BENG 278: Magnetic Resonance Imaging Lab Course - Winter 2013

Bioengineering 278: Magnetic Resonance Imaging Lab
Winter Quarter 2013

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 and Fridays 2:00-3:50 PM
Keck Center for fMRI 3T West Scanner - Room 1023
Lab reports are due at 2PM on Wednesday the week after the lab
and should be turned in by email.
Matlab code for all calculations should be included with each lab.
Office Hour: Tuesdays 1-2, or by Appointment:
Keck Center for FMRI Room 1011
Teaching Assistant: Aaron Simon
Office Hour: Tuesdays 11-12
(you will need at least one of these two):
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.
Grading: One lab report per week.

Class Information:

  1. Syllabus ** UPDATED 2013.01.22 **
  2. Simple K-Space demo in Matlab or Mathematica
  3. Coherence Diagrams Klaus Scheffler

From previous BE278 classes:

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

Lecture Slides:

  1. Lecture 1 Hardware Overview, Nuclear magnetization, Excitation, The NMR signal
  2. Lecture 2 Fourier Transforms, K-space, the basic 2D imaging pulse sequence
  3. Lecture 3 Spin Echoes, Gradient Echoes, and Coherence pathways
  4. Lecture 4 Fast Imaging: Echo Planar Imaging, Fast Spin Echo, balanced SSFP
  5. Lecture 5 RF pulses
  6. Lecture 6 Phase Contrast and Diffusion
  7. Lecture 7 Cardiac MRI

Lab Assignments:

  1. Lab 1 Image reconstruction, B1 mapping
  2. Lab 2 Basic 2D imaging, chemical shift
  3. Lab 3 Spin Echoes, Gradient Echoes, and Coherence pathways
  4. Lab 4 Fast Imaging: EPI, bSSFP, FSE
  5. Lab 5 RF pulses: spatial spectral and 1D linear
  6. Lab 6 Diffusion Imaging
  7. Lab 7 Cardiac MRI

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)