COL 786: Advanced Functional Brain Imaging


Course Outline


Week Number

Topics to be covered



Introduction to the course and nervous system

o   Principles of Neural Science, 4th Edition by Eric Kandel, James Schwartz and Thomas Jessell, Chapter 2

o   At Medical Neuroscience by Leonard E. White, Units 1-2 and 1-3

o   Chapter 1 of Clinical Neuroanatomy Seventh Edition, by Richard S. Snell.

o   TED Talk-- Vilayanur Ramachandran: The neurons that shaped civilization


Basic neuroanatomy, introduction to FSL

o   Medical Neuroscience, Units 1-1 and 1-4 to 1-9

o   MIT Introduction to Neuroanatomy Series (parts 1-6)

o   Introduction to FSL

o   TED talk: A map of the brain

o   TED talk by Miguel Nicolelis, A monkey that controls a robot with its thoughts


MRI imaging basics

o   Paul Callaghan Videos on MRI

o   MRI Physics for Biomedical Researchers, Book By Gordon E. Sarty, Chapters 1, 5, 7, 8 and 14


fMRI basics -- Protocol design, fMRI processing pipeline and details

o   TED talk: A neural portrait of the human mind

o   Principles of fMRI 1 and 2 course by Johns Hopkins University at

o   Uludag, Kâmil, David J. Dubowitz, and Richard B. Buxton. "Basic principles of functional MRI." Clinical MRI. Elsevier, San Diego (2005): 249-287.


Introduction to statistics, formal notations

o   Introduction to the Science of Statistics, by Joseph C. Watkins. Chapters 12, 14, 16, 17

o   Multivariate Gaussian Distributions

o   Properties of Multivariate Gaussian Distributions


GLM statistics, multi-subject statistics, Multiple comparison problem, Bonferroni correction, FDR correction

o   Lazar, Nicole. The statistical analysis of functional MRI data. Springer Science & Business Media, 2008.

o   Mark W. Woolrich, Christian F. Beckmann, Thomas E. Nichols, Stephen M. Smith, Statistical Analysis of fMRI Data

o   A shorter reference on fMRI analysis


Connectivity analysis and statistics

o   Raichle, Marcus E., and Abraham Z. Snyder. "A default mode of brain function: a brief history of an evolving idea." Neuroimage 37.4 (2007): 1083-1090.

o   Van Den Heuvel, Martijn P., and Hilleke E. Hulshoff Pol. "Exploring the brain network: a review on resting-state fMRI functional connectivity." European Neuropsychopharmacology 20.8 (2010): 519-534.


ISC analysis and statistics

o   Kauppi, Jukka-Pekka, Juha Pajula, and Jussi Tohka. "A versatile software package for inter-subject correlation based analyses of fMRI." Frontiers in neuroinformatics 8 (2015).

o   Pajula, Juha, Jukka-Pekka Kauppi, and Jussi Tohka. "Inter-subject correlation in fMRI: method validation against stimulus-model based analysis." PloS one 7.8 (2012): e41196.

o   Hasson, Uri, et al. "Neurocinematics: The neuroscience of film." Projections 2.1 (2008): 1-26.


Multi-voxel pattern analysis and brain dynamics using fMRI

o   Norman, Kenneth A., et al. "Beyond mind-reading: multi-voxel pattern analysis of fMRI data." Trends in cognitive sciences 10.9 (2006): 424-430.

o   Kay, Kendrick N., et al. "Identifying natural images from human brain activity." Nature 452.7185 (2008): 352-355.

o   TED talk: Could future devices read images from our brains?

o   Nishimoto, Shinji, et al. "Reconstructing visual experiences from brain activity evoked by natural movies." Current Biology 21.19 (2011): 1641-1646.


Other concepts in Neuroscience and project presentations

o   The Secret Life of the Brain, PBS Documentary (all six episodes)

o   The Man With The 7 Second Memory ITV1 Documentary

o   The Woman Who Could Not Forget

o   PBS NOVA Documentary – Memory Hackers


Grading structure (tentative)

·         Exams — 40 (Minors — 20, Majors — 20)

·         Assignments, project — 45 (Assignments — 30, Project  — 15)

·         Quizzes/home work/class participation — 15