585.741.81 - MR Imaging in Medicine

Expanded Course Description

Prerequisites/Co-requisites

585.409—Mathematical Methods for Applied Biomedical Engineering OR 535.441—Mathematical Methods for Engineers OR a written permission from the instructor.

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 (Wen) to Day 7 (next Tue) respectively. The Modules can be accessed by clicking Course Modules on the left menu. A module can have several sections including the Overview, Content, Readings, Discussions, 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

Basic Physics of Magnetic Resonance

• - Nuclear spins
• - Magnetization
• - Precession

Principles of MR Imaging – Part I

• - Rotating versus stationary frame of reference
• - Radiofrequency pulse and Resonance
• - Block equation

Principles of MR Imaging – Part II

• - Relaxation (T1, T2, T2*)
• - Signal detection
• - Free induction decay
• - Spin and gradient echoes

MR imaging Spatial Encoding

• - Selective excitation
• - Frequency encoding
• - Phase encoding
• - K-space
• - Sampling

MR image contrast

• - T1, T2, proton density
• - Spin echo
• - Gradient echo
• - Inversion recovery

Diffusion MRI – Part I

• - Acquisition gradients
• - Diffusion weighted imaging
• - Diffusion tensor imaging

Diffusion MRI – Part II

• - Practical considerations
• - Diffusion indices (contrast)
• - Fiber tracking
• - Higher order models

FMRI  - Background & Theory

FMRI – Acquisition Methods

FMRI - Preprocessing

FMRI – Applications / Example Studies

Cardiovascular MRI – Part I

• - Black blood versus bright blood imaging
• - Cardiac motion (still imaging versus cine imaging)
• - Dealing with respiratory motion (Fast imaging)

Cardiovascular MRI – Part II

• - Selective tissue saturation
• - Preparatory pulses
• - Late enhanced imaging
• - Coronary imaging
• - Velocity encoding
• - Perfusion imaging
• - Tagged MRI

MRI noise, resolution, general artifacts

Course Goals

To identify and explain basic principles involved in MRI signal generation and image construction. To apply this understanding to conduct medical research using structural and functional neuro and cardiovascular MR imaging and to identify and remedy pitfalls associated with these techniques.

Course Learning Outcomes (CLOs)

• State & explain physical principles behind magnetic resonance (MR) signal generation and detection.
• Describe pulse excitation phenomenon and Identify characteristics of generated MR signals.
• Discuss principals of spatial localization of MR signal and techniques used to construct MR images.
• Discuss concept of MR image contrast and approaches to manipulate this contrast.
• Identify different MR image artifacts and to propose potential remedies to rectify the problem.
• Characterize the micro-structure of tissue using diffusion MR measurements.
• Apply post-processing techniques to generate diffusion indices at each image voxel.
• Describe structural and functional analysis of cardiovascular disorders with MR based techniques.
• Apply post-processing techniques to quantify cardiac function using tagged MRI.

Textbooks

Required

1. Z.-P. Liang, P.C. Lauterbur; Principals of Magnetic Resonance Imaging: A Signal Processing Perspective, Wiley-IEEE Press; 1 edition (November 1, 1999). ISBN-13: 978-0780347236. ISBN-10: 0780347234.

2. Mori, S., & Tournier, J. D. (2013). Introduction to Diffusion Tensor Imaging: And Higher Order Models. Academic Press. ISBN-13: 978-0123983985. ISBN-10: 0123983983

   1. Available Free online from JHU library: https://catalyst.library.jhu.edu/catalog/bib_4684420.

3. Plein, S., Greenwood, J., & Ridgway, J. P. (2011). Cardiovascular MR manual. Springer Science & Business Media. ASIN: B011DC4CCU.

   1. Available Free online from JHU library: https://catalyst.library.jhu.edu/catalog/bib_4684116.

Optional

R.W. Brown, Y.-C. N. Cheng, E. M. Haacke, M. R. Thompson, R. Venkatesan; Magnetic Resonance Imaging: Physical Principles and Sequence Design, Wiley-Blackwell; 2 ed. (June 23, 2014).

ISBN-13: 978-0471720850
ISBN-10: 0471720852

Required Software

MATLAB

Freely accessible from Hopkins: https://ep.jhu.edu/faculty-staff/getting-started/software-and-hardware-purchases-and-downloads/

For further help needed, students should refer to Help & Support on the left menu for a general listing of all the course technical requirements.

Student Coursework Requirements

It is expected that each module will take approximately 10–13 hours per week to complete. Here is an approximate breakdown: Reading the assigned texts or outside reading (approximately 3–4 hours per week), listening to the audio annotated slide presentations (approximately 3–4 hours per week), and writing assignments (approximately 4–5 hours per week).

There is one single final test for this course at the end of Module 14; covering all the topics. This final test will count for 20% of total grade. The details for the test format, timing etc. will be shared later via a separate document.

Apart from that the course will require following three basic student activities for successful completion:

Preparation and Participation (Discussions/Debates; 10% of final grade)

Each student is responsible for carefully reading all assigned material and being prepared for discussion. Additional reading maybe assigned to supplemental text readings. The grading system for this requirement will work as follows:

Post your initial response to the discussion questions by creating a new thread by the due date for that module week. Posting the new thread as a response to the discussion question is part one of your grade for module discussions (i.e., Timeliness).

Part two of your grade for module discussion is your interaction (i.e., responding to classmate postings with thoughtful responses) with at least two classmates (i.e., Critical Thinking). This activity could go beyond the module week, but you should engage in this interaction by the due dates.

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

Instructors will monitor module 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: 

Homework 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 xof 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 end of the day 7 for each module, unless otherwise stated.

Late submission will incur a penalty of 10% per day. For example, if your score was 95% on an assignment or project, your grade would be reduced to 85% if submitted 0 to 24 hours after the deadline and 75% if submitted 24 to 48 hours after the deadline (no exceptions without prior coordination with the instructors).

Qualitative assignments are evaluated by the following grading elements:

Course Projects (Two Small Projects During Modules 6-13; 40% of Final Grade Calculation)

During the weeks 6-13 of the course, you will work on 2 instructor-assigned projects. First project is running for 3 weeks and the second project is running for 2 weeks. The details of deliverable etc. will vary and will be provided along with each project.

Students will be provided with raw data and will be challenged to write their own code or use a software tool (as and if instructed). The code should be original and written with detailed comments, and can be easily executable by instructors, without warnings/errors.

For each project, you will be expected to follow the instructions to submit brief report, if requested, or provide complete response to questions and include executable source code by the end of the Day 7 of the due module as mentioned in course outline document.

You are encouraged to discuss/brainstorm among each other throughout the process; however, you should refrain from copying each other’s work or other sources and/or collaborating. You are also strongly discouraged to help others in the form of already built code – in full or parts.

These projects together will comprise 40% of the student final grade (Projects 1, 25% of final grade and projects 2, 15% of final grade).

The grading is based on the clear presentation of the idea, detailed description of methodology including the mathematics if necessary, presentation and accuracy of the results, solid conclusion, and clean, understandable source codes that can be executed successfully.

Projects are graded as follows: 

Late submission follows the same role as described for homework assignments.

Grading Policy

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

Instructors generally do not directly grade spelling and grammar. However, egregious violations of the rules of the English language willbe 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.

EP uses a +/- grading system (see “Grading System”, Graduate Programs catalog, p. 10). The following grades are used for the courses: A+, A, A– (excellent), B+, B, B– (good), C (unsatisfactory), 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 system, with the following breakdown:

Final grades will be determined by the following weighting:
 

Course Policies

Academic Integrity Course

You will be enrolled in an academic integrity training course shortly after registering for your first class at Johns Hopkins Engineering for Professionals. This course covers the fundamental values of academic integrity, as well as information related to our academic misconduct policy. You will receive guidance on proper citation, and learn how to avoid mistakes like plagiarism and other violations of academic misconduct.

The academic integrity training course can be accessed through Blackboard and will take approximately 30 minutes to complete. This is a pass/fail course and the grade will be posted to your transcript. All students are expected to complete the academic integritycourse within their first term. For more information on our academic misconduct policy, please visit: https://ep.jhu.edu/student-services/academic-services/academic-regulations/

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.