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.

Recent Publications

Beha GH, Stemmerik MG, Boer VO, van der Ploeg AT, van der Beek NAME, Andersen H, Marsman A, Jacobsen LN, Theunissen MTM, Petersen ET, Vissing J. 2025. Quantification of muscle glycogen distribution in Pompe disease using 7 Tesla 13C NMR spectroscopy. JNNP. Accepted.

Güler S, Zivkovic I, Boer VO, Zhurbenko V, Petersen ET. 2025. The mode of operation of high-impedance coils and shielded coaxial cable coils: A comparative study. NMR Biomed. 38(8): e70071. https://doi.org/10.1002/nbm.70071

London A, Schaufuss A, Povazan M, Dichman M-L, Merhout J, Dirksen C, Madsbad S, Siebner HR, Lundsgaard A, Fritzen AM, Kiens B, Bojsen-Møller KN. 2025. Effects of acute iso- and hypocaloric carbohydrate restriction on liver fat and glucose and lipid metabolism. J Clin Endocrinol Metab. dgaf382, https://doi.org/10.1210/clinem/dgaf382

Güler S, Povazan M, Zhurbenko V, Zivkovic I. 2025. An 8Tx/32Rx head-neck coil at 7T by combining 2Tx/32Rx Noval coil with 6TRx shielded coaxial cable elements. Magn Reson Med. 93(2): 864-872. https://doi.org/10.1002/mrm.30297

Madelung CF, Løkkegaard A, Fuglsang SA, Marques MM, Boer VO, Madsen KH, Hejl A-M, Meder D, Siebner HR. 2025. High-resolution mapping of substantia nigra in Parkinson’s disease using 7 tesla magnetic resonance imaging. Npj Parkinsons Dis. 11(113). https://doi.org/10.1038/s41531-025-00972-7

London A, Richter MM, Sjøberg KA, Wewer Albrechtsen NJ, Povazan M, Drici L, Schaufuss A, Madsen L, Øyen J, Madsbad S, Juul Holst J, van Hall G, Siebner HR, Richter EA, Kiens B, Lundsgaard A, Bojsen-Møller KN. 2024. The impact of short-term eucaloric low- and high-carbohydrate diets on liver triacylglycersol content in males with overweight and obesity: a randomized crossover study. Am J Clin Nutrition. 120(2): 283-293. https://doi.org/10.1016/j.ajcnut.2024.06.006

Madsen MAJ, Povazan M, Wiggermann V, Lundell H, Blinkenberg M, Romme Christensen J, Sellebjerg F, Siebner HR. 2024. Association of cortical lesions with regional glutamate, GABA, N-Acetylaspartate, and Myoinositol levels in patients with multiple sclerosis. Neurology. 103(1): e209543. https://doi.org/10.1212/WNL.0000000000209543

Stærkind H, Jensen K, Müller JH, Boer VO, Polzik ES, Petersen ET. 2024. High-field optical cesium magnetometer for magnetic resonance imaging. PRX Quantum. 5(2): 020320. https://doi.org/10.1103/PRXQuantum.5.020320

Stærkind H, Jensen K, Müller JH, Boer VO, Petersen ET, Polzik ES. 2023. Precision measurement of the excited state Landé g-factor and diamagnetic shift of the Cesium D2 line. Phys Rev X. 13(2): 021036. https://doi.org/10.1103/PhysRevX.13.021036

Boer VO, Pedersen JO, Arango N, Kuang I, Stockmann J, Petersen ET. 2022. Improving brain B0 shimming using an easy and accessible multi-coil shim array at ultra-high field. MAGMA. 35(6): 943-951. https://doi.org/10.1007/s10334-022-01014-6

Andersen M, Laustsen M, Boer V. Accuracy investigations for volumetric head-motion navigators with and without EPI at 7 T. 2022. Magn Reson Med. 88(3): 1198-1211. https://doi.org/10.1002/mrm.29296

Madsen MAJ, Wiggermann V, Marques MFM, Lundell H, Cerri S, Puonti O, Blinkenberg M, Romme Christensen J, Sellebjerg F, Siebner HR. 2022. Linking lesions in sensorimotor cortex to contralateral hand function in multiple sclerosis: a 7 T MRI study. Brain. 145(10): 3522-3535. https://doi.org/10.1093/brain/awac203

Sandström KO, Baltzersen OB, Marsman A, Lemvigh CK, Boer VO, Bojesen KB, Nielsen MØ, Lundell H, Sulaiman DK, Sørensen ME, Fagerlund B, Lahti AC, Syeda WT, Pantelis C, Petersen ET, Glenthøj BY, Siebner HR, Ebdrup BH. 2022. Add-on memantine to dopamine antagonism to improve negative symptoms at first psychosis – the AMEND trial protocol. Front Psychiatry. 13: 889572. https://doi.org/10.3389/fpsyt.2022.889572

Madelung CF, Meder D, Fuglsang SA, Marques MM, Boer VO, Madsen KH, Petersen ET, Hejl A-M, Løkkegaard A, Siebner HR. 2022. Locus coeruleus shows a spatial pattern of structural disintegration in Parkinson’s disease. Movement Disord. 37(3): 479-489. https://doi.org/10.1002/mds.28945

Selected Recent Conference Abstracts

Engel K, Wiggermann V, Ronen I, Lundell H. Correction of phase fluctuations in diffusion-weighted MRS at high b-values with external phantom reference. ISMRM annual meeting. 05/2025,

Madsen MAJ, Christiansen L, Povazan M, Wiggermann V, Siebner HR. Regional glutamate but not GABA concentration scales with TMS-based measures of cortical excitability – a combined 7T MR spectroscopy and TMS study of the human primary motor hand area. Brain Stimulation, Kyoto, Japan, 02/2025 [Brain Stimulation 18(1) 576, 2025]

Madsen MAJ, Wiggermann V, Lundell H, Christiansen L, Romme Christensen J, Blinkenberg M, Sellebjerg F, Siebner HR. The impact of pathway-specific cortical and white matter pathology on trans-callosal conduction and inhibition in multiple sclerosis, ECTRIMS, Copemhagen, Denmark, 09/2024

Madsen MAJ, Wiggermann V, Christiansen L, Povazan M, Lundell H, Puonti O, Romme Christensen J, Sellebjerg F, Siebner HR. The ipsilateral silent period and its link to cortical lesions in multiple sclerosis, Brain Stimulation, Lisbon, Portugal, 02/2023, [Brain Stimulation 14(6) 1628, 2023]

Stemmerik M, Beha G, Boer V, Marsman A, Jacobsen L, Petersen E, Vissing J. 2022. Using high-field magnetic resonance spectroscopy to measure muscle glycogen in patients with McArdle disease. Neuromuscular Disorders. 32. S73-S74.

Beha G, Stemmerik M, Boer V, Marsman A, Jacobsen L, Petersen E, Vissing J. 2022. Quantification of glycogen distribution in late-onset Pompe patients using 7 Tesla C13 NMR spectroscopy. Neuromuscular Disorders. 32. S73.

Madsen MAJ, Wiggermann V, Povazan M, Lundell H, Boer VO, Marsman A, Blinkenberg MB, Romme Christensen J, Sellebjerg FT, Siebner HR. 2022. Linking cortical demyelination to changes in brain metabolism in multiple sclerosis: a 7T MR spectroscopy study. ECTRIMS annual (virtual) meeting.

Güler S, Costa G, Boer V, Paulides M, Baltus P, Petersen E, Zivkovic I. 2022. Shielded coaxial cable coils: the array configuration for maximized central SNR at 7T MRI. Joint Annual Meeting ISMRM-ESMRMB, 31^st annual ISMRM meeting.

Güler S, Zhurbenko V, Zivkovic I, Boer V, Petersen ET. 2022. Second resonance mode ensure intrinsic low coupling between elements on shielded-coaxial-cable coil designs. Joint Annual Meeting ISMRM-ESMRMB, 31^st annual ISMRM meeting.