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Readings

Textbook

Huettel, S. A., A. W. Song, and G. McCarthy. Functional Magnetic Resonance Imaging. Sunderland, MA: Sinauer Associates, Inc, 2004. ISBN 0878932887.

Required reading for lectures.

Supplementary readings are also suggested for those of you with less background in the areas of neuroscience and statistics.

Required Readings

Readings Table.
SeS #	TOPICS	READINGS
Overview
1	Lec 1 Introduction to Course Introduction to Functional Magnetic Resonance Imaging	Savoy, R. L. "History and Future Directions of Human Brain Mapping and Functional Neuroimaging." Acta Psychologica 107 (2001): 9-42.
Functional Neural Systems
2-4	Lec 2 Overview of Neural Systems: Neural Systems I Lab 1 Introduction to Lab, Viewing MR Images, and MatLab®. Safety Video Lec 3 Overview of Neural Systems: Neural Systems II Rec 1 Human Subjects Safety Issues Lec 4 Overview of Neural Systems: Neural Systems III Lab 2 MRI Tour	Required Course Textbook: Huettel, S. A., A. W. Song, and G. McCarthy. Functional Magnetic Resonance Imaging. Sunderland, MA: Sinauer Associates, Inc, 2004, pp. 359-367, and 377-379. ISBN: 0878932887. Nolte, John. The Human Brain. 5th ed. Philadelphia, PA: Elsevier, 2001, Chapters 1, 3, 6, 13, 17, and 22. ISBN: 0323013201. Hanaway, J., et al. The Brain Atlas: A Visual Guide to the Human Central Nervous System. 2nd ed. New York, NY: Wiley & Sons, 2002, pp. 222-225. ISBN: 0471430587. Gazzaniga, M. Chapter 53 in The Cognitive Neurosciences. 3rd ed. Cambridge, MA: MIT Press, 2004. ISBN: 0262072548. Optional Kosslyn, S. M., et al. "Neural foundations of imagery." Nat Rev Neurosci 2, no. 9 (2001): 635-642. Hanaway. pp. 202-203. Course Textbook. Chapter 6, 13. Downar, J., A. P. Crawley, D. G. Mikulis, and K. D. Davis. "A Multimodal Cortical Network for the Detection of Changes in the Sensory Environment." Nat Neuro 3, no. 3 (2000): 277-283. Krüger, G., and G. H. Glover. "Physiological Noise in Oxygenation-Sensitive Magnetic Resonance Imaging." Magnetic Res in Med 46 (2001): 631-637. Mountcastle, V. B. "The Columnar Organization of the Neocortex." Brain 120 (1997): 701-722. Moore, C. I., S. B. Nelson, and M. Sur. "Dynamics of Neuronal Processing in Rat Somatosensory Cortex." TINS 22, no. 11 (1999): 513-520. Vanduffel, W., et al. "Visual Motion Processing Investigated Using Contrast Agent-Enhanced fMRI in Awake Behaving Monkeys." Neuron 32 (2001): 565-577. Logothetis, N. K., et al. "Neurophysiological Investigation of the Basis of the fMRI Signal." Nature 412, no. 6843 (2001): 150-157 Bush, G., P. Luu, and M. I. Posner. "Cognitive and Emotional Influences in Anterior Cingulate Cortex." Trends in Cog Sci 4, no. 6 (2000): 215-222. Bush, G., et al. "Dorsal Anterior Cingulate Cortex: A Role in Reward-based Decision Making." PNAS 99 no. 1 (2002): 507-512. Gusnard, D. A., and M. E. Raichle. "Searching for a Baseline: Functional Imaging and the Resting Human Brain." Nat Rev Neuro 2 (2001): 685-694. Fletcher, P. C., and R. N. A. Henson. "Frontal Lobes and Human Memory." Brain 124 (2001): 849-881. Milner, B., L. R. Squire, and E. R. Kandel. "Cognitive Neuroscience and the Study of the Memory." Neuron 20 (1998): 445-468. Functional Neuroanatomy Reading List (PDF) Functional Neural Systems (PDF)
Imaging Physiology
5-8	Lec 5 Overview of Imaging Physiology Applied Respiratory and Cardiovascular Physiology I Rec 2 See Bibliography Lec 6 Applied Respiratory and Cardiovascular Physiology II Lab 3 Introduction to fMRI Data Acquisition and Viewing Lec 7 Cerebrovascular Anatomy and Neural Regulation of CNS Blood Flow Rec 3 Review of Imaging Physiology The Big Picture of HST 583 Lec 8 Neurovascular Coupling. Global vs. Regionally Specific Changes in CBF and Metabolism Lab 4 Biophysical Basis of fMRI Signal. Introduction and Lab	Waldvogel, D., P. van Gelderen, W. Muellbacher, U. Ziemann, I. Immisch, and M. Hallett. "The relative metabolic demand of inhibition and excitation." Nature 406, no. 6799 (Aug 31, 2000): 995-8. Chillon, J. M., and G. L. Baumbach. "Autoregulation: Arterial and Intracranial Pressure." Chapter 25 in Cerebral Blood Flow and Metabolism. 2nd ed. Edited by L. Edvinsson, and D. N. Krause. Baltimore, MD: Lippincott Williams & Wilkins, 2002, pp. 395-412. ISBN: 0781722594. Buxton, R., ed. Chapters from Introduction to Functional Magnetic Resonance Imaging: Principles and Techniques. Cambridge, UK: Cambridge University Press, 2002. ISBN: 0521581133. - Chapter 1: "Energy Metabolism in the Brain," 4-21. - Chapter 2: "Cerebral Blood Flow," 22-40. - Chapter 3: "Brain Activation," 41-62. Edvinsson, L., and D. N. Krause. Chapters from Cerebral Blood Flow and Metabolism. ISBN: 0781722594. - Chapter 1: "General and Comparative Anatomy of the Cerebral Circulation." L. Edvinsson and E. T. MacKenzie, 71-87. - Chapter 9: "Neurotransmitters." P. J. Magistretti, L. Pellerin, and G. Bonvento, 162-171. - Chapter 10: "Neurovascular Control of the Cerebral Circulation." P. J. Goadsby and L. Edvinsson, 172-189. Respiratory and Circulatory Physiology for Brain Imagers (PDF) Special Features of Cerebral Circulation (PDF)
Experiment Design
9-10	Lec 9 General Principles of Experimental Design, point 1 Rec 4 See Bibliograhy Lec 10 General Principles of Experimental Design, point 2 Psychological State Variables in Imaging Rec 5 TBD	O'Craven, K. M., B. R. Rosen, K. K. Kwong, A. Treisman, and R. Savoy. "Voluntary attention modulated fMRI activity in human MT-MST." Neuron, 18 (1997): 591-598. Schultz, Gauther, et al. "Abnormal Ventral Temporal Cortical Activity During Face Discrimination Among Individuals With Autism and Asperger Syndrome." Arch Gen Psychiatry 57 (April 2000): 331. Hadjikhani, Joseph, Snyder, et al. "Activation of the fusiform gyrus when individuals with autism spectrum disorder view faces." NeuroImage 22 (2004): 1141-1150. Blood, A. J., A. W. Flaherty, J. K. Choi, F. H. Hochberg, D. N. Greve, G. Bonmassar, B. R. Rosen, and B. G. Jenkins. "Basal ganglia activity remains elevated after movement in focal hand dystonia." Ann Neurol 55, no. 5 (2004): 744-8. Friston, K. J., A. P. Holmes, and K. J. Worsley. "How Many Subjects Constitute a Study?" NeuroImage 10 (1999): 1-5. Jezzard, P., P. M. Matthews, and S. M. Smith. Chapters from Functional MRI: An Introduction to Methods. New York, NY: Oxford University Press, 2003. ISBN: 019852773X. - Chapter 9: "Effective Paradigm Design." D. I. Donaldson, and R. L. Buckner, 177-195.
Physics of Image Acquisition
11-17	Lec 11 Overview of Structural and Functional MRI Signal Acquisition Lab 5 Biophysical Basis of fMRI Signals, part 2 Lec 12 MRI Physics I Rec 6 Movement Artifacts in fMRI Lec 13 MRI Physics II Lab 6 Improving fMRI Signal using Physiological Data Lec 14 MRI Physics III Rec 7 TBD Lec 15 MRI Physics IV Lab 7 Extra Lab Session Lec 16 Physics of Diffusion Weighted Imaging Rec 8 TBD Lec 17 Diffusion Weighted Imaging II Lab 8 Diffusion Gradients Lab	Buxton, R. Chapters from Introduction to Functional Magnetic Resonance Imaging: Principles and Techniques. Cambridge, UK: Cambridge University Press, 2002. ISBN: 0521581133. - Chapter 4: "Nuclear Magnetic Resonance," 64-85. - Chapter 5: "Magnetic Resonance Imaging," 86-103. - Chapter 6: "Imaging Functional Activity," 104-120. - Chapter 7: "Basic Physics of Magnetism and NMR," 124-154. - Chapter 8: "Relaxation and Contrast in MRI," 155-184. - Chapter 10: "Mapping the MR Signal," 218-248. - Chapter 11: "MRI Techniques," 249-273. - Chapter 12: "Noise and Artifacts in MR Images," 274-303. - Chapter 16: "The Nature of the Blood Oxygenation Level Dependent Effect," 390-416. - Chapter 17: "Mapping Brain Activation with BOLD-fMRI," 417-444. Hall, D. A., et al. "Sparse Temporal Sampling in Auditory fMRI." Hum Brain Mapping 7 (1999): 213-223. Guimaraes, A. R., et al. "Imaging Subcortical Auditory Activity in Humans." Hum Brain Mapping 6 (1998): 33-41. Bihan, D. Le, et al. "Diffusion Tensor Imaging: Concepts and Applications." J Mag Res Imaging 12, no. 4 (2001): 534-546. Norris, D. G. "The Effects of Microscopic Tissue Parameters on the Diffusion Weighted Magnetic Resonance Imaging Experiment. NMR Biomed 14, no. 20 (2001): 77-93. Barbier, E., L. Lamalle, and M. Décorps. "Methodology of Brain Perfusion Imaging." J Mag Res Imaging 13 (2001): 496-520.
	Mid-term Exam
Statistical Analysis
18-23	Lec 18 Overview of fMRI Statistical Analysis. Stats I Lab 9 Statistical Analysis of fMRI Data, part 1 Lec 19 Overview of fMRI Statistical Analysis. Stats II Rec 9 TBD Lec 20 Overview of fMRI Statistical Analysis. Stats III Lab 10 Statistical Analysis of fMRI Data, part 2 Lec 21 Overview of fMRI Statistical Analysis. Stats IV Rec 10 TBD Lec 22 Overview of fMRI Statistical Analysis. Stats V Lab 11 Morphometric Analysis Lec 23 Overview of fMRI Statistical Analysis. Stats VI Rec 11 TBD	Leite, F. P., D. Tsao, W. Vanduffel, D. Fize, Y. Sasaki, L. L. Wald, A. M. Dale, K. K. Kwong, G. A. Orban, B. R. Rosen, R. B. Tootell, and J. B. Mandeville. "Repeated fMRI using iron oxide contrast agent in awake, behaving macaques at 3 Tesla." NeuroImage 16, no. 2 (June, 2002): 283-94. Kenet, T., D. Bibitchkov, M. Tsodyks, A. Grinvald, and A. Arieli. "Spontaneously emerging cortical representations of visual attributes." Nature 425, no. 6961 (Oct 30, 2003): 954-6. Ikegaya, Y., G. Aaron, R. Cossart, D. Aronov, I. Lampl, D. Ferster, and R. Yuste. "Synfire chains and cortical songs: temporal modules of cortical activity." Science 304, no. 5670 (Apr 23, 2004): 559-64. Dale, A. M., and R. L. Buckner. "Selective Averaging of Rapidly Presented Individual Trials Using fMRI." Hum Brain Mapping 5 (1997): 329-340. Burock M. A., and A. M. Dale. "Estimation and Detection of Event-Related fMRI Signals with Temporally Correlated Noise: A Statistically Efficient and Unbiased Approach." Hum Brain Mapping 11 (2000): 249-260. Jezzard, P., P. M. Matthews, and S. M. Smith. Chapters from Functional MRI: An Introduction to Methods. New York, NY: Oxford University Press, 2003. ISBN: 019852773X. - Chapter 11: "Overview of fMRI Analysis." S. M. Smith, 215-228. - Chapter 12: "Preparing fMRI Data for Statistical Analysis." S. M. Smith, 229-242. - Chapter 13: "Head Motion and its Correction." M. J. Brammer, 243-250. - Chapter 14: "Statistical Analysis of Activation Images." K. J. Worsley, 251-270. (With annotations from Mark Vangel.) Genovese, C. R., N. A. Lazar, and T. Nichols. "Thresholding of Statistical Maps in Functional Neuroimaging Using the False Discovery Rate." NeuroImage 15, (2002): 870-878. Makris, N., et al. "Diffusion Tensor Imaging." Chapter 27 in Neuropsychopharmacology. Baltimore, MD: Lippincott Williams & Wilkins, 2002. ISBN: 0781728371. Brett, M., I. S. Johnsrude, and A. M. Owen. "The Problem of Functional Localization in the Human Brain." Nat Rev Neuroscience 3 (2002): 243-249.
Structural and Functional Analysis
24-25	Lec 24 Spatial Normalization for Anatomical Analysis. DTI Applications Lec 25 Surface-based Anatomical Analysis	Fischl, B., and A. M. Dale. "Measuring the Thickness of the Human Cerebral Cortex from Magnetic Resonance Imaging." PNAS 97, no. 20 (2000): 11050-11055. Dale, A. M., et al. "Dynamic Statistical Parametric Mapping: Combining fMRI and MEG for High-resolution Imaging of Cortical Activity." Neuron 26, no. 1 (2000): 55-67.
	Final Exam

Supplementary Reading

Suggested for Students with no Prior Neuroscience Background

Nolte, John. Chapters from The Human Brain. 5th ed. Philadelphia, PA: Elsevier, 2001. ISBN: 0323013201.

Chapter 1: "Introduction to the Nervous System."
Chapter 3: "Gross Anatomy and General Organization of the Central Nervous System."

Suggested for Students with no Prior Statistics Background

DeGroot, M. H., and M. J. Schervish. Chapters from Probability and Statistics. 3rd ed. Reading, MA: Addison-Wesley Press, 2001. ISBN: 0201524880.

Chapter 1: "Introduction to Probability."
Chapter 2: "Conditional Probability."

Texts to Supplement Physiology Lectures

West, John B. Pulmonary Physiology and Pathophysiology: An Integrated, Case-Based Approach . 1st ed. Baltimore, MD: Lippincott Williams & Wilkins Publishers, 2001. ISBN: 0781729106. [Paperback. Widely used by medical students. Not much depth on neurophysiology of breathing, but good for gas exchange etc.]

Richardson, Daniel R., David C. Randall, and Dexter F. Speck. Cardiopulmonary System. 1st ed. Raleigh, NC: Hayes Barton Press, 1998. ISBN: 1889325309. [Paperback. This book is not known to me, but Dexter Speck is a good respiratory neurophysiologist.]

Levitzky, Michael G. Pulmonary Physiology. 5th ed. New York, NY: McGraw-Hill Professional Publishing, 1999. ISBN: 0781729106.
[I am told by a colleague this is a good book.]

Vander, Arthur, James Sherman, and Dorothy Lucian. Human Physiology: The Mechanisms of Body Function, 8th ed. New York, NY: McGraw-Hill Higher Education, 2000. ISBN: 0072378441. [This is a readable and reliable text covering all systems. We have used it for years in my department.]

Pruessmann K. P., Weiger M., Scheidegger M. B., and Boesiger P. "SENSE: Sensitivity Encoding for Fast MRI." Magnetic Resonance in Medicine 42 (1999): 952-962.

Sodickson D. K., and Manning W. J. "Simultaneous Acquisiiton of Spatial Harmonics (SMASH): Fast Imaging with Radiofrequency Coil Arrays." Magnetic Resonance in Medicine 38 (1997): 591-603.

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