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Title Imaging in Neuroscience: with a Focus on Functional Magnetic Resonance Imaging Methods
Course number 5522
Programme Neurovetenskap
Language English
Credits 1.5
Date 2023-09-26 -- 2023-11-14
Responsible KI department Institutionen för klinisk neurovetenskap
Specific entry requirements Background in cognitive sciences, psychology, medicine, biomedicine, biology, medical imaging, computational biology or any humanistic discipline where neuroimaging is used as an experimental tool.
Purpose of the course The main purpose of the course is to enable the students to acquire solid understanding of the tools available to analyze brain activity data measured with functional magnetic resonance imaging (fMRI). The students will develop the ability to critically review results provided by different methods, to select the most adequate tools and experimental designs to answer different questions and to compare their relative advantages.
Intended learning outcomes After attending the course the student should be able to: 1) describe the usual preprocessing steps of fMRI; 2) give a brief overview of different methods to analyze the data and explain when to use them; 3) conducte simple fMRI analysis using several methods; 4) be acquainted with experimental designs to answer different questions using fMRI; 5) give a brief overview of the usage of magnetic resonance imaging to study brain structure and function; 6) give a brief overview of other techniques to study brain function non-invasively and describe their relative merits and challenges.
Contents of the course The course focuses on experimental design and analysis of fMRI data. We will briefly introduce the basis of the blood-oxygen-level dependent (BOLD) signal and how it is measured. The image processing steps, before statistical analysis, will be explained. The application of general linear model analysis to fMRI data will be explained, including random effects analysis and correction for multiple comparisons. We will discuss experimental designs for fMRI studies. The study of functional connectivity using fMRI data will be explained. We will also introduce machine learning techniques for analysis of fMRI data. Finally, structural measures of gray and white matter will be introduced as well as other techniques to measure functional and metabolic brain activity non-invasively.

Teaching and learning activities The course consists of lectures, hands-on sessions, group discussions and student presentations.
Compulsory elements Attendance of at least 90 % on all parts of the course moments is compulsory.
In certain cases students can be exempted from participation in a moment of the course. In these cases the student can be asked to complete a compensatory assignment.
Examination The learning outcomes will be assessed throughout the course during the hands-on sessions where the students have to perform data analyses. The students will also complete a more extensive assignment based on one of the hands-on sessions. In the final day of the course the students will present and discuss their assignments with the rest of the group.
Literature and other teaching material Recommended literature:

Poldrack, Mumford and Nichols, Handbook of Functional MRI Data Analysis, Cambridge University Press, New York, 2011.

Haynes, A primer on pattern-based approaches to fMRI: principles, pitfalls, and perspectives, Neuron 87: 257-270, 2015.
Lindquist and Wager, Principles of functional Magnetic Resonance Imaging, in Handbook of Neuroimaging Data Analysis. London: Chapman & Hall, CRC Press, 2014.
Jenkinson and Chappel, Introduction to neuroimaging analysis. Oxford University Press 2018.
Van Dijk et al. Intrinsic Functional Connectivity As a Tool For Human Connectomics: Theory, Properties, and Optimization, Journal of Neurophysiology 103: 297–321, 2010.
Number of students 8 - 15
Selection of students Selection will be based on 1) the relevance of the course syllabus for the applicant's doctoral project (according to written motivation), 2) start date of doctoral studies (priority given to earlier start date)
More information The course will take place from 9.00 to 12.00 on the following days: 26th of September, 3rd of October, 10th of October, 17th of October, 24th of October, 31st of October, 7th of November; and from 9.00 to 15.00 on the 14th November. This course is planned and offered in cooperation with the Department of Linguistics and the Department of Psychology at Stockholm University. The course is overlapping with the course Imaging in neuroscience: with a focus on functional magnetic resonance imaging methods, 1.5 higher education credits, offered at Stockholm University; and partly overlapping with the course with the same name but with 7.5 higher education credits at Stockholm University. The classes will be at Stockholm University Brain Imaging Center (SUBIC), Svante Arrhenius väg 16 A.
Additional course leader Peter Fransson, Institutionen för klinisk neurovetenskap; Jonathan Berrebi, Stockholm University Brain Imaging Center
Latest course evaluation Course evaluation report
Course responsible Rita Almeida
Institutionen för klinisk neurovetenskap

rita.almeida@ki.se
Contact person Rita Almeida
Institutionen för klinisk neurovetenskap

rita.almeida@ki.se


Peter Fransson
Institutionen för klinisk neurovetenskap

Peter.Fransson@ki.se