fMRI Course

Cognitive Science 260 (B00) [4 Units]- Winter 2020

Fundamentals of Functional Neuroimaging

Course Faculty: Thomas Liu, Alan Simmons, Amanda Bischoff-Grethe, Lisa Eyler, Christine Fennema-Notestine, Maryam Falahpour, Frank Haist

Lectures: Monday/Wednesday, 2:00-3:20pm; CFMRI Conference Room (subject to change depending on enrollment)

Course Overview: Covers the basic principles underlying magnetic resonance imaging (MRI), functional MRI, structural and functional connectivity, and perfusion imaging. Students will gain an understanding of key concepts in the processing, analysis, and interpretation of neuroimaging data with hands-on exercises using standard neuroimaging analysis software packages.

Prerequisites: Graduate standing or consent of instructor. Prior course in statistics is strongly recommended.

Course Materials: Access for registered students will be through

Preliminary Syllabus for Winter 2020 (Subject to Change)

Week 1  
Monday 1/6 Basics of fMRI – Physics and Physiology
Wednesday 1/8 The fMRI signal model; General Linear Model (GLM)
Week 2  
Monday 1/13 Task-based fMRI; Experimental Designs; Statistical Tests
Wednesday 1/15 Confounds and Nuisance Regression; Motion-related Artifacts; Physiological Noise
Week 3  
Monday 1/20 MLK Holiday; NO CLASS
Wednesday 1/22 Anatomical Image Processing; Alignment; Standard Space
Week 4  
Monday 1/27 Distortion Correction; Volume Registration; Minimal Processing Pipeline;
Wednesday 1/29 Quality Assurance; Data Organization; Outliers and Data Censoring
Week 5  
Monday 2/3 Group Analysis Part I
Wednesday 2/5 Group Analysis Part II
Week 6  
Monday 2/10 Multiple Comparisons; Clustering
Tuesday 2/12 Functional Connectivity Part I
Week 7  
Monday 2/17 President’s Day Holiday; NO CLASS
Wednesday 2/19 Functional Connectivity Part II
Week 8  
Monday 2/24 Diffusion MRI Physics; Diffusion Tensor Imaging; Multishell
Wednesday 2/26 Diffusion MRI Analysis; Tractography
Week 9  
Monday 3/2 Diffusion MRI processing
Wednesday 3/4 Human Connectome Project (HCP); Surface-based analysis
Week 10  
Monday 3/9 HCP Pipeline and Applications
Wednesday 3/11 Arterial Spin Labeling and Emerging Methods
Week 11  
Monday 3/16 Final Exam Period (3 to 6 pm)