Psy 5065 fMRI: Hands-on Training (Spring 2019)

3 credits

Regular meeting time: 1:25-4:25pm, Fridays, 530B Bruininks Hall
On the following days we will instead be at the CMRR:
Feb. 15 (3TA)
Feb. 22 (3TA)
Mar. 29 (3TB)
Apr. 5 (3TB)
Apr. 26 (1-2:30 on 3TA; 2-4 on 3TB)
May 3 (1-5 on 3TB)

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 Wednesdays from 1:30-3:30 in N264 Elliott Hall.

Interesting Links

Different people have different ways of explaining MRI. Here are some that have been helpful.
   http://www.xrayphysics.com/contrast.html
   www.imaios.com/en (4th section has interactive course on MRI)
   practicalfmri.blogspot.com
   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.

Exams

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 8	Midterm. Word format; pdf.	Mar 15
May 3	Final, written portion. Word format; pdf. We'll have a work time in 530B Bruininks from 10:30-12:30 on May 13 if you need to finish anything up.	May 13

Data from the course

Our data will be on BLiSS. Here are the instructions for setting up remote access to BLiSS and connecting to the compute resource are at: latisresearch.umn.edu/using-computecla, and here are some more verbose instructions for getting NX Client working on your machine.

All data can be stored on on BLiSS (lts.cla.umn.edu), in /pkg/classes/psy5065/Data. Each day's data are stored there in the 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.

Assignments and Readings

Reading	HW	Date Assigned	Topic	Due Date
none	HW1	Jan 25	Basic NMR	Jan 30 answer key
term search	HW2	Feb 1	FID and linewidth (Fourier transform) code, if you want it.	Feb 6 answer key
			Matlab FFT Tutorial (input data)	N/A
Huettel, Ch. 3	HW3	Feb 8	Gradients	Feb 13 answer key
Huettel, Ch. 4	HW4	Feb 15	k-space	Feb 20 answer key
Huettel, Ch. 5	HW5	Feb 22	FLASH vs. EPI	Feb 27 answer key
	HW6	Mar 1	Relaxation	Mar 6 answer key
Mori et al		Mar 8	DTI and Ernst angle (Matlab demo code )	(midterm due Mar. 15)
Carr et al. 3T Safety Manual	HW7	Mar 15	Safety and Experiment Design	Mar 25
			Spring break
Krueger et al.	HW8	Mar 29	SNR	Apr 3
Gorno-Tempini et al.	HW9	Apr 8	Distortion and drop-out	Apr 17
			Sample commands for using FSL's FUGUE sample commands and TOPUP or AFNI's QWARP .
Pruessman et a.	HW10	Apr. 19	Parallel imaging	Apr. 24
Waehnert et al.	HW11	Apr 19	Cortical segmentation	May 1
Sign-up		April 26	Get your own data!	May 3
	Final	May 3	TBD	Final due May 13

Lectures

Click here for links to pdf and .pptx files.

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 YouTube
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