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SYLLABUS Fall 2009
BME 425: Basics of Biomedical Imaging
(Dr. Manbir Singh)
Course Goals, Learning Objectives and Relationship to Program Outcomes
Course Goals:
The goals are to introduce you to the underlying physics, mathematics and engineering
concepts of most prevailing biomedical imaging modalities for in-vivo human imaging
including x-rays, nuclear medicine, MRI and ultrasound.
Learning Objectives and Relationship to Program Outcomes*:
(*BME program outcomes are listed at the end of the syllabus)
After successfully completing this course, you should be able to:
1. Understand the basic physical concepts of how biological components
(parameters) of our bodies lead to contrast in: a) x-ray imaging, b) x-ray
computed tomography, c) nuclear medicine including single photon emission
computed tomography (SPECT) and positron emission tomography (PET), d)
magnetic resonance imaging (MRI) and e) ultrasound imaging. You should be
able to relate the physical and biological parameters to engineering design of the
imaging instruments. (OUTCOME 1)
2. Compare and contrast the role of different imaging modalities in providing
anatomical and physiological information about the human body within limits
imposed by the physical and engineering design constraints of each modality.
(OUTCOME 1)
3. Obtain a basic understanding of how data are acquired by each scanner, how data
are processed, how images are reconstructed, how these data are analyzed and
how the results are interpreted (OUTCOMES 1 and 2)
4. Understand and write basic software codes to simulate the effect of system point
spread function on data that would be acquired by an imaging system.
(OUTCOME 3)
5. Develop an individual project based on either (a) technological review of a current
topic in biomedical imaging with original suggestions for future work, (b)
development of software codes to perform a computer simulation of data
acquisition and image reconstruction by a biomedical scanner, or (c) development
of codes to process raw experimental data acquired by a biomedical scanner.
Present and discuss project at an initial (midterm) and final stage and submit
written report. Interact in class with other students during discussion of your
project. (OUTCOMES 5,6,7)
6. Have a basic understanding of how images from various scanners provide
complimentary information toward clinical diagnosis of various diseases and
acquire a conceptual knowledge of how a particular scanner is selected in a
specific instance. Be able to relate the value of imaging technology and proper
engineering design to health care. (OUTCOMES 8,9)
7. Acquire a basic understanding of how the engineering of biomedical imaging
scanners contributes to medicine and biological sciences and be able to engage in
further interdisciplinary education in these areas. (OUTCOME 10)
Below is an outline of topics that will be covered on a weekly basis. These topics are used
as a guideline and it is possible that there may be some changes in the order of
presentations. Also some topics may be discussed in more detail than others depending on
the level of interest and dynamics of the class.
WK 1:
Overview of Various Imaging Modalities I
Introduction. Discussion of course requirements, exams and paper topics. Overview of
X-ray imaging, computed tomography, nuclear medical imaging.
WK 2:
Overview of Various Imaging Modalities II
Magnetic resonance imaging and spectroscopy, ultrasonic imaging, neuromagnetic
imaging.
WK 3: Basic Parameters of Biomedical Imaging, Conventional X-ray Imaging and
Digital Radiography
Spatial resolution, temporal resolution, sensitivity, point spread function, line spread
function, modulation transfer function, contrast, photon statistics, signal to noise ratio.
Interaction of X-rays with matter, photoelectric interaction, coherent and incoherent
scattering, linear attenuation coefficients, contrast formation, contrast enhancement,
fluorescent screens, quantum limits, fluoroscopy and image intensifiers, principles of
digital radiography, system configuration, digital subtraction angiography. Homework:
computer design of an object to be imaged (phantom) and a code to simulate the
effect of point spread function in imaging.
WK 4:
X-Ray Computed Tomography I
Principles of computed tomography, linear and angular sampling, sampling frequency,
limited angular sampling, image reconstruction techniques, simple backprojection,
iterative algorithms, Fourier and Direct reconstruction algorithms I.
WK 5:
X-Ray Computed Tomography II
Fourier and Direct reconstruction algorithms II, X-ray sources, radiation detectors, first to
fifth generation CT scanners, beam hardening artifacts.
WK 6:
Conventional Nuclear Medical Imaging
Radioactive tags of biochemical function, scintillation detectors, basics of collimation,
scintillation cameras, scattered radiation, clinical applications.
WK 7:
Emission Computed Tomography I: SPECT
Introduction to single photon emission computed tomography (SPECT), Image
reconstruction in SPECT, Variations in sensitivity, line spread function and related
problems, attenuation and scatter correction, quantification, clinical applications of
SPECT.
WK 8:
Emission Computed Tomography II: PET
Basics of positron emission tomography (PET), electronic collimation, scatter and
attenuation correction, image reconstruction, instrumentation, time-of-flight techniques in
PET, clinical applications.
WK 9:
Introduction to Magnetic Resonance Imaging (MRI) Physical concepts,
classical and quantum mechanics, Bloch equations, spin density, relaxation times.
MIDTERM I: OUTLINE PRESENTATIONS (ORAL)
WK 10: MIDTERM II: Written exam
WK 11:
MRI 2
Pulse sequences, Fourier imaging, k-space, Phase encoding, Fast imaging techniques,
clinical applications.
WK 12: MRI 3
Functional MRI (fMRI), Applications of fMRI, Introduction to Diffusion Tensor Imaging
(DTI)
WK 13:
MRI 4, Ultrasonic Imaging
MRI Instrumentation, resistive and superconducting magnets, RF coils, gradient coils.
Physical principles of ultrasonic imaging, various modes, transducers, system
configuration, tissue characterization, applications.
WK 14:
imaging
FINAL Presentation of Papers by students or Review of misc. topics in
WK 15: FINAL Presentation of Papers by students
WK 16: FINAL EXAM
LIST OF COURSE READINGS
Text-book (recommended)
Foundations of Medical Imaging, Z. H. Cho, Joie Jones and Manbir Singh,
John Wiley & Sons, Inc. New York, 1993.
Additional reading (recommended)
1. Radiological Imaging: The theory of image formation, detection, and processing
Vol. 1 and 2, H.H. Barrett and W. Swindell, Academic Press, New York, 1981.
2. Principles of Computerized Tomographic Imaging, A. C. Kak and M. Slaney,
IEEE Press, 1987.
3. Physics in Nuclear Medicine, James Sorenson and Michael Phelps, Grune and
Stratton, New York, 1980.
4. Scientific Basis of Medical Imaging, P.N.T. Wells, Churchill Livingstone, New
York, 1982.
5. All You Really Need to Know about MRI Physics, Moriel NessAiver, University
of Maryland Medical Center, [email protected]. Published in 1996.
6. Principles of Magnetic Resonance Imaging; A Signal Processing Perspective, Z.
P. Liang and Paul C. Lauterbur, IEEE Series in Biomedical Engineering, ISBN 07803-4723-4, 2000.
EXAMS
Midterm:
The midterm has two parts.
Part I: A 5-minute presentation of the outline of the student’s paper and submission of a
one-page outline on the day of the midterm presentation.
Part II: A 2.5 hour written exam, closed-book.
Final:
The Final exam has three parts:
Part I: A 15-minute presentation of the student’s paper (to be presented during the last
two weeks of classes).
Part II: A 15-page written final paper submitted on the scheduled day of the Final.
Part III: A two-hour written exam on the scheduled day of the Final.
Grading policy:
Midterm part I: 5% of final grade (presentation)
Midterm part II: 15% of final grade (Written Exam)
Final part I: 25% of final grade (Presentation)
Final part II: 30% of final grade (Written paper)
Final part III: 15% of final grade (Written Exam)
Homework, Attendance and Interactions in class: 10% of final grade
Office Hours: The instructor and teaching assistant will hold office hours every week.
This is for your benefit and you are welcome to utilize the office hours for individual or
small-group discussions.
Disability Statement: Students requesting academic accommodations based on a
disability are required to register with Disability Services and Programs (DSP) each
semester. A letter of verification for approved accommodations can be obtained from
DSP when adequate documentation is filed. Please be sure the letter is delivered to the
instructor within the first few weeks of the semester. DSP is open Monday-Friday, 8:305:00. The office is in Student Union 301 and the phone number is (213) 740-0776.
List of BME Program Outcomes
Students who complete successfully the Biomedical Engineering Program should be able to:
1.
Apply knowledge of mathematics, physical sciences, life sciences and engineering to formulate and
study or solve engineering problems, including problems at the interface of engineering, medicine, and
biology.
2.
Plan and conduct experiments as well as analyze and interpret experimental measurements
collected on physical systems and living systems.
3.
Design electronic, mechanical and/or computer-based devices and software for applications
including medical instrumentation, physiological measurement and signal processing, prosthesis
development, and engineering simulation of living systems.
4.
Understand the professional, ethical and societal responsibilities pertinent to the practice of
engineering.
5.
Communicate effectively using appropriate technology and information resources to document
work, analyze engineering problems and solutions, and present project results.
6.
Lead a team of student engineers performing a laboratory exercise or a class project; participate in
various roles to the team and understand the contribution of each role to the team's effort.
7.
Be independent learners who can master new knowledge and technologies.
8.
Utilize their broad liberal education to explore and analyze the impact of engineering and
technology solutions on society and healthcare.
9.
Select and use modern engineering tools for analysis, design,experimentation and testing.
10.
Successfully engage in further education in engineering, medicine and biomedical sciences.