PSC290(4) Analysis of fMRI Data
Schedule
(subject to change)
Week 1, January 4, 2006
Organization 
fMRI Data Center; Computing at a distance
Introduction to Unix/Linux
Matlab
The zen of programming
Workspaces
	Matlab vs Unix
	variables
	functions and parameters
Data analysis packages: FSL, SPM
Data formats
Data viewers
Emacs
Batch processing
Assignment 1 (due Monday Jan. 16): Identify datasets to analyze.

Week 2, January 11, 2006
SPM and FSL graphical user interfaces
SPM and FSL data flow and data structures
Readying the data for analysis
	Organizing the data
	Rudimentary quality checks - Is the data worthy of analysis?
Image pre-processing -- 
	Spatial coregistration.
	Motion estimation and correction.
	Spatial normalization.
	Slice-timing correction
	Pre-whitening
Assignment 2 (due Jan. 25): Preprocess data (using at least 2 different strategies)

Week 3, January 18, 2006
Design matrix construction/Statistics. Block designs. Event-related designs.
Assignment 3 (due February 1): Construct design matrices

Week 4, January 25, 2006 (Assignment 2 due)
1. Pre-processing presentations
2. Design matrix construction, Statistics

Week 5, February 1, 2006
Region of interest (ROI) analyses
Masking
Anatomy toolbox
Obtaining time-courses
HRF estimation
Assignment 4 (due February 15): ROI analyses

Week 6, February 8, 2006
Multivariate methods - ICA, partial least-squares, coherence, effective connectivity

Week 7, February 15, 2006 (Assignment 3 due)
ROI presentations
Multivariate methods - ICA, partial least-squares, coherence, effective connectivity

Week 8, February 22, 2006
Flat-mapping & Meta-analysis

Week 9, March 1, 2006
Flat-mapping & Meta-analysis

Week 10, March 8, 2006
Final Presentations

March 15, 2006
Final Project write-ups due