
This class aims to teach the basic principles of MRI.
Fundamentals of MRI including signaltonoise ratio, resolution,
and contrast as dictated by physics, pulse sequences, and instrumentation.
Image reconstruction via 2D FFT methods. Fast imaging reconstruction via
convolutionback 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 highfield MRI, hyperpolarization methods, small animal MRI,
cardiac MRI, stemcell tracking, functional MRI, parallel imaging and
compressedsensing MRI.
Instructor
Michael (Miki) Lustig
506 Cory Hall
(510) 6439338
mlustig@eecs.berkeley.edu
Office Hours
Th 23p Cory 5064 Priority EE225EBIOE265
W 45p Cory 506/4 Priority EE123
Lab GSI
Wenwen Jiang
<jiangwenwen1231@gmail.com>
GSI office hours: 5:006:00pm,Wed @ Cory 557
Class Time and Location
11:30–1:00 WF
299 Cory Hall
Lab Sessions:
We are going to use Piazza for discussion and announcements. The link is TBD.
D. Nishimura Principles of Magnetic Resonance Imaging Lulu.com 2010
You can get in paperback(35$) and hardcover(45$) from http://lulu.com.
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: 0471351288.
Richard B. Buxton, An Introduction to Functional Magnetic Resonance Imaging: Principles and Techniques, ISBN: 0521581133. Publisher: Cambridge University Press.
Grading (subject to adjustment):
Weekly assignments consisting of problem sets and potentially some matlab programming. (15%)
Two wet labs (10%)
One midterms towards 2/3 of the semester (40%)
Final project (35%)
No late hw, makeup midterms etc. without prior concent from the instructor.
Midterm dates:
Homework Instruction
We will use a paperless submission system. Please submit your homework using the bcourses in PDF format. I strongly recommend using Latex for formatting, but you can use anything you wish. A Latex template can be downloded from here. The document should include your answers to the questions, matlab code and plots as required.
Please use the standard file name which is: Firstname_Lastname_hwxx_sol.pdf. for example: Miki_Lustig_hw01_sol.pdf.
There will be self grading – self grading is due 3 days after posting of the solutions.
Labs:
Dry Matlab asignments, almost weekly.
Lab 1: Wet MRI experiments with an high field 7T NMR system
Lab 2: Wet MRI experiments at the Brain Imaging Center's 3T scanner
Project:
Research Topics for the project can be downloaded from Here
Lecture Notes
Introduction Notes
Overview of MRI – Chapter 03 Color, Print
Notes on Tomography  Here
Conrast Notes
A beatiful paper on Magnetic Susceptibility by Schenck.
Lecturenotes from Chunlei Liu's guest lecture here
Lecturenotes from Peder Larson's guest lecture here and here
Assignments:
Homework 1 can be downloaded from Here.
The LBNL Report 51983, 26March2003 Vitaliy Fadeyev and Carl Haber can be downloaded from Here.
HW1 Due Jan 29th, 11:59pm, self grading due Feb 1st
Homework 2 can be downloaded from Here.
Here's mysinc.m and myjinc.m
HW2 Due Feb 5th, 11:59pm, self grading due Feb 8th
Homework 3 can be downloaded from Here.
HW3 Due Feb 12th, 11:59pm, self grading due Feb 15th
Solutions and selfgrading in the class bcourse page
Homework 4 can be downloaded from Here.
HW4 Due Feb 19th, 11:59pm, self grading due Feb 22nd
The Matlab question uses a Bloch simulator that was written by Brian Hargreaves. You will need bloch.c, bloch.m for the simulator. For visualization you will need: rotatePoints.m, arrow3D.m, visualizeMagn.m. These were downloaded from MatlabCentral
Here are compiled mex files: Linux 64bit, Mac OSX Intel and Windows Vista
Homework 5 can be downloaded from Here.
HW5 Due Feb 26th, 11:59pm, self grading due Feb 29th
Matlab files for question 6: se_t1_sag_data.mat and phantom.mat
Matlab file for question 7: hw5_img.mat.
Homework 6 can be downloaded from Here.
HW6 Due Mar 4th, 11:59pm, self grading due Mar 7th
Homework 7 can be downloaded from Here.
You will also need diffSim.m and T2Sim.m.
HW7 Due Mar 18th, 11:59pm, self grading due Mar 21st
Homework 8 can be downloaded from Here.
HW8 Due April 1st, 11:59pm, self grading due April 4th
Homework 9 can be downloaded from Here.
HW 9 Due April 8th, 11:59pm, self grading due April 11th