MRI analysis, second level

Second level analysis

N-back hands-on group study

December 21st: MRI analysis, second level inference

Contrasts, plotting and visualizations.
N-back hands-on second level inference.

Selected Publications

Siebner, Thomas Hartwig, Stefan Fuglsang, Christopher Fugl Madelung, Annemette Løkkegaard, Flemming Bendtsen, Jens Dahlgaard Hove, Morten Damgaard, Jan Lysgård Madsen, and Hartwig Roman Siebner. “Gastric Emptying Is Not Delayed and Does Not Correlate With Attenuated Postprandial Blood Flow Increase in Medicated Patients With Early Parkinson’s Disease.” Frontiers in Neurology 13 (2022). https://www.frontiersin.org/article/10.3389/fneur.2022.828069.

Madelung, Christopher F., David Meder, Søren A. Fuglsang, Marta M. Marques, Vincent O. Boer, Kristoffer H. Madsen, Esben T. Petersen, Anne-Mette Hejl, Annemette Løkkegaard, and Hartwig R. Siebner. “Locus Coeruleus Shows a Spatial Pattern of Structural Disintegration in Parkinson’s Disease.” Movement Disorders 37, no. 3 (2022): 479–89. https://doi.org/10.1002/mds.28945.

Siebner, Thomas Hartwig, Christopher Fugl Madelung, Flemming Bendtsen, Annemette Løkkegaard, Jens Dahlgaard Hove, and Hartwig Roman Siebner. “Postprandial Increase in Mesenteric Blood Flow Is Attenuated in Parkinson’s Disease: A Dynamic PC-MRI Study.” Journal of Parkinson’s Disease 11, no. 2 (January 1, 2021): 545–57. https://doi.org/10.3233/JPD-202341.

Herz, Damian M., David Meder, Julia A. Camilleri, Simon B. Eickhoff, and Hartwig R. Siebner. “Brain Motor Network Changes in Parkinson’s Disease: Evidence from Meta-Analytic Modeling.” Movement Disorders 36, no. 5 (2021): 1180–90. https://doi.org/10.1002/mds.28468.

Lohse, Allan, David Meder, Silas Nielsen, Anders Elkjær Lund, Damian M Herz, Annemette Løkkegaard, and Hartwig R Siebner. “Low-Frequency Transcranial Stimulation of Pre-Supplementary Motor Area Alleviates Levodopa-Induced Dyskinesia in Parkinson’s Disease: A Randomized Cross-over Trial.” Brain Communications 2, no. 2 (July 1, 2020): fcaa147. https://doi.org/10.1093/braincomms/fcaa147.

Haagensen, Brian N., Damian M. Herz, David Meder, Kristoffer H. Madsen, Annemette Løkkegaard, and Hartwig R. Siebner. “Linking Brain Activity during Sequential Gambling to Impulse Control in Parkinson’s Disease.” NeuroImage: Clinical 27 (January 1, 2020): 102330. https://doi.org/10.1016/j.nicl.2020.102330.

Betts, Matthew J., Evgeniya Kirilina, Maria C. G. Otaduy, Dimo Ivanov, Julio Acosta-Cabronero, Martina F. Callaghan, Christian Lambert, et al. “Locus Coeruleus Imaging as a Biomarker for Noradrenergic Dysfunction in Neurodegenerative Diseases.” Brain 142, no. 9 (September 1, 2019): 2558–71. https://doi.org/10.1093/brain/awz193.

Meder, David, Damian Marc Herz, James Benedict Rowe, Stéphane Lehéricy, and Hartwig Roman Siebner. “The Role of Dopamine in the Brain - Lessons Learned from Parkinson’s Disease.” NeuroImage, Mapping diseased brains, 190 (April 15, 2019): 79–93. https://doi.org/10.1016/j.neuroimage.2018.11.021.

Irmen, Friederike, Andreas Horn, David Meder, Wolf-Julian Neumann, Philip Plettig, Gerd-Helge Schneider, Hartwig Roman Siebner, and Andrea A. Kühn. “Sensorimotor Subthalamic Stimulation Restores Risk-Reward Trade-off in Parkinson’s Disease.” Movement Disorders 34, no. 3 (2019): 366–76. https://doi.org/10.1002/mds.27576.

Meder, David, and Hartwig Roman Siebner. “Spectral Signatures of Neurodegenerative Diseases: How to Decipher Them?” Brain 141, no. 8 (August 1, 2018): 2241–44. https://doi.org/10.1093/brain/awy195.

Lehericy, Stéphane, David E. Vaillancourt, Klaus Seppi, Oury Monchi, Irena Rektorova, Angelo Antonini, Martin J. McKeown, et al. “The Role of High-Field Magnetic Resonance Imaging in Parkinsonian Disorders: Pushing the Boundaries Forward.” Movement Disorders 32, no. 4 (April 1, 2017): 510–25. https://doi.org/10.1002/mds.26968.

Correia, M. M., Rittman, T., Barnes, C. L., Coyle-Gilchrist, I. T., Ghosh, B., Hughes, L. E. & Rowe, J. B.
Towards accurate and unbiased imaging-based differentiation of Parkinson's disease, progressive supranuclear palsy and corticobasal syndrome.
Brain communications. 2, 1, p. 1-18, fcaa051. 2020.

Kaalund, S. S., Passamonti, L., Allinson, K. S. J., Murley, A. G., Robbins, T. W., Spillantini, M. G. & Rowe, J. B.
Locus coeruleus pathology in progressive supranuclear palsy, and its relation to disease severity.
Acta neuropathologica communications. 8, 1, p. 1-11, 11. 2020.

van der Vegt, J. P. M., Hulme, O. J., Madsen, K. H., Buhmann, C., Bloem, B. R., Münchau, A., Helmich, R. C. & Siebner, H. R.
Dopamine agonist treatment increases sensitivity to gamble outcomes in the hippocampus in de novo Parkinson's disease.
NeuroImage. Clinical. 28, p. 1-8, 102362. 2020.

Dogonowski, A. M., Andersen, K. W., Sellebjerg, F., Schreiber, K., Madsen, K. H. & Siebner, H. R.
Functional neuroimaging of recovery from motor conversion disorder: A case report.
NeuroImage. 190, p. 269-274, 2019.

Dubbioso, R., Manganelli, F., Siebner, H. R. & Di Lazzaro, V.
Fast Intracortical Sensory-Motor Integration: A Window Into the Pathophysiology of Parkinson's Disease.
Frontiers in Human Neuroscience. 13, p. 1-14, 111. 2019.

van Eimeren, T., Antonini, A., Berg, D., Bohnen, N., Ceravolo, R., Drzezga, A., Höglinger, G. U., Higuchi, M., Lehericy, S., Lewis, S., Monchi, O., Nestor, P., Ondrus, M., Pavese, N., Peralta, M. C., Piccini, P., Pineda-Pardo, J. Á., Rektorová, I., Rodríguez-Oroz, M., Rominger, A., Seppi, K., Stoessl, A. J., Tessitore, A., Thobois, S., Kaasinen, V., Wenning, G., Siebner, H. R., Strafella, A. P. & Rowe, J. B.
Neuroimaging biomarkers for clinical trials in atypical parkinsonian disorders: Proposal for a Neuroimaging Biomarker Utility System.
Alzheimer's & Dementia: Diagnosis, Assessment & Disease Monitoring. 11, p. 301-309, 2019.

Siebner, Hartwig R., David Meder, and Damian M. Herz. “FMRI in Parkinson’s Disease.” In FMRI: Basics and Clinical Applications, edited by Stephan Ulmer and Olav Jansen, 417–31. Cham: Springer International Publishing, 2020. https://doi.org/10.1007/978-3-030-41874-8_26

Thomsen, B. L. C., Herz, D. M., Siebner, H. R. & Løkkegaard, A.
Dyskinesier ved Parkinsons sygdom: opdatering om nye billeddannende metoder og behandlingsmuligheder.
Ugeskrift for Laeger. 12, 2017, p. 2-6, 2017.

Lehéricy, S., Vaillancourt, D. E., Seppi, K., Monchi, O., Rektorova, I., Antonini, A., McKeown, M. J., Masellis, M., Berg, D., Rowe, J. B., Lewis, S. J. G., Williams-Gray, C. H., Tessitore, A., Siebner, H. R. & International Parkinson and Movement Disorder Society -Neuroimaging Study Group.
The role of high-field magnetic resonance imaging in parkinsonian disorders: Pushing the boundaries forward.
Movement disorders. 32, 4, p. 510-525, 2017.

Løkkegaard A, Herz DM, Haagensen BN, Lorentzen AK, Eickhoff SB, Siebner HR (2016) Altered sensorimotor activation patterns in idiopathic dystonia - an activation likelihood estimation meta-analysis of functional brain imaging studies. Hum Brain Mapp 37:547-557.

Herz DM, Haagensen BN, Nielsen SH, Madsen KH, Løkkegaard A, Siebner HR (2016) Resting-state connectivity predicts levodopa-induced dyskinesias in Parkinson’s disease. Mov Disord 31:521-529.

Herz DM, Haagensen BN, Christensen MS, Madsen KH, Rowe JB, Løkkegaard A, Siebner HR (2015) Abnormal dopaminergic modulation of striato-cortical networks underlies levodopa-induced dyskinesias in humans. Brain 138:1658-1666.

Herz DM, Haagensen BN,Christensen MS, Madsen KH, Rowe J, Løkkegaard A, Siebner HR (2014) The acute brain response to levodopa heralds dyskinesias in Parkinson’s disease. Ann Neurol 75:829-836.

Herz DM, Eickhoff SB, Løkkegaard A, Siebner HR (2014) Functional neuroimaging of motor control in Parkinson’s disease: A meta-analysis. Hum Brain Mapp 35:3227-3237.

van der Vegt JPM, Hulme OJ, Zittel S, Madsen KH, Weiss MM, Buhmann C, Bloem BR, Münchau A, Siebner HR (2013) Attenuated neural response to gamble outcomes in drug-naive patients with Parkinson’s disease. Brain 136:1192-1203.