CMPUT616
Fundamentals of Medical Imaging
CMPUT616 - Autumn 2011
Fundamentals of Medical Imaging
Every Monday, 15h00 to 17h30 Room
349
General Description:
The course starts by reviewing signal processing theory with example from medical
imaging. We will then study six general medical imaging modalities: projection
radiography, computed tomography, magnetic resonance imaging, nuclear
imaging, ultrasound, and confocal microscopy. The goal will be to understand these
modalities in terms familiar to a computer scientist. Following the study of modalities, we
will then review basic 3D image processing such as filtering, registration, segmentation,
and data driven physical simulation. Flexibility exists for the instructor to vary the depth
of each topic area after determining the general background and experience of the
students.
Syllabus:
Lecture 1: History of Modalities:
 Powerpoint files: Introduction.ppt,
Lecture 2: Basics of Linear Systems:
 Powerpoint files: LinearSystems-I.ppt,
Lecture 3: Convolution and 1-D Fourier Transform:
 Powerpoint files: LinearSystems-II.ppt,
Lecture 4: 2-D Fourier Transform:
 Powerpoint files: LinearSystems-III.ppt,
Lecture 5: Sampling Theorem:
 Powerpoint files: LinearSystems-IV.ppt,
Lecture 6: Discrete Fourier Transform:
 Powerpoint files: LinearSystems-V.ppt,
Lecture 7: Hankel Transform:
 Powerpoint files: LinearSystems-VI.ppt,
Lecture 8: 3-D Slicer
 Powerpoint files: Slicer3Minute_SPujol.pdf,
 3D Slicer website
 Tutorials
Lecture 9: Fundamental of X-Ray Physics-I:
 Powerpoint files:xRayPhysics-I.ppt,
 Movies: XRay General.avi
Lecture 10: Fundamental of X-Ray Physics-II:
 Powerpoint files: xRayPhysics-II.ppt,
 Movies: Source Obliquity.avi
 XRay Depth Dependence.avi
Lecture 11: X-Ray Distortion and Non-linearity:
 Powerpoint files: xRayPhysics-III.ppt
 Movies: xray source blurring.avi
Lecture 12: Statistical Model of X-Ray Images:
 Powerpoint files: xRayPhysics-IV.ppt
 Movies: screem capture.avi
 xray_contrast_and noise.avi
Lecture 13: X-ray CT-I:
 Powerpoint files: CT-I.ppt
 Movies: CTscanBasic.avi
 CTbackProjDivx.avi
Lecture 14: X-ray CT-II:
 Powerpoint files: CT-II.ppt
Lecture 15: Fundamental of MRI:
 Powerpoint files: MR-I.ppt
 Movies: MR Proton Precession.avi
 MR Transceiver Signal.avi
Lecture 16: MRI Image Formation Overview:
 Powerpoint files: MR-II.ppt,
 Movies: MR Gradient Coil Fields.avi
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MR spin vector field.avi
Moviews: MXY under gradient vector fields
MXY with effects of B0 inhomogeneity
Moviews: MXY with effects of B0 inhomogeneity
MXY with B0 inhomogeneity with spin echo
Lecture 17: Nuclear Imaging:
 Powerpoint files: Nuclear.ppt
Lecture 18: Ultrasound Imaging Systems:
 Powerpoint files: Ultrasound.ppt
Lecture 19: Fluoroscopy and Confocal Microscopy
 Powerpoint files: Confocal.ppt
Lecture 21: Multi-modal Non-linear Filtering
 Powerpoint files: Filtering.ppt
Lecture 22: Multi-modal Registration
 Powerpoint files: Registration.ppt
Lecture 23: Multi-modal Segmentation
 Powerpoint files: Segmentation.ppt
Lecture 24: From Segmentation to Physical Simulation and Surgical Planning
 Powerpoint files: Simulation.ppt
Textbook:
The following textbook is used to provide both the engineering, mathematical, and
physics background necessary for this course. I will lecture from the class notes but I
will refer to the textbook from time to time and some of the assignment will be from the
textbook.
J.L. Prince and J.M. Links, Medical Imaging: Signals and Systems,
Pearson Prentice Hall Bioengineering
Homework
Homework will generally be handed out during a lecture and will be due on the following
week. Some parts of the homework may involve SLICER exercises. There will be
approximately 5 problem sets. Don't be misled by the relatively few points assigned to
homework grades in the final grade calculation. While the grade that you get on your
homework is at most a minor component of your final grade, working the problems is a
crucial part of the learning process and will invariably have a major impact on your
understanding of the material.
SLICER-Based Project and Exercises
One of the best ways of learning much of the material in this course is by exploring
many of the concepts with Slicer. In addition to traditional homework problems, this
subject will have a computer exercise component based on the Slicer software
package.
Course Project
There will be an individual semester project, culminating in a final 8 pages report in
IEEE format and a 20 minutes presentation during a one day workshop in December.
Progress and check points before the final due date will count toward the final grade.
Course Grade
The final grade for the course is based on our best assessment of your understanding
of the material, as well as your commitment and participation. The SLICER project,
problem sets, and the final projects are combined to give a final grade:
ACTIVITIES
WEIGHT
Final Project
60%
Problem Sets
20%
SLICER Project(s)
20%
Links:
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Introduction to various technologies from HowStuffWorks.com
o X-rays
o CT
o MRI
o Ultrasound
Joseph Hornak, The Basics of MRI
Online resource, available at http://www.cis.rit.edu/htbooks/mri/ (Introduction to
MRI)
MRI safety (flying objects) [simplyphysics.com]
The Ottawa Medical Physics Institute has a series of interesting and relevant
Seminars
The Visible Human Project
Interactive Visible Human Viewer
The Computer Vision Test Image Database has many databases relevant to
image processing. Some contain medical images
The MedPix Database has X-ray and CT and MRI images.
Physionet.org / Images
digimorph.org X-Ray CT views of living and extinct vertebrates.
Online Computer vision books
P. K.Kaiser; The Joy of Visual Perception, Online book, 1996.
Kak, M. Slaney. Principles of Computerized Tomographic Imaging, Society of
Industrial and Applied Mathematics, 2001.
Martin Spahn Flat detectors and their clinical applications Eur Radiol (2005) 15:
1934-1947