Functional Magnetic Resonance Imaging

NEUROBIO 381
Fall 2005

Time
Wednesdays, 3:00-6:00 PM.
Places
Due to space constraints and the number of individuals interested in the course, we will be splitting the Lecture and Laboratory components of the course into separate rooms.
LECTURES (3:00-4:20): 101L Bryan Research Building (Neurobiology)
LABS / DISCUSSIONS (4:30-6:00): 251 Bell Research Building (BIAC)
Materials
The primary text will be Functional Magnetic Resonance Imaging, by Huettel, Song, and McCarthy. It can be ordered from Sinauer Associates, Inc. Any additional readings will be provided by the instructors and/or posted on the website.
Course Director
Scott Huettel, Ph.D.
Departments of Psychiatry, Neurobiology, and Psychology
Brain Imaging and Analysis Center (Bell 254D)
email: phone: 681-9527
Office Hours
Bell Building, Room 254D
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 or research staff. 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, weekly short answer questions, and a final practicum research project. There may also be one take-home test at the discretion of the instructor. All assignments are primarily pedagogical, not evaluative. The class projects may be presented in early December.

Auditors are welcome (and encouraged) to take the course, but regular attendance and participation is required. Auditors will be expected to complete the same assignments as the students, or they will not be allowed to participate in the course.

Course web page: http://www.biac.duke.edu/education/courses/

Course Preliminary Outline

8/31

Lecture:

Introduction to fMRI (ppt) (html)

Huettel

 

Laboratory:

Visit to MR Scanner, Real-time fMRI

Voyvodic

 

Readings:

CH 1, CH 2; Schenck (2000); AJR Safety Readings (WhitePaper; Kanal; Shellock)

 

9/7

Lecture:

Basic Physical Principles (ppt) (html)

Voyvodic

 

Laboratory:

Exploring Brain Anatomy (pdf)

 

 

Readings:

CH 3

 

9/7

Lecture:

Basic Physical Principles (ppt) (html)

Voyvodic

 

Laboratory:

Exploring Brain Anatomy (pdf)

 

 

Readings:

CH 3

 

9/14

Lecture:

Image Formation (ppt) (html)

Song

 

Laboratory:

MATLAB and BIAC tools (pdf)

 

 

Readings:

CH 4; Damadian (1971); Lauterbur (1973)

 

9/22

Course session rescheduled due to CCN Retreat (original date 9/21)

 

Lecture:

Contrast Mechanisms and Pulse Sequences (ppt) (html)

Song

 

Laboratory:

Understanding K-Space

 

 

Readings:

CH 5

 

9/28

Lecture:

From Neuronal to Hemodynamic Activity (ppt) (html)

McCarthy

 

Laboratory:

Image types and contrasts (pdf)

 

 

Readings:

CH 6; Attwell (2002); Hyder (2002); Raichle (2002)

 

10/5

Lecture:

BOLD Contrast (ppt) (html)

McCarthy

 

Laboratory:

Working with fMRI datasets (pdf)

 

 

Readings:

CH 7; Ogawa (1990); Kwong (1992); Blamire (1992)

 

10/12

Lecture:

Spatial and Temporal Properties (ppt) (html)

Huettel

 

Laboratory:

Limits on Resolution, Understanding refractory effects

 

 

Readings:

CH 8; Dale (1997); Huettel (2000); Menon (1998)

 

10/19

Lecture:

Signal and Noise Properties, Preprocessing (ppt) (html)

Huettel

 

Discussion:

Ethics, Publicity, and Wild Speculations

 

 

Readings:

CH 9, 10

 

10/26

Lecture:

Experimental Design (ppt) (html)

Huettel

 

Discussion:

The BIAC preprocessing pipeline and tools

Gadde

 

Readings:

CH11

 

11/2

Lecture:

Statistical Analysis (ppt) (html)

Huettel

 

Laboratory:

Effects of Temporal Sampling (pdf)

 

 

Readings:

CH 12

 

11/9

Lecture:

The Role of fMRI in Cognitive Neuroscience

Pelphrey

 

Discussion:

Limits of neuroimaging

BIAC faculty

 

Readings:

CH 13

 

11/16

Lecture:

Integrating fMRI with Other Approaches

McCarthy

 

Laboratory:

Work on projects

 

 

Readings:

CH 15; Logothetis (2001); Huettel (2004)

 

11/23

No Class - Thanksgiving Holiday

11/30

Lecture:

Advanced fMRI Techniques (Week of SFN)

Song

 

Laboratory:

Work on projects

 

 

Readings:

CH 14; Nakahara (2002); Kim (2000)