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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

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.

 

Selected Publications

Gregersen, F., Eroğlu, H. H., Göksu, C., Puonti, O., Zuo, Z., Thielscher, A. & Hanson, L. G.
MR imaging of the magnetic fields induced by injected currents can guide improvements of individualized head volume conductor models.
Imaging Neuroscience. 2, p. 1-15, https://doi.org/10.1162/imag_a_00176 (2024).

Göksu, C., Gregersen, F., Scheffler, K., Eroğlu, H. H., Heule, R., Siebner, H. R., Hanson, L. G. & Thielscher, A. Volumetric measurements of weak current-induced magnetic fields in the human brain at high resolution. Magn Reson Med.  DOI: 10.1002/mrm.29780 (2023).

Hosseini, S., Puonti, O., Treeby, B., Hanson, L. G. & Thielscher, A.
A Head Template for Computational Dose Modelling for Transcranial Focused Ultrasound Stimulation. NeuroImage. p. 120227. DOI: 0.1016/j.neuroimage.2023.120227 (2023).

Rahbek, S., Mahmood, F., Tomaszewski, M. R., Hanson, L. G. & Madsen, K. H. Decomposition-based framework for tumor classification and prediction of treatment response from longitudinal MRI, Phys in Med and Biol. DOI: 10.1088/1361-6560/acaa85, 2023.

Rahbek, S., Schakel, T., Mahmood, F., Madsen, K. H., Philippens, M. E. P. & Hanson, L. G. Optimized flip angle schemes for the split acquisition of fast spin-echo signals (SPLICE) sequence and application to diffusion-weighted imaging. Magn Reson Med, DOI: 10.1002/mrm.29545, 2023.

Laustsen, M., Andersen M., Xue, R., Madsen, K. H., & Hanson, L. G., Tracking of rigid head motion during MRI using an EEG system, Magn Reson Med, DOI: 10.1002/mrm.29251, 2022.

Gregersen, F., Göksu, C., Schaefers, G., Xue, R., Thielscher A., & Hanson L. G., Safety evaluation of a new setup for Transcranial Electric Stimulation during Magnetic Resonance Imaging, Brain Stimulation. 14, 3, p. 488-497, 2021.

Göksu, C., Scheffler, K., Gregersen, F., Eroğlu, H. H., Heule, R., Siebner, H. R., Hanson, L. G. & Thielscher, A. Sensitivity and resolution improvement for in vivo magnetic resonance current-density imaging of the human brain. Magn. Reson. Med. 86, p. 3131-3146, 2021.

Rahbek, S., Madsen, K. H., Lundell, H., Mahmood, F. & Hanson, L. G. Data-driven separation of MRI signal components for tissue characterization. J. Mag. Res. 333, p. 1-11. 2021.

Busoni, S., Bock, M., Chmelik, M., Colgan, N., De Bondt, T., Hanson, L. G., Israel, M., Kugel, H., Maieron, M., Mazzoni, L. N., Seimenis, I. & Vestergaard, P. ADDENDUM to EFOMP Policy statement No.14 "The role of the Medical Physicist in the management of safety within the magnetic resonance imaging environment: EFOMP recommendations". Physica Medica. 89, p. 303-305, 2021.

Sánchez-Heredia, J. D., Olin, R. B., McLean, M. A., Laustsen, C., Hansen A., Hanson, L.G., & Ardenkjaer-Larsen, J. H., Multi-Site Benchmarking of Clinical 13C RF Coils at 3 T, J Magn Reson, 318:106798, 2020.

Olin, R. B., Sánchez-Heredia, J. D., Schulte, R. F., Bøgh, N., Hansen, E. S. S., Laustsen, C., Hanson, L. G. & Ardenkjaer-Larsen, J. H. Three-dimensional accelerated acquisition for hyperpolarized 13 C MR  with blipped stack-of-spirals and conjugate-gradient  SENSE. Magn Reson Med 84, p. 519-34, 2020.

Pedersen, J. O., Hanson, C. G., Xue, R. & Hanson, L. G. Inductive measurement and encoding of k-space trajectories in MR raw data. MAGMA 32, p. 655-667, 2019.

Göksu, C., Scheffler K., Siebner H. R., Thielscher, A., & Hanson, L. G. The stray magnetic fields in Magnetic Resonance Current Density Imaging (MRCDI), Phys Med 59, p. 142-150, 2019.

Pedersen, J. O., Hanson, C. G., Xue, R. & Hanson, L. G. Regularization of Digitally Integrated, Inductive k-Space Trajectory Measures.
ISMRM 27th Annual Meeting & Exhibition 2019.

Pasquinelli, C., Hanson, L. G., Siebner, H. R., Lee, H. J. & Thielscher, A. Safety of transcranial focused ultrasound stimulation: A systematic review of the state of knowledge from both human and animal studies. Brain Stimulation. 12, 6, p. 1367-1380, 2019.

Hansen, R. B., Sánchez-Heredia, J. D., Bøgh, N., Hansen, E. S. S., Laustsen C., L. G. Hanson & Ardenkjær-Larsen,  J. H. Coil profile estimation strategies for parallel imaging with hyperpolarized 13 C MRI, Magn Reson Med 82, p. 2104-17, 2019.

Göksu, C., Scheffler K., Siebner H. R., Thielscher, A., & Hanson, L.G. The stray magnetic fields in Magnetic Resonance Current Density Imaging (MRCDI), Phys Med 59, 142-150, 2019.

Magnusson, P., Boer, V., Marsman, A., Paulson, O. B., Hanson, L. G. & Petersen, E. T. Gamma-aminobutyric acid edited echo-planar spectroscopic imaging (EPSI) with MEGA-sLASER at 7T, Magn Reson Med, 81(2), p. 773-780, 2019.

Pedersen, J. O. Encoding of non-MR signals in Magnetic Resonance Imaging data. PhD thesis, Technical University of Denmark, Electrical Engineering, 2018.

Pedersen, J. O., Hanson, C. G., Xue, R.  & Hanson, L. G. General Purpose Electronics for Real-Time Processing and encoding of non-MR Data in MR Acquisitions, Concepts in Magn Reson B, 48B(2), e21385, 2018.

Eldirdiri, A., Posse, S., Hanson, L. G., Hansen, R. B., Holst, P., Schøier, C., Kristensen, A. T., Johannesen, H. H., Kjaer, A., Hansen, A. E.  & Ardenkjær-Larsen, J. H. Development of a Symmetric Echo Planar Spectroscopic Imaging Framework for Hyperpolarized 13C Imaging in a Clinical PET/MR Scanner, Tomography, 4(3), p. 110-22, 20184(3), p. 110-22, 2018.

Wilhjelm J. E., Duun-Henriksen J. & Hanson L. G., A virtual scanner for teaching fundamental magnetic resonance in biomedical engineering, Comput Appl Eng Educ, 26(6), p. 2197-2209, 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.

Laustsen, M., Andersen, M., Lehmann, P. M., Xue, R., Madsen, K. H. & Hanson, L. G. Slice-wise motion tracking during simultaneous EEG-fMRI. Joint Annual Meeting ISMRM-ESMRMB 2018.

Petersen, J. R., Pedersen, J. O., Zhurbenko, V., Ardenkjær-Larsen, J. H. & Hanson, L. G. Ultra-low power transmitter for encoding non-MR signals in Magnetic Resonance  recordings. Joint Annual Meeting ISMRM-ESMRMB 2018.

Göksu, C., Hanson, L. G., Siebner, H. R., Ehses, P., Scheffler, K. & Thielscher, A. Comparison of two alternative sequences for human in-vivo brain MR Current Density Imaging (MRCDI). Joint Annual Meeting ISMRM-ESMRMB 2018.

Göksu, C., Hanson, L. G., Siebner, H. R., Ehses, P., Scheffler, K. & Thielscher, A. Human In-vivo Brain MR Current Density Imaging (MRCDI) based on Steady-state Free Precession Free Induction Decay (SSFP-FID). Joint Annual Meeting ISMRM-ESMRMB 2018.

Andersen, M., Hanson, L. G., Madsen, K. H., Wezel, J., Boer, V., van der Velden, T., van Osch, M. J. P., Klomp, D., Webb, A. G. & Versluis, M. J. Measuring motion-induced B0 -fluctuations in the brain using field probes. Magnetic Resonance in Medicine, 75(5):2020-30, 2016.

Andersen, M., Towards Motion-Insensitive Magnetic Resonance Imaging Using Dynamic Field Measurements. PhD thesis, Technical University of Denmark, Electrical Engineering. 109 p., 2016.

Hanson, L. G. The Ups and Downs of Classical and Quantum Formulations of Magnetic Resonance. Book chapter in Anthropic Awareness: The Human Aspects of Scientific Thinking in NMR Spectroscopy and Mass Spectrometry. Edited by: C Szantay, Jr. Elsevier, Chap. 3, p. 141-171, 2015.

de Nijs, R., Miranda, MJ., Hansen, LK., Hanson, LG. Motion correction of single-voxel spectroscopy by independent component analysis applied to spectra from nonanesthetized pediatric subjects. Magn Reson Med 2009, 62(5), 1147-1154.

Hanson, LG. Is quantum mechanics necessary for understanding magnetic resonance? Concepts in Magnetic Resonance Part A 2008, 32A(5), 329-340.

Hanson, LG. A graphical simulator for teaching basic and advanced MR imaging techniques. Radiographics 2007, 27(6), e27.

Hanson, LG., Lund, TE., Hanson, CG. Encoding of electrophysiology and other signals in MR images. J. Magn Reson Imaging 2007, 25(5), 1059-1066. 

Hanson, LG., Lund, TE., Hanson, CG. Encoding and transmission of signals as RF signals for detection using an MR apparatus. WO/2005/116676, PCT/DK2005/000343 2005.

Andersen, IK., Szymkowiak, A., Rasmussen, CE., Hanson, LG., Marstrand, JR., Larsson, HB. & Hansen, LK. Perfusion quantification using Gaussian process deconvolution. Magn Reson Med 2002, 48(2), 351-361.

Hanson, LG., Adalsteinsson, E., Pfefferbaum, A., Spielman, DM. Optimal voxel size for measuring global gray and white matter proton metabolite concentrations using chemical shift imaging. Magn Reson Med 2000, 44(1), 10-18.

Hanson, LG., Schaumburg, K., Paulson, OB. Reconstruction strategy for echo planar spectroscopy and its application to partially undersampled imaging. Magn Reson Med 2000, 44(3), 412-417.

News & Events

Group Members

Lars G. Hanson

Group Leader

External Collaborators

Section for MR, DTU Health Tech

Technical University of Denmark, Lyngby

Institute of Biophysics

Chinese Academy of Sciences, Beijing, China

Max Planck Institute for Biological Cybernetics

Tübingen, Germany