COMP-329:
Introduction to Computer-Integrated Surgery
Fall 2014
Course
Outline
This
course is designed for 3rd and 4th year life science and
generally non-computing and non-engineering students. The course is designed to
introduce you the concepts and some of the most relevant issues of
computer-integrated surgery; a field in the intersection of computer science,
electrical engineering, mechanical engineering, life sciences, and medicine.
Throughout the course, you will learn to ask questions and look for answers the
way clinical engineers study and build computer-integrated surgery systems. The
course will review underlying technologies, such as medical imaging, tracking,
navigation, treatment planning, surgical guidance and navigation techniques. We
will study the use of medical images for surgical guidance and review specific
challenges of ultrasound, X-ray, fluoroscopy, computed tomography and magnetic
resonance imaging. We will study concepts, methods, and clinical systems
introduced through series of applications that are currently in clinical use or
under development at various research institutions, including the Perk Lab (http://perk.cs.queensu.ca) at Queen’s University.
Prerequisites
4U MATH or
MATH-006*
Or
Instructor’s Approval
__________________________________________
ANNOUNCEMENTS
__________________________________________
COURSE DESCRIPTION
Instructor
Gabor Fichtinger, PhD
Professor and Cancer Care Ontario Research Chair
School of Computing, Queen’s University
Office: Goodwin Hall, Room 725
Homepage: www.cs.queensu.ca/~gabor
Email: gabor@cs.queensu.ca
ß PREFERRED WAY OF COMMUNICATION
Course Website
http://www.cs.queensu.ca/home/cisc330
Teaching Assistant
Sadly, we have no TA this year…
Class
Times & Location
Mon 11:30 – 13:00 Goodwin Hall 247
Thu 13:00 – 14:30 Goodwin Hall 247
Course
Schedule & Lecture Notes
Tue 10:00 – 11:30 (Goodwin
725)
Fri 10:00 – 11:30 (Goodwin
725)
Please always email me the day before you wish to see me in office hour.
Office hours are usually crowded, I want to make sure that you receive enough
time and attention.
I strongly encourage you to use the office hours for in-person
consultation, especially if you have questions or problems with materials in
class or with the homework assignments. I suggest you come to see me in the
posted office hours. Please always email me beforehand! If you miss me in
office, always send me an email note so that I know that you came to see me
(which shows that you care about your grade.) Generally, never be embarrassed
to ask questions. Asking questions and seeking help will always have a positive
impact on your grade. I consider this as an important gauge of your overall
interest and commitment. I want you to understand and learn the material, so
that I can reward you with a good grade.
Classes
The dominant format is classroom presentations, with as much discussion
as time permits. There may be occasional guest lecturers, presenting on
various topics of interest. Guest lecturers will be scheduled flexibly
depending upon their availability.
Class attendance is highly recommended, because lecture notes are mostly
without words and you will have to take notes. We will move fast in the
classroom and often cover material outside the course notes. Every assignment
will involve some details that are not in the course notes but will be
discussed in class. Students who tend to miss classes tend to do poorly in this
course.
Class
Notes
I will post on this website PDF copies of the power point presentations
shown in class. I often change the presentation in the last minute, in order to
adjust to the flow of the course.
The slides do not contain many words and sometimes no word at all. I
recommend that you download and/or print out the slides and take notes, either
electronically or manually. If you miss a class, you still may like to print
out the handouts for the following time, because lectures tend to be grouped by
themes, rather than by calendar. As there is no concise textbook for the
course, your notes will serve as primary reference in the assignments.
Lab Sessions
There will be two mandatory hands-on lab sessions to experiment with
image guided surgery navigation systems. Each session will take about 90
minutes to compete. The lab sessions will replace two cancelled class sessions.
You will perform image-guided needle placements interventions in non-biohazardous subjects (so called phantoms) that may contain
actual human body parts. (This is as close to cadaver trials as is gets in an
engineering establishment.)
You will not be required to prepare lab notes from the sessions and your
performance will not be graded. During the lab sessions, you will be asked to
participate in human performance studies that investigate the use and
effectiveness of novel surgical guidance techniques developed in the Perk Lab.
You will be given an informed consent form to describe the study and its
voluntary nature. Your participation in the study will help our research in the
Perk Lab (http://perk.cs.queensu.ca).
You can decline participation in the study, but you will have to show up for
your sessions.
The lab sessions will be scheduled individually and flexibly to fit your
schedule. The lab sessions are expected to be sometime in November / December
and they will be coordinated by Zsuzsanna Keri, MD (keri@cs.queensu.ca). Sometime in October
or early November I will instruct the class to email Dr. Keri to make
appointment for the lab sessions.
Assignments
Assignments involve problems pertinent to medical image computing and
computer-assisted surgical navigation.
The assignments do not include programming, though using software will
be considered a plus.
The assignments will be posted on this website, under Announcements.
Four assignments and one final project are planned.
There will be about two weeks (10 working days) for each assignment,
from posting date to submission date.
The final project will be posted in the last week of classes and it will
be due in the last week of the exam period.
The assignments and final project will take a fair bit of time (this is
an understatement). Do not leave them for the last day or two, when you will
discover that you have difficulties. Start on them early, size up the problem
and formulate a solid work plan. Come to office hours when you encounter
difficulties. Consultation will not only save you from a poor grade, but it
will also show genuine concern about your grade and will add positively to your
record.
I will try to adjust submission deadlines to avoid mass collision with
midterm exams. To this end, I urge you to consult with your classmates and
bring constructive suggestions to class to adjust our schedule.
Once the cut-off date and time are set, there will be no extension or
exception, unless you produce written evidence of a medical reason or other
extenuating circumstances.
There will be 5% per day penalty for late submission without cause. (For
example, if your submission is worth 90 points out of 100, but you are late by
one day, you will receive 85 points.)
You may be asked to come in for a “walk-through” of your submission, to
explain what, why and how you did in the assignment.
Submission
·
Submit the assignments
in PDF format, by email to me with copying the TA. You will receive an
acknowledgment of receipt. If you do not get one before or shortly after the
deadline, resend the submission with noting the original date of submission.
·
Do not wait with the
submission until the last minute.
·
When you submit
multiple files, order them and zip them together into a single file.
·
Use a file / folder
name that includes your full name and identifies the assignment, such as
“Lastname-Firstname-Assgn-1.gz”.
·
Your submission will
often include handwritten inserts, figures and math, which you should convert
into PDF and zip with the rest of the files.
·
Write your full name
and student number in the pages.
·
Number the pages.
Software components
o Work out your programs in MATLAB (unless specifically instructed
otherwise).
o Submit your code in MATLAB file format (m files).
o Include screen capture or some evidence that the code runs and produces
the results you claim.
o Include some README or instruction for running your code.
o Your code must be complete and self-contained.
o I and the TA must be able to run your assignment in a common MATLAB
environment. If you use special libraries, you must include those with your
source, with exact reference to the source where they came from.
o Include a proper header in each program file.
Notes on Integrity and
originality
o You can use any publicly available book, website, article, and
open-source software, and you must always fully reference the source.
o Any attempt to submit fake results will be penalized.
o I encourage you to study in groups, but I require independent work in
the submitted artifacts.
o If you brainstorm with another person, you must acknowledge this in your
submission.
o Do not share any part of the written assignment, including software
code, with anyone.
o You will be penalized if you copy someone else's work or allow your work
to be copied.
Tests
There will be none :-)
Midterm
Exam
There will be none :-)
Final
Exam
There will be none :-) The final project will replace it.
All components in this course will receive numerical percentage marks
and an overall percentage score will be calculated as the weighted average of
the scores from the components. The assignments will approximately weigh about
the same each and the final project will probably weigh a bit more. The weights
are not known exactly at this time, because the contents of the assignments and
project are undecided at this time and they will be adjusted to our progress
with the material.
If your percentage mark is on the borderline between two letter grades
(see chart below), I will consider overall diligence, interest and commitment,
progress, timeliness in submission, and participation in class discussions.
The final grade you receive will be derived by converting your numerical
mark to a letter grade, according to Grade Conversion Scale I received from the
Faculty of Arts and Science.
|
Grade |
Numerical Range |
|
A+ |
90-100 |
|
A |
85-89 |
|
A- |
80-84 |
|
B+ |
77-79 |
|
B |
73-76 |
|
B- |
70-72 |
|
C+ |
67-69 |
|
C |
63-66 |
|
C- |
60-62 |
|
D+ |
57-59 |
|
D |
53-56 |
|
D- |
50-52 |
|
F |
49 and below |
Academic
Integrity & Dishonesty
Queen's policy for Academic Integrity & Dishonesty will be enforced.
Academic Integrity is constituted by the five core fundamental values of
honesty, trust, fairness, respect and responsibility (see
www.academicintegrity.org). These values are central to the building, nurturing
and sustaining of an academic community in which all members of the community
will thrive. Adherence to the values expressed through academic integrity forms
a foundation for the "freedom of inquiry and exchange of ideas"
essential to the intellectual life of the University (see the Senate Report on
Principles and Priorities)
Students are responsible for familiarizing themselves with the regulations
concerning academic integrity and for ensuring that their assignments conform
to the principles of academic integrity. Information on academic integrity is
available in the Arts and Science Calendar (see Academic Regulation 1) on the
Faculty of Arts and Science website.
Departures from academic integrity include plagiarism, use of
unauthorized materials, facilitation, forgery and falsification, and are
antithetical to the development of an academic community at Queen's. Given the
seriousness of these matters, actions which contravene the regulation on
academic integrity carry sanctions that can range from a warning or the loss of
grades on an assignment to the failure of a course to a requirement to withdraw
from the university.
Specifically in this course, the following activities
are examples of violations of Academic Integrity:
·
Sharing a partial or complete solution to a marked assignment with
another student (not even after the submission deadline).
·
Looking at another student's partial or complete solution to a marked
assignment -- with or without their permission
·
Asking another person to write code or pseudo-code for you for a marked
assignment
·
Asking for help with a marked assignment from an online site
Statement on copyright for inclusion on all course
materials
The material on
this website, linked course notes, lectures and assignments is copyrighted and
is for the sole use of students registered in this course. The material on this
website may be downloaded for a registered student’s personal use, but shall
not be distributed or disseminated to anyone other than students registered in
this course. Failure to abide by these conditions is a breach of copyright, and
may also constitute a breach of academic integrity under the University Senate’s
Academic Integrity Policy Statement.
Recommended
Books
The books listed below are not mandatory, but I can highly recommend
reading them. They are available online and some in the campus bookstore.
- [Peters] Image-Guided Interventions:
Technology and Applications, by Terry Peters & Kevin Cleary (Eds.)
2008, ISBN: 978-0-387-73856-7, Springer.
- [Wolbarst] Looking
Within: How X-Ray, Ct, MRI, Ultrasound, and Other Medical Images Are
Created, and How They Help Physicians Save Lives by Anthony Brinton Wolbarst, Gordon Cook (Illustrator). Amazon price was
$15.96 when I checked the last time. This book is an easy, yet very useful
introduction to the fundamentals of the most popular medical imaging
devices. I recommend that you buy a personal copy.
- [Kevles] Naked to the
Bone: Medical Imaging in the Twentieth Century by Bettyann
Kevles Amazon price was $14.40 when I checked
the last time. The book provides rich historical and social background to
the evolution of medical imaging devices. It is plenty of fun to read and
not at all hard on your valet. I recommend that you buy a personal copy.
Please monitor this
site during the term, as I may post here some reprints that you may find useful
in the assignments.
Articles available from
http://perk.cs.queensu.ca under “Publications”
·
[Kazanzides]
Kazanzides P, Fichtinger G, Hager GD, Okamura AM, Whitcomb LL, Taylor RH.
Surgical and Interventional Robotics: Core Concepts, Technology, and Design. IEEE
Robot Autom Mag. 2008 Jun 1;15(2):122-130
·
[Fichtinger]
Fichtinger G, Kazanzides P, Okamura AM, Hager GD, Whitcomb LL, Taylor RH.
Surgical and Interventional Robotics: Part II: Surgical CAD-CAM Systems. IEEE
Robot Autom Mag. 2008 Sep 1;15(3):94-102.
·
[Hager]
Hager GD, Okamura AM, Kazanzides P, Whitcomb LL, Fichtinger G, Taylor RH.
Surgical and Interventional Robotics: Part III: Surgical Assistance Systems.
IEEE Robot Autom Mag. 2008 Dec 1;15(4):84-93.
Course Schedule & Lecture Notes
The schedule is subject to changes, depending on our
progress in the classroom. I WILL KEEP REVISING THE COURSE NOTES, PLEASE CHECK
THE LATEST VERSION SHORTLY BEFORE CLASS. 
|
SESSION |
CLASS SUBJECT |
|
COURSE NOTES |
OTHER REFERENCES |
|
[1]
Sep 8 Mon |
Introduction |
|
||
|
[2]
Sep 11 Thu |
Math primer (Vector geometry) Math primer (Transformations) |
HW1 on Math Library POSTED |
||
|
[3]
Sep 15 Mon |
Maggie Hess |
|
|
|
|
[4]
Sep 18 Thu |
CANCELLED
FOR MICCAI’14 |
|
|
|
|
[5]
Sep 22 Mon |
Coordinate
systems and transforms |
|
|
|
|
[6]
Sep 25 Thu |
Tracking
devices |
HW1 IN |
|
|
|
[7]
Sep 29 Mon |
Calibration |
HW2 on Surgical tool tracking POSTED |
|
|
|
[8]
Oct 1 Thu |
Calibration
(continued) |
|
|
|
|
[9]
Oct 6 Mon |
X-ray and Fluoroscopy |
|
X-ray
and Fluoroscopy |
|
|
[10] Oct 9 Thu |
Fluoroscopy
guided interventions |
|
|
|
|
[11] Oct 13 Mon |
CANCELLED FOR THGV |
HW2 IN HW3 on Fluoroscopy guidance POSTED |
|
|
|
[12]
Oct 16
Thu |
CT-guided
interventions |
|
|
|
|
[13]
Oct 20
Mon |
CT-guided
interventions |
|
|
|
|
[14]
Oct 23 Thu |
CT-guided
interventions (cont’d) |
|
|
|
|
[15]
Oct 27 Mon |
Radiosurgery |
|
|
|
|
[16]
Oct 30 Thu |
Radiosurgery
– Gamma Knife |
HW3 IN HW4 on Radiosurgery POSTED |
|
|
|
[17]
Nov 3 Mon |
Prostate
Cancer, Brachytherapy |
|
|
|
|
[18]
Nov 6 Thu |
Brachytherapy
(continued) |
|
|
|
|
[19]
Nov 10 Mon |
Tracked
ultrasound navigation |
|
|
|
|
[20]
Nov 13 Thu |
Interventional
robotics |
|
|
|
|
[21]
Nov 17
Mon |
Interventional
robotics |
HW4 IN |
|
NO ASSIGNMENT FROM THIS DAY FORWARD |
|
[22]
Nov 20 Thu |
Robot
calibration & registration |
Final Project on Interventional Robotics POSTED |
|
|
|
[23]
Oct 24 Mon |
Tele-manipulation,
haptics, DaVinci robot |
|
|
|
|
[24]
Nov 27 Thu |
Augmented
Reality |
|
|