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 Å. Nielsen, Andrew P. Holmes, Thomas Kolenda, Robert Savoy and Lars Kai Hansen
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