Overview

Lecture 9/4
History and future directions of human brain mapping and functional neuroimaging." R. L. Savoy. Acta Psychologica (2001), 107, 9-42.

Functional Neural Systems (Weeks 2 & 3)

Lab 9/9
Physiological Noise in Oxygenation-Sensitive Magnetic Resonance Imaging. G. Krüger and G. H. Glover. Magnetic Res in Med (2001), 46, 631-637.

Lecture 9/9
A multimodal cortical network for the detection of changes in the sensory environment. J. Downar, A. P. Crawley, D. G. Mikulis, K. D. Davis. Nat Neuro (2000), 3 (3), 277-283.

Lecture 9/11
The columnar organization of the neocortex. V. B. Mountcastle. Brain (1997), 120, 701-722.
Dynamics of neuronal processing in rat somatosensory cortex. C. I Moore, S. B. Nelson, M. Sur. TINS (1999), 22 (11), 513-520.
Visual Motion Processing Investigated Using Contrast Agent-Enhanced fMRI in Awake Behaving Monkeys. W. Vanduffel, et al. Neuron (2001), 32, 565-577.
Neurophysiological investigation of the basis of the fMRI signal. N. K. Logothetis, et al. Nature (2001), 412 (6843), 150-157.

Discussion 9/11
Distributed and Overlapping Representations of Faces and Objects in Ventral Temporal Cortex. J. V. Haxby, et al. Science (2001), 293, 2425-2430.
The Fusiform Face Area: A Module in Human Extrastriate Cortex Specialized for Face Perception. N. Kanwisher, J. McDermott, M. M. Chun. J Neurosci (1997), 17 (11), 4302-4311.

Lecture 9/16
Cognitive and emotional influences in anterior cingulate cortex. G. Bush, P. Luu, M. I. Posner. Trends in Cog Sci (2000), 4 (6), 215-222.
Dorsal anterior cingulate cortex: A role in reward-based decision making. G. Bush, et al. PNAS (2002), 99 (1), 507-512.
Searching for a baseline: Functional imaging and the resting human brain. D. A. Gusnard, M. E. Raichle. Nat Rev Neuro (2001), 2, 685-694.
Frontal lobes and human memory. P. C. Fletcher, R. N. A. Henson. Brain (2001), 124, 849-881.
Cognitive Neuroscience and the Study of the Memory. B. Milner, L. R. Squire, E. R. Kandel. Neuron (1998), 20, 445-468.

Imaging Physiology (Weeks 3, 4 & 5)

Discussion 9/18
Neural mechanisms of blood flow regulation during synaptic activity in cerebellar cortex. C. Iadecola, J. Li, S. Xu and G. Yang. J Neurophysiol. (1996), 75 (2), 940-850.
Blood flow and oxygen delivery to human brain during functional activity: Theoretical modeling and experimental data. M. A. Mintun, et al. PNAS (2001), 98 (12) 6859-6864.

Lecture 9/25
Chapters from Cerebral Blood Flow and Metabolism. L. Edvinsson and D. N. Krause, eds. Second edition. Lippincott, Williams & Wilkins (2002). ISBN 0-7817-2259-4.
- Ch. 25: Autoregulation: Arterial and Intracranial Pressure. J. M. Chillon and G. L. Baumbach, 395-412.

Discussion 9/25
To be determined

Lectures 9/30 and 10/2
Chapters from Introduction to Functional Magnetic Resonance Imaging: Principles and Techniques. R. Buxton, ed. Cambridge University Press (2002). ISBN 0-521-58113-3.
- Ch. 1: Energy Metabolism in the Brain, 4-21.
- Ch. 2: Cerebral Blood Flow, 22-40.
- Ch. 3: Brain Activation, 41-62.
Chapters from Cerebral Blood Flow and Metabolism. L. Edvinsson and D. N. Krause.
- Ch. 1: General and Comparative Anatomy of the Cerebral Circulation. L Edvinsson and E. T. MacKenzie, 71-87.
- Ch. 9: Neurotransmitters. P. J. Magistretti, L. Pellerin, and G. Bonvento, 162-171.
- Ch. 10: Neurovascular Control of the Cerebral Circulation. P. J. Goadsby and L. Edvinsson, 172-189.

Discussion 10/2
Functional MRI at 1.5 tesla: A comparison of the blood oxygenation level-dependent signal and electrophysiology. E. A. Disbrow, D. a. Slutsky, T. P. L. Roberts, and L. A. Krubitzer. PNAS (2000), 97 (17), 9718-9723.
Regionally Specific Sensitivity Difference in fMRI and PET: Where do they come from? D. J. Veltman, K. J. Friston, G. Sanders, and C. J. Price. NeuroImage (2000), 11, 575-588.

Physics Of Image Acquisition (Weeks 6 -10)

Lectures 10/7, 10/9, 10/16, 10/21, 10/23, 10/28
Chapters from Introduction to Functional Magnetic Resonance Imaging: Principles and Techniques. R. Buxton
- Ch. 4: Nuclear Magnetic Resonance, 64-85.
- Ch. 5: Magnetic Resonance Imaging, 86-103.
- Ch. 6: Imaging Functional Activity, 104-120.
- Ch. 7: Basic Physics of Magnetism and NMR, 124-154.
- Ch. 8: Relaxation and Contrast in MRI, 155-184.
- Ch. 10: Mapping the MR Signal, 218-248.
- Ch. 11: MRI Techniques, 249-273.
- Ch. 12: Noise and Artifacts in MR Images, 274-303.
- Ch. 16: The Nature of the Blood Oxygenation Level Dependent Effect, 390-416.
- Ch. 17: Mapping Brain Activation with BOLD-fMRI, 417-444.

Discussion 10/9
To be determined

Discussion 10/16
To be determined

Lecture 10/23
"Sparse" Temporal Sampling in Auditory fMRI. D. A. Hall, et al. Hum. Brain Mapping (1999), 7, 213-223.
Imaging Subcortical Auditory Activity in Humans. A. R. Guimaraes, et al. Hum. Brain Mapping (1998), 6, 33-41.

Discussion 10/23
To be determined

Lecture 10/30
Diffusion tensor imaging: Concepts and applications. D Le Bihan, et al. J Mag Res Imaging (2001), 12 (4), 534-546.
The effects of microscopic tissue parameters on the diffusion weighted magnetic resonance imaging experiment. D. G. Norris. NMR Biomed (2001), 14 (20), 77-93.
Methodology of Brain Perfusion Imaging. E. Barbier, L. Lamalle, M. Décorps. J Mag Res Imaging (2001), 13, 496-520.

Discussion 10/30
Turbo ASL: Arterial Spin Labeling with Higher SNR and Temporal Resolution. E. C. Wong, W. Luh, T. T. Liu. Mag Res Med (2000), 44, 511-515.

Lecture 11/4
Chapter from Functional MRI: An Introduction to Methods. P. Jezzard, P. M. Matthews, S. M. Smith, eds. Oxford University Press (2001). ISBN 0-19-263071-7
- Ch. 8: Quantitative measurement using fMRI. R. D. Hoge, G. B. Pike, 159-174.
Chapter from Introduction to Functional Magnetic Resonance Imaging: Principles and Techniques. R. Buxton
- Ch. 15: Arterial Spin Labeling Techniques, 351-388.

Experimental Design (Weeks 11 & 12)

Lecture 11/13 and 11/18
How Many Subjects Constitute a Study? K. J. Friston, A. P. Holmes, and K. J. Worsley. NeuroImage (1999), 10, 1-5.
Chapters from Functional MRI: An Introduction to Methods. P. Jezzard, P. M. Matthews, S. M. Smith
- Ch. 9: Effective paradigm design. D. I. Donaldson and R. L. Buckner, 177-195.

Discussion 11/13
Prefrontal cortex dysfunction during working memory performance in schizophrenia: Reconciling discrepant findings. D. S. Manoach. (Schizophrenia Research, in press)
When zero is not zero: The problem of ambiguous baseline conditions in fMRI. C. E. L. Stark, L. R. Squire. PNAS (2001), 98 (22), 12760-12766.

Statistical Analysis (Weeks 13 & 14)

Lecture 11/20
Chapters from Functional MRI: An Introduction to Methods. P. Jezzard, P. M. Matthews, S. M. Smith
- Ch. 11: Overview of fMRI analysis. S. M. Smith, 215-228.

Lab 11/25
Chapters from Functional MRI: An Introduction to Methods. P. Jezzard, P. M. Matthews, S. M. Smith
- Ch. 12: Preparing fMRI data for statistical analysis. S. M. Smith, 229-242.
- Ch. 13: Head motion and its correction. M. J. Brammer, 243-250.

Lecture 11/25
Selective Averaging of Rapidly Presented Individual Trials Using fMRI. A. M. Dale and R. L. Buckner. Hum. Brain Mapping (1997), 5, 329-340.
Estimation and Detection of Event-Related fMRI Signals with Temporally Correlated noise: A Statistically Efficient and Unbiased Approach. M. A. Burock and A. M. Dale. Hum. Brain Mapping (2000), 11, 249-260.

Lecture 11/27
Chapters from Functional MRI: An Introduction to Methods. P. Jezzard, P. M. Matthews, S. M. Smith
- Ch. 14: Statistical analysis of activation images. K. J. Worsley, 251-270. (with annotations from Mark Vangel)
Thresholding of Statistical Maps in Functional Neuroimaging Using the False Discovery Rate. C. R. Genovese, N. A. Lazar, and T. Nichols. NeuroImage (2002), 15, 870-878.

Lecture 12/4
Diffusion Tensor Imaging. N. Makris, et al. Neuropsychopharmacology, Lippincott, Williams & Wilkins (2002). (Ch. 27).
The problem of functional localization in the human brain. M. Brett, I. S. Johnsrude and A. M. Owen. Nat. Rev. Neuroscience (2002), 3, 243-249.

Discussion 12/4
Optimal Experimental Design for Event-Related fMRI. A. M. Dale. Hum. Brain Mapping (1999), 8, 109-114.

Structural Analysis (Week 15)

Lecture 12/9
Measuring the thickness of the human cerebral cortex from magnetic resonance imaging. B. Fischl and A. M. Dale. PNAS (2000), 97 (20), 11050-11055.

Lecture 12/11
Dynamic statistical parametric mapping: combining fMRI and MEG for high-resolution imaging of cortical activity. A. M. Dale, et al. Neuron (2000), 26 (1), 55-67.

Discussion 12/11
To be determined

 

Supplementary Reading

Suggested for students with no prior neuroscience background

• Chapters from The Human Brain: An Introduction to Its Functional Anatomy. J. Nolte
  - Ch. 1: Introduction to the Nervous System
  - Ch. 3: Gross Anatomy and General Organization of the Central Nervous System

Suggested for students with no prior statistics background

• Chapters from Probability and Statistics. M. H. DeGroot and M. J. Schervish
  - Ch. 1: Introduction to Probability
  - Ch. 2: Conditional Probability

Texts to supplement physiology lectures:

• Pulmonary Physiology and Pathophysiology: An Integrated, Case-Based Approach by John B. West, Paperback 1st edition (January 15, 2001) Lippincott Williams & Wilkins Publishers; ISBN: 0781729106
  Amazon Price: $31.95
  Widely used by medical students. Not much depth on neurophysiology of breathing, but good for gas exchange etc.
• Cardiopulmonary System, Daniel R. Richardson, David C. Randall, Dexter F. Speck, Paperback - (January 15, 1998) 353 pages, Amazon Price: $25.95
  This book not known to me, but Dexter Speck is a good respiratory neurophysiologist
• Pulmonary Physiology, Michael G. Levitzky, 320 pages 5th edition (1999) McGraw-Hill Professional Publishing; ISBN: 0071345434, Amazon Price: $29.95
  I'm told by a colleague this is a good book.
• Human Physiology: The Mechanisms of Body Function, Arthur Vander, James Sherman, Dorothy Lucian 864 pages 8th edition Book&CDROM (2000) Amazon Price: $119.45 McGraw-Hill Higher Education; ISBN: 0072378441
  This is a readable and reliable text covering all systems -- We have used it for years in my department.

 

Materials on reserve in Schering-Plough Library (E25-131):

Reference Books

• Cerebral Blood Flow and Metabolism. L. Edvinsson and D. N. Krause, eds. Second edition. Lippincott, Williams & Wilkins (2002). ISBN 0-7817-2259-4.
• Introduction to Functional Magnetic Resonance Imaging: Principles and Techniques. R. Buxton, ed. Cambridge University Press (2002). ISBN 0-521-58113-3.
• Functional MRI: An Introduction to Methods. P. Jezzard, P. M. Matthews, S. M. Smith, eds. Oxford University Press (2001). ISBN 0-19-263071-7
• The Human Brain: An Introduction to Its Functional Anatomy. J. Nolte. Fifth edition. Mosby Press (2002).
• Probability and Statistics. M. H. DeGroot and M. J. Schervish. Addison-Wesley Press (2002).
• Magnetic Resonance Procedures: Health Effects and Safety, F.G. Shellock, CRC Presss, (2001).
• Human Physiology: the mechanisms of body function, A.J. Vander, J.H. Sherman, D.S. Luciano, 3rd Edition, (1980).

Introductory material on Fourier transforms:

• Signals and Systems Made Ridiculously Simple. Z. Z. Karu, ZiZi Press (1995). Chapter 16: Fourier Transforms

Miscellaneous Useful Materials:

• Chapters from Magnetic Resonance Imaging: Physical Principles and Sequence Design. Haacke, Brown, Thompson and Venkatesan
  - Ch. 1: Magnetic Resonance Imaging: A Preview
  - Ch. 2: Clasical Nucleus in Magnetic Field
  - Ch. 3: Rotating Reference Frames and Resonance
  - Ch. 4: Magnetization, Relaxation and the Bloch Equation
  - Ch. 41: MRI I: The Quantum View of Nuclear Magnetic Resonance Imaging
  - Ch. 42: MRI II: The Classical View of Nuclear Magnetic Resonance Imaging
  - Ch. 43: MRI III: Relaxation Times, Pulse Sequences, and Image Contrast
  - Ch. 44: MRI IV: Imaging
• Chapters from The Fast Fourier Transform and its applications. E. O. Brigham
  - Ch. 2: The Fourier Transform
  - Ch. 3: Fourier Transform Properties
  
• Chapters from NMR Tomography, Diffusometry, Relaxometry. R. Kimmich
  - Ch. 24: Survey
  - Ch. 25: Fundamentals of NMR Imaging
• Chapters from: Functional MRI. C.T.W. Moonen and P.A. Bandettini (1999)
  - Ch. 11: Basic Theoretical Models of BOLD Signal Change. R. M. Weisskoff
  - Ch. 13: Echo-Planar Imaging and Functional MRI. M. S. Cohen
  - Ch. 16: Physiological Noise: Strategies for Correction. P. Jezzard.
• An Introduction to NMR Imaging: From the Bloch equation to the imaging equation. W. S. Hinshaw and A. H. Lent, Proc. IEEE, Vol. 71, No. 3, March 1983.
• M. Mesulam, From Sensation to Cognition, Brain (1998), 121, 1013-1052.