Psyc 7215: Principles of fMRI


Course description

Functional Magnetic Resonance Imaging (fMRI) is the most widely used technique for investigating the living, functioning human brain as people perform tasks and experience mental states. It is a convergence point for multidisciplinary work from many disciplines. Psychologists, statisticians, physicists, computer scientists, neuroscientists, medical researchers, behavioral scientists, engineers, public health researchers, biologists, and others are coming together to advance our understanding of the human mind and brain. In this course we provide an introduction to fMRI, including physics and acquisition, experimental design, analysis, and inferences about brain and mind. We discuss both theoretical considerations and practical aspects of conducting fMRI studies, with an emphasis on statistical analysis. The course is appropriate for scholars from all disciplines who want to learn more about fMRI, and for researchers engaged in fMRI studies.

This course is taught by Tor Wager at CU Boulder and (on video) Martin Lindquist from JHU.

Office Hours: Tues, 3:15 - 5:15 pm, D261d Muen

Take the course on (coming soon!):

Preparation for the class

The lectures do not assume extensive background knowledge, but fMRI analysis draws from different fields, and there may be many “holes” to fill in.

If we cover practical data analysis, then you will need a laptop running Matlab and SPM.

Course schedule

Video Lectures


Watch the YouTube lectures each week, and be prepared to answer basic questions on them.

Emerging methods

These lectures cover the basics. In addition, the class will engage in “emerging methods” discussions. Each class member identifies a paper from the literature that they think is particularly informative on the topic. They bring a synopsis of the paper to class, and we will discuss the papers and what current “best practices” might be. We will store the synopses in a shared Google Drive folder, here. Before class, upload your files to the folder. These include:

1. One Powerpoint (or equivalent) slide to present 2. A 1/2 page synopsis of the paper in a Word document 3. The PDF of the paper and any key supporting references

Final project

Students will do a final project to be presented the last day of class (likely the final exam day). Projects are intended to serve students' research goals, and can be one of several types:

1. fMRI data analysis on a dataset the student is working on, ideally designed for publication 2. fMRI data analysis on an instructor-supplied dataset comparing methods (preprocessing or modeling steps) 3. Literature review on an MRI-related methodological topic (one not covered or one that goes beyond the material covered) 4. A tutorial on an MRI methods-related topic

Each student will submit a 5-page paper (double-spaced, including figures) describing the project and results. We will discuss the projects twice: Once at mid-term, and once at the end of the course.


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20% Watch video lectures, quizzes

20% Discussion

20% Summaries

20% Final project


Further Reading

BOOK: Principles of fMRI, Coming soon

Lindquist, M. A. & Wager, T. D. (2014) “Principles of functional Magnetic Resonance Imaging.” Handbook of Neuroimaging Data Analysis. London: Chapman & Hall, CRC Press.

Wager, T. D., Lindquist, M. A. (2011). Essentials of Functional Magnetic Resonance Imaging. In: Decety, J., Cacioppo, J. T. (Eds.), Handbook of Social Neuroscience. Oxford University Press.

Wager. T. D., Lindquist, M., and Hernandez, L. (2009). Essentials of functional neuroimaging. In: Handbook of Neuroscience for the Behavioral Sciences.

Wager, T. D., Hernandez, L., Jonides, J., & Lindquist, M. (2007). Elements of functional neuroimaging. In J. T. Cacioppo, L. G. Tassinary & G. G. Berntson (Eds.), Handbook of Psychophysiology (4th ed., pp. 19-55). Cambridge: Cambridge University Press.

Hernandez, L., Wager, T.D., & Jonides, J. (2002). Introduction to Functional Brain Imaging. In John Wixted and Hal Pashler (Eds.), Stevens Handbook of Experimental Psychology, Third Edition, Volume 4: Methodology in Experimental Psychology. New York: John Wiley and Sons,Inc.

Functional Magnetic Resonance Imaging, S. Huettel, A. Song, G. McCarthy, Sinauer Associates, 2004

Functional MRI – an introduction to Methods, Editors P. Jezzard, P. Matthews, S. Smith, Oxford University Press, 2002

Introduction to Functional Magnetic Resonance Imaging, R. Buxton, Cambridge University Press, 2003

Principles of Magnetic Resonance Imaging, Z-P Liang and P. Lauterbur, IEEE Press, 2000

Magnetic Resonance Imaging –Physical Principles and Sequence Design, E.M. Hacke, R. Brown, M. Thompson, R. Venkatesan, Wiley, 1999

The Friedman, Hastie, and Tibshirani classic book

More resources

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