Analysis Methods in Functional Magnetic Resonance Imaging

ECE595/CS591/PSYCH650

Spring Semester, 2007

Location: ECE 310

 

Time: Tuesdays and Thursdays, 12:30-1:45pm

 

Instructor: Vince D Calhoun

Email: vcalhoun (at) unm.edu

Phone: 272-1817

Office: ECE 224B

Office Hours: TBA and by appointment

 

 Text (required):

Computing Brain Activity Maps from FMRI Time-Series Images (ISBN 0521868262)

Gordon Sarty

 

 Article for Term Paper:

Plurality and Resemblance in fMRI Data Analysis NeuroImage, Volume 10, Issue 3, September 1999, Pages 282-303 Nicholas Lange, Stephen C. Strother, Jon R. Anderson, Finn . Nielsen, Andrew P. Holmes, Thomas Kolenda, Robert Savoy and Lars Kai Hansen

 

 Course Description/Syllabus:

 

Software (SPM5, GIFT, MRIcro)

 

Data (visuomotor task, auditory oddball, description of auditory oddball)

 

Lectures (Jan 15-May 12) [disclaimer: many of the lecture slides are borrowed from others]:

1)      Jan 16: Course Intro: Overview of MRI Physics (Noll, pg 1-7)

2)      Jan 18: Introduction to fMRI (Noll, pg 8-14)

3)      Jan 23: Basic brain anatomy (Anatomy Primer)

4)      Jan 25: Preliminaries (Sarty Chapter 1, Matlab Primer [1, 2, 2 (files), 3, 3 (files)], Matrix Primer) [Book chapters are password protected...contact instructor for password]

5)      Jan 30: Preprocessing I (Sarty: 2.1-2.3, Oakes Comparison, Friere Similarity Measure)

6)   Feb 1: Preprocessing II

7)      Feb 6: Preprocessing III: Anatomic transformation to standard brain spaces (Sarty: 2.4-2.6)

8)      Feb 8: Preprocessing IV: Temporal Filtering (Glover; RETROICOR, Kruger Physiologic Noise)

9)      Feb 13 Paradigm design (blocked and event-related) (Sarty Chapter 3) (Burock, rapid fMRI; Monty GLM Critique)

10)      Feb 15: The GLM‑univariate approaches (Sarty: 4.1)

11)  Feb 20: The GLM-second-level (Sarty: 4.1)

12)  Feb 22: NO CLASS

13)  Feb 27: (quiz handed out) Random effects/multiple comparisons (Sarty: 4.2, Sarty: 4.3)

14)  Mar 1: (quiz due) Data Collection at the MIND Institute

15)  Mar 6: Modeling the hemodynamic response/Discussion of project details (buxton balloon model)

16)  Mar 8: Deconvolution-Andy Mayer

17)  Mar 13: NO CLASS (Spring Recess)

18)  Mar 15: NO CLASS (Spring Recess)

19)  Mar 20: Bayesian & Nonparametric methods (Sarty: 4.4-4.5, Genovese)

20)  Mar 22: Fourier methods/Repeatability and comparison of methods (Sarty: 4.6-4.7)

21)  Mar 27: The GLM‑multivariate approaches/PLS (Sarty: 5.1) [PLS toolbox]

22)  Mar 29: Functional connectivity (correlation) (Sarty: 5.5)

23)  Apr 3 (term paper due): Principal and independent component analysis (Sarty: 5.2) [review article]

24)  Apr 5: Independent component analysis (group analysis) (Sarty: 5.2)

25)  Apr 10: Clustering methods (Sarty: 5.4)

26)  Apr 12: Real time fMRI (Sarty: 4.8)

27)  Apr 17: Wavelet methods (Sarty: 5.3) [review article]

28)  Apr 19: Effective connectivity (SEM/DBN) (Sarty: 5.6)

29)  Apr 24: Integration with other modalities: EEG

30)  Apr 26: Integration with other modalities: part II

31)  May 1: Ultra Low-Field MRI (slides 1), (slides 2): John Moser

32)  May 3: (projects due): Student Presentations

33)  May 8: Student Presentations

34)  May 10 Student Presentations