BME 327 - Biomedical Engineering

BME 327: Magnetic Resonance Imaging
2013 Winter Quarter
Lecture Time and Room: TuTh 9:30 am-10:50 pm, Tech M120
Instructors:
Michael Markl, PhD, Associate Professor of Radiology and BME
Tel: 312-695-1799
E-mail: mmarkl@northwestern.edu
Office hr: Tu, Th 9:30-10:50 am
Room: Tech-M120
Guest-Instructor: Prof. Fluckiger, NWU Radiology
Prerequisite:
General Physics and
BME 305 (Biomedical Signals Analysis)
or permission of instructor
Required Textbooks:
Principles of Magnetic Resonance Imaging
by D. G. Nishimura
(Available for purchase in Norris Center Bookstore)
References:
Magnetic Resonance Imaging: Physical Principles and Sequence Design
by E. Mark Haacke, et al.
1999 John Wiley & Sons, Inc.
(Engineering Library)
Principles of Magnetic Resonance Imaging: A Signal Processing Perspective
by Zhi-Pei Liang et al.
2000 The Institute of Electrical and Electronic Engineers, Inc.
(Engineering Library)
Magnetic Resonance Imaging: Theory and Practice
by M. T. Vlaardingerbroek, et al.
1999 Springer-Verlag, Berlin.
(Medical School Library)

Grading System
Item % of final grade Comments
Homework 30% Assigned once per week, scored 0-10
Midterm 25% open book, scored 0-100
Final 40% open book, scored 0-100
Presentation 5% open book, scored 0-5
Grading scale:
>=93 A
90-93 A-
87-90 B+
83-87 B
80-83 B-
77-80 C+
73-77 C
70-73 C-
Course Management System (CMS) will be used for passing out assignments, solutions,
class notes, handouts, and announcements.
Course Description:
Magnetic resonance imaging (MRI) is an emerging technique that has found widespread
applications in medical imaging research and clinical applications in recent years. It has the
potential to provide a variety of information about the human body, including anatomy,
function, blood flow, and metabolism. This course will provide fundamentals and basic
concepts of magnetic resonance imaging and their applications to disease diagnosis.
This course will first introduce the basic physics of MRI, including magnetic
moments and resonance, nuclear spin interactions with applied magnetic fields, and
magnetic relaxation. The second portion of the course will discuss basic concepts of image
formation, including radiofrequency pulse excitation, magnetic field gradients, imaging
equation, Fourier Transform, k-space, and two-dimensional spatial encoding. The final
portion of the course will introduce practical imaging methods and applications, such as
image artifacts, fast imaging methods, signal-to-noise, contrast-to-noise, resolution, MR
imaging of heart and blood vessels, and MR imaging of the neural system.
At the end of the class, students are expected to have (1) a basic but systematic
understanding of the MRI fundamentals; (2) a basic understanding of major technical
issues in MRI; (3) general knowledge of clinical applications of MRI. This will prepare
students to perform advanced research on MR imaging in the future.

Course Objectives:
The students should:
1. understand the basic physics of magnetic resonance imaging, including:
a. nuclear spin interactions with applied magnetic fields
b. magnetic resonance
c. magnetic relaxations: Bloch equation
2. understand the fundamentals of image formation, including:
a. radiofrequency pulse excitation
b. phase of magnetization as a function of magnetic field gradients
c. frequency and phase encoding
d. Fourier transform relationship between image and k-space: Imaging equation
e. basic signal sampling requirements for magnetic resonance imaging and image
artifacts if the Nyquist sampling rate is not met (aliasing)
f. resolution
g. image contrast (T1, T2, and spin-density weighted imaging)
3. understand main factors affecting images, including:
a. magnetic resonance signal and contrast as functions of tissue parameters
b. effects of field inhomogeneities on images
c. sources of image noise
d. effects of contrast agents on image signal intensity
e. definition and formation of echoes in spin-echo and gradient-echo sequences
4. learn to determine k-space trajectories from magnetic field gradient waveforms and
vise versa,
5. learn to analyze changes in signal-to-noise and contrast-to-noise ratios as functions of
imaging parameters,
6. become aware of basic clinical applications of magnetic resonance imaging in
diagnosing diseases of heart, blood vessels, body, and neural systems.

Syllabus for BME 327: Magnetic Resonance Imaging
1 01/08 Introduction, overview, basic concepts of MRI
2 01/10 Basic mathematics related to MR Physics
3 01/15
4 01/17
5 01/22
6 01/24
Spin physics: Nuclear Spin, interactions with applied
magnetic fields, rf-excitation, FID
T1, T2, T2* Relaxation, Bloch equations, Chemical shift
& MR spectroscopy
Imaging principles: magnetic field gradients, spatial
localization, frequency encoding, imaging equation
Imaging principles: Fourier transform, slice selection,
phase encoding, echoes, k-space
7 01/29 Fundamental MRI techniques: Spin echo
8 01/31 Fundamental MRI techniques: Gradient echo
9 02/05
10 02/07
Lab: Introduction to MRI hardware, tour of imaging
facility (Prof. Fluckiger at CTI)
Imaging principles: k-space, finite sampling, aliasing,
resolution, Mid-term review
11 02/12 Midterm Exam
12 02/14
13 02/18
14 02/21
15 02/26
16 02/28
Imaging principles: rf-excitation revisited, slice
selection, inversion recovery
Imaging considerations: contrast manipulation, noise,
steady state. saturation pulses
Imaging considerations: field inhomogeneity, T2*,
contrast agent
Imaging considerations: MR-signal phase, phasecontrast
MRI
Imaging considerations: Fast imaging, parallel imaging,
3D imaging, final review
Nishimura: Chaps.
1 & 3
Nishimura: Chaps.
2
Nishimura: Chap.
4, 6.1
Nishimura: Chap.
4
Nishimura: Chap.
5
Nishimura: 5.2,
5.3, 2.2, 6.2
Nishimura: 7.1,
Handout
Nishimura: 7.3,
Handout
Nishimura: 2.4,
5.6.2
Nishimura: 5.7
Nishimura: Chap.
6 Handout
Nishimura: 7.2 -
7.5
Nishimura: 7.1.
Handout
Handout
17 03/05 Advanced applications I: cardiovascular None
18 03/07 Advanced applications II: TBD None
19 03/12 Advanced applications III: TBD None
20 03/14 Student presentations Papers