
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
W 11a12 Cory 506 Priority EE225E/BIOE265
Th 3p5p Cory 506 Priority EE123
Lab GSI
Christine Leon Swisher
Christine.Leon@berkeley.edu
GSI office hours: W 25pm Cory 367
Class Time and Location
1:00–2:00 MWF
293 Cory Hall
Lab Sessions:
We are going to use Piazza for discussion and announcements. The link is here.
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.
Course outline:
A list of the topics that will be covered is given here, in the order that they will be covered. This may change based on class interest, and time.
Grading:
Weekly assignments consisting of problem sets and potentially some matlab programming. (20%)
Two minterms (yes min, not mid), one in the middle (30%) and one at the end (30%) of the semester.
Final project (20%)
No late hw, makeup midterms etc. without prior concent from the instructor.
Homework Instruction
We will use a paperless submission system. Please submit your homework using the DROPBOX in BSPACE 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.
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:
Lecture Notes
Lecture 01+02 01/22/2014 Notes,
Lecture 03 Notes
Lecture 04 Notes
Lecture 05 Notes
Lecture 06 Notes
Lecture 07 Notes
Lecture 08 Notes
A beatiful paper on Magnetic Susceptibility by Schenck.
Lecture 09 Notes
Lecture 10 Notes
Lecture 11 Notes
Lecture 12 Notes
Lecture 13 Notes
Lecture 14 Notes
Lecture 15 Notes
Lecture 16 Notes
Lecture 17 Notes
Lecture 18 Notes
Lecture 19 Notes
Lecture 20 Notes
Lecture 21 Notes
Assignments:
Homework 1 can be downloaded from Here.
The LBNL Report 51983, 26March2003 Vitaliy Fadeyev and Carl Haber can be downloaded from Here.
HW Due Jan 31st, 11:59pm, self grading due Feb 3rd
Solutions and selfgrading in the class bspace page
Homework 2 can be downloaded from Here.
Here's mysinc.m and myjinc.m
Solutions and selfgrading in the class bspace page
Homework 3 can be downloaded from Here.
Solutions and selfgrading in the class bspace page
Homework 4 can be downloaded from Here.
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
Solutions and selfgrading in the class bspace page
Homework 5 can be downloaded from Here.
Matlab files for question 5: se_t1_sag_data.mat and phantom.mat
Matlab file for question 6: hw5_img.mat.
Solutions and selfgrading in the class bspace page
Homework 6 can be downloaded from Here.
Solutions and selfgrading in the class bspace page
Homework 7 can be downloaded from Here.
You will also need diffSim.m and T2Sim.m.
Solutions and selfgrading in the class bspace page
Homework 8 can be downloaded from Here.
Solutions and selfgrading in the class bspace page
Homework 9 can be downloaded from Here.
Solutions and selfgrading in the class bspace page
Homework 10 can be downloaded from Here.
Homework 11 (optional) can be downloaded from Here.
A link to Pruessmann's SENSE paper is here.
The matlab data sense_2dft.mat.
Announcements: