Functional Magnetic Resonance Imaging: Data Acquisition and Analysis

Readings

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.

SES #	READINGS
Functional neural systems
1	Required 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) Supplemental 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. 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.
2	Discussion Human Subjects in fMRI research Notes (PDF) Slides (PDF)
3	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.
4	Required Course text: Chapter 6 “From Neuronal to Hemodynamic Activity” Discussion 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
5	Required 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. Discussion Ekstrom, L. B., et al. “Bottom-Up Dependent Gating of Frontal Signals in Early Visual Cortex.” Science 321 (2008): 414-417.
6	Discussion 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
7	Required 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.
8	Discussion Swisher, Jascha D., et al. “Visual Topography of Human Intraparietal Sulcus.” The Journal of Neuroscience 27, no. 20 (May 16, 2007): 5326 -5337.
9	Discussion Napadow, V. et al. “Brain Correlates of Autonomic Modulation: Combining Heart Rate Variability with fMRI.” NeuroImage 42 (2008): 169-177.
Experimental designs
10	Required Savoy, Robert L. “Experimental Design in Brain Activation MRI: Cautionary Tales.” Brain Research Bulletin 67, no. 5 (November 15, 2005): 361-367.
11	Required Course text: Chapter 9 “Signal and Noise in fMRI”
Statistical analysis
12	Background 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.
13	Discussion Lin, F-H, et al. “Event-related Single-shot Volumetric Functional Magnetic Resonance Inverse Imaging of Visual Processing.” NeuroImage 42 (2008): 230-247.
14	Discussion 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.
15	Required 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
16	Background Devlin, J. T., and R. A. Poldrack. “In Praise of Tedious Anatomy.” NeuroImage 37 (2007): 1033-1041.
17	Background 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.