Functional Magnetic Resonance Imaging

Fall 2002

Time and Place
Wednesdays, 3:30-6:30 PM in the BIAC laboratory (251 Bell Building).
Computers for lab exercises are available in rooms 251.
The primary text is Introduction to Functional Magnetic Resonance Imaging, by Richard Buxton. Readings from this text will be assigned for most class sessions. Additional readings will be provided by the instructors. A more printable PDF copy of the syllabus may be found here.
Course Director
Scott Huettel, Ph.D.
Departments of Psychiatry, Neurobiology, and Psychology
Brain Imaging and Analysis Center
email: phone: 681-9527
Office Hours
Room 254D Bell Building
Given the size of the class, office hours will be by appointment.

Course Information

This course is intended to provide a comprehensive and rigorous introduction to the technique of functional magnetic resonance imaging (fMRI). Students will learn the basic physics underlying MRI, the biological principles of fMRI, the principles of experimental design, the processing steps associated with data analysis, and the use of available software packages.

Each week’s session will be composed of a lecture and laboratory. Each part will be led by one or more BIAC faculty members. Where possible, the laboratory topics will be flexible so that students with more experience can explore the issues covered in more detail.

As this is a graduate course, grades will reflect a certification of training, rather than a competition between students. Therefore, all grades can be raised to “E” by demonstrating understanding of the material. Grades will be based on participation in course sessions, completion of laboratory exercises, one take-home test at the middle of the semester, and a final practicum research project.

Auditors are welcome (and encouraged) to take the course, but regular attendance and participation is required. It is strongly recommended that auditors attend both the lecture and laboratory sessions, if possible, as they will be designed to complement each other.

Course Outline

Please note: you must have a BIAC login to access the readings. We apologize for the inconvenience. Also, additional readings and lecture notes will appear here as the semester progresses. If you want a printed copy of the handouts, we recommend opening the Powerpoint version and selecting Print As: Handout from the Print dialog. This will save ink and paper.

8/28 Lecture: Introduction to fMRI (Huettel) (html) (ppt)

Laboratory: Visit to MR Scanner, Real-time fMRI (Voyvodic)

Readings: "An Introduction...", Matthews

9/4 Lecture: From Neuronal to Hemodynamic Activity (McCarthy) (html) (ppt)

Laboratory: Matlab and BIAC tools (handout) (exercises)

Readings: Buxton, Ch. 1-3; Smith (2002); Hyder(2002); Raichle (2002)

9/11 Lecture: MR Physics: Basic Principles (Song) (html) (ppt)

Laboratory: Matlab and BIAC tools: II (guide to showsrs2) (exercises)

Readings: Buxton Ch. 4,7

9/18 Lecture: MR Physics: Image Formation (Song) (html) (ppt)

Laboratory: Creating a MR Image (exercises)

Readings: Buxton, Ch. 5,10; Damadian (1971); Lauterbur (1973)

9/25 Lecture: MR Physics: Pulse Sequences and Contrast (Song)

Laboratory: Analysis of functional data: Introduction (exercises)

Readings: Buxton, Ch. 8,11

10/2 Lecture: BOLD fMRI Imaging (Huettel) (html) (ppt)

Laboratory: Working with fMRI datasets

Readings: Buxton, Ch. 6, 16; Ogawa (1990, 1992); Blamire (1992); Kwong (1992)

10/9 Lecture: Cartography and Chronometry of fMRI (Huettel) (html) (ppt)

Laboratory: Limits on Resolution, Understanding refractory effects (exercises)

Readings: Buxton, Ch. 17; Dale (1997); Huettel (2000)

10/16 Lecture: Signal and Noise in fMRI (Huettel) (html) (ppt)

Laboratory: Effects of sampling upon functional images (exercises)

Readings: Buxton, Ch. 12; Huettel (2001)

10/23 Lecture: Data preprocessing (Huettel) (html) (ppt)

Readings: To be announced

10/30 Lecture: Issues in Experimental Design (Huettel) (html) (ppt)

Laboratory: Comparison of Different Design Types

Readings: Buxton, Ch. 19

11/13 Lecture: Statistical Analysis (Huettel, McKeown) (huettel html) (huettel ppt) (mckeown html) (mckeown ppt)

Readings: Buxton, Ch. 18

11/20 Lecture: Functional Brain Anatomy (McCarthy)

Readings: To be announced

11/27 Lecture: Advanced functional MR imaging techniques (Song)
[To be rescheduled]

Laboratory: To be announced

Readings: Buxton, Ch. 9, 13-15