“Neuroimaging Methods and Theory: from image to inference”

16:26:830: 512; Sem in Cog Sci IV

Instructors; S. Hanson and C. Hanson

Time: W 2:30-5pm

Place: Fishbowl, SMITH HALL Newark-Campus


We are now at an unprecedented point in the field of neuroscience: We can watch the human brain in action as it sees, thinks, decides, reads, and remembers. Functional magnetic resonance imaging (fMRI) is the only method that enables us to monitor local neural activity in the normal human brain in a noninvasive fashion and over cognitively relevant time spans with excellent spatial resolution. The goals of this course are to help students become savvy and critical users of the current neuroimaging methods, to understand the strengths and weaknesses of the technique, and to design their own cutting-edge, theoretically motivated studies. Lectures and discussions will cover fMRI methods and experimental design. The course is primarily intended for students who will use neuroimaging techniques in their own thesis projects, and need to have a solid understanding of the physical and computational and mathematical principles behind these tools in order to acquire good data and analyze them appropriately. The basic statistical considerations for neuroimaging and new methods that use multivariate analysis (MPVA/PD) and Network/Connectivity analysis will be discussed.  

Students will be expected to do a project using the RUBIC facilities and develop a testable hypothesis using methods discussed in the course.   (These dates may change below; shown for topic only).






Introduction to MRI: Theory and Practice

No Readings



MRI: basics and biophysics:  we are all just water!

Poldrack Chapter 1, . McRobbie  9 (online)


Collecting Data/MR Parameters/Pulse sequences
(Level I training/ Safety)

McRobbie:  Chapter  3, Chapter 10 (online)


Work Flow/Image processing/Preprocessing

 Poldrack Chapter 2, Chapter 3


Brain structures/Spatial Normalization/Atlases

 Poldrack Chapter 4


Statistical analysis/BOLD Signal and Noise/FSL Lab

outside Speaker; functional focus

 Poldrack  Chapter 5, Chapter 6


Statistical Inferences on Images/FSL Lab

outside Speaker; functional focus

 Poldrack Chapter 7


MIDTERM First pass on Project ideas and modeling

 Draft proposals


Modeling Brain Connectivity/IMAGES

 Poldrack Chapter 8


MVPA/Predictive Decoding

 Poldrack Chapter 9


Visualization and Localization of fMRI data

 Poldrack Chapter 10


Project Scanning

 RUBIC—scheduled times per group


Project Scanning

 RUBIC—schedule times per group.


Final Project presentations


Handbook of Functional MRI Data Analysis, Russell A. Poldrack, Jeanette Mumford, Thomas Nichols, Cambridge, 2011.
MRI from Picture to Proton Edition 1 by Donald W. McRobbie, Elizabeth A. Moore, Martin J. Graves, Martin R. Prince, Cambridge, 2003.