Psy 5065 fMRI: Hands-on Training

3:45 &ndash 4:45 pm Wednesdays, Room S204 Elliott Hall
3 &ndash 5 pm Fridays, 3T Scanner, CMRR
3 credits

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

Interesting Links

Different people have different ways of explaining MRI. Here are some that have been helpful.
   Jeff Hornak's MRI Web-book
   Brian Hargreaves' animations of spin physics
   MR-TIP, a resource for MR professionals

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 requird only pencil and paper to complete.

Date Assigned	Exam	Due Date
Oct 19	Midterm. Word format . pdf.	Oct 26
Dec 12	Final. Word format . pdf.	Dec 21

Data from the course

All data are on BLiSS (bliss.socsci.umn.edu), in /labs/olmanlab/PSY5065. Each day's data is 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 has been converted to Nifti format. In addition, data from a few days have been 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 instructor if you want help moving, copying, converting or analyzing the data.

Assignments

All assignments will use one of the two functions below to simulate the scanner:
FLASH.m
EPI.m

	Date Assigned	Topic	Due Date
HW1	Sept 7	Basic Matlab. Instructions.	Sept 14
HW2	Sept 14	FID and linewidth (Fourier transform)	Sept 21
		FFT Tutorial (input data)	N/A
HW3	Sept 21	Image resolution (input data)	Sept 28
HW4	Sept 28	T₁ contrast (input data)	Oct 5
HW5	Oct 5	EPI vs. FLASH (input data)	Oct 19
HW6	Nov 5	Pulse sequences Blank diagrams	Nov 9
HW7	Nov 16	Experiment design	Nov 30
		Simulations with brain data.

Past Lectures

Date	Topic
Sept 12	Introduction to NMR
Sept 19	Introduction to RF Coils
Sept 26	Gradient echo pulse sequences
Oct 3	Excitation and relaxation
Oct 10	Tracking magnetization through pulse sequences
Oct 17	Pulse sequences
Oct 24	Pulse sequences II
Oct 31	Human subjects: Screening & Safety NIMH Workgroup Report
Nov 14	Experiment design
Nov 21	Distortion
Nov 28	Drop-out
Dec 5	Parallel imaging; course summary
Dec 12	Data from last lab: DTI, ICA & GLM

	Topic	Buxton	Haacke	Huettel
Module 1	NMR	p. 64-72, 124-135	Ch. 1, 2, 25	Ch. 1, p.49-63
	Fourier transform		Ch. 11
	Excitation		Ch. 3, 7, 8	p. 64-72
Module 2	Gradients	p. 72-81, 86-94	Ch. 27	Ch. 2
	k-space	Ch. 10	Ch. 9, 10, 12	Ch. 4
Module 3	T₁, T₂, contrast		Ch. 4	p. 99-110
Module 4	Fast imaging	p. 261-273	Ch. 19, 26	p. 120-126
Module 5	Noise	p. 274-288	Ch. 15	Ch. 9
	Fieldmaps	p. 288-306	Ch. 20
Module 6	Signal loss		Ch. 20?