Course Text

The course text readings cited in the following table are from the 1st edition (2004):

Huettel, S. A., A. W. Song, and G. McCarthy. Functional Magnetic Resonance Imaging. 1st edition. Sunderland, MA: Sinauer Associates, Inc., 2004. ISBN: 9780878932887.

The 2nd edition of this book (2009) was published after the Fall 2008 term, and Dr. Gollub recommends its use. Interested students should consult the corresponding sections in this edition:

Huettel, S. A., A. W. Song, and G. McCarthy. Functional Magnetic Resonance Imaging. 2nd ed. Sunderland, MA: Sinauer Associates, Inc., 2009. ISBN: 9780878932863.

Functional neural systems


Course text

  • Box 6.2 “Primer on Neuroanatomy” (pp. 149-155)

  • Ch. 13.1 – 13.3 “Applications of fMRI” (pp. 359-367)

  • Ch. 13.4.2 “Topic Areas: Memory” (pp. 377-379)


Nolte, John. The Human Brain. 5th ed. Philadelphia, PA: Elsevier, 2002, chapters 1, 3, 6, 17, and portions of 22, pp. 506-525 and 547-561. ISBN: 9780323013208.

Buy at MIT Press Gazzaniga, M. The Cognitive Neurosciences. 3rd ed. Cambridge, MA: MIT Press, 2004, chapter 53. ISBN: 9780262072540.

Kosslyn S. M., et al. “Neural Foundations of Imagery.” Nat Rev Neurosci 2, no. 9 (2001): 635-642.



Human Subjects in fMRI research

Notes (PDF)

Slides (PDF)


Required for lab 2

Kelley, W. M., et al. “Finding the Self? An Event-Related fMRI Study.” Journal of Cognitive Neuroscience 14, no. 5 (2002): 785-794.

Raichle, M. E., et al. “A Default Mode of Brain Function.” PNAS 98, no. 2 (January 16, 2001): 676-682.



Course text: Chapter 6 “From Neuronal to Hemodynamic Activity”


Moore, C. I., and R. Cao. “The Hemo-Neural Hypothesis: On The Role of Blood Flow in Information Processing.” J Neurophysiol 99 (2008): 2035-2047.

Physics of image acquisitions


Course text:

  • Chapter 3: “Basic Principles of MR Signal Generation.”
  • Chapter 4: “Basic Principles of MR Signal Formation.”
  • Chapter 5: “MR Contrast Mechanisms and Pulse Sequences.”
  • Chapter 9: “Signal and Noise in fMRI.”

Students who feel they need additional support in grasping all the concepts could also read as a supplement the same material in:

Buxton, R., ed. Chapters from Introduction to Functional Magnetic Resonance Imaging: Principles and Techniques. Cambridge, UK: Cambridge University Press, 2001. ISBN: 9780521581134.

  • Chapter 4: “Nuclear Magnetic Resonance.” pp. 64-85.
  • Chapter 5: “Magnetic Resonance Imaging.” pp. 86-103.
  • Chapter 6: “Imaging Functional Activity.” pp. 104-120.
  • Chapter 7: “Basic Physics of Magnetism and NMR.” pp. 124-154.
  • Chapter 8: “Relaxation and Contrast in MRI.” pp. 155-184.
  • Chapter 10: “Mapping the MR Signal.” pp. 218-248.
  • Chapter 11: “MRI Techniques.” pp. 249-273.
  • Chapter 12: “Noise and Artifacts in MR Images.” pp. 274-303.
  • Chapter 16: “The Nature of the Blood Oxygenation Level Dependent Effect.” pp. 390-416.
  • Chapter 17: “Mapping Brain Activation with BOLD-fMRI.” pp. 417-444.


Ekstrom, L. B., et al. “Bottom-Up Dependent Gating of Frontal Signals in Early Visual Cortex.” Science 321 (2008): 414-417.



Thakkar, K. N., et al. “Response Monitoring, Repetitive Behaviour and Anterior Cingulate Abnormalities in ASD.” Brain 131, no. 9 (2008): 2464-2478. (PDF - 4.2 MB)

Imaging physiologys


Course text:

  • Chapter 6: “From Neuronal to Hemodynamic Activity”

  • Chapter 7: “Bold fMRI”

  • Chapter 8: “Spatial and Temporal Properties of fMRI”

Buxton, R., ed. Introduction to Functional Magnetic Resonance Imaging: Principles and Techniques. Cambridge, UK: Cambridge University Press, 2001, chapters 16 and 17. ISBN: 9780521581134.



Swisher, Jascha D., et al. “Visual Topography of Human Intraparietal Sulcus.” The Journal of Neuroscience 27, no. 20 (May 16, 2007): 5326 -5337.



Napadow, V. et al. “Brain Correlates of Autonomic Modulation: Combining Heart Rate Variability with fMRI.” NeuroImage 42 (2008): 169-177.

Experimental designs


Savoy, Robert L. “Experimental Design in Brain Activation MRI: Cautionary Tales.” Brain Research Bulletin 67, no. 5 (November 15, 2005): 361-367.



Course text: Chapter 9 “Signal and Noise in fMRI”

Statistical analysis


Smith, Stephen M. “Overview of fMRI Analysis.” Chapter 11 in Functional MRI: An Introduction to Methods. Edited by P. Jezzard, P. M. Matthews, and S. M. Smith. New York, NY: Oxford University Press, 2003. ISBN: 9780198527732.



Lin, F-H, et al. “Event-related Single-shot Volumetric Functional Magnetic Resonance Inverse Imaging of Visual Processing.” NeuroImage 42 (2008): 230-247.



Jenkins, A. C., C. N. Macrae, and J. P. Mitchell. “Repetition Suppression of Ventromedial Prefrontal Activity During Judgments of Self and Others.” PNAS 105, no. 11 (March 18, 2005): 4507-4512.



Lazar, Nicole. “Multivariate Approaches.” Chapter 7 in The Statistical Analysis of Functional MRI Data. New York, NY: Springer, 2008. ISBN: 9780387781907.

Andersen, A. H., D. M. Gash, and M. J. Avison. “Principal Component Analysis of the Dynamic Response Measured by fMRI: A Generalized Linear Systems Framework.” Magnetic Resonance Imaging 17, no. 6 (1999): 795-815.

Hyvärinen, A. and E. Oja. “Independent Component Analysis: Algorithms and Applications.” Neural Networks 13 (2000): 411-430.

Structural and functional analysis


Devlin, J. T., and R. A. Poldrack. “In Praise of Tedious Anatomy.” NeuroImage 37 (2007): 1033-1041.



Gholipour, A., et al. “Brain Functional Localization: A Survey of Image Registration Techniques.” IEEE Transactions on Medical Imaging 26, no. 4 (April 2007): 427-451.

Brett, M., I. S. Johnsrude, and A. M. Owen. “The Problem of Functional Localization in the Human Brain.” Nature Reviews Neuroscience 3 (March 2002): 243-249.

Course Info
As Taught In
Fall 2008
Learning Resource Types
assignment_turned_in Problem Sets with Solutions
grading Exams with Solutions
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