COMP-230: Introduction to Computer Integrated Surgery
Fall 2009
__________________________________________
COURSE ANNOUNCEMENTS 
Office hours Tuesday
8:30 am – 10:00, Goodwin 725
__________________________________________
HOMEWORK ASSIGNMENTS
HW-1 is posted HERE.
HW-2 is posted HERE.
HW-2 is coming…
__________________________________________
_______________________________________________________________
COURSE DESCRIPTION
Instructor
Gabor Fichtinger, Ph.D.,
Associate Professor
School of Computing,
Goodwin Hall 725
Homepage: www.cs.queensu.ca/~gabor
Phone: (613) 533-3258 ß I DO NOT
CHECK OFFICE VOICEMAIL
Email: gabor@cs.queensu.caß PREFERRED
WAY OF COMMUNICATION
Course Website:
http://www.cs.queensu.ca/home/comp230
Teaching Assistant:
Alexandra
(Sacha) Pompeu-Robinson
Email: sacharobinson@gmail.com
Phone: (613) 533-6000 Ext. 32797
Class Times & Location
Monday 1:00 - 2:30, BIO
1120
Wednesday 11:30 - 1:00, BIO 1120
Course Schedule & Lecture Notes
Office Hours
GF: Tuesday 8:30 am – 10:00,
Goodwin 725
TA: BY APPOINTMENT, email sacharobinson@gmail.com
I strongly encourage you to use
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 or the TA in the posted office hours.
Always email me beforehand! If you miss me in office, always leave an
email note so that I know that you came to see me. Generally, never be shy or 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 learn and understand the material, so that I can
reward you with a good grade.
Prerequisites
4U MATH or MATH-006*
Or Instructor’s Approval
Course Outline
This course is designed to introduce
you the concepts and some of the most relevant issues of computer-integrated
surgery (CIS). CIS is 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 engineers study and build CIS
systems. The course will review underlying technologies, such as medical image
processing (segmentation, registration, and statistical atlases), optimization
schemes, and error estimation and propagation methods. Surgical guidance and
navigation techniques will be discussed, covering medical robotics, passive
restraints, augmented reality, and navigation systems. We will study the use of
medical images for surgical guidance and review specific technical challenges
of ultrasound (US), fluoroscopy, computed tomography (CT), magnetic resonance
imaging (MRI), and nuclear medicine (PET, SPECT, etc.) We will emphasize
on concepts and systems introduced through series of applications that are
currently in clinical use or under development at various research
institutions, including Queen’s University.
Classes
The dominant format is classroom
presentations, with a lot of discussion. There may be several guest
lecturers, presenting various topics of interest. Guest lecturers will be
scheduled flexibly, depending upon their availability. I will try to schedule
guest lectures when I am away.
Although I will not register
attendance, it will be used as one of the metrics of your commitment to
achieving a good grade. Class attendance is highly recommended, because lecture
handouts do not contain a lot of words, will move fast and also cover material
outside the notes. All said, if you miss classes, you will stay behind.
Class Notes
I will post PDF copies of the power
point presentations shown in class HERE. I will also
print a hard copy and distribute them in class. The slides have only a few
words. You will have to take notes into these printouts. If you miss a class,
make sure you print out the handouts for the next time. As there is no
textbook, your notes will serve as primary reference in studying for the exams.
This is one more reason for you not to miss classes. Do not print out notes
much in advance, because they always change until almost the last minute.
Lab Session
We plan an optional hands-on
lab component to experiment with an augmented reality surgical guidance system
called Perk Station. Due to the limited availability of the Perk
Station and lab assistant, participation in the lab will not be mandatory.
Nonetheless, 3 hours or longer successful participation in the lab will yield a
bonus. Students will perform augmented
reality and laser guided needle placements in non-biohazardous subjects (so
called phantoms) that contain actual human body parts. (This is as close to cadaver trials as we can
push it in an engineering establishment.)
The lab will be open flexibly in afternoon and evening hours. There will be more info about the lab
sessions during the semester. The lab will count as an “assignment” and your
average grade will be calculated from one more data point. As almost everybody
who completes the lab receives an ‘A’ for it, you can use this as a booster to
your overall grade.
Assignments
Homework assignments will involve
problems pertinent to medical image processing and surgical navigation. No
computer programming will be necessary or required to complete the assignment.
However, solving the homework with the use of computer programming would be a
plus (in form of bonus points) and thus it will reflect favorably in your
grade. The simple rules:
·
I
only accept typed & printed homeworks. Your work may include hand-written
inserts for math.
·
Always
staple your work. Paperclip is not secure enough.
·
I
encourage you to study in groups, but I require independent work in the
assignments.
·
If
you brainstorm with another student, you must acknowledge his/her name in your
assignment.
·
You
will be severely penalized if you copy someone else's work or allow your work
to be copied.
·
Any
attempt to fake results will be severely penalized.
Always remember to present your
general approach and solution carefully (using unknowns, parametric equations,
etc.) Once the general approach is clear and well explained, plug specific
values into the equations to calculate the results. You can collect plenty of points
for a correct generic solution, numerical mistakes (unless otherwise important)
will not be judged harshly. Always
examine your results and always conduct a “sanity check” whether the results
make sense and they turn out to be in the range where they were supposed to
fall. If you really want to impress me
(and I know you want to do so) then always estimate the results before
you solve the problem numerically. This will demonstrate to me that you really
“own” the problem and have it under control.
Assignments will take a fair bit of
time. Do not leave the homework for the last day or days, when you will
discover that you have difficulties. Instead, come to the office hours and ask
for consultation. This will not only save you from a poor grade, but will show
your concern about the grade and will add positively to your record. The
assignments will be posted on the course’s home page.
I tend to be flexible in setting the
deadline dates. We will determine the upcoming deadline sensibly in class and
then I will post it here on the website. Therefore, I urge you to with your
classmates beforehand and bring constructive suggestion to class. This will be
your opportunity to shape your schedule dynamically. But remember: you must
negotiate with me as a group. Once we
set the cut-off date and time, there will be no exception. There will be 5
points per day late submission penalty.
If your homework is worth 80 points out of 100, but you are late by one
day, you receive only 75 points. You must email the TA about late submission,
because otherwise the drop box will not be checked and you will accumulate more
late submission penalty. Your TA has been instructed to acknowledge the
reception from any note from you in email.
You will have plenty of time to
complete the assignments. Deadlines, therefore, will have to be enforced. You
must make sure that your paper is turned in for you by the deadline. There will
be a drop box for the assignments in Goodwin Hall 2nd Floor. If you know that you will be late, notify me
and the TA in email well in advance and explain your situation.
I plan to give you 5 assignments.
(There may be fewer, depending how we progress with the material.)
Exams
There will
be one midterm exam and final exam. If you know that you will miss the test, then you have to
discuss that with me in advance: provide sufficient reasons and obtain my
explicit permission. If you miss the test for medical reasons, I require an
official medical record. Failing these conditions, there will be no make-up for
a missed test.
The Midterm Exam will be
administered in class, on Nov 2, when I will be out of town. The final exam
administered by the University.
Your grade will be calculated as the
weighted average of the scores from the assignments and exams. Of the total
100%, the assignments are worth ~60%, the midterm is ~15%, and final is ~25%.
This is approximate at this point, because the number of assignments and
contents may change. If your mark is on the borderline, I will consider your
overall diligence, interest and commitment, etc. Some factors to be considered:
class attendance, participation in class discussions, elective lab, and above
all: coming to office hours and consultation.
You will notice that in any given
assignment or exam, the total points will add up to less than 100, to about 95
or so. This means that if you do everything that the assignment/problem
demands, then you will get leas than 100 (about 95 or so.) In order to receive a higher score, you will
have to do more than it is required by the text of the assignment. I will not tell you how you can get the extra
points – this you must figure out yourself, but there always be ways to get
bonus points. You may think about alternative solutions or high-quality
computer program. (As you remember, no programming will be required in the
class, but if you generate good code, then I will reward you with bonus
points.)
Academic Dishonesty
Queen's policy for Academic
Dishonesty (http://www.queensu.ca/secretariat/senate/policies/acaddish.html) 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 at http://www.queensu.ca/secretariat/senate/policies/princpri/
)
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 (Regulation 1.), on the
Arts and Science website at
http://www.queensu.ca/calendars/artsci/Regulation_1____Academic_Integrity.html.
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.
Recommended Books:
None of the books below is
mandatory, but I can highly recommend them.
·
[Peters]
Image-Guided Interventions: Technology and Applications, by
·
[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.
·
Selected
readings and references are linked to the course time table below.
Course Schedule & Links to
I WILL KEEP REVISING THE
COURSE NOTES, THEY WILL CHANGE RIGHT UNTIL CLASS
|
SESSION |
CLASS SUBJECT |
|
COURSE NOTES |
OTHER REFERENCES |
|
[1]
Sep 14 Mon |
Course
info CIS
Intro |
|
|
Peters
Ch9 |
|
[2]
Sep 16 Wed |
X-ray |
|
Peters
Ch9 |
|
|
[3]
Sep 21 Mon |
Math primer – vectors & lines Fluoroscopy
& Cardiac imaging Dr.
Pascal Fallavollita |
GF AWAY HW1 out (Basic math) |
Math Abundance Peters Ch9 |
|
|
[4]
Sep 23 Wed |
Intra-vascular interventions (coils,
stents, clips, etc.) Guest:
Dr. Pascal Fallavollita |
GF AWAY |
TO BE POSTED |
Peters
Ch9 |
|
[5]
Sep 28 Mon |
Fluoroscopy
& CT |
|
|
|
|
[6]
Sep 30 Wed |
Biplane
fluoroscopy target reconstruction |
HW1 in HW2 out (Biplane
fluoro) |
|
|
|
[7]
Oct 5 Mon |
Cardiac Arrhythmia
Ablation Guest: Dr. Pascal
Fallavollita |
GF AWAY |
|
|
|
[8]
Oct 7 Wed |
Cancer
Intro |
|
Peters
Ch9 |
|
|
[9]
Oct 12 Mon |
THANKSGIVING,
NO CLASS |
|
|
|
|
[10] Oct
14 Wed |
CT-guided
interventions – AR |
|
|
Peters
Ch2 |
|
[11] Oct 19 Mon |
Tracking
devices |
|
Peters
Ch6, Ch7 |
|
|
[12]
Oct 21 Wed |
Tracking
devices |
|
|
Peters
Ch2 Peters
Ch13 |
|
[13]
Oct 26 Mon |
Tracked
navigation systems |
HW3 out (Pointer
calibration) |
Peters
Ch9 |
|
|
[1]
Oct 28 Wed |
Percutaneous
Robots |
|
||
|
[2]
Nov 2 Mon |
MIDTERM EXAM – IN CLASS |
GF AWAY |
|
|
|
[3]
Nov 4 Wed |
Radiosurgery |
HW4 out
(Stereotactic) |
Peters
Ch16 |
|
|
[4]
Nov 9 Mon |
Radiation
Oncology |
|
Peters
Ch17 |
|
|
[5]
Nov 11 Wed |
Radiation
Oncology |
|
Peters
Ch17 |
|
|
[6]
Nov 16 Mon |
Prostate
cancer Brachytherapy
|
HW5 out
(Brachytherapy) |
Peters
Ch15 |
|
|
[7]
Nov 17 Wed |
Brachytherapy |
|
Peters
Ch15 |
|
|
[8]
Nov 23
Mon |
Magnetic
Resonance Imaging MRI-guided
interventions |
|
TO BE POSTED |
Peters
Ch14 |
|
[9]
Nov 29 Wed |
Orthopedic
Surgery Robodoc |
|
Peters
Ch12 |
|
|
[10]
Nov 30 Mon |
Laparoscopy Telesurgery
robots |
Study for exam |
|
|
|
[11]
Dec 2 Wed |
Surgical
Assistant Systems |
study for exam |
TO BE POSTED |