|
CMPUT616 |
|
Fundamentals
of Medical Imaging |
|
Fundamentals of Medical
Imaging Friday 16h00 to 18h00 in CSC 2-49 |
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,
and ultrasound. 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:
Short History of Modalities:
- Powerpoint files: Introduction.pptx
- From Medical Imaging to Patient
Specific Modelling for Surgical Planning and Image Guided Surgery
- Slicer4.5minute_SoniaPujol.pdf
- Slicer4.5
Data Loading Tutorial
- 3D
Slicer website
- Slicer 3D
Tutorials
- Assignment 1 (Due Sept. 14)
Lecture 2:
Basics of Linear Systems:
- Powerpoint files: LinearSystems-I.pptx
- Further Reading: Linear Systems in
Wikipedia
Lecture 3: Multi-modal
Filtering
·
Powerpoint
files: LinearSystems-II.pptx, Filtering.pptx
- Further Reading: Convolution.pdf
·
Assignment 2 (Due Sept. 21)
Lecture 4:
Fourier Transform:
- Powerpoint files: LinearSystems-III.pptx,
- Further Readings:
Lecture 5:
Sampling Theorem:
- Powerpoint files: LinearSystems-IV.pptx,
Lecture 7:
Fundamental of X-Ray Physics-I:
- Powerpoint files:xRayPhysics-I.pptx, xRayPhysics-Modalities.pptx
- Further Reading: X-Rays.pdf
- Assignment 3 (Due Oct. 19)
Lecture 8:
Fundamental of X-Ray Physics-II:
- Powerpoint files: xRayPhysics-II.pptx,
Lecture 9:
X-Ray Distortion and Non-linearity:
- Powerpoint files: xRayPhysics-III.pptx
Lecture 10:
Statistical Model of X-Ray Images:
- Powerpoint files: xRayPhysics-IV.pptx
Lecture 11:
X-ray CT-I:
- Powerpoint files: CT-I.pptx
- Further Reading: Backprojection.pdf
Lecture 12:
X-ray CT-II:
- Powerpoint files: CT-II.pptx
- Further Reading: AlgebraicReconstruction.pdf
- Assignment 4 (Due Oct. 26)
Lecture 13:
Fundamental of MR:
- Powerpoint files: MR-I.pptx
Lecture 14:
MRI Image Formation Overview:
- Powerpoint files: MR-II.pptx, MR-III.pptx
- Further Reading: MRI.pdf
- Assignment 5 (Due Nov. 16)
Lecture 15:
Nuclear Imaging:
- Powerpoint files: Nuclear.pptx
Lecture 16: Multi-modal Registration
·
Powerpoint
files: Registration.pptx
·
Assignment 6 (Due Nov 30)
Lecture 17: Ultrasound Imaging Systems:
·
Powerpoint
files: Ultrasound.pptx
Lecture 18: From Segmentation to
Physical Simulation and Surgical Planning
·
Powerpoint
files: Segmentation.pptx, Simulation.pptx
·
Assignment 7 (Due Dec 7)
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
You
can get access to the book at: https://bookshelf.vitalsource.com/#/books/9780133583168
The username and passwd will be distributed in class.
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 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.
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 |
65% |
|
7 x Problem
Sets |
35% |
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