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HST.583

Functional Magnetic Resonance Imaging: Data Acquisition and Analysis

2-3-7 units · Graduate

Provides background necessary for designing, conducting, and interpreting fMRI studies in the human brain. Covers in depth the physics of image encoding, mechanisms of anatomical and functional contrasts, the physiological basis of fMRI signals, cerebral hemodynamics, and neurovascular coupling. Also covers design methods for stimulus-, task-driven and resting-state experiments, as well as workflows for model-based and data-driven analysis methods for data. Instruction in brain structure analysis and surface- and region-based analyses. Laboratory sessions include data acquisition sessions at the 3 Tesla MRI scanner at MIT and the Connectom and 7 Tesla scanners at the MGH/HST Martinos Center, as well as hands-on data analysis workshops. Introductory or college-level neurobiology, physics, and signal processing are helpful.

Fall 2008

This team-taught multidisciplinary course provides information relevant to the conduct and interpretation of human brain mapping studies. It begins with 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, and building and applying statistical models for fMRI data; and human subject issues including informed consent, institutional review board requirements and safety in the high field environment. ##### {{< anchor "fellows" >}}{{< /anchor >}}Additional Faculty Div Bolar Dr. Bradford Dickerson Dr. John Gabrieli Dr. Doug Greve Dr. Karl Helmer Dr. Dara Manoach Dr. Jason Mitchell Dr. Christopher Moore Dr. Vitaly Napadow Dr. Jon Polimeni Dr. Sonia Pujol Dr. Bruce Rosen Dr. Mert Sabuncu Dr. David Salat Dr. Robert Savoy Dr. David Somers Dr. A. Gregory Sorensen Dr. Christina Triantafyllou Dr. Wim Vanduffel Dr. Mark Vangel Dr. Lawrence Wald Dr. Susan Whitfield-Gabrieli Dr. Anastasia Yendiki

Readings

  • The course text readings cited in the following table are from the 1st edition (2004):
    Listed reading
  • Huettel, S. A., A. W. Song, and G. McCarthy. Functional Magnetic Resonance Imaging. 1st edition. Sunderland, MA: Sinauer Associates, Inc., 2004. ISBN: 9780878932887.
    Listed reading
  • 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:
    Listed reading
  • Huettel, S. A., A. W. Song, and G. McCarthy. Functional Magnetic Resonance Imaging . 2nd ed. Sunderland, MA: Sinauer Associates, Inc., 2009. ISBN: 9780878932863. ↗
    Listed reading
  • 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.
    Listed reading
  • Buy at MIT Press Gazzaniga, M. The Cognitive Neurosciences . 3rd ed. Cambridge, MA: MIT Press, 2004, chapter 53. ISBN: 9780262072540. ↗
    Listed reading
  • Kosslyn S. M., et al. “Neural Foundations of Imagery.” Nat Rev Neurosci 2, no. 9 (2001): 635-642.
    Listed reading
  • Kelley, W. M., et al. “Finding the Self? An Event-Related fMRI Study.” Journal of Cognitive Neuroscience 14, no. 5 (2002): 785-794.
    Required
  • Raichle, M. E., et al. “A Default Mode of Brain Function.” PNAS 98, no. 2 (January 16, 2001): 676-682.
    Required
  • Course text: Chapter 6 “From Neuronal to Hemodynamic Activity”
    Required
  • 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.
    Listed reading
  • Chapter 3: “Basic Principles of MR Signal Generation.”
    Required
  • Chapter 4: “Basic Principles of MR Signal Formation.”
    Required
  • Chapter 5: “MR Contrast Mechanisms and Pulse Sequences.”
    Required
  • Chapter 9: “Signal and Noise in fMRI.”
    Required
  • Buxton, R., ed. Chapters from Introduction to Functional Magnetic Resonance Imaging: Principles and Techniques . Cambridge, UK: Cambridge University Press, 2001. ISBN: 9780521581134.
    Required
  • Chapter 4: “Nuclear Magnetic Resonance.” pp. 64-85.
    Required
  • Chapter 5: “Magnetic Resonance Imaging.” pp. 86-103.
    Required
  • Chapter 6: “Imaging Functional Activity.” pp. 104-120.
    Required
  • Chapter 7: “Basic Physics of Magnetism and NMR.” pp. 124-154.
    Required
  • Chapter 8: “Relaxation and Contrast in MRI.” pp. 155-184.
    Required
  • Chapter 10: “Mapping the MR Signal.” pp. 218-248.
    Required
  • Chapter 11: “MRI Techniques.” pp. 249-273.
    Required
  • Chapter 12: “Noise and Artifacts in MR Images.” pp. 274-303.
    Required
  • Chapter 16: “The Nature of the Blood Oxygenation Level Dependent Effect.” pp. 390-416.
    Required
  • Chapter 17: “Mapping Brain Activation with BOLD-fMRI.” pp. 417-444.
    Required
  • Ekstrom, L. B., et al. “Bottom-Up Dependent Gating of Frontal Signals in Early Visual Cortex.” Science 321 (2008): 414-417.
    Listed reading
  • 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 ) ↗
    Listed reading
  • Chapter 6: “From Neuronal to Hemodynamic Activity”
    Required
  • Chapter 7: “Bold fMRI”
    Required
  • Chapter 8: “Spatial and Temporal Properties of fMRI”
    Required
  • Buxton, R., ed. Introduction to Functional Magnetic Resonance Imaging: Principles and Techniques . Cambridge, UK: Cambridge University Press, 2001, chapters 16 and 17. ISBN: 9780521581134.
    Required
  • Swisher, Jascha D., et al. “Visual Topography of Human Intraparietal Sulcus.” The Journal of Neuroscience 27, no. 20 (May 16, 2007): 5326 -5337.
    Listed reading
  • Napadow, V. et al. “Brain Correlates of Autonomic Modulation: Combining Heart Rate Variability with fMRI.” NeuroImage 42 (2008): 169-177.
    Listed reading
  • Savoy, Robert L. “Experimental Design in Brain Activation MRI: Cautionary Tales.” Brain Research Bulletin 67, no. 5 (November 15, 2005): 361-367.
    Required
  • Course text: Chapter 9 “Signal and Noise in fMRI”
    Required
  • 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.
    Listed reading
  • Lin, F-H, et al. “Event-related Single-shot Volumetric Functional Magnetic Resonance Inverse Imaging of Visual Processing.” NeuroImage 42 (2008): 230-247.
    Listed reading
  • 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.
    Listed reading
  • Lazar, Nicole. “Multivariate Approaches.” Chapter 7 in The Statistical Analysis of Functional MRI Data . New York, NY: Springer, 2008. ISBN: 9780387781907.
    Required
  • 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.
    Required
  • Hyvärinen, A. and E. Oja. “Independent Component Analysis: Algorithms and Applications.” Neural Networks 13 (2000): 411-430.
    Required
  • Devlin, J. T., and R. A. Poldrack. “In Praise of Tedious Anatomy.” NeuroImage 37 (2007): 1033-1041.
    Listed reading
  • 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.
    Listed reading
  • 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.
    Listed reading
  • Huettel, S. A., A. W. Song, and G. McCarthy. Functional Magnetic Resonance Imaging. 1st edition. Sunderland, MA: Sinauer Associates, Inc., 2004. ISBN: 9780878932887.
    Required
  • Note : The 2nd edition of this book was published after the Fall 2008 term, and Dr. Gollub recommends its use. Huettel, S. A., A. W. Song, and G. McCarthy. Functional Magnetic Resonance Imaging . 2nd ed. Sunderland, MA: Sinauer Associates, Inc., 2009. ISBN: 9780878932863. ↗
    Required

Prerequisites & course information

Same subject as 9.583[J] Prereq: 18.05 and ( 18.06 or permission of instructor) Acad Year 2027-2028: Not offered Acad Year 2028-2029: G (Fall) 2-3-7 units

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