MR Imaging: from Spins to Brains

BCS 513- 91447, NSC 513 - 91472, PHY 513 - 74727, BME 513 - 91587

FALL 2004

CLASS TIME: 3:30-6:00 pm on Tuesdays
LOCATION: Kresge Room in Meliora Hall
(Except for hands-on that will be at the MR Center in the Annex)

Instructors:
Jianhui Zhong - jianhui.zhong@rochester.edu
Daphne Bavelier - daphne@bcs.rochester.edu

Hands-on help:
Aaron Newman - anewman@bcs.rochester.edu (BOLD)
Jennifer Vannest - jvannest@bcs.rochester.edu (BOLD)
Arnaud Guidon - aguidon@bcs.rochester.edu (Cortical Flattening/Volume studies)
Aparna Sapre - asapre@bcs.rochester.edu (Cortical Flattening/Volume studies)
Edmund Kwok - edmund_kwok@urmc.rochester.edu (Pulse sequence programming)
Tong Zhu - tozhu@seas.rochester.edu (DTI)
Hongyan Ni - Hongyan_Ni@URMC.Rochester.edu (DTI)

There will be no office hours; students should contact their assigned advisor through email and arrange directly with him/her for a meeting.

Course Description

This course will introduce students to the basic physics of MRI and review its application in biomedical imaging. We will discuss how the MR technique can take advantage of physiological principles and tissue structure to provide diagnostic image for clinicians and researchers. We will then cover what can be learned about brain functions through MRI. In particular, students will be introduced to functional brain imaging (fMRI) and related issues in data analysis. The goal of the class is to provide students with a comprehensive background of the MR imaging technique and its application to medical or research issues.

Prerequisites and Requirements

Since the course is open to students with either neuroscience or physics/engineering background, students need some of the following background knowledge, but are also willing to acquire others during the course.

- Good command of basic statistics
- Familiarity with linear algebra
- Familiarity with neuroscience

Students with no background in Physics are required to study the following materials:

http://www.simplyphysics.com/IntroToMRI.html
http://www.cis.rit.edu/htbooks/mri/inside.htm

Students with no background in Biology/Neuroscience are required to read the following materials:

Biological Psychology by Kalat, James W.; Hardcover (Wadsworth Pub Co, July 1, 2003), 8th bk&cd edition, (http://isbn.nu/0534588166)

This book is used by BCS 110 and is on reserve at the University library.

Readings:

Material from both textbooks may be presented in lectures. Both books are reserved in Carlson Library for one-day loan, and can be purchased at the University bookstore

For students with physics/engineering background -
Author: Dwight Nushimura (Stanford University)
Titled: Principles of Magnetic Resonance Imaging $25 / copy

For students with neuroscience background -
Author: Scott A. Huettel, Allen W. Song, Gregory McCarthy
Titled: Functional Magnetic Resonance Imaging
Hardcover / Sinauer Associates Incorporated / June 2004 / 0878932887

SYLLABUS

Tips on Viewing PowerPoint Files

All readings are based on the Huettel et al. book unless otherwise mentioned. Supplementary readings and homework questions may be assigned from Nishimura book for physics/engineering students.

Sept 7 : Introduction - Zhong and Bavelier - Readings: ch. 1 and 2

Sept 14 : MR signal generation and formation - Zhong - Readings: ch. 3 and 4

Notes (pdf) Slides (ppt)

Sept 21 : From neuronal to hemodynamic activity - Bavelier - Readings: ch. 6

Sept 28 : Hands-on I (DB AND JZ OUT)

Visit of MR Center - Vannest/Newman, Kwok and Sapre - Safety issues reviewed, data collection, coil, stimulus delivery (Three groups: 40 min per group)

Oct 5 : MR contrast mechanism and pulse sequence (pdf) - Zhong - Readings: ch. 5 and 7

Oct 12: Experimental Design - Bavelier - Readings: ch. 11

Oct 19: Experimental Design - Bavelier / BOLD and more - Zhong

Oct 26: Spatial/temporal properties of fMRI/more BOLD - Zhong/Bavelier - Readings: ch. 7 and 8

First Homework due - Students are to present the outline of a project that they will carry in the remainder of the class (typed outline needs to include the rationale for the project and the method(s) to be used).

Project Assignment Sheet

Nov 2: Hands-on II

X11 & OSX pdf

Neuroscience: BOLD fMRI data analysis - Newman and Vannest - Readings: ch. 10 and 12

http://www.rcbi.rochester.edu/analysis/

Engineering/Physics: Pulse sequence - Tong Zhu and Zhong - Readings From Nishimura?

Nov 9: Hands-on III - Choose 2 out of the 4:

Diffusion Tensor Imaging - Zhu

Advanced topics in pulse sequence programming - Zhong

Nov 16: Hands-on IV (DB OUT)

Segmentation - Methods and Applications (mpeg movie file: Control- or right-click to save movie to desktop)

Volumetric studies and Cortical Flattening - Guidon and Sapre

MR center open to students + access to all instructors for help on their project

Nov 23: Signal and noise in fMRI - Zhong - Readings: ch. 9

Nov 30: Other brain imaging techniques - Bavelier - Readings: ch. 15 (JZ OUT)

Dec 7: Advanced fMRI methods - Zhong - Readings: ch 14

Final version of homework due (should include the goal of the project, and all the methodological details - be it programs developed, design of analyses etc); not to exceed 5 pages.