Principles of MRI

Spring 2021

Course Description

This class aims to teach the basic principles of MRI.

Fundamentals of MRI including signal-to-noise ratio, resolution, and contrast as dictated by physics, pulse sequences, and instrumentation. Image reconstruction via 2D FFT methods. Fast imaging reconstruction via convolution-back projection and gridding methods and FFTs. Hardware for modern MRI scanners including main field, gradient fields, RF coils, and shim supplies. Software for MRI including imaging methods such as 2D FT, RARE, SSFP, spiral and echo planar imaging methods. Fundamental tradeoffs of tailoring hardware and pulse sequences to specific applications. The modern MRI toolbox will be introduced, including selecting a slice or volume, fast imaging methods to avoid image artifacts due to physiologic motion, and methods for functional imaging. The fundamentals of MRI image artifacts (motion, magnetic susceptibility variations, RF field variations) will also be covered. The last part of the class will present emerging research opportunities and concomitant engineering research challenges including high-field MRI, hyperpolarization methods, small animal MRI, cardiac MRI, stem-cell tracking, functional MRI, parallel imaging and compressed-sensing MRI.

Instructor:

Michael (Miki Lustig)

506 Cory Hall(510)643-9338mlustig@eecs.berkeley.edu

Office Hours

TBD

GSIs:

Ekin Karasan

Discussion: Wednesday 3-4pm (Zoom: https://berkeley.zoom.us/j/9 9777519642)Office Hours: Monday 5-6pm (Zoom: https://berkeley.zoom.us/j/99777519642)ekin_karasan@berkeley.edu

Required Text

D. Nishimura Principles of Magnetic Resonance Imaging Lulu.com 2010

You can get in paperback(35$) and hardcover(45$) from http://lulu.com.

(Please don't buy from amazon scammers)

Optional references

Bernstein, King and Zhou, Handbook of MRI Pulse Sequences Elsevier/Wiley, 2004
You can get it from Amazon here. This is an excellent book, which anyone working in MRI will want to have.
Z.-P. Liang, P. Lauterbur, Principles of Magnetic Resonance Imaging: A Signal Processing Perspective, IEEE Press. A link to Amazon Here
Haacke, Brown, Thompson, and Venkatesan, Magnetic Resonance Imaging: Physical Principles and Sequence Design, John Wiley & Sons New York, NY 1999. ISBN: 0-471-35128-8.
Richard B. Buxton, An Introduction to Functional Magnetic Resonance Imaging: Principles and Techniques, ISBN: 0521581133. Publisher: Cambridge University Press.

Grading (subject to change)

Weekly assignments consisting of problem sets and potentially some matlab programming. (20%)
Two wet labs (20%)
One midterms towards 2/3 of the semester (30%)
Final project (30%)
No late hw, makeup midterms etc. without prior concent from the instructor.

Labs:

Dry Matlab/Python asignments, almost weekly.
Lab 1: Wet MRI experiments - Lab 1 Sign-Up, Lab 1 PDF
Lab 2: Wet MRI experiments - Lab 2 Sign-Up, Lab 2 PDF, Subject Screening Form (for reference)

Project:

Lecture Notes:

Intro: Lecture 1/2
Prereq: Lecture 3/3.5
Chapter 3: Lecture 4/5/6
Chapter 4: Lecture 7/8
Chapter 5: Here
Chapter 6: Here
Chapter 7: Here
Chapter 8: Here

Discussion Videos:

Assignments:

Homework 1: Due Feb 2nd, 11:59PM, Self grading due Feb 9th, 11:59PM

The LBNL Report 51983, 26-March-2003 Vitaliy Fadeyev and Carl Haber can be downloaded from here.

Homework 2: Due Feb 9th, 11:59PM, Self grading due Feb 16th, 11:59PM

Jupyter Notebook can be found here. Matlab Live Script and functions can be found here.

Homework 3: Due Feb 16th, 11:59PM, Self grading due Feb 23th, 11:59PM

Jupyter Notebook can be found here. Matlab Live Script and functions can be found here.

Homework 4: Due Feb 23rd, 11:59PM, Self grading due Mar 2nd, 11:59PM