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Course Overview

This team taught, multidisciplinary course covers the fundamentals of magnetic resonance imaging relevant to the conduct and interpretation of human brain mapping studies. The challenges inherent in advancing our knowledge about brain function using fMRI are presented first to put the work in context. The course then provides in depth coverage of the physics of image formation, mechanisms of image contrast, and the physiological basis for image signals. Parenchymal and cerebrovascular neuroanatomy and application of sophisticated structural analysis algorithms for segmentation and registration of functional data are discussed. Additional topics include fMRI experimental design including block design, event related and exploratory data analysis methods, building and applying statistical models for fMRI data. Human subjects issues including informed consent, institutional review board requirements and safety in the high field environment are presented.


Linear Algebra (e.g. 18.06) and Differential Equations (e.g. 18.03). Introductory or college level courses in neurobiology (e.g. 9.01), physiology, probability (e.g. 6.041), and physics (e.g. 8.01 and 8.02) are preferred.

Required Textbook

Amazon logo Huettel, S. A., A. W. Song, and G. McCarthy. Functional Magnetic Resonance Imaging. Sunderland, MA: Sinauer Associates, Inc, 2004. ISBN: 9780878932887.

This book will be supplemented by readings in the research literature and other books.

Course Format

The course employs two 60-minute lectures per week, along with weekly laboratory and recitation sessions. Laboratory sessions will include fMRI data acquisition sessions and data analysis workshops. Assignments include reading of the primary textbook chapters and primary literature, fMRI data analysis in the laboratory, and several problem sets.

Course Outline

  • Overview
  • Functional Neural Systems
  • Imaging Physiology
  • Physics of Image Acquisition
  • Experiment Design
  • Statistical Analysis
  • Structural Analysis