MR Imaging: from Spins to Brains Fall 2005

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

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First lecture and organizational meeting:

Friday Sept. 9th at 4:00 PM -- Meliora Hall, Kresge Room (Room 269)

Tentative Times:

Main Lectures: Wednesdays 4:00 - 5:45 PM -- Meliora Hall, Kresge Room (Room 269)

Special Hands-on Track: Fridays 4:00 - 5:15 PM -- Meliora Hall, Kresge Room (Room 269)

FINAL TIME AND PLACE SUBJECT TO CHANGE. Please email the instructors if you are interested in attending but cannot make the first meeting, on Friday, September 9th, at 4:00 PM.

Course Description

This course will introduce students to the basic physics of MRI and 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. The course is set up with one lecture and one hands-on session per week. Students are required to attend all the regular lectures and all the hand-on sessions.

Two different tracks are available for hand-on experience: neuroimaging analysis and MRI physics. In the neuroimaging analysis track, students will be introduced to several common software packages for functional brain imaging (fMRI) and related issues in data analysis and study design. In the MRI physics track, students will gain more in-depth knowledge of imaging physics and pulse sequence designs. Although some sessions are common to both tracks, students should attend the session corresponding to their track when applicable and complete homeworks and final project of their declared track. Students need to declare their track by the end of September.

Instructors:

Jianhui Zhong - jianhui.zhong[at]rochester.edu
Daphne Bavelier - daphne[at]bcs.rochester.edu

Hands-on help:

Arnaud Guidon - aguidon[at]rcbi.rochester.edu (Cortical Flattening/DTI)
Tianliang Gu - tgu[at]rcbi.rochester.edu (Pulse sequences)
Aparna Sapre - asapre[at]rcbi.rochester.edu (Volume studies)
Jennifer Vannest - jvannest[at]bcs.rochester.edu (BOLD)
Tong Zhu - tozhu[at]seas.rochester.edu (DTI)

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

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 should also be 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).
Read the chapters titled: The Major Issues; Nerve Cells and Nerve Impulses; Communication Within the Body; Synapses and Hormones; Anatomy of the Nervous System.
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.

Author: Dwight Nushimura (Stanford University)
Titled: Principles of Magnetic Resonance Imaging, $25/copy
with more MRI physics and math

Author: Scott A. Huettel, Allen W. Song, Gregory McCarthy
Titled: Functional Magnetic Resonance Imaging, $81.95/copy
Hardover / Sinauer Associates Incorporated / June 2004 / 0878932887
with more fMRI applications

Syllabus

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.

Week of Sept. 5th: Sept 9 : Introduction to class (Bavelier); Intro to MR (Zhong) – Readings: ch. 1 and 2
Week of Sept. 12th: Sept 14 Main Lecture: MR signal generation (Zhong); Image evaluation (Bavelier) - Readings: ch. 1 and 3; Sept 16 COMMON Hands-on: Visit to the RCBI - Safety issues reviewed, data collection, coil, stimulus delivery. Sapre, Guidon, and Mithun
Week of Sept. 19th: Sept 21 : MR Image formation (Zhong) - Readings: ch. 3 and 4; Sept 23 COMMON: FSL lecture I – Vannest and Sapre
Week of Sept. 26th: Sept 28 : From neuronal to hemodynamic activity (Bavelier) – Readings: ch. 6; Sept 30 COMMON: FSL lecture II – Vannest and Sapre
Week of Oct. 3rd: Oct 5 : Experimental Design (Bavelier) – Readings: ch. 11; Oct 7 : Neuroimaging Track: Volumetric Studies Analyses – Sapre
MRI Physics Track: Fourier transform and other math topics - Gu
Week of Oct. 10th: Oct 12 : MR contrast mechanism and pulse sequence (Zhong) – Readings: ch. 5 and 7; Oct 15 : Neuroimaging Track: Volumetric Studies Analyses - Sapre
MRI Physics Track: RF pulses and gradients - Gu
Week of Oct. 17th: Oct 19 : Spatial/temporal properties of fMRI/more BOLD (Bavelier) - Readings: ch. 7 and 8; Oct 21 COMMON: BOLD fMRI Analyses I – Vannest/Guidon; Home Work 1 due on volumetric analyses (neuroimaging track) or imaging formation (Engineer/physics track)
Week of Oct. 24th: Oct 26 : MR contrast mechanism and pulse sequence (Zhong) – Readings: ch. 5 and 7; Oct 28 : Neuroimaging Track - BOLD fMRI Analyses II – Vannest
MRI Physics Track: Basic pulse sequences –Gu/Zhong
Week of Oct. 31st: Nov 2 : BOLD and more (Zhong) – Readings: ch. 9; Nov 5 : Neuroimaging Track - BOLD fMRI Analyses III – Vannest/Guidon
MRI Physics Track: Basic pulse sequences – Gu/Zhong
Week of Nov. 7th: Nov 9 : Cortical Flattening and Retinotopic Mapping (Bavelier); Nov 11 : Neuroimaging Track - Cortical flattening implementation – Guidon/Schneider
MRI Physics Track: advance imaging techniques; Home Work 2 due on BOLD analyses (neuroimaging track) or special topic (MRI physics track) - Final Project Assigned
Week of Nov. 14th: Nov 16 : DTI and its application (Zhong); Nov 18 COMMON: DTI software and analyses – Guidon/Zhu
Week of Nov. 21st No class – Thanksgiving
Week of Nov 28th: Nov 30 : Advanced fMRI methods (Zhong) – Readings: ch 14; Dec 2 : Student presentation
Week of Dec 5th: Dec 7 : Other brain imaging techniques – Bavelier – Readings: ch. 15; Dec 9 : Student presentation; Final project (written part) due on Dec 14th

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