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 canvas.ucsd.edu
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) |