Topic outline

  • General

    Overview:

    The course in 2019 is organized during Periods III and IV which spans the time period from Tuesday, 8 January (kick-off meeting) until Tuesday, 9 April (exam), that is, the weeks 2-15. Note that unlike the Oodi calendar says, the course room is F254 as the original room F158 is nowadays a yoga-room. 

    The course consists of weekly learning packages which are to be studied and learned by the students independently. The learning objectives for each week are listed in Materials section along with pointers to book chapters, electronic materials, and summary videos containing the information. Quizzes and home work exercises, that are discussed during the weekly contact sessions, are used to monitor the learning. Additionally, there are compulsory project works and an examination.

    Prerequisites:

    Basic courses in mathematics and physics. Basic Matlab knowledge.

    Kick-off meeting and contact sessions:

    The only compulsory contact session was the kick-off meeting on Tuesday, January 8 at 14:15-16:00. There are no compulsory contact sessions during the course, but there are voluntary weekly sessions, where you can join to discuss the exercises and to get help in solving them. The voluntary sessions are held in F254 (Otakaari 3) every Tuesday 14:15-16:00, beginning Tuesday, 15 January. During the sessions, the teachers will assist either personally or via Adobe Connect (https://connect.funet.fi/aalto_mri_2019/).

    Exam:

    Examination is 9th of April, 14:00-17:00, auditorium F239a in Otakaari 3. The second exam is on Monday 16th September 2019, 16:30-19:30. The exam is included in the retake exam system of Aalto. Sign in WebOodi by 9.9.2019.

    Grading:

    The grading of the course is based on the exam, mandatory project works, and exercises.

    Personnel:

    The main lecturer/organizers are Prof. Simo Särkkä (simo.sarkka@aalto.fi) and Lecturer Lauri Palva (lauri.palva@aalto.fi). The teaching assistant is Toni Karvonen (toni.karvonen@aalto.fi). 


  • Materials

    The main course book is

    • Robert W. Brown, Y.-C. Norman Cheng, E. Mark Haacke, Michael R. Thompson, Ramesh Venkatesan, "Magnetic Resonance Imaging: Physical Principles and Sequence Design", 2nd Edition, Wiley, 2014.

    which is available as an e-book via Aalto University library (https://ebookcentral-proquest-com.libproxy.aalto.fi/lib/aalto-ebooks/detail.action?docID=1676112). The following books are also useful on the course, but the exercises will be taken from Brown's book:

    • Zhi-Pei Liang, Paul C. Lauterbur, "Principles of Magnetic Resonance Imaging: A Signal Processing Perspective", Wiley-IEEE, 1999
    • Donald W. McRobbie, Elizabeth A. Moore, Martin J. Graves, Martin R. Prince, "MRI from Picture to Proton", 2nd Edition, 2007

    The pointers to other materials will be provided on this page. The tentative list of weekly learning objectives is below (chapter, problem numbers and page references are to Brown's book). Contact sessions are meant for discussion about the current week's exercises. The exercises are returned on MyCourses in two batches: rounds 1-4 by 19.2. and rounds 5-8 by 16.4.

    Note that the electronic materials shown in the exercise session ("Brief Recap of Chapter X of Brown et al. (2014)") are also linked below – but – the exercise answers that are presented in the exercise sessions will not be uploaded here, because they are home works. If you want to see them, you need to attend the session.

    1. Overview of MRI (week 3)
    2. Spins and magnetization (week 5)
      • Chapter 2: Classical Response of a Single Nucleus to a Magnetic Field (pp. 19-36)
      • Brief Recap of Chapter 2 of Brown et al. (2014)
      • Contact session on Tuesday 29.1. (14:15-16:00, F254, Otakaari 3)
      • Youtube videos:
      • Exercise 2
      • Quiz 2
    3. Rotating frame (week 6)
      • Chapter 3: Rotating Reference Frames and Resonance (pp. 37-51)
      • Brief Recap of Chapter 3 of Brown et al. (2014)
      • Contact session on Tuesday 5.2. (14:15-16:00, F254, Otakaari 3)
      • Youtube videos:
        • 90 degree pulse and relaxation: https://goo.gl/84UgZL
        • Spin resonance and the rotating frame (this contains some quantum mechanics not required on this course but hopefully helps visualizing the rotating frame): https://goo.gl/eJaeeQ
      • Exercise 3
      • Quiz 3
    4. Bloch equations (week 7; Exercises for weeks 1-4 to be returned by 19.2.)
      • Chapter 4: Magnetization, Relaxation, and the Bloch Equation (pp. 53-66)
      • Brief Recap of Chapter 4 of Brown et al. (2014)
      • Contact session on Tuesday 12.2. (14:15-16:00, F254, Otakaari 3)
      • Youtube videos:
      • Exercise 4
      • Quiz 4
    5. Signal detection (week 9)
      • Chapter 7: Signal Detection Concepts (pp. 95-111)
      • Brief Recap of Chapter 7 of Brown et al. (2014)
      • Contact session on Tuesday 26.2. (14:15-16:00, F254, Otakaari 3)
      • Youtube videos:
      • Exercise 5
      • Quiz 5
    6. Spatially varying fields and echoes (week 10)
    7. Basics of Fourier imaging (week 11)
      • Chapter 9: One-Dimensional Fourier Imaging, k-Space, and Gradient Echoes (pp. 141-164)
      • Brief Recap of Chapter 9 of Brown et al. (2014)
      • Contact session on Tuesday 12.3. (14:15-16:00, F254, Otakaari 3)
      • Youtube videos:
      • Exercise 7
      • Quiz 7
    8. Multidimensional Fourier imaging (week 12; Exercises for weeks 5-8 and the Matlab exercise to be returned by 16.4.)

  • Assignments

    This page will contain the home work exercises as well as the place to return the answers. There are 8 exercise sets in total, each containing two problems (plus a Matlab exercise). Exercises 1-4 are to be submitted by Tuesday, February 19 and exercises 5-8 by Tuesday April 16. You can either write your answers by hand and scan them or use e.g. Word or LaTeX.

    There are voluntary exercise sessions, held in F254 (Otakaari 3) on most Tuesdays at 14:15-16, beginning on Tuesday, January 15. During the sessions, the teachers will assist either personally or via Adobe Connect. See Timetable for more information.

    EXERCISE 1

    EXERCISE 2

    EXERCISE 3
    EXERCISE 4

    Exercises 1 to 4 are to be returned on MyCourses by February 19. Submission of exercises 1-4.

    EXERCISE 5
    EXERCISE 6 (in Problem 6.2, it may be easier to use Equation (8.30) instead of (8.31))
    EXERCISE 7
    EXERCISE 8

    Exercises 5 to 8 are to be returned on MyCourses by April 16. Submission of exercises 5-8.

    MATLAB EXERCISE

    Matlab exercise is to be returned on MyCourses by April 16. Submission of Matlab exercise. Data files for the exercise are available here.

  • Timetable

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    This is a preliminary timetable of the course. Changes, in particular in Period IV, are possible, but the contact session are always held on Tuesdays at 14:15-16:00. See Materials for topics that will be covered during each week.

    January 8

    • Kick-off meeting, 14:15-16:00, room F254, Otakaari 3

    January 15

    • Contact session (exercise round 1; Chapter 1), 14:15-16:00, room F254, Otakaari 3
    January 22

    • No contact session

    January 29

    • Contact session (exercise round 2; Chapter 2), 14:15-16:00, room F254, Otakaari 3

    February  5

    • Contact session (exercise round 3; Chapter 3), 14:15-16:00, room F254, Otakaari 3

    February 12

    • Contact session (exercise round 4; Chapter 4), 14:15-16:00, room F158, Otakaari 3
    February 19

    February 26

    • Contact session (exercise round 5; Chapter 7), 14:15-16:00, room F254, Otakaari 3

    March 5

    • Contact session (exercise round 6; Chapter 8), 14:15-16:00, room F254, Otakaari 3

    March 12

    • Contact session (exercise round 7; Chapter 9), 14:15-16:00, room F254, Otakaari 3

    March 19

    • Contact session (exercise round 8; Chapter 10), 14:15-16:00, room F254, Otakaari 3

    March 26

    • Contact session (Matlab exercise), 14:15-16:00, room F254, Otakaari 3

    April 2

    • Recap, 14:15-16:00, room F254, Otakaari 3
    April 9

    • Exam, 14:00-17:00, auditorium, Otakaari 3

    April 16

    April 29

    • Deadline for returning the project work report.

  • Quizzes

    Quizzes do not affect grading.

  • Project work

    There is a mandatory project work that involves either writing an essay on an imaging method presented in the book or doing a lab work. The essay / lab work report must be returned by April 29.

    Laboratory work

    The laboratory work consists of six MRI tasks completed using a mini-sized MRI system. The student

    1. Adjusts the system frequency of the MRI device;
    2. Adjusts the radiofrequency pulse duration for a 90° flip angle;
    3. Adjusts shimming so as to achieve a homogeneous B0 field;
    4. Experiments with changing the repetition time;
    5. Experiments with parameters of a spin echo sequence;
    6. Acquires an MR image of a phantom or an object of their choosing (that needs to fit in a 10 mm diameter test tube) using a 2D spin echo sequence and also reconstructs the image from raw k-space data with Fourier transform.
    If none of the time slots suits you and you wish to do the laboratory work, contact toni.karvonen@aalto.fi. The written report on the laboratory work must be returned by April 29.

    Select time slot for the laboratory work

    Submission of the lab work report

    Files:

    Laboratory work manual

    Data preprocessing MATLAB function

    Essay

    Another option is to write an essay (4 to 6 pages) on an advanced MR imaging topic. The possible topics are (chapters and page numbers refer to those in the course book by Brown et al.):

    • Water-fat separation (Chapter 17; pp. 413-446)
    • Fast steady-state imaging (Chapter 18; pp. 447-508)
    • Partial reconstruction and EPI (Chapter 19; pp. 511-566)
    • Diffusion imaging (Chapter 21; pp. 619-636)
    • Sequence design (Chapter 26; pp. 779-821)
    • Parallel imaging (Chapter 28; pp. 859-889)

    The essay must be returned by April 29.

    Submission of the essay

  • Grading

    The grading of the course is based on a combination the exam, mandatory project works, and exercises.

    • To pass the course, you must complete the project work (either a laboratory work or an essay).
    • There will be five questions in the exam, each worth 5 points for the total of 25 points. You must receive at least 10 points (Any extra points are not included. That is, you do not pass the course if you get 5 points from the exam even if you have done all the exercises and submitted course feedback) to pass the course.
    • By completing the 8 regular exercise sets, you can receive a maximum of 3 extra points for the exam. Furthermore, the Matlab exercise at the end of course and course feedback after the exam are both worth 1 extra point. That is, by completing most of the exercises and giving course feedback you can get up to 5 extra points for the exam.
    • The grade brackets are 1: 10 to 12 points; 2: 13 to 15 points; 3: 16 to 19 points; 4: 20 to 22 points; 5: 23 to 25 points.

  • Results

    These files contain course results. Results for assignments contains points obtained from doing the regular course exercises, MATLAB exercise, and completing the course feedback form. Exam results and grades contains the exam results and final grades. See Grading for the grade brackets and on how doing the exercises affects grading.

    Completion of the mandatory Project work is not indicated in these files. Your project work report has been accepted if you have not received an email requesting clarifications or corrections.