Functional Magnetic Resonance Imaging

NEUROBIO 381
Fall 2003

Time and Place
Wednesdays, 3:30-6:30 PM. Most lectures will be held in the Chen Conference room in Radiology (Duke North Hospital). Other lectures will be held in the BIAC laboratory (251 Bell).
Computers for lab exercises are available in rooms 251 and 166.
Materials
The primary text will be Functional Magnetic Resonance Imaging, by Huettel, Song, and McCarthy. As this book will not be published until the spring, we will provide chapters directly to the students. Additional suggested readings are listed at the end of each chapter, and will be placed in the class directory if PDFs are available.
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. 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. All assignments are primarily pedagogical, not evaluative.

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 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.

8/27

Lecture:

Introduction to fMRI (html) (powerpoint)

Huettel

 

Laboratory:

Visit to MR Scanner, Real-time fMRI

Voyvodic

 

Readings:

CH 1 (self-assessment)

 

9/3

Lecture:

From Neuronal to Hemodynamic Activity (html) (powerpoint)

McCarthy

 

Laboratory:

Exploring Brain Anatomy (exercises)

 

 

Readings:

CH 2 (self-assessment)

 

9/10

Lecture:

MR Physics: Basic Principles (html) (powerpoint)

Song

 

Laboratory:

Matlab and BIAC tools (exercises)

 

 

Readings:

CH 3 (self-assessment)

 

9/17

Lecture:

MR Physics: Image Formation (html) (powerpoint)

Song

 

Laboratory:

Understanding K-Space (exercises)

 

 

Readings:

CH 4 (self-assessment)

 

9/24

Lecture:

MR Physics: Pulse Sequences and Contrast (html) (powerpoint)

Song

 

Laboratory:

Working with fMRI datasets (exercises)

 

 

Readings:

CH 5 (self-assessment)

 

10/1

Lecture:

BOLD fMRI Imaging (html) (powerpoint)

Huettel

 

Laboratory:

Working with fMRI datasets, cont.

 

 

Readings:

CH 6 (self-assessment)

 

10/8

Lecture:

Spatial and Temporal Resolution (html) (powerpoint)

Huettel

 

Laboratory:

Working with fMRI datasets, cont.

 

 

Readings:

CH 7 (self-assessment)

 

10/15

Lecture:

Signal and Noise Properties (html) (powerpoint)

Huettel

 

Laboratory:

Effects of Trial Averaging (exercises)

 

 

Readings:

CH 8 (self-assessment)

 

10/22

Lecture:

Data preprocessing, Basic Design (html) (powerpoint)

Huettel

 

Laboratory:

Effects of Trial Averaging, cont.

 

 

Readings:

CH 9 (self-assessment), CH 10 (self-assessment)

 

10/29

Lecture:

Experimental Analysis, Advanced Design (html) (powerpoint)

Huettel

 

Laboratory:

Effects of Temporal Sampling (exercises)

 

 

Readings:

CH 10 (self-assessment), CH 11 (self-assessment)

 

11/5

Lecture:

Integrating fMRI with other Techniques

McCarthy

 

Laboratory:

Class project analysis

 

 

Readings:

CH 13 (self-assessment), CH 14

 

11/12

Lecture:

Advanced fMRI

Song

 

Laboratory:

Class project analysis

 

 

Readings:

CH 12 (self-assessment)

 

11/19

Lecture:

Clinical fMRI and its Implications

Voyvodic

 

Laboratory:

Class project analysis

 

 

Readings:

To be announced