Neuroscience: From Molecules to Systems to Behavior
Princeton University, NEU 502B, Spring 2023
Time: M/W 1:00–4:00 pm
Location: PNI A03
Instructor: Sam Nastase (snastase@princeton.edu)
AI: Gili Karni (gili@princeton.edu)
Syllabus: Syllabus
GitHub: GitHub
Scratch: Scratch
This lab course covers the methodological landscape of human cognitive neuroscience research. Students will learn the fundamentals of experimental design, data collection, preprocessing, and statistical analysis for fMRI, EEG/MEG, and ECoG, with an emphasis on best practices in reproducible neuroscience. Lectures will set the conceptual foundation for interactive, hands-on lab work using Jupyter notebooks. Advanced topics include multivariate pattern analysis (MVPA), representational similarity analysis (RSA), functional connectivity, intersubject correlation (ISC) analysis, and regularized encoding models. Students will be expected to design, analyze, and write up an fMRI experiment as a final project.
Lecture schedule
| Date | Topic | Slides/code | Homework | Optional reading |
|---|---|---|---|---|
| M 1/30 | Introduction and computing tools; MR physics | Slides Code | Logothetis et al., 2001 Buxton, 2013 | |
| W 2/1 | Biological basis of BOLD | Slides Code | Ogawa et al., 1992 Bandettini et al., 1992 Kwong et al., 1992 | |
| M 2/6 | fMRI experimental design | Slides Code | Boynton et al., 1996 Dale & Buckner, 1997 | |
| W 2/8 | fMRI confounds and preprocessing | Slides Code | Esteban et al., 2019 Power et al., 2012 | |
| M 2/13 | Subject-level modeling (GLM) Homework 1 (due 2/22) | Slides Code | Homework 1 | Friston et al., 1994 Lindquist, 2008 |
| W 2/15 | Group-level analysis and correction for multiple tests | Slides Code | Nichols & Holmes, 2002 Eklund et al., 2016 | |
| M 2/20 | Best practices in reproducible neuroimaging | Slides Code | Carp, 2012 Nichols et al., 2017 Poldrack et al., 2019 | |
| W 2/22 | Multivariate pattern analysis (MVPA) | Slides Code | Haxby et al., 2001 Norman et al., 2006 Tong & Pratte, 2012 | |
| M 2/27 | Representational similarity analysis Homework 2 (due 3/8) | Slides Code | Homework 2 | Edelman, 1998 Kriegeskorte et al., 2008 |
| W 3/1 | Searchlight analysis | Slides Code | Kriegeskorte et al., 2006 | |
| M 3/6 | Voxelwise encoding models | Slides Code | Mitchell et al., 2008 Naselaris et al., 2011 Huth et al., 2016 | |
| W 3/8 | Naturalistic design, intersubject correlation, hyperalignment | Slides Code | Hasson et al., 2004 Nastase et al., 2019 Haxby et al., 2020 | |
| M 3/13 | No class (spring recess) | |||
| W 3/15 | No class (spring recess) | |||
| M 3/20 | Structural and functional connectivity | Slides Code | Bullmore & Sporns Biswal et al., 2010 Yeo et al., 2011 | |
| W 3/22 | EEG preprocessing; project proposal presentations | Slides Code | Buzsáki et al., 2012 Gramfort et al., 2013 | |
| M 3/27 | Class canceled | Peirce et al., 2019 | ||
| W 3/29 | EEG facility demonstration | |||
| M 4/3 | fMRI data collection | |||
| W 4/5 | fMRI data collection | |||
| M 4/10 | fMRI data collection | Hillyard & Kutas, 1983 Kutas & Federmeier, 2010 | ||
| W 4/12 | EEG ERP and time-frequency analysis | Slides Code | Fries, 2015 Cohen, 2017 | |
| M 4/17 | ECoG preprocessing and analysis | Slides Code | Mukamel et al., 2012 Parvizi & Kastner, 2018 | |
| W 4/19 | Parallel distributed processing | Code | Rumelhart et al., 1986 McClelland et al., 2010 | |
| M 4/24 | Progress report presentations | |||
| W 4/26 | Deep learning | Slides Code | Richards et al., 2019 Hasson et al., 2020 | |
| M 5/8 | No class (final written report due) |
The content of this course is inspired by related courses designed by Leigh Nystrom, Jonathan Cohen, Jody Culham, and Jim Haxby.
Supplementary reading
Huettel, S. A., Song, A. W., & McCarthy, G. (2014). Functional Magnetic Resonance Imaging (3rd Ed.). Sinauer Associates. link
Poldrack, R. A., Mumford, J. A., & Nichols, T. E. (2011). Handbook of Functional MRI Data Analysis. Cambridge University Press. DOI
Bandettini, P. A. (2020). fMRI. MIT Press. link
Luck, S. J. (2014). An Introduction to the Event-Related Potential Technique (2nd ed.). MIT Press. link
McClelland, J. L. (2015). Explorations in Parallel Distributed Processing: A Handbook of Models, Programs, and Exercises (2nd ed.). MIT Press. PDF
Duvernoy, H. M. (1999). The Human Brain: Surface, Three-Dimensional Sectional Anatomy with MRI, and Blood Supply (2nd ed.). Springer. DOI