CISC-472: Medical Informatics

 

Winter 2016

 

Course Outline

 

This course is designed for 3rd and 4th year biomedical computing students and  it is mandatory in the Biomedical Computing Honor’s Program at the Queen’s School of Computing.  This course is a continuation of CISC-330 Computer Integrated Surgery, a subject in the intersection of computer science, engineering, medical physics, life sciences and medicine. We will study concepts, methods, component technologies and clinical systems that are currently in clinical use or development at various research institutions including Queen’s.  To see the detailed contents of the course click at CISC-472-Contents .pdf.

 

Prerequisite

CISC-330* - Please note that this prerequisite cannot be waived.

 

__________________________________________­­­­­­­­­­­­

ANNOUNCEMENTS image001 

 

Final Project is posted – Image Processing, Project Data, Due April 18, 09:00AM

 

Assignment 3 is posted – Transrectal Robot Navigation, Due March 18. 09:00AM

 

Assignment 2 is posted – Stereotactic Targeting, Due Feb 23. 09:00AM

 

Assignment 1 is posted – Marker Registration, Due Feb 3. 09:00AM

 

__________________________________________

 

COURSE DESCRIPTION

 

Instructor

Gabor Fichtinger, PhD

Professor and Cancer Care Ontario Research Chair

School of Computing, Queen’s University

 

Office: Goodwin 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/cisc472

 

Teaching Assistant

TA for CMPE 472 cohort

Amani Ibrahim (9ai15@queensu.ca), MSc Candidate    

Office hours: Monday 11:30 - 2:30 and Wednesday 10:00 - 12:00.

(Email by 4pm the day before, indicate time, and question/subject to be discussed.

Office: Goodwin 757 (for individual) or Goodwin 747 (for group)

 

Grader

Kyle Sunderland (1krs1@queensu.ca), MSc Candidate    

            Please note that Kyle will assist in grading and will not hold regular office hours.

 

Class Times & Location

Tuesday          11:30 – 13:00  Mc E202

Friday             13:00 – 14:30  Mc E202

 

Office Hours

Tue 09:30 – 11:00, Goodwin 747, Perk Lab conf. room

Fri 11:00 – 12:30, Goodwin 747, Perk Lab conf. room

 

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. Please always email me the day before you wish to see me in office hour. Office hours are often crowded, I want to make sure that you receive sufficient time and attention. When you arrive and I am not in in the Perk Lab conference room, please find me in Goodwin 725, ask Perk Lab members to find me. If you do not find me for some reason, send me an email note so that I know that you came to see me.

 

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. When I must be away for some reason (conference, etc.) I will arrange for guest lectures if possible, instead of cancelling classes or setting makeup classes.

 

Class attendance is strongly 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 fall behind quickly tend to do poorly in this course.

 

Course Notes

I will post on this website PDF copies of the power point presentations shown in class. I sometimes change the presentation in the last minute, in order to adjust to the flow of the course. Slides do not contain many words and sometimes no words 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.

 

Assignments & Project

The assignments will involve problems pertinent to medical image computing and computer-assisted surgery. The assignments will be posted on this website, under Announcements above. Each assignment will include concept, software development, testing and analysis elements.

 

Four assignments and one final project are planned. The assignments are due in the sessional period. There will be about two weeks for each, from posting date to submission date.  The Final Project will be due in the exam period, with a somewhat longer time to complete. The assignments and project will take a fair bit of time (this is an understatement). Do not leave them for the last few days, 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 individual extension, unless you produce written evidence of a medical reason or other extenuating circumstances.

 

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 the TA with copy to me. 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.

·         When you submit multiple files, order them and zip them together into a single file.

·         Use a file name “Lastname-Firstname-Assgn-x.gz” to indicate your identity.

·         Your submission will often include handwritten inserts, figures and math – scan these into PDF and zip it with the rest of the submission; number the pages sensibly.

·         Write your full name and student number in the submission.

·         Software components

·         Work out your programs in MATLAB.

·         Submit your code in MATLAB file format (m files).

·         Include screen capture or some evidence that the code runs and produces the results you claim.

·         Include some README or instruction for running your code.

·         Your code must be complete and self-contained.

·         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.

·         You must include a proper header in each program file and for each routine; you must follow good software practices you learned in your other courses – this does count in your marks.

 

Notes on Integrity and originality

·         You can use any publicly available book, website, article, and open-source software unless otherwise instructed.

·         You must always fully reference any external source.

·         Any attempt to submit fake results will be penalized.

·         I encourage you to study and brainstorm in groups, but independent work is required in the submitted material.

·         If you brainstorm with another person, you must acknowledge this in your submission.

·         Do not share any part of the written assignment, including software code or pseudo code, with anyone.

·         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 :-)

 

Grading

Each component will receive numerical grade on the 0–100 scale, from which an overall numerical score will be calculated as the weighted average. Typically, all components weigh the same. (The exact weights are not known at this time, because the assignments and project may be adjusted to our progress with the material.) 

 

The final letter grade will be computed by converting the numerical grade to a letter grade by using conversion algorithm mandated by the Queen’s Faculty of Arts and Science, published at the address below:

http://www.queensu.ca/artsci/sites/default/files/grading_policy.pdf.

 

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.

 

The following activities are some 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.

 

 

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 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 – WORK IN PROGRESS

The schedule is subject to changes, depending on our progress in the classroom. I WILL KEEP REVISING THE COURSE SCGHESULE NOTES, PLEASE CHECK THE LATEST VERSION SHORTLY BEFORE CLASS.

 

SESSION

CLASS SUBJECT

NOTES

COURSE NOTES

[1]     Jan 5  Tue    

Introduction

Refresher from CISC 330

 

Part 1: Geometry

Part 2: Transforms

[2]     Jan 8  Fri    

Refresher from CISC 330

 

 

[3]     Jan 12  Tue    

Marker registration (point markers)

 

 

[4]     Jan 15  Fri    

Marker registration (point objects)

 

Rigid Registration

Arun’s Paper

[5]     Jan 19  Tue    

Medical Images (modalities, representations, DICOM)

Jan 20 HW1 posted

 

[6]     Jan 22  Fri    

Image Filters

(Thresholding, histograms, window/level)

 

[7]     Jan 26  Tue    

 

 

 

[8]     Jan 29  Fri    

 

 

[9]     Feb 2  Tue    

HW1 DUE Feb 3

 

[10] Feb 5  Fri    

 

 

[11] Feb 9  Tue     

 

Percutaneous Robots

[12] Feb 12  Fri    

 

MRI Prostate Robot

[13] Feb 16  Tue    

READING WEEK – NO CLASS

 

[14] Feb5  19 Fri    

READING WEEK – NO CLASS

 

[15] Feb 23  Tue    

Anatomical Segmentation

(Manual methods)

HW2 DUE Feb 23

 

[16] Feb 26  Fri    

Robot  kinematics

 

 

[17] Mar  1 Tue    

CANCELLED

 

 

[18] Mar 4  Fri    

Free discussion

 

 

[19] Mar  8 Tue    

Segmentation and model reconstruction

Segmentation basics

[20] Mar 11  Fri    

Segmentation and model reconstruction

 

 

[21] Mar  15 Tue    

Segmentation and model reconstruction

 

 

[22] Mar 18  Fri    

Image registration (workflow, optimization, similarity metrics)

HW4 IN

Surface registration

[23] Mar  22 Tue    

 

 

[24] Mar 25  Fri    

 

 

[25] Mar  29 Tue    

GOOD FRIDAY – NO CLASS

 

 

[26] Apr 1  Fri    

Project Consultation (Kyle Sunderland)