Instructor
Brad Sutton
Professor
Expected Course Outcomes
By the end of class, students will be able to:
- Describe the basic physics behind the MRI signal
- Simulate spin echo gradient echo MRI experiments using a Bloch simulator
- Understand the relationship between pulse sequence components of RF pulses and gradients to image parameters
- Understand the SNR/spatial resolution/ acquisition time trade-offs of traditional imaging
- Perform basic image reconstruction steps, including from Cartesian and non-Cartesian acquisitions
- Understand the basic physics and processing steps for diffusion tensor imaging and functional MRI
Required Materials
Background material
-
Noll Primer on imaging: http://web.eecs.umich.edu/~dnoll/primer2.pdf
-
E-mri applets for learning basics of MRI (registration is free): https://www.imaios.com/en/e-Courses/e-MRI
Primary source for the course: Liang. Principles of Magnetic Resonance Imaging: A signal processing perspective. Free access on campus or through VPN: https://ieeexplore.ieee.org/book/5264284
Homework
OFFICE HOURS, Wednesday, 2/26, 2-3 PM in 2128 EVERITT.Here is a tutorial for how to submit homework with gradescope: https://gradescope-static-assets.s3.amazonaws.com/help/submitting_hw_guide.pdf
- Homework 1 (basic MRI physics, Due 2/20):
- Homework 2 (Pulse Sequence Design, Due 2/25):
- Handout of assignment: https://courses.engr.illinois.edu/bioe572/sp2020/secure/Sutton/hw2.pdf
- Homework 3 (Gridding for Image Reconstruction, Due 2/27):
- Handout of assignment: https://courses.engr.illinois.edu/bioe572/sp2020/secure/Sutton/hw3.pdf
- Matlab code: https://courses.engr.illinois.edu/bioe572/sp2020/secure/Sutton/Gridding1DCode.zip
- Homework 4 (Functional MRI: Not Graded, No due date.)
- Step-by-step analysis on AWS of fMRI data: https://courses.engr.illinois.edu/bioe572/sp2020/secure/Sutton/fMRI_Analysis_Manual.pdf
- Getting fMRI data to analyze: https://courses.engr.illinois.edu/bioe572/sp2020/secure/Sutton/LINKtoDATA.pdf
Schedule
- LECTURE 1 - 2/11 Introduction to MRI
- Overview: Intro slides
- LECTURE 2 - 2/13: From spins to signal
- Lecture Notes:2020-02-13.pdf
- LECTURE 3 - 2/18: Signal to sequence components
- Lecture Notes:2020-02-18.pdf
- LECTURE 4 - 2/20: Pulse sequence design
- Lecture Notes:2020-02-20.pdf
- LECTURE 5 - 2/25: Image reconstruction
- Lecture Notes: Slides: 2020-02-25-slides.pdf
- LECTURE 6 - 2/27: functional MRI of brain