Overview

Lecture 9/6

First chapter of course textbook after lecture 1.
Second chapter of course textbook before lab 1.

Lab 9/11

Human Subjects Safety Handout.
Optional:
1: Northoff G, Heinzel A, de Greck M, Bermpohl F, Dobrowolny H, Panksepp J.
Self-referential processing in our brain--a meta-analysis of imaging studies on
the self. Neuroimage. 2006 May 15;31(1):440-57. Epub 2006 Feb 7.

Functional Neural Systems

Lecture 9/13 - 9/18

Please note: reading that are assigned from texts other than the course textbook are supplementary.

1. Course textbook, pp 359-367; John Nolte, The Human Brain, chapters 1 and 3; optional: remainder of Ch 13; Nolte chapter 22

2. Course book, pp 377-379; Nolte 547-561 optional: remainder of Ch 13; Hanaway, pp 222-225; Michael Gazzaniga, The Cognitive Neurosciences, chapter 53

3. Nolte, Chapter 17; Nolte, Ch 22 (pp 506-525) optional: Kosslyn SM et al., Neural foundations of imagery. Nat Rev Neurosci 2001;2(9):635-642; Hanaway, 202-203; remainder of Nolte Ch 22

4. Nolte, Ch 6

5. Course book, chapter 6

MRI Physics

Lecture 10/4 - 10/23

Ch. 3: Basic Principles of MR Signal Generation
Ch. 4: Basic Principles of MR Signal Formation
Ch. 5: MR Contrast Mechanisms and Pulse Sequences
Ch. 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 by Rick Buxton (this book ison reserve for them).

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.

General Principles of Experimental Design

Lecture 10/30 - 11/6

Course textbook
Ch. 9: Signal & Noise in fMRI
Ch. 11: Experimental Design

fMRI Statistical Analysis

Lecture 11/13 - 11/29

Course textbook
Ch. 10: Preprocessing of fMRI Data
Ch. 12: Statistical Analysis

fMRI Structural and functional analysiss

Lecture 12/4 - 12/11

Course textbook
Ch. 8: Spatial and temporal properties of fMRI
Ch. 13: Applications of fMRI
Ch. 14: Advanced fMRI methods
Ch. 15: Converging Operations

 

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

 

Materials currently or to be soon found on reserve in the Hayden Science Library (14S-100):
(there are currently two copies of Nolte; one on reserve and the other in science reference.)

Reference Books

• 1. Functional Magnetic Resonance Imaging, S. A. Huettel, A. W. Song, and G. McCarthy, Sinauer, April 2004, ISBN 0-87893-288-7.
• 2. The Human Brain: An Introduction to Its Functional Anatomy, J. Nolte, C. V. Mosby, 5th edition, January 2002, ISBN 0-32301-320-1.
• Functional MRI: An Introduction to Methods. P. Jezzard, P. M. Matthews, S. M. Smith, eds. Oxford University Press (2001). ISBN 0-19-263071-7
• 3. Cerebral Blood Flow and Metabolism. L. Edvinsson and D. N. Krause, eds. Second edition. Lippincott, Williams & Wilkins (2002). ISBN 0-7817-2259-4.
• 4. Introduction to Functional Magnetic Resonance Imaging: Principles and Techniques. R. Buxton, ed. Cambridge University Press (2002). ISBN 0-521-58113-3.
• 5. Functional MRI: An Introduction to Methods. P. Jezzard, P. M. Matthews, S. M. Smith, eds. Oxford University Press (2001). ISBN 0-19-263071-7
• 6. Vander, Sherman, Luciano's Human Physiology: The Mechanisms of Body Function. Eric P. Widmaier, Hershel Raff, Kevin T. Strang. McGraw Hill (2002). 9th edition. ISBN 0-0724-3793-6.
• 7. Probability and Statistics. M. H. DeGroot and M. J. Schervish. Addison-Wesley Press (2001). 3rd edition. ISBN 0-201-52488-0.
• 8. Cognitive Neuroscience. Michael S. Gazzaniga, Richard B. Ivry, George R. Mangun. Norton & Company (2002). 2nd edition. ISBN 0-393-97777-3.
• 9. The Brain Atlas. Joseph Hanaway, Thomas A. Woolsey, Mokhtar Gado, Melville P. J. R. Roberts. Wiley & Sons Inc. (1998). ASIN 1891786067.

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.