Psy 5065 fMRI: Hands-on Training (Spring 2016)

Lecture: 1:30-3:30pm, Mondays, S150 Elliott Hall
Lab, Section 1: 1:30-2:30pm, Fridays, 3T Scanner & Seminar room, CMRR
Lab, Section 2: 2:30-3:30pm, Fridays, 3T Scanner & Seminar room, CMRR
3 credits

Please see the syllabus for the course description and topics that will be covered.

Getting questions answered ...

You can come ask Cheryl questions during her office hours, which are Mondays, 11-12, and Thursdays at 2:15.


Interesting Links

Different people have different ways of explaining MRI. Here are some that have been helpful. (4th section has interactive course on MRI)
   Jeff Hornak's MRI Web-book
   Brian Hargreaves' animations of spin physics
   MR-TIP, a resource for MR professionals
   Revise MRI
   PHET MR simulations
Please suggest the addition of any links/resources you like.


The mid-term and final exams will be take-home & open book. They should require only pencil and paper to complete.

Date Assigned Exam Due Date
Mar 7 Midterm. Word format pdf. Mar 11
May 2 Final, written portion. Word format . pdf. May 6

Data from the course

All data can be stored on on BLiSS (, in /pkg/classes/psy5065/Data. Each day's data are stored there in its original format -- a "study" directory for each "subject," which contains a different DICOM directory for each scan. In most of the study directories, some of the DICOM data have been converted to Nifti format. Nifti files from a few days will be moved to topical directories (DistortionCompensation and DTI), to demonstrate pre-processing or analysis steps.

A brief guide to converting and viewing (and analyzing ... although that section is very brief) is provided here . Don't hesitate to contact the TA if you want help moving, copying, converting or analyzing the data.


Most assignments will use one of the two functions below to simulate the scanner:

  Date Assigned Topic Due Date
HW1 Jan 25 Basic NMR & BLiSS. Old instructions. New instructions.
Instructions for setting up remote access to BLiSS:
Jan 29 answer key
HW2 Feb 1 FID and linewidth (Fourier transform) code, if you want it. Feb 5 answer key
    FFT Tutorial (input data) N/A
HW3 Feb 8 Gradients  Feb 12 answer key
HW4 Feb 15 DICOM handling and aliasing Feb 19 answer key
HW5 Feb 22 FLASH vs EPI: chemical shift   mriSims website Feb 26 answer key
HW6 Feb 29 Contrast in the real world   mriSims Mar 6 answer key
HW7 Mar 22 Experiment design   Mar 26 answer key
HW8 Mar 28 Handling data; basic AFNI analysis Apr 1 answer key
HW9 Apr 4 SNR maps, using FSL command-line tools Apr 8 answer key
  Ernst angle demo code Ernst angle calculations N/A
HW10 Apr 11 Distortion compensation, using FSL's FUGUE sample commands and TOPUP or AFNI's QWARP . Apr 15 answer key
HW11 Apr 18 Freesurfer reconstructions Apr 22 answer key
HW12 Apr 25 Experiment design Apr 29


Click here for links to pdf and .pptx files.

Suggested background readings

All books should be available in the CMRR library (please do not check them out, and leave them as reference for your classmates. In addition, some relevant chapters from Huettel will be handed out.
Topic Buxton Haacke Huettel
NMR p. 64-72, 124-135 Ch. 1, 2, 25 Ch. 1, history; Ch. 3, p.57-63, 68-77 precession
Magnetization & Excitation   Ch. 3, 7, 8 p. 62-68; 75-88
Fourier transform   Ch. 11 Fourier notes
Handy website
Gradients p. 72-81, 86-94 Ch. 27 Ch 2 , esp. pp. 31-41
k-space Ch. 10 Physics notes Ch. 9, 10, 12 Ch 4
T1, T2, contrast   Ch. 4 Bloch notes Ch 5
Fast imaging p. 261-273 Ch. 19, 26 p. 120-126
Noise p. 274-288 Ch. 15 Ch. 9
Kruger et al., MRM 2001
Bodurka et al., NeuroImage 2007
Fieldmaps p. 288-306 Ch. 20  
Signal loss   Ch. 20?
Gorno-Tempini et al, NeuroImage 2002
Chen et al, NeuroImage 2003
Weiskopf et al NeuroImage 2006
DTI     Mori & Zhang Neuron 2006