CMPUT616 |
Fundamentals of Medical Imaging |
|
Fundamentals of Medical
Imaging Tuesday and Thursday, 15h30 to 17h00
CSC B41 |
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:
Lecture 2:
Basics of Linear Systems:
Lecture 3:
Convolution and 1-D Fourier Transform:
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
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 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.
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.
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:
·
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