Description of the courses, emphasizing upper level undergraduate and introductory graduate courses:

Curriculum Overview

The proposed program consists of four core courses and three additional courses that are accessible to advanced undergraduates and first year graduate students. The MRI Technology course (3 units) emphasizes the mathematics, physics, signal processing and design of the MRI system. The prerequisites are a broad base of rigorous freshman physics (such as in Halliday, Resnick) and junior or senior level education in Linear Systems and Fourier Transforms. The course provides required knowledge for all MRI pulse sequence, signal and image processing research and development projects. The MR Systems Laboratory (4 units) will provide hands-on experience with the 0.6T system. The student will gain an introduction to MRI experimentation for industrial applications. The MRI Current Concepts I and MRI Current Concepts II courses (3 units each) is designed to cover advanced theoretical topics, newer applications, and the latest research results in MRI at a technical level. The prerequisite will be the successful completion of the Mathematics of MRI course, or consent of instructor. The MRI instrumentation course (3 units) is a lecture/laboratory course designed to provide the student with practical first-hand experience with MRI hardware. The lecture portion will cover in stepwise fashion all basic hardware components of the MRI instrument, with the lab designed to illustrate each topic covered in the lecture. This course will enable the student to understand each part of the MRI and its use in obtaining data, eliminating the unproductive "black box" approach to MRI. In addition, the student will be taught intelligent hardware parameter selection to optimize data collection. Design of pulse sequences will be covered with a focus on how hardware performance specifications dictate experimental design. Programming of the MR scanner, linking of software and data flow to the operating system reconstruction programs, and to the display algorithms will be covered in detail. The students will use the pulse programming language on the Omega 7T imaging system (located at NMR Facility), the Tecmag pulse programming language on the 0.6 Tesla NMR imaging systems (both also located at NMR Facility), and the EPIC pulse programming language of Signa 1.5T GE Signa (located at UC Davis Med Center) MRI operating system. There will be laboratory manuals for each of the programming environments, and separate laboratory manuals for experiment description and procedure. The course entitled Introduction to MRI in Biomedicine (2 units) consists of twenty 60-minute lectures using 35 mm slides on MRI covering the physics of magnetic resonance, biophysical properties of tissue, imaging hardware, image generation, factors influencing image contrast and quality. These lectures are directed at biomedical engineering advanced undergraduates and first year graduate students. The undergraduate Introduction to Magnetic Resonance course (3 units) will cover the broad applications of magnetic resonance in biomedicine and engineering. Faculty will also be available for independent study courses to give students an introduction to magnetic resonance research. A weekly MRI Research Seminar (1 unit taught at least one quarter every other year) will bring students and faculty from diverse MRI applications together for discussion and practice presentations.

Outlines and sample schedules

MRI Technology (Mathematics of MRI)

This course is taught yearly, in the spring quarter. Last taught Spring Quarter 1997.

From 1997…

MRI Technology (Mathematics of MRI) -- Spring Quarter 1997
MW, 7:30 - 8:50 AM, 1070 Bainer Hall (Televised and videotaped)
Instructor: Michael H. Buonocore

Lecture #	Date	Topics		Details
1	M, Mar 31	Topic #1: Properties of nuclear spin systems		Larmor relation, nuclear magneton, gyromagnetic ratio.
2	W, April 2	Topic #1: Properties of nuclear spin systems		Thermal equilibrium, transitions, Boltzman factor, equilibrium magnetization of tissue
3	M, April 7	Topic #2: Spin dynamics: Schrodinger and Bloch equations	HW #1	Fundamental postulates of Quantum Mechanics. Quantization of angular momentum. Derivation of two component Schrodinger equation. Introduction to spinors.
4	W, April 9	Topic #2: Spin dynamics: Schrodinger and Bloch equations		Schrodinger equation for spin 1/2 particle -- steady state spin dynamics -- connection between spin and magnetization. Expectation values.
5	M, April 14	Topic #2: Spin dynamics: Schrodinger and Bloch equations	HW #2	Conversion from Spinor dynamics to magnetization dynamics.
6	W, April 16	Topic #2: Spin dynamics: Schrodinger and Bloch equations		Bloch Equation
7	M, April 21	Topic #3: Biophysical basis of T1, T2	HW #3	Water in biological systems, exchange model, origin of T1 and T2 relaxation, T1 dependences such as field strength. QM explanation of T1 and T2: Ensemble averaging, spin transitions, rotational and translational correlation functions
8	W, April 23	Topic #4: Hardware Design		Gradient coil design
9	M, April 28	Topic #4: Hardware Design	HW #4	Gradient and RF coil design
10	W, April 30	Topic #4: Hardware Design		RF coil design and expression for signal to noise. Comparison with experimental data.
11	M, May 5	Topic #5: Image Generation	HW #5	k-space and imaging parameter relations:
12	W, May 7	Topic #5: Image Generation		k-space and imaging parameter relations: k-space trajectories and image reconstruction.
13	M, May 12	Topic #5: Image Generation	HW #6	k-space trajectories and image reconstruction continued.
14	W, May 14	Topic #5: Image Generation		k-space trajectories and image reconstruction continued.
15	M, May 19	Topic #5: Image Generation	HW #7	k-space trajectories and image reconstruction continued.
16	W, May 21	Topic #6: Imaging Parameters		How choice of imaging parameters affects spatial resolution and signal-to-noise SNR. Understanding sources of signal and sources of noise.
17	M, May 26	Topic #7: Generation of Tissue contrast	HW #8	Spin echo and inversion recovery sequences: writing out spin equilibrium equations, approximating and solving signal equations
18	W, May 28	Topic #7: Generation of Tissue contrast		Gradient recalled echo sequences: approximating spin dynamics.
19	M, June 2	Topic #8: Effects of Flow and Motion	HW #9	Modeling objects that are moving during a scan. Predicting location, amplitude and phase of ghost artifacts.
20	W, June 4	Topic #9: Review questions
Final Week	June 6-12	Final Exam		Answers provided to all homework questions -- open question period.
Grades in	June 17

From 1995…

"Mathematics of MRI" course outline (3 units): Spring 1995
Instructor:		MH Buonocore, MD PhD, Dept. of Radiology, UC Davis Medical Center, 734-3766
TIME/LOCATION:			TTh 3:10-4:30 PM	159 Chemistry Building, UC Davis Main Campus
Tu April 4	Properties of nuclear spin systems: Larmor relation, nuclear magneton, gyromagnetic ratio.
Th April 6	Properties of nuclear spin systems: Thermal equilibrium, transitions, Boltzmann factor, equilibrium magnetization of tissue
Tu April 11	Spin dynamics: Schrodinger equation for spin 1/2 particle -- steady state spin dynamics -- connection between spin and magnetization.
Th April 13	Spin dynamics: Bloch equations, relaxation terms, rotating frame.
Tu April 18	Theory of T1 and T2 relaxation terms: Water in biological systems, exchange model, origin of T1 and T2 relaxation, T1 dependencies such as field strength
Th April 20	Theory of T1 and T2 relaxation terms: QM explanation of T1 and T2: Ensemble averaging, spin transitions, rotational and translational correlation functions
Tu April 25	MRI Hardware: Gradient coil design
Th April 27	MRI Hardware: RF coil design
Tu May 2	Image generation: Slice selection, range of RF pulse excitation
Th May 4	Image generation: Phase and frequency encoding
Tu May 9	Imaging generation: k-space and image-space relationships
Th May 11	Imaging parameters: Origins and expressions for signal and noise in imaging.
Tu May 16	Imaging parameters: How MR parameters affect spatial resolution and signal to noise
Th May 18	Generation of Tissue contrast: Spin echo and inversion recovery sequences: writing out spin equilibrium equations, approximating and solving signal equations
Tu May 23	Generation of Tissue contrast: Gradient recalled echo sequences: writing out spin equilibrium equations, approximating and solving signal equations
Th May 25	Image artifacts and how to avoid them: Artifacts due to the body (e.g. physiological motion of breathing, blood flow, voluntary and involuntary muscle motion, tissue susceptibility, etc.).
Tu May 30	Image artifacts and how to avoid them: Artifacts due to the body continued (e.g. physiological motion of breathing, blood flow, muscle motion, tissue susceptibility, etc.)
Th June 1	NO CLASS
Tu June 6	Image artifacts and how to avoid them: Artifacts from system (Gibbs, inhomogeneities, nonlinearities).
Th June 8	Velocity compensation and velocity mapping

MRI Systems Laboratory

1997…

EBS 239

Magnetic Resonance Imaging of

Biological Materials

Instructor:

Michael J. McCarthy

Departments of Biological and Agricultural Engineering

and

Food Science and Technology

Office: 231 Cruess Hall

Phone: 752-8921

Email: mjmccarthy@ucdavis.edu

Course Location: Bainer Hall 2045

Course Time: Tu/Th 10:30 to 11:50 AM

Relaxation weighted image of a Kiwi, 0.1 Tesla field strength.

Lecture Schedule - EBS-239 Fall 1997

Month	Date	Topic
September	25	Magnetic Resonance Fundamentals
	30	Spin dynamics, spin-spin relaxation, spin-lattice relaxation
October	2	Pulse sequences, inversion recovery, spin-echo, basic imaging sequences
	7	Quantitative magnetic resonance, solutions to the Bloch equations (** lecture in room 2033)
	9	Localized spectroscopy, chemical shift, magnetic susceptibility (** lecture in room 2033)
	14	MR imaging, spin-echo sequences, fast imaging
	16	Diffusion in a magnetic field gradient, spin phase mapping
	21	Restricted diffusion, measurement of characteristic length scales
	23	Flow measurements, time-of-flight, phase mapping
	28	Flow measurements, acceleration, turbulence
	30	MIDTERM
November	4	Design of MR experiments
	6	Measurement of porosity and phase volumes
	11	Colloidal Systems
	13	Cellular Systems
	18	Physical properties
	20	Engineering quantities, transport coefficients
	25	Practical considerations, signal-to-noise, spatial resolution, field strength
December	2	Student project presentations
	4	Student project presentations

Grading:

Homework 20%

Midterm 30%

Oral Presentation 10%

Proposal 40%

REFERENCES

M.J. McCarthy, Magnetic Resonance Imaging in Foods, Chapman & Hall, New York 1994.

P.T. Callaghan, Principles of Nuclear Magnetic Resonance Microscopy, Clarendon Press, Oxford 1991.

C-N. Chen and D. I. Hoult, Biomedical Magnetic Resonance Technology, Adam Hilgar, New York, 1989.

E. Fukushima and S.B.W. Roeder, Experimental Pulse NMR: A Nuts and Bolts Approach, Addison-Wesley Publishing Company, Reading, Massachusetts 1981.

T.C. Farrar, Pulse NMR, Farragut Press, Madison, WI, 1989.

See the following web sites:

http://www.nmr.ucdavis.edu/

http://galaxy.einet.net/editors/doug-morris/mri.html

From 1995…

This course is taught every other year, in the fall quarter. Last taught 1995, scheduled Fall 1997.

"MRI Systems Laboratory" course outline (4 units), Fall Quarter
Instructor:		Mike McCarthy PhD, 231 Cruess Hall, 752-8921 (office)
TIME/LOCATION:			TUES/THURS 11-12:30	1336 BAINER HALL
Th Sept 30	Magnetic Resonance Fundamentals; Bloch Equations
Tu Oct. 5	Pulse sequences; spin-echo, inversion recovery, selective pulses
Th Oct. 7	Simple imaging pulse sequences; projection reconstruction; Fourier imaging
Tu Oct.12	Quantitative localized spectroscopy and multinuclear imaging
Th Oct.14	Phase separation in colloidal systems, influence of temperature one-dimensional relaxation weighted imaging.
M. Oct. 18	Sedimentation; quantification of porosity with NMRI derived Patterson functions
Tu Oct. 19	Spin phase mapping - propagator approach -I
Th Oct. 21	Spin phase mapping - propagator approach - II
Tu Oct. 26	Measurement of diffusion in unbounded systems
Th Oct. 28	Measurement of diffusion in bounded systems; droplet size distributions
Tu Nov. 2	Flow imaging; laminar flow
Th Nov. 4	Flow imaging; influence of shear, influence of acceleration
Tu Nov. 9	Spin echo signals for turbulent flow; eddy diffusivities
Th Nov. 11	Simultaneous measurement of diffusion and flow
Tu Nov. 16	Microcirculation and flow in porous media; complex geometries
Th-Nov. 18	Instrumental weight functions; influence of length scales
Tu-Nov. 23	Limitations of MRI measurements; temporal and spatial
Th-Nov. 25	Holiday
Tu-Nov. 30	Process Control using MRI
Th-Dec. 2	Relationship of MRI to x-ray and gamma ray imaging
Tu-Dec. 7	Relationship of MRI to industrial tomographics systems
Th-Dec. 9	Design of MRI pulse sequences and data analysis for industrial applications

Laboratory component: 2 - 1 hour lectures per week; 1 - 3 hour laboratory per week

M. Oct. 6	Introduction to operating systems; setting sequence parameters
M. Oct. 13	Relaxation time measurements; Inversion recovery, CPMG, Spin-echos
M. Oct. 20	Selective pulses; measurement of slice thickness
M. Oct. 27	Simple 1-D imaging; simple 2-D imaging
M. Nov. 1	Chemical shift imaging of emulsions; diffusion measurements
M. Nov. 8	Flow imaging
M. Nov. 15	q-space imaging and Patterson functions
M. Nov. 22	Fast imaging; gradient recalled echos, FLASH
M. Nov. 29	Quantitative MRI project-determination of an unknown
M. Dec. 6	Quantitative MRI project continued.

Current Concepts in MRI

This course is being taught for the first time Fall 1997.

Title: Current Concepts in Magnetic Resonance Imaging (BIM 247)
Time-Place: Fall Quarter 1997, TR, 7:30 - 8:50 AM, 2170 Bainer Hall
Instructor: Michael H. Buonocore

NOTE: Being the first year that the class is taught, this is an approximate schedule. The current plan is to have bi-weekly homework assignments, and a take-home final exam. NOTE ADDED 10/08/97: Course will be extended through Winter quarter.

Lecture #	Date	Topic	Details
1	Th, Sep 25	Introduction	Review of all topics, start Topic #1
2	Tu, Sep 30	Topic #1: Velocity encoding	Modeling phase accumulation in presence of motion, gradient moment nulling and encoding waveforms, 2 and 4 point encoding methods.
3	Th, Oct 2	Topic #2: Echo planar (EPI) and spiral imaging	Review of k-space encoding, single shot EPI, Hybrid EPI, EPI point response.
4	Tu, Oct 7		Ghost artifact correction for EPI and hybrid EPI
5	Th, Oct 9		Spiral scan, design to provide necessary spatial resolution, interleaved spiral, accelerated spiral, image reconstruction of spiral data.
6	Tu, Oct 14	Topic #3: RF spoiling and refocusing of Transverse magnetization	Review of MRI contrast mechanisms, generation of spin equilibrium equations, distinction between refocussing, delayed refocussing, and spoiling.
7	Th, Oct 16		Effect of imaging system point response on image intensity, special cases, and numerical results.
8	Tu, Oct 21		The need for spoiling, Identifying spin populations with identical phase, Setting up numerical problem to find effective spoiling techniques.
9	Th, Oct 23		Catch-up day, review day.
10	Tu, Oct 28	Topic #4: Fast spin echo imaging	Basic principles of data acquisition in k-space, "fast" principle, derivation of point response, reason for bright fat signal.
11	Th, Oct 30	Topic #5: RF pulse design	Spinor notation, modeling actions of gradient and RF pulses with spinors.
12	Tu, Nov 4		RF pulse train approximation, digital filter representation, inverse solution method, representation of common RF pulse types.
13	Th, Nov 6		Pictorial representation of the RF pulse design solution. Connnection with other solution methods. Hilbert transform and other necessities.
14	Tu, Nov 11	Topic #6: Computer simulation of MRI	Value of an exact simulation. Ellipse model, reducing the equation to a standard form.
15	Th, Nov 13		Solving the integral, solution in special cases of MRI, full solution using asymptotic analysis.
16	Tu, Nov 18	Topic #7: Diffusion weighted imaging	Basic methodology, importance in applications, complexity of diffusion effect and modeling
17	Th, Nov 20		Path integral approach to modeling diffusion in the presence of field gradients. Effective and ineffective gradient waveforms for measuring diffusion.
18	Tu, Nov 25	Topic #8: Magnetization transfer	Introduction of what it is and its importance. Four compartment tissue model, agreement between theory and experiment.
19	Th, Nov 27	(thankgiving, no class)	NO CLASS
20	Dec 1	(RSNA meeting, no class)	Will have makeup during end of quarter as catch-up day.
21	Dec 5	(RSNA meeting, no class)	No makeup planned.
	Dec 8-13	FINALS WEEK.	Take home final examination.
	Dec 16:	Grades in

This course is being taught for the first time Fall 1997.

"MRI Current concepts" course outline (3 units) Fall Quarter 1997
Instructor:		MH Buonocore, MD PhD, Dept. of Radiology, UC Davis Medical Center, 734-3766
TIME/LOCATION:			Wednesday, 3:10-4:30 PM	Fall Quarter 1997
Topic 1	Velocity encoded phase imaging sequences (k-space, moment analysis, flow encoding and contrast mechanisms)
Topic 2	Contrast mechanisms in fast pulse sequences
Topic 3	Echo planar and spiral fast scanning pulse sequences (k-space, tissue contrast)
Topic 4	Fast-spin echo pulse sequence: (k-space coverage and generation of tissue contrast)
Topic 5	RF pulse design (including inverse scattering, SLR algorithms)
Topic 6	Magnetization transfer imaging (theory and experiments)
Topic 7	Diffusion/perfusion imaging (theory and MR measurement)
Topic 8	First-pass contrast studies (modeling of transport phenomenon)
Topic 9	Accurate computer simulation of MRI

MRI Instrumentation

This course is taught yearly, in the winter quarter.

"MRI Instrumentation" course outline (3 units)
Instructors:		Jeffrey deRopp, PhD. NMR Facility, UC Davis, 752-7677. Jeffrey Walton, PhD. NMR Facility, UC Davis, 752-7794
TIME/LOCATION:			NMR Facility, UC Davis	Winter 1996
Topic 1	Main magnet, shims, gradients and their functions
Topic 2	Basic electronics review
Topic 3	MRI console building blocks and block diagram
Topic 4	Probe design and tuning - tricks of the trade
Topic 5	RF hardware - pulses and their shaped and phasing
Topic 6	Gradient generation hardware; eddy currents
Topic 7	Detection of FID; Nyquist theorem, receiver gain
Topic 8	ADC; digital resolution
Topic 9	Fourier Transform; signal conditioning
Topic 10	2D + Multi-D FTs
Topic 11	Pulse sequences - design
Topic 12	Combined RF + gradient sequences - implementation
Topic 13	Multichannel RF experiments
Topic 14	Gradient echoes
Topic 15	Signal suppression

Introduction to MRI in Biomedicine

This course is taught yearly, in the spring quarter.

From 1997 …

Introduction to MRI: A Slide Presentation -- Spring Quarter 1997
MW 9:10 - 10:00 AM, 1070 Bainer Hall (Televised and videorecorded)
Instructor: Michael H. Buonocore

Lecture #	Date	Topic
1	M, Mar 31	Spin and signal concepts
2	W, Apr 2	MR hardware
3	W, April 9	MR Safety / Image generation
4	F, April 11	Image generation
5	M, April 14	NO CLASS
6	W, April 16	NO CLASS
7	M, April 21	Image generation (board)
8	W, April 23	Image generation (board)
9	M, April 28	Generation of image contrast
10	W, April 30	Generation of image contrast
11	M, May 5	Generation of image contrast (board)
12	W, May 7	Clinical imaging, brain
13	M, May 12	Biophysical basis of T1, T2
14	W, May 14	Appearance of Hemorrhage
15	M, May 19	Scan parameters
16	W, May 21	Scan parameters
17	M, May 26	Scan parameters
18	W, May 28	Scan parameters
19	M, June 2	Artifacts and their elimination
20	W, June 4	Artifacts and their elimination
Final Week	June 6-12	Final exam
Grades in	June 17

From 1995 …

"Introduction to MRI in Biomedicine" slide course (2 units), Spring Quarter 1995
Instructor:	MH Buonocore MD PhD, Dept. of Radiology, UC Davis Medical Center, 734-3766
TIME/LOCATION:			Tu 4:40-6:00 PM	159 Chemistry Building, UC Davis
Tu April 4		Spin and signal concepts (38 slides)
Th April 6		MR hardware (48 slides)
Tu April 11		MR Safety/Image generation -- overview (44 slides)
Th April 13		Image generation -- frequency and phase encoding (40 slides)
Tu April 18		Generation of image contrast -- spin echo sequences (30 slides)
Th April 20		Generation of image contrast -- gradient echo sequences (42 slides)
Tu April 25		Clinical imaging, Brain (64 slides)
Th April 27		Biophysical basis for T1 and T2 -- molecular mechanisms (30 slides)
Tu May 2		Biophysical basis for T1 and T2 -- tissue characteristics (37 slides)
Th May 4		Appearance of hemorrhage -- hemorrhage evolution (42 slides)
Tu May 9		Appearance of hemorrhage -- typical appearance in brain lesions (42 slides)
Th May 11		Scan parameters -- affecting contrast, resolution and signal to noise (45 slides)
Tu May 16		Scan parameters -- lesion detectability and scan time (50 slides)
Th May 18		Artifacts and their elimination -- physiological motion effects (53 slides)
Tu May 23		Artifacts and their elimination -- compensation and reduction techniques (53 slides)
Th May 25		Artifacts and their elimination -- other (65 slides)
Tu May 30		NO CLASS
Th June 1		Flow effects / Cardiovascular MRI (42 slides)
Tu June 6		MR angiography (76 slides)
Th June 8		Introduction to MRI research (60 slides) -- lecture not given in 1995.

Introduction to Magnetic Resonance

This course has not yet been offered.

Undergraduate "Introduction to Magnetic Resonance" course (3 units)
Instructors:		Robert L. Powell PhD, Dept. of Chemical Engineering, UC Davis, 752-8779Mike McCarthy PhD, Dept. of Food Science and Technology, UC Davis 752-8921MH Buonocore MD PhD, Dept. of Radiology, UC Davis Medical Center, 734-3766
Topic 1	What is magnetic resonance in chemistry?
Topic 2	What is non-invasive testing?
Topic 3	Why do we need non-invasive testing in life sciences and industry?
Topic 4	What is the history of imaging done with x-rays, sound waves and other older imaging methods?
Topic 5	How is magnetic resonance different from imaging with x-rays and sound waves?
Topic 6	Case studies involving anatomical imaging and detection of tumors and musculoskeletal injuries.
Topic 7	What kind of information about tissues does MRI provide? Additional case studies on measurement of cardiac function, vessel anatomy using angiographic techniques, and imaging neural activation in the brain.
Topic 8	What information about foods can MRI provide? Case studies involving measurement of particle size distributions in emulsions with PFGSE techniques, measurement of rheological properties of fluids.
Topic 9	What information about industrial processes can MRI provide? Case studies involving measurement of moisture transport in food systems.
Topic 10	Introduction to the theory of MRI: Bloch equations, relaxation in tissues, influence of motion on the signal and basic pulse sequences, RF probe and gradient coil design.