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

Webb JL, Troise L, Hansen NW, Olsson C, Wojciechowski AM, Achard J, Brinza O, Staacke R, Kieschnick M, Meijer J, Thielscher A, Perrier J-F, Berg-Sørensen K, Huck A, Andersen UL. 2021. Detection of biological signals from a live mammalian muscle using an early stage diamond quantum sensor. Scientific Reports. 11(1):1-11. https://doi.org/10.1038/s41598-021-81828-x

von Conta J, Kasten FH, Ćurčić-Blake B, Aleman A, Thielscher A, Herrmann CS. 2021. Interindividual variability of electric fields during transcranial temporal interference stimulation (tTIS). Scientific Reports. 11(1):1-12. https://doi.org/10.1038/s41598-021-99749-0

Splittgerber M, Borzikowsky C, Salvador R, Puonti O, Papadimitriou K, Merschformann C, Biagi MC, Stenner T, Brauer H, Breitling-Ziegler C, Prehn-Kristensen A, Krauel K, Ruffini G, Pedersen A, Nees F, Thielscher A, Dempfle A, Siniatchkin M, Moliadze V. 2021. Multichannel anodal tDCS over the left dorsolateral prefrontal cortex in a paediatric population. Scientific Reports. 11(1):1-15. https://doi.org/10.1038/s41598-021-00933-z

Shirinpour S, Mantell K, Li X, Puonti O, Madsen K, Haigh Z, Casillo EC, Alekseichuk I, Hendrickson T, Xu T. 2021. New tools for computational modeling of non-invasive brain stimulation in SimNIBS. Brain Stimulation: Basic, Translational, and Clinical Research in Neuromodulation. 14(6):1644. https://doi.org/10.1016/j.brs.2021.10.180

Saturnino GB, Madsen KH, Thielscher A. 2021. Optimizing the electric field strength in multiple targets for multichannel transcranial electric stimulation. Journal of Neural Engineering. 18(1): Article 014001. https://doi.org/10.1088/1741-2552/abca15

Numssen O, Zier A-L, Thielscher A, Hartwigsen G, Knösche TR, Weise K. 2021. Efficient high-resolution TMS mapping of the human motor cortex by nonlinear regression. NeuroImage. 245:1-11. https://doi.org/10.1016/j.neuroimage.2021.118654

Montanaro H, Pasquinelli C, Lee HJ, Kim H, Siebner HR, Kuster N, Thielscher A, Neufeld E. 2021. The impact of CT image parameters and skull heterogeneity modeling on the accuracy of transcranial focused ultrasound simulations. Journal of Neural Engineering. 18(4):1-28. https://doi.org/10.1088/1741-2552/abf68d

Mezger E, Rauchmann B-S, Brunoni AR, Bulubas L, Thielscher A, Werle J, Mortazavi M, Karali T, Stöcklein S, Ertl-Wagner B, Goerigk S, Padberg F, Keeser D. 2021. Effects of bifrontal transcranial direct current stimulation on brain glutamate levels and resting state connectivity: multimodal MRI data for the cathodal stimulation site. European Archives of Psychiatry and Clinical Neuroscience. 271(1):111-122. https://doi.org/10.1007/s00406-020-01177-0

Karadas M, Olsson C, Winther Hansen N, Perrier J-F, Webb JL, Huck A, Andersen UL, Thielscher A. 2021. In-vitro Recordings of Neural Magnetic Activity From the Auditory Brainstem Using Color Centers in Diamond: A Simulation Study. Frontiers in Neuroscience. 15:1-17. https://doi.org/10.3389/fnins.2021.643614

Gregersen F, Göksu C, Schaefers G, Xue R, Thielscher A, Hanson LG. 2021. Safety Evaluation of a New Setup for Transcranial Electric Stimulation during Magnetic Resonance Imaging. Brain Stimulation. 14(3):488-497. https://doi.org/10.1016/j.brs.2021.02.019

Göksu C, Scheffler K, Gregersen F, Eroğlu HH, Heule R, Siebner HR, Hanson LG, Thielscher A. 2021. Sensitivity and resolution improvement for in vivo magnetic resonance current-density imaging of the human brain. Magnetic Resonance in Medicine. 86(6):3131-3146. https://doi.org/10.1002/mrm.28944

Eroğlu HH, Puonti O, Göksu C, Gregersen F, Siebner HR, Hanson LG, Thielscher A. 2021. On the reconstruction of magnetic resonance current density images of the human brain: Pitfalls and perspectives. NeuroImage. 243:1-15. https://doi.org/10.1016/j.neuroimage.2021.118517

Dubbioso R, Madsen KH, Thielscher A, Siebner HR. 2021. The myelin content of the human precentral hand knob reflects interindividual differences in manual motor control at the physiological and behavioral level. The Journal of Neuroscience: the official journal of the Society for Neuroscience. 41(14):3163-3179. https://doi.org/10.1523/JNEUROSCI.0390-20.2021

Antonenko D, Grittner U, Puonti O, Flöel A, Thielscher A. 2021. Estimation of individually induced e-field strength during transcranial electric stimulation using the head circumference. Brain Stimulation. 14(5):1055-1058. https://doi.org/10.1016/j.brs.2021.07.001

Antonenko D, Grittner U, Saturnino G, Nierhaus T, Thielscher A, Flöel A. 2021. Inter-individual and age-dependent variability in simulated electric fields induced by conventional transcranial electrical stimulation. NeuroImage. 224:1-9. https://doi.org/10.1016/j.neuroimage.2020.117413

Weise K, Numssen O, Thielscher A, Hartwigsen G, Knösche TR. 2020. A novel approach to localize cortical TMS effects. NeuroImage. 209:1-17. Available from: 10.1016/j.neuroimage.2019.116486

Puonti O, Van Leemput K, Saturnino GB, Siebner HR, Madsen KH, Thielscher A. 2020. Accurate and robust whole-head segmentation from magnetic resonance images for individualized head modeling. NeuroImage. 219:1-17. Available from: 10.1016/j.neuroimage.2020.117044

Puonti O, Saturnino GB, Madsen KH, Thielscher A. 2020. Value and limitations of intracranial recordings for validating electric field modeling for transcranial brain stimulation. NeuroImage. 208:1-14. Available from: 10.1016/j.neuroimage.2019.116431

Pasquinelli C, Montanaro H, Lee HJ, Hanson LG, Kim H, Kuster N, Siebner HR, Neufeld E, Thielscher A. 2020. Transducer modeling for accurate acoustic simulations of transcranial focused ultrasound stimulation. Journal of Neural Engineering. 17(4):1-22. Available from: 10.1088/1741-2552/ab98dc

Habich A, Fehér KD, Antonenko D, Boraxbekk C-J, Flöel A, Nissen C, Siebner HR, Thielscher A, Klöppel S. 2020. Stimulating aged brains with transcranial direct current stimulation: Opportunities and challenges: Opportunities and challenges. Psychiatry Research - Neuroimaging. 306:1-9. Available from: 10.1016/j.pscychresns.2020.111179

Boayue NM, Csifcsák G, Aslaksen P, Turi Z, Antal A, Groot J, Hawkins GE, Forstmann B, Opitz A, Thielscher A, Mittner M. 2020. Increasing propensity to mind-wander by transcranial direct current stimulation? A registered report. European Journal of Neuroscience. 51(3):755-780. Available from: 10.1111/ejn.14347

Bikson M, Hanlon CA, Woods AJ, Gillick BT, Charvet L, Lamm C, Madeo G, Holczer A, Almeida J, Antal A, Ay MR, Baeken C, Blumberger DM, Campanella S, Camprodon J, Christiansen L, Colleen L, Crinion J, Fitzgerald P, Gallimberti L, Ghobadi-Azbari P, Ghodratitoostani I, Grabner R, Hartwigsen G, Hirata A, Kirton A, Knotkova H, Krupitsky E, Marangolo P, Nakamura-Palacios EM, Potok W, Praharaj SK, Ruff CC, Schlaug G, Siebner HR, Stagg CJ, Thielscher A, Wenderoth N, Yuan T-F, Zhang X, Ekhtiari H. 2020. Guidelines for TMS/tES Clinical Services and Research through the COVID-19 Pandemic. Brain Stimulation. 13(4):1124-1149. Available from: 10.1016/j.brs.2020.05.010

Saturnino GB, Siebner HR, Thielscher A, Madsen KH Accessibility of cortical regions to focal TES: Dependence on spatial position, safety, and practical constraints. Neuroimage. 2019 doi: 10.1016/j.neuroimage.2019.116183

Saturnino GB, Madsen KH, Thielscher A Electric field simulations for transcranial brain stimulation using FEM: an efficient implementation and error analysis. J Neural Eng. doi: 10.1088/1741-2552/ab41ba, 2019

Pasquinelli C, Hanson LG, Siebner HR, Lee HJ, Thielscher A Safety of transcranial focused ultrasound stimulation: A systematic review of the state of knowledge from both human and animal studies Brain Stimul. doi: 10.1016/j.brs.2019.07.024, 2019

Korshøj AR, Sørensen JCH, von Oettingen G, Poulsen FR, Thielscher A Optimization of tumor treating fields using singular value decomposition and minimization of field anisotropy. Phys Med Biol. 64(4):04NT03. 2019

Saturnino GB, Thielscher A, Madsen KH, Knösche TR, Weise K. A principled approach to conductivity uncertainty analysis in electric field calculations. Neuroimage. 188:821-834, 2019

Karadas M, Wojciechowski AM, Huck A, Dalby NO, Andersen UL, Thielscher A. Feasibility and resolution limits of opto-magnetic imaging of neural network activity in brain slices using color centers in diamond. Sci Rep. 8(1):4503, 2018.

Nielsen JD, Madsen KH, Puonti O, Siebner HR, Bauer C, Madsen CG, Saturnino GB, Thielscher A Automatic skull segmentation from MR images for realistic volume conductor models of the head: Assessment of the state-of-the-art. Neuroimage. 174:587-598, 2018.

Göksu, C., Hanson, L. G., Siebner, H. R., Ehses, P., Scheffler, K. & Thielscher, A. Human in-vivo brain magnetic resonance current density imaging (MRCDI). NeuroImage. 171, p. 26-39, 2018.

Göksu C, Scheffler K, Ehses P, Hanson L.G, Thielscher A. Sensitivity Analysis of Magnetic Field Measurements for Magnetic Resonance Electrical Impedance Tomography (MREIT), Magnetic Resonance in Medicine. 79, p. 748-760, 2018.

Bungert, A., Antunes, A., Espenhahn, S. & Thielscher, A. Where does TMS Stimulate the Motor Cortex? Combining Electrophysiological Measurements and Realistic Field Estimates to Reveal the Affected Cortex Position. Cerebral cortex, 27(11):5083-5094, 2017.

Minjoli, S., Saturnino, G. B., Blicher, J. U., Stagg, C. J., Siebner, H. R., Antunes, A. & Thielscher, A. The impact of large structural brain changes in chronic stroke patients on the electric field caused by transcranial brain stimulation. NeuroImage. Clinical. 15, p. 106-117, 2017.

Saturnino, G. B., Madsen, K. H., Siebner, H. R. & Thielscher, A. How to target inter-regional phase synchronization with dual-site Transcranial Alternating Current Stimulation.
NeuroImage. 163, p. 68-80, 2017.

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, 1205-1208, 2015

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

Moisa, M., Siebner, H.R., Pohmann, R., Thielscher, A. Uncovering a context-specific connectional fingerprint of human dorsal premotor cortex. J Neurosci 32, 7244-7252, 2012.

Thielscher, A., Opitz, A., Windhoff, M. Impact of the gyral geometry on the electric field induced by transcranial magnetic stimulation. Neuroimage 54, 234-243, 2011