Analysis Methods in Functional Magnetic Resonance Imaging


Spring Semester, 2009

Location: ECE 237


Time: Tuesdays, 3:00-5:30pm


Instructor: Vince D Calhoun

Email: vcalhoun (at)

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


 Course Description/Syllabus:


Software (SPM5, GIFT, MRIcro)


Data (visuomotor task, auditory oddball, description of auditory oddball, data collected in class)


Lectures (Jan 20-May 5) [disclaimer: many of the lecture slides are borrowed from others]:

1)   Jan 20: Course Intro: Overview of MRI Physics & Basics of BOLD fMRI [Noll, pg 1-7, MRI Made Easy (almost)]

2)   Jan 27: Basic brain anatomy, basic mathematics and software tools (Anatomy Primer, Sarty Chapter 1, Matlab Primer [1, 2, 2 (files), 3, 3 (files)], Matrix Primer) [Book chapters are password instructor for password]

3)   Feb 5: Data collection at the Mind Research Network

4)  Feb 10: Preprocessing I & II (Sarty: 2.1-2.3, Oakes Comparison, Friere Similarity Measure, Viola Mutual Information)

4)   Feb 17: Preprocessing III & IV: Anatomic transformation to standard brain spaces (Sarty: 2.4-2.6), Temporal Filtering (Glover; RETROICOR, Kruger Physiologic Noise)

5)   Feb 24 Paradigm design (blocked and event-related) (Sarty Chapter 3) (Burock, rapid fMRI; Monty GLM Critique), The GLM‑univariate approaches (Sarty: 4.1)

6)  Mar 3: (quiz handed out [due Friday March 6th], approval of critique paper) Random effects/multiple comparisons (Sarty: 4.3),

7)  Mar 10: Modeling the hemodynamic response (buxton balloon model) (Sarty: 4.2), Bayesian & Nonparametric methods (Sarty: 4.4-4.5, Genovese)

9)  Mar 17: NO CLASS (Spring Recess)

10)  Mar 24: Functional connectivity (correlation) (Sarty: 5.5), Effective connectivity (SEM/DBN) (Sarty: 5.6)

11)  Mar 31: Principal and independent component analysis (Sarty: 5.2) [review article]

12)  Apr 7: (term paper due) Group ICA

13)  Apr 14: Wavelet methods (Sarty: 5.3) [review article], Clustering methods (Sarty: 5.4), The GLM‑multivariate approaches/PLS (Sarty: 5.1) [PLS toolbox]

14)  Apr 21: Fourier methods/Repeatability and comparison of methods (Sarty: 4.6-4.7), Real time fMRI (Sarty: 4.8)

15)  Apr 28: Integration with other modalities: EEG, DTI, genetics

16)  May 5: (projects due): Student Presentations