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 ( at Queen’s University.



4U MATH or MATH-006*

Or Instructor’s Approval











Gabor Fichtinger, PhD

Professor and Cancer Care Ontario Research Chair

School of Computing, Queen’s University


Office: Goodwin Hall, Room 725




Course Website


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

            CLICK HERE


Office Hours

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.



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 ( 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 ( Sometime in October or early November I will instruct the class to email Dr. Keri to make appointment for the lab sessions.



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.



·         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.



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.



Numerical Range


























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 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.





Recommended Articles

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 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. Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: Description: C:\ERC\QUEENS\TEACHING\CISC330\index_files - Copy\image001.gif







[1]     Sep 8      Mon



Introduction to CIS

[2]     Sep 11   Thu

Math primer (Vector geometry)

Math primer (Transformations)

HW1 on

Math Library


Math-1 (Vectors & Lines)

Math-2 (Matrices & Transformations)

Math Abundance

[3]     Sep 15   Mon

Maggie Hess




[4]     Sep 18   Thu




[5]     Sep 22   Mon

Coordinate systems and transforms




[6]     Sep  25   Thu

Tracking devices 




[7]     Sep 29    Mon


HW2 on

Surgical tool tracking




[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



HW3 on

Fluoroscopy guidance




[12]  Oct  16  Thu

CT-guided interventions


CT Guidance


[13]  Oct  20   Mon

CT-guided interventions





[14]  Oct 23    Thu

CT-guided interventions (cont’d)




[15]  Oct 27    Mon





[16]  Oct 30     Thu

Radiosurgery – Gamma Knife


HW4 on Radiosurgery




[17]  Nov 3    Mon

Prostate Cancer, Brachytherapy


Prostate Cancer Intro

Prostate Brachytherapy


[18]  Nov 6   Thu

Brachytherapy (continued)



[19]  Nov 10   Mon

Tracked ultrasound navigation



[20]  Nov 13   Thu

Interventional robotics


Robotic Prostate Interventions


[21]   Nov 17   Mon

Interventional robotics




[22]  Nov 20   Thu

Robot calibration & registration

Final Project on

Interventional Robotics




[23]  Oct 24    Mon

Tele-manipulation, haptics, DaVinci robot




[24]  Nov 27  Thu

Augmented Reality