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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

Dunås T, Wåhlin A, Nyberg L, Boraxbekk C-J. 2021. Multimodal Image Analysis of Apparent Brain Age Identifies Physical Fitness as Predictor of Brain Maintenance. Cerebral Cortex. 31(7):3393-3407. https://doi.org/10.1093/cercor/bhab019

Hansen AL, Boraxbekk C-J, Petersen ET, Paulson OB, Andersen O, Siebner HR, Marsman A. 2021. Do glia provide the link between low-grade systemic inflammation and normal cognitive ageing? A 1H magnetic resonance spectroscopy study at 7 tesla. Journal of Neurochemistry. 159(1):185-196.

Nyberg L, Magnussen F, Lundquist A, Baaré W, Bartrés-Faz D, Bertram L, Boraxbekk CJ, Brandmaier AM, Drevon CA, Ebmeier K, Ghisletta P, Henson RN, Junqué C, Kievit R, Kleemeyer M, Knights E, Kühn S, Lindenberger U, Penninx BWJH, Pudas S, Sørensen Ø, Vaqué-Alcázar L, Walhovd KB, Fjell AM. 2021. Educational attainment does not influence brain aging. Proceedings of the National Academy of Sciences of the United States of America. 118(18):1-3. https://doi.org/10.1073/pnas.2101644118

Sandberg P, Boraxbekk C-J, Zogaj I, Nyberg L. 2021. Ancient Mnemonic in New Format-Episodic Memory Training With the Method of Loci in a Smart Phone Application. Journals of Gerontology - Series B Psychological Sciences and Social Sciences. 76(4):681-691. https://doi.org/10.1093/geronb/gbaa216

Vidal-Pineiro D, Wang Y, Krogsrud SK, Amlien IK, Baaré WF, Bartres-Faz D, Bertram L, Brandmaier AM, Drevon CA, Düzel S, Ebmeier K, Henson RN, Junqué C, Kievit RA, Kühn S, Leonardsen E, Lindenberger U, Madsen KS, Magnussen F, Mowinckel AM, Nyberg L, Roe JM, Segura B, Smith SM, Sørensen Ø, Suri S, Westerhausen R, Zalesky A, Zsoldos E, Walhovd KB, Fjell A. 2021. Individual variations in 'brain age' relate to early-life factors more than to longitudinal brain change. eLife. 10:1-19. https://doi.org/10.7554/eLife.69995

Lind, A., Boraxbekk, C.J., Petersen, E.T., Paulsson, O., Siebner, H., & Marsman, A. (2020). Regional myo-inositol, creatine and choline levels are higher at older age and scale negatively with visuo-spatial working memory: A cross-sectional proton MR spectroscopy study at 7 tesla on normal cognitive ageing. Journal of Neuroscience, 40(42), 8149-8159.

Nyberg, L., Boraxbekk, C.J., Eriksson Sörman, D., Hansson, P., Herlitz, A., Kauppi, K., Ljungberg, J.K., Lövheim, H., Lundquist, A., Nordin Adolfsson, A., Oudin, A., Pudas, S., Rönnlund, M., Stiernstedt, M., Sundström, A., & Adolfsson, R. (2020). Biological and environmental predictors of heterogeneity in neurocognitive ageing: Evidence from Betula and other longitudinal studies. Ageing Research Reviews.

Gylling AT, Bloch-Ibenfeldt M, Eriksen CS, Ziegler AK, Wimmelmann CL, Baekgaard M, Boraxbekk CJ, Siebner HR, Mortensen EL, & Kjaer M. (2020). Maintenance of muscle strength following a one-year resistance training program in older adults. Experimental Gerontology, 139.

Eskilsson, T., Fjellman-Wiklund, A., Ek Malmer, E., Stigsdotter Neely, A., Malmberg Gavelin, H., Slunga Järvholm, L., Boraxbekk, C-J. & Nordin, M.(2020). Hopeful struggling for health: Experiences of participating in computerized cognitive training and aerobic training for persons with stress-related exhaustion disorder. Scandinavian Journal of Psychology.

Friedman, B. B., Suri, S., Solé-Padullés, C., Düzel, S., Drevon, C. A., Baaré, W. F. C., Bartrés-Faz, D., Fjell, A. M., Johansen-Berg, H., Madsen, K. S., Nyberg, L., Penninx, B. W. J. H., Sexton, C., Walhovd, K. B., Zsoldos, E. & Budin-Ljøsne, I. (2020). Are People Ready for Personalized Brain Health? Perspectives of Research Participants in the Lifebrain Consortium. The Gerontologist.

Hansen, A. L., Boraxbekk, C-J., Petersen, E. T., Paulson, O. B., Siebner, H. R. & Marsman, A. (2020). Regional glia-related metabolite levels are higher at older age and scale negatively with visuo-spatial working memory: A cross-sectional proton MR spectroscopy study at 7 tesla on normal cognitive ageing. Cold Spring Harbor Protocols. 36 p., 864496.

Karalija, N., Jonassson, L., Johansson, J., Papenberg, G., Salami, A., Andersson, M., Riklund, K., Nyberg, L. & Boraxbekk, C-J. (2020). High long-term test-retest reliability for extrastriatal 11C-raclopride binding in healthy older adults.
Journal of cerebral blood flow and metabolism.

Wheeler, M. J., Green, D. J., Ellis, K. A., Cerin, E., Heinonen, I., Naylor, L. H., Larsen, R., Wennberg, P., Boraxbekk, C-J., Lewis, J., Eikelis, N., Lautenschlager, N. T., Kingwell, B. A., Lambert, G., Owen, N. & Dunstan, D. W. (2020).
Distinct effects of acute exercise and breaks in sitting on working memory and executive function in older adults: a three-arm, randomised cross-over trial to evaluate the effects of exercise with and without breaks in sitting on cognition.
British Journal of Sports Medicine.

Bangsbo, J., Blackwell, J., Boraxbekk, C-J., Caserotti, P., Dela, F., Evans, A. B., Jespersen, A. P., Gliemann, L., Kramer, A. F., Lundbye-Jensen, J., Mortensen, E. L., Lassen, A. J., Gow, A. J., Harridge, S. D. R., Hellsten, Y., Kjaer, M., Kujala, U. M., Rhodes, R. E., Pike, E. C. J., Skinner, T., Skovgaard, T., Troelsen, J., Tulle, E., Tully, M. A., van Uffelen, J. G. Z. & Viña, J. (2019). Copenhagen Consensus statement 2019: physical activity and ageing. British Journal of Sports Medicine. 53, 14, p. 856-858.

Bojsen-Møller, E., Boraxbekk, C-J., Ekblom, Ö., Blom, V. & Ekblom, M. M. (2019). Relationships between Physical Activity, Sedentary Behaviour and Cognitive Functions in Office Workers.
International Journal of Environmental Research and Public Health. 16, 23, p. 1-15, 4721.

Düzel, E., Acosta-Cabronero, J., Berron, D., Biessels, G. J., Björkman-Burtscher, I., Bottlaender, M., Bowtell, R., Buchem, M. V., Cardenas-Blanco, A., Boumezbeur, F., Chan, D., Clare, S., Costagli, M., de Rochefort, L., Fillmer, A., Gowland, P., Hansson, O., Hendrikse, J., Kraff, O., Ladd, M. E., Ronen, I., Petersen, E., Rowe, J. B., Siebner, H., Stoecker, T., Straub, S., Tosetti, M., Uludag, K., Vignaud, A., Zwanenburg, J. & Speck, O. (2019). European Ultrahigh-Field Imaging Network for Neurodegenerative Diseases (EUFIND). Alzheimer's & dementia (Amsterdam, Netherlands). 11, p. 538-549.

Hedlund, M., Lindelöf, N., Johansson, B., Boraxbekk, C-J. & Rosendahl, E. (2019). Development and Feasibility of a Regulated, Supramaximal High-Intensity Training Program Adapted for Older Individuals. Frontiers in physiology. 10, p. 1-12, 590.

Holm, S. K., Madsen, K. S., Vestergaard, M., Born, A. P., Paulson, O. B., Siebner, H. R., Uldall, P. & Baaré, W. F. C. (2019). Previous glucocorticoid treatment in childhood and adolescence is associated with long-term differences in subcortical grey matter volume and microstructure. NeuroImage. Clinical. 23, p. 1-11, 101825. 

Jonasson, L. S., Nyberg, L., Axelsson, J., Kramer, A. F., Riklund, K. & Boraxbekk, C-J. (2019). Higher striatal D2-receptor availability in aerobically fit older adults but non-selective intervention effects after aerobic versus resistance training. NeuroImage. 202, p. 1-10, 116044.

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

Månsson, K. N. T., Lindqvist, D., Yang, L. L., Svanborg, C., Isung, J., Nilsonne, G., Bergman-Nordgren, L., El Alaoui, S., Hedman-Lagerlöf, E., Kraepelien, M., Högström, J., Andersson, G., Boraxbekk, C-J., Fischer, H., Lavebratt, C., Wolkowitz, O. M. & Furmark, T. (2019). Improvement in indices of cellular protection after psychological treatment for social anxiety disorder. Translational psychiatry. 9, p. 1-10, 340.

Marsman, A. & Pol, H. H. (2019). Glutamaterge neurotransmissie. Handboek schizofreniespectrumstoornissen. 2nd udg. De Tijdstroom/Boom, Bind 2019. p. 370-385..

Malmberg Gavelin, H., Eskilsson, T., Boraxbekk, C.J., Josefsson, M., Stigsdotter Neely, A., & Slunga Järvholm L. (2018). Rehabilitation for improved cognition in patients with stress-related exhaustion disorder: RECO – a randomized clinical trial. Stress.

Boraxbekk, C.-J. (2018). Non-invasive brain stimulation and neuro-enhancement in aging. Clinical Neurophysiology, 129, 464-65.

Baruël Johansen, L., Madsen, K. S., Andersen, K. W., Madsen, K. H., Siebner, H. R. & Baaré, W. F. C. (2017) Reduced orbitofrontal functional network centrality characterizes high neuroticism across childhood and adolescence.

Stomby, A., Otten, J., Ryberg, M., Nyberg, L., Olsson, T. & Boraxbekk, C-J. (2017). A Paleolithic Diet with and without Combined Aerobic and Resistance Exercise Increases Functional Brain Responses and Hippocampal Volume in Subjects with Type 2 Diabetes. Frontiers in Aging Neuroscience. 9, 391.

Jonasson, L. S., Axelsson, J., Riklund, K. & Boraxbekk, C.-J. (2017). Simulating effects of brain atrophy in longitudinal PET imaging with an anthropomorphic brain phantom.
Physics in Medicine and Biology. 62, 13, p. 5213-5227.

Gavelin, H. M., Neely, A. S., Andersson, M., Eskilsson, T., Järvholm, L. S. & Boraxbekk, C-J. (2017). Neural activation in stress-related exhaustion: Cross-sectional observations and interventional effects.
Psychiatry Research. 269, p. 17-25.

Flodin, P., Jonasson, L. S., Riklund, K., Nyberg, L. & Boraxbekk, C.-J. (2017). Does Aerobic Exercise Influence Intrinsic Brain Activity?: An Aerobic Exercise Intervention among Healthy Old Adults.Frontiers in Aging Neuroscience. 9, p. 267.

Eskilsson, T., Slunga Järvholm, L., Malmberg Gavelin, H., Stigsdotter Neely, A. & Boraxbekk, C-J. (2017). Aerobic training for improved memory in patients with stress-related exhaustion: a randomized controlled trial. BMC Psychiatry. 17, 322, p. 1-10, 322.

Bas-Hoogendam, J. M., van Steenbergen, H., Nienke Pannekoek, J., Fouche, J. P., Lochner, C., Hattingh, C. J., Cremers, H. R., Furmark, T., Månsson, K. N. T., Frick, A., Engman, J., Boraxbekk, C.-J., Carlbring, P., Andersson, G., Fredrikson, M., Straube, T., Peterburs, J., Klumpp, H., Phan, K. L., Roelofs, K., Veltman, D. J., van Tol, M. J., Stein, D. J. & van der Wee, N. J. A. (2017). Voxel-based morphometry multi-center mega-analysis of brain structure in social anxiety disorder. NeuroImage: Clinical. 16, p. 678-688.

Jonasson, L.S., Nyberg, L., Kramer, A.F., Lundquist, A., Riklund, K., & Boraxbekk, C.-J. (2017). Aerobic exercise intervention, cognitive performance, and brain structure: Results from the physical influences on brain in aging (PHIBRA) study. Frontiers in Aging Neuroscience; 8, 336.

Boraxbekk, C.-J., Salami, A., Wåhlin, A., & Nyberg, L. (2016). Physical activity over a decade modifies age-related decline in perfusion, gray matter volume, and functional connectivity of the posterior default mode network - a multimodal approach. NeuroImage; 131, 133-141

Group Members

Naiara Demnitz

Group Leader

Sussi Larsen

External Collaborators

Prof. Erik Lykke Mortensen

Department of Public Health, Copenhagen University

Prof. Michael Kjær

Department of Clinical Medicine, Bispebjerg Hospital, University of Copenhagen

Prof. Gunhild Waldemar

Department of Neurology, Copenhagen University Hospital Rigshospitalet 

Prof. Lars Nyberg

Umeå Center for  Functional Brain Imaging