BIOM5200 / BMG5200 / SYSC5304 / ELG5127 - Medical Image Processing
Mathematical models of image formation based on the image modality
and tissue properties. Linear models of image degradation and
reconstruction. Inverse problems and regularization for image
reconstruction. Image formation in Radiology, Computed Tomography,
Magnetic Resonance Imaging, Nuclear Medicine, Ultrasound,
Positron Emission Tomography, Electrical Impedance Tomography.
OCIECE and OCIBME graduate students.
Office: Minto 7040
Phone: +1-613-520-2600 x 8785
Office hours will be available by appointment.
Please email the instructor to organize a convenient time.
Times and Locations
Monday 11:30 - 13:00
Wednesday 11:30 - 13:00
There is no assigned text for the course.
Lectures will be taken from the following resources:
− Project proposal
− Midterm report
- Assignments will be submitted at the beginning
of class on the day indicated.
Work may be in English or French.
- While it will be accepted to do programming in any computer
language, I recommend
Access to Matlab is available from almost all PCs in the
graduate labs. For home use, you may
1) purchase the student version of Matlab,
2) use octave (free under the GNU GPL license).
Information on installing octave is
Proposal is 1-2 pages (double spaced). Include problem
description, proposed techniques, and references.
Report is a minimum of 5 pages (double spaced). Describe
project progress to date. Discuss any current challenges.
Presentations will be (≤10 minutes) in English.
Marks are based on technical content, clarity of
presentation, and ability to answer questions.
Apr. 2 − Apr. 4
The report will be 10−20 pages (double spaced) and written in
English or French. Include an introduction, methods, results and
discussion. Ensure that the report synthesizes and
discusses the material. Do not simply restate
Marks are based on the technical content, and clarity of its
- Students are encouraged to select projects of interest
or relevant to their studies. Projects can be
- A review of a technique or topic
- An analysis or critique of a technique
- A comparison between two techniques
- An implementation or simulation of a technique
- The following is a rough list of possible project
−Applications of CT
−Beam hardening and its effects in CT
−Specialized CT imaging systems
−Use of a specific contrast agent for CT
−Problems and limitations of CT for a specific application
−SPECT image reconstruction algorithms
−Detectors and technologies for PET
−Considerations for spatial resolution of PET
−Specialized PET imaging systems
−Considerations for 3D PET imaging
−Problems and limitations of PET for a specific application
−Design considerations for MRI electronics
−Design considerations for MRI signal processing
−Fast MRI: Electronics, Imaging, Applications, etc.
−Cardiac / Respiratory gated MRI
−Specialized MRI techniques: Echo planar imaging, etc.
−Other applications of NMR
−Physical limits to NMR resolution
−MRI of a non-water compound, ie. Xenon
−Electronics HW and signal processing for EIT
−Imaging algorithms for dynamic EIT
−Imaging algorithms for static EIT
−Problems and limitations of EIT for a specific application
−Ultrasound for 3D
−Optical flow techniques for ultrasound
−Electronics HW and signal processing for ultrasound
−Problems and limitations of EIT for a specific application
−Image processing techniques for enhanced visualization
−Medical image interpretation for specific application
−Multi-modality image fusion
−Calibration approaches for multimodality images
−Virtual Environments applied to medical imaging
−Automated image classification, search, archiving
−Applications of expert systems / AI for medical imaging
Exams (Midterm and Final)
- Midterm exam is Feb. 26 in class.
The instructions for the midterm are:
You have 80 miutes to complete this exam. The exam has
four questions; you are required to answer any three
of them. Each question is worth equal marks. This is a
closed book exam; however, you are permitted to bring one
(1) 8.5"×11" sheet of notes into the exam. You are
permitted to use a non-programmable calculator. You may
not communicate with anyone during the exam except the
- Final exam is Apr. 18, 1130−1300
- For all exams, you will be permitted a calculator and
one (1) 8.5" × 11"
paper sheet containing any information you choose (double sided).
- Late work = 20% off for first week.
- More than 1 week late = don't bother submitting without
- If you wish to do a single (larger) assignments,
assignment for two graduate courses, you
must obtain written permission from
all profs involved. Otherwise, you may
find yourself in a position of academic fraud.
- If you have a question about a mark you have received,
fill out, sign and submit
- Academic fraud will be taken very seriously.
Cooperation between students for assignments is expected and
encouraged, however, copying of another's work
is not. You should not be leaving a discussion with
copies of another student's work.
Please refer to Carleton Universities
on this subject.
One further note: the excuse of not being aware of
the university plagiarism policy is not acceptable.
Students with Disabilities
Students with disabilities requiring academic accommodations in this
course are encouraged to contact a coordinator at the Paul Menton Centre
for Students with Disabilities to complete the necessary letters of
accommodation. After registering with the PMC, make an appointment
to meet and discuss yours needs with me at least two weeks prior to
the first in-class test or CUTV midterm exam. This is necessary in
order to ensure sufficient time to make the necessary arrangements.
Please note the following deadlines for submitting completed forms to
the Paul Menton Centre: March 9th, 2007 for the Winter Term.
Introduction to medical imaging technology
Introduction to Medical Imaging
X-ray imaging. Computed Tomography.
Nuclear Medical Imaging, PET, SPECT
Algebraic Reconstruction Technique
Magnetic Resonance Imaging
The Basics of MRI
Notes: Inversion Recovery signal 180-90
at 180 pulse, s0= -[ 1-exp(-(TR-TI)/T1) ],
and s(t)= kρ[ 1- (1-s0)×exp(-t/T1)) ]
s(TI)= kρ[ 1- (1+(1-exp(-TR/T1)exp(TI/T1))exp(-TI/T1)) ]
= kρ[ 1- 2exp(-TR/T1) + exp(TI/T1))
Perception of images / Human Visual System
Representation of Images / Image Quality and information content
Human visual System
Study Break (No class)
Midterm Exam (in class)
For practice, here are the
The midterm reflects the approximately the first two
questions in the 2006 final.
Removal of Artefacts
− Wiener filters (in the Fourier and Matrix domain
− Histogram Transforms (page 3)
Code to implement histogram equalization:
m=min(im0(:));M=max(im0(:)); N=255; % or any large number
hv= conv2(hv, [.5,.5], 'valid'); %spread weights
im2=reshape( map(floor(im1)+1), size(im0) );
(Guest lecture by
Regions of Interest
Marr/Hildreth Edge Detection
Canny Edge Detection
Circular Hough Transform
Active contours (Snakes)
Analysis of Shape / Analysis of Texture
Texture and Applications
Project Reports due (before 16h30)
(or by email with paper copy to follow at exam)
Final Exam. 11h30−13h00 Loeb LA-B149
For practice, here are the
final exams, and
2007 midterm exam.
Note that the course content is significantly different from
previous years. Thus previous exams should be taken as an indication
of my style of exam writing.
- Introduction to various technologies from
Joseph Hornak, The Basics of MRI
Online resource, available at
(Introduction to MRI)
MRI safety (flying objects) [simplyphysics.com]
Ottawa Medical Physics Institute has
a series of interesting and relevant
- The Visible Human Project
- Browse the
sections from the Visible Human
- Interactive Visible Human
- 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.
- The Bristol Biomed image archive has several interesting
images [registration required]
- Physionet.org / Images
X-Ray CT views of living and extinct vertebrates.
- Unfortunately, I'm not aware on an online source for
raw medical image data. This in not surprising. Most vendors
won't let you see raw data because this will expose
the limits of the hardware design.
- Medical Imaging in Canada
Report from Canadian Institute for Health Information (CIHI).
- Online Computer vision books
- D.H. Hubel;
Eye Brain and Vision ,
Scientific American Library, 1988, ISBN 0-7167-5020-1.
- P. K.Kaiser;
The Joy of Visual Perception, Online book, 1996.
- A. 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
Notes (from previous years)
$Date: 2007-11-24 01:39:40 -0500 (Sat, 24 Nov 2007) $