CMPUT616 |
Fundamentals
of Medical Imaging |
|
Fundamentals of Medical
Imaging Friday 13h00 to 16h00 in CSC 363 |
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 medical practitioners. 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:
Lecture 2:
Basics of Linear Systems:
Lecture 3:
Convolution and 1-D Fourier Transform:
·
Assignment 2 (Due Sept. 26)
Lecture 4:
2-D Fourier Transform:
Lecture 5:
Sampling Theorem:
Lecture 6:
Discrete Fourier Transform:
Lecture 7:
Hankel Transform:
Lecture 8:
3-D Slicer
Lecture 9:
Fundamental of X-Ray Physics-I:
Lecture 10:
Fundamental of X-Ray Physics-II:
Lecture 11:
X-Ray Distortion and Non-linearity:
Lecture 12:
Statistical Model of X-Ray Images:
Lecture 13:
X-ray CT-I:
Lecture 14:
X-ray CT-II:
Lecture 15:
Fundamental of MR:
Lecture 16:
MRI Image Formation Overview:
Lecture 17:
Nuclear Imaging:
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
·
Assignment 6 (This is a supplementary
assignment and it is voluntary)
Lecture 23: Multi-modal Segmentation
·
Powerpoint
files: Segmentation.ppt
Lecture 24: From Segmentation to
Physical Simulation and Surgical Planning
·
Powerpoint
files: Simulation.ppt
·
Assignment 7 (This is a supplementary
assignment and it is voluntary)
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
Bio-engineering
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 6
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.
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.
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 |
40% |
Links:
·
Introduction
to various technologies from HowStuffWorks.com
o X-rays
o CT
o MRI
·
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.
·
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