585.704.81 - Principles of Medical Imaging

Expanded Course Description

Medical Imaging is undergoing a tremendous technological advances in last few years. It is one of the most important topic for a biomedical engineer. On the fundamental level, the imaging technique, the process and the art draws from some basic principles; primarily derived from physics of radiation and its interaction with biological matter. In this new, online course the students will focus on learning the fundamentals of major imaging methods and thus touch upon many branches of physics and engineering. With an emphasis on the physical principles behind modern medical imaging, the course will cover topics such as mathematical and physical foundations of imaging; image construction and interpretation; image quality and image processing. Individual modules will cover various imaging modalities to provide an advanced understanding of the physics of the signal and its interaction with biological tissue; image formation or reconstruction; modality specific issues for image quality; clinical applications; biological effects and safety. Final modules will briefly touch upon image analysis and describe applications for clinical diagnosis and/or treatment.

Course Structure

The course is divided into 14 modules. Each module will run for one week from Wednesday through Tuesday. In what follows, these days will be referred to as Day 1 (Wed) to Day 7 (Next Tue) respectively. The Modules can be accessed by clicking Course Modules on the left menu. A module will have several sections including the Overview, Content, Readings, Discussions, Quizzes and Assignments. Students are encouraged to preview all sections of the module before starting.

Students should regularly check the Calendar and Announcements for assignment Due Dates.

Course Topics

Medical Imaging Modalities
- Intro to Imaging
- X-rays Radiography
- X-rays CT
- MRI
- Nuclear Imaging (PET/SPECT)
- Ultrasound Imaging
- Intro to Image Processing: Registration/Segmentation

Course Goals

By the end of this course, you will be able to:

• Explain the underlying physical principles behind major medical imaging techniques
• Relate these to principles to major medical imaging protocols
• Apply these foundational principles to real world problems in diagnosis
• Apply the basic ideas learnt towards effective image processing
• Critique a medical imaging study from the standpoint of a physician
• Synthesize medical literature about specific pathologies or imaging techniques used at all levels of biomedical engineering – from bench to bedside
• Communicate via presentations, essays and reports the basic interdisciplinary concepts in imaging from an engineering standpoint.

Textbooks

Textbooks: Required

• Suetens, P. Fundamentals of Medical Imaging (2009, 2nd Ed, Cambridge University Press).
  ISBN-10: 0521519152
  ISBN-13: 978-0521519151
  Edition: 2
  
  
• Webb, A. Introduction to Biomedical Imaging (2002 1st Ed, Wiley-IEEE Press).
  ISBN-10: 0471237663
  ISBN-13: 978-0471237662
  Edition: 1
  
  

Textbooks: Optional

Additionally, any of the following texts may be useful for this course, especially if you find yourself struggling with specific skills. The instructor may use excerpts from these books about specific topics

1. Principles of Medical Imaging (1st Ed, 1992)
   Shung, K. Kirk, Michael Smith, and Benjamin MW Tsui. Principles of medical imaging. Academic Press, 1992.
   ISBN-10: 0126409706
   ISBN-13: 978-0126409703
   
   
2. Medical Imaging Signals and Systems (2nd Ed, 2014)
   Prince, Jerry L., and Jonathan M. Links. Medical imaging signals and systems. Upper Saddle River, NJ: Pearson Prentice Hall, 2014.
   ISBN-10: 0132145189
   ISBN-13: 978-0132145183
   
   
3. Medical Imaging Physics (4th Ed, 2002)
   Hendee, William R., and E. Russell Ritenour. Medical imaging physics. John Wiley & Sons, 2002.
   ISBN-10: 0471382264
   ISBN-13: 978-0471382263
   
   
4. The Essential Physics of Medical Imaging (3rd North American Ed, 2011)
   Bushberg, Jerrold T., and John M. Boone. The essential physics of medical imaging. Lippincott Williams & Wilkins, 2011.
   ISBN-10: 0781780578
   ISBN-13: 978-0781780575

Required Software

MATLAB is available for free for instructors and students through the myJHU portal. Please visit the portal, log in, and look for "Technology" on the left hand side of the page. From there, please click on "mySoftware," and then follow the link to access the Software Catalog. Under the Software Catalog, please click "Order Software" and search for MATLAB.

Student Coursework Requirements

Coursework Requirements

It is expected that each module will take approximately 7–10 hours of work per week to complete. Here is an approximate breakdown: Reading the assigned sections of the texts (approximately 2–3 hours per week) as well as some outside reading, listening to the audio annotated slide presentations (approximately 2–3 hours per week), and writing assignments and/or prepare presentations (approximately 3–4 hours per week).

There will be an end-of-the-term final test for this course. The test scores will be worth 40% of your grade. For more details on the test, please refer to the “Test Guide” document available under the ‘Syllabus & Course Info’ link on Black Board site for the course.

Apart from that, the course will consist of the following basic student requirements for successful completion:

1. Preparation and Participation (Quizzes, Discussions & Office Hours; 10% of final grade)

Quizzes (7% of Grade Points): There will be a graded 10-questions quiz every odd numbered week starting from week 1 (Weeks 1, 3, 5, 7, 9, 11, 13). These will be designed to check your preparation of required reading material and participation in reviewing video content etc. each quiz will be a 10-point quiz, with 7 quizzes amounting to be a total of 70 points. These will be then counted towards a total of 7% points in your final grade.

Discussion Forums & Office Hours (3% Grade Points): Each student is responsible for carefully reading all assigned material and being prepared for discussions online as well as live discussions during office hours. The majority of readings are from the course texts. Additional reading may be assigned to supplemental text readings. The grading system for this requirement will work as follows:

Your grade for module participation during office hours is your interaction (i.e., responding to classmate postings with thoughtful responses). In order to gain your full 3% points on this requirement, you are expected to attend a minimum of 6 office hour sessions with meaningful participation.

Just responding to a question is not sufficient; we want you to interact with your classmates. Be detailed in your responses to your classmates' postings. Feel free to discuss and agree or disagree with your classmates. Please ensure that your responses are civil and constructive.

The instructors will monitor discussions and will respond to some of the discussions as discussions are posted. In some instances, instructors will summarize the overall discussions and post the summary for the module.

Evaluation of preparation and participation is based on contribution to discussions.

Preparation and participation is evaluated by the following grading elements:

1. Timeliness (50%)
2. Critical Thinking (50%)

Preparation and participation is graded as follows:

2. Written Assignments (30% of Final Grade Calculation)

Assignments will include a mix of qualitative assignments (e.g. literature reviews, summaries), and/or quantitative problem sets. Include a cover sheet with your name and assignment identifier. Also include your name and a page number indicator (i.e., page x of y) on each page of your submissions. Each problem should have the problem statement, assumptions, computations, and conclusions/discussion delineated. All Figures and Tables should be captioned and labeled appropriately.

All written assignments will be due as per the calendar dates posted in the Course Calendar each week. Typically this is day 7 for each module, unless otherwise stated. Late submissions will be reduced by one letter grade for each day of lateness (No exceptions without prior coordination with the instructors).

If, after submitting a written assignment a student is not satisfied with the grade received, the student is encouraged to contact the instructors with a request to re-do. The re-do requests must be emailed to the instructors within 3 days after the grade is posted (inclusive of the day of posting). The approval is fully at the discretion of the instructors, with a deadline for resubmission pre-decided by them.

Qualitative assignments are evaluated by the following grading elements:

3. Student Presentations (20% of Final Grade; 10% presentation + 10% comments)

Each student will be required to present one or two “online presentations”  (depending on the class population) and address questions from the entire class towards 10% of his/her grade; PLUS s/he will be required to constructively post meaningful questions/comment on other student’s presentations towards another 10%.

There won’t be any presentation for weeks 1-2. During these weeks, the students will individually discuss with Dr. Maybhate about the possible topics and week of his/her seminar.

Weeks 3-12 will be open for signing up for a presentation, with 1 slot for each week. Students must sign up for their preferred week by the end of week 2 before the Module 3 starts. 

The topics could be anything of your personal choice that is related with the core topics in the course. It could be anything directly/indirectly related to topics covered until that week; any updates in technology; any sensor with its design/application or anything that excites you, as pre-approved by Dr. Maybhate.

Each student presentation will last for maximum 10-15 minutes each containing maximum 8-10 easily readable slides. The presentations will be in the form of Voice-over-PowerPoint videos, posted using VoiceThread.

VoiceThread tutorials about creating and sharing a presentation are available at https://jhu.voicethread.com/myvoice/#tutorials with JHU login required. After the presentation, the student will be asked to share the presentation and the slides with the entire class (PDF file). Please do NOT use commenting in VoiceThread. Commenting should be ONLY done on the provided discussion forum.

If you are not the presenter for that week, you are expected to view the presentation and post questions/comment etc. by the end of Day 6, which the presenter will address by the end of Day 7. The presentation and the commenting will be graded as follows:

Grading Policy

Student assignments are due according to the dates in the Calendar and Assignments items in the corresponding modules. Dr. Maybhate will post grades one week after assignment due dates.

I generally do not directly grade spelling and grammar. However, egregious violations of the rules of the English language will be noted without comment. Consistently poor performance in either spelling or grammar is taken as an indication of poor written communication ability that may detract from your grade.

A grade of A indicates achievement of consistent excellence and distinction throughout the course—that is, conspicuous excellence in all aspects of assignments and discussion in every week.

A grade of B indicates work that meets all course requirements on a level appropriate for graduate academic work. These criteria apply to both undergraduates and graduate students taking the course.

WSE/EP uses a signed (+/-) grading system (see “Grading System”, Graduate Programs catalog). The following grades are used for the courses: A+, A, A– (excellent), B+, B, B– (good), C+,C,C- (unsatisfactory), D (poor), F(failure), I (incomplete), W (official withdrawal), and AU (audit). The last two are not assigned by instructors.

This course will use the same grading scheme, with the following breakdown:

• o 100–98 = A+; 97–94 = A; 93 –90 = A−
• o 89–87 = B+; 86–83 = B; 82–80 = B−;
• o 79–77 = C+; 76-73 = C; 72-70 = C-;
• o 69-67 = D+, 66-63 = D;
• o <63 = F.

Final grades will be determined by the following weighting distribution

Academic Policies

Deadlines for Adding, Dropping and Withdrawing from Courses

Students may add a course up to one week after the start of the term for that particular course. Students may drop courses according to the drop deadlines outlined in the EP academic calendar (https://ep.jhu.edu/student-services/academic-calendar/). Between the 6th week of the class and prior to the final withdrawal deadline, a student may withdraw from a course with a W on their academic record. A record of the course will remain on the academic record with a W appearing in the grade column to indicate that the student registered and withdrew from the course.

Academic Misconduct Policy

All students are required to read, know, and comply with the Johns Hopkins University Krieger School of Arts and Sciences (KSAS) / Whiting School of Engineering (WSE) Procedures for Handling Allegations of Misconduct by Full-Time and Part-Time Graduate Students.

This policy prohibits academic misconduct, including but not limited to the following: cheating or facilitating cheating; plagiarism; reuse of assignments; unauthorized collaboration; alteration of graded assignments; and unfair competition. Course materials (old assignments, texts, or examinations, etc.) should not be shared unless authorized by the course instructor. Any questions related to this policy should be directed to EP’s academic integrity officer at ep-academic-integrity@jhu.edu.

Students with Disabilities - Accommodations and Accessibility

Johns Hopkins University values diversity and inclusion. We are committed to providing welcoming, equitable, and accessible educational experiences for all students. Students with disabilities (including those with psychological conditions, medical conditions and temporary disabilities) can request accommodations for this course by providing an Accommodation Letter issued by Student Disability Services (SDS). Please request accommodations for this course as early as possible to provide time for effective communication and arrangements.

For further information or to start the process of requesting accommodations, please contact Student Disability Services at Engineering for Professionals, ep-disability-svcs@jhu.edu.

Student Conduct Code

The fundamental purpose of the JHU regulation of student conduct is to promote and to protect the health, safety, welfare, property, and rights of all members of the University community as well as to promote the orderly operation of the University and to safeguard its property and facilities. As members of the University community, students accept certain responsibilities which support the educational mission and create an environment in which all students are afforded the same opportunity to succeed academically. 

For a full description of the code please visit the following website: https://studentaffairs.jhu.edu/policies-guidelines/student-code/

Classroom Climate

JHU is committed to creating a classroom environment that values the diversity of experiences and perspectives that all students bring. Everyone has the right to be treated with dignity and respect. Fostering an inclusive climate is important. Research and experience show that students who interact with peers who are different from themselves learn new things and experience tangible educational outcomes. At no time in this learning process should someone be singled out or treated unequally on the basis of any seen or unseen part of their identity. 
 
If you have concerns in this course about harassment, discrimination, or any unequal treatment, or if you seek accommodations or resources, please reach out to the course instructor directly. Reporting will never impact your course grade. You may also share concerns with your program chair, the Assistant Dean for Diversity and Inclusion, or the Office of Institutional Equity. In handling reports, people will protect your privacy as much as possible, but faculty and staff are required to officially report information for some cases (e.g. sexual harassment).

Course Auditing

When a student enrolls in an EP course with “audit” status, the student must reach an understanding with the instructor as to what is required to earn the “audit.” If the student does not meet those expectations, the instructor must notify the EP Registration Team [EP-Registration@exchange.johnshopkins.edu] in order for the student to be retroactively dropped or withdrawn from the course (depending on when the "audit" was requested and in accordance with EP registration deadlines). All lecture content will remain accessible to auditing students, but access to all other course material is left to the discretion of the instructor.