BENG 278: Magnetic Resonance Imaging Lab Course - Winter 2015

Bioengineering 278: Magnetic Resonance Imaging Lab
Winter Quarter 2015

Instructor: Eric Wong PhD MD
Keck Center for FMRI Room 1011
(858) 822-0564
Lectures: Mondays, 1:00-1:50 PM
Keck Center for fMRI Conference Room 1014
Map to Center
Labs: Wednesdays 2:00-3:50 and Fridays 2:00-2:50 PM
Keck Center for fMRI 3T West Scanner - Room 1023
Office Hour: Tuesdays 1-2, or by Appointment:
Keck Center for FMRI Room 1011
1) Principles of MRI by D.G. Nishimura
2) Handbook of MRI Pulse Sequences by Matt A. Bernstein (also here )
Prerequisites: BENG 280A or consent of intructor.
  • Class Participation: 20%
  • Lab Reports: 80%
    • Lab 1: 10%; Lab 2: 10%; Lab 3: 20%; Lab 4: 40%
  • Late labs: 20% off per day late
  • Turn in by email to
  • Matlab code for all calculations should be included with each lab
  • Submit each lab as a single pdf file containing both writeup and Matlab code

Class Information:

  1. Syllabus


  1. MRI Hardware: Three Fields
  2. MRI: Introduction to K-space
  3. MRI: Coherence Pathways
  4. MRI: Sampling and SNR
  5. MRI: Excitation K-Space

Lab Assignments:

Reports Due Wednesdays at 2PM.
  1. Lab 1: Image reconstruction, EPI, Due Week 2
  2. Lab 2: Coherence Pathways, Due Week 4
  3. Lab 3: Project 1, Due Week 7
  4. Lab 4: Final Project, Due Finals Week

From previous BE278 classes:

  1. Website for BE278 Winter 2014
  2. Website for BE278 Winter 2013
  3. Website for BE278 Winter 2012
  4. Website for BE278 Winter 2011
  5. Website for BE278 Winter 2010
  6. MRI: Fast Imaging Sequences
  7. Coherence Pathways by Klaus Scheffler
  8. Cross-Vendor Lexicon The Rosetta Stone of MRI Terms
  9. Safety Information Safety Lecture and online Safety Test are required for entry into scan room
  10. Gridding (resampling) stuff from Brian Hargreaves
  11. For Compressed Sensing Lab: Random Gaussian Sampling in 1D and 2D
  12. For Compressed Sensing Lab: Simple stand alone script for wavelet transforms
  13. For Compressed Sensing Lab: Some example code to get you started
  14. Matlab Code for Magnetic Field of a Loop from Matlab Central, and a test function
  15. EPI/Spiral blurring simulation code
  16. Code to generate smiley face
  17. Original Paper on the Birdcage Coil by Hayes
  18. Magnetic Field of a Loop
  19. DENSE Motion Mapping Han Wen

Related Links:

  1. A full course on the Fourier Transform from Stanford
  2. SpinBench an MRI pulse sequence simulator
  3. A one page summary of Fourier Transforms
  4. Duke Virtual Imaging Lab
  5. The Basics of NMR by Joseph Hornak (an animated on-line book)
  6. MRI Educational Links from the ISMRM site
  7. Lots of cool links and software from Brian Hargreaves' site
  8. Compressed sensing stuff from Michael Lustig's site
  9. MRI Tutorials and Q&A from ReviseMRI
  10. MRI Tutorial from Stuart Clare's Dissertation
  11. MRI Artifacts
  12. Convolution Website

Related Classes on the Web:

  1. BE280A Principles of Biomedical Imaging (taught by Tom Liu at UCSD, the prerequisite to this course)
  2. SOM276A-C fMRI Courses in the UCSD School of Medicine
  3. BME530 Medical Imaging Systems (taught by W. Block at Univ. Wisconsin Madison)
  4. BME516 Medical Imaging Systems (taught by D. Noll at Univ. Michigan )
  5. EE369C Medical Image Reconstruction (taught by J. Pauly at Stanford)
  6. EE591 MRI (taught by K. Nayak at USC)
  7. EE691 Advanced Topics in MRI (taught by K. Nayak at USC)
  8. BE248 MRI (taught by M. Tyszka at Caltech)