MIT OpenCourseWare
  • OCW home
  • Course List
  • about OCW
  • Help
  • Feedback
    • Support MIT OCW

 » MIT OpenCourseWare » Health Sciences and Technology » Functional Magnetic Resonance Imaging: Data Acquisition and Analysis, Fall 2002

Readings

Required Reading

LEC # LECTURE READINGS LAB READINGS
Overview

1

Savoy, R. L. "History and Future Directions of Human Brain Mapping and Functional Neuroimaging." Acta Psychologica 107 (2001): 9-42.
Functional Neural Systems
2

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.
3

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.
4

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.
Imaging Physiology
5
6 Chillon, J. M., and G. L. Baumbach. "Autoregulation: Arterial and Intracranial Pressure." Chap. 25 in Cerebral Blood Flow and Metabolism. 2nd ed. Edited by L. Edvinsson and D. N. Krause. Lippincott Williams & Wilkins, 2002, pp. 395-412.
7

Buxton, R., ed. Chapters from Introduction to Functional Magnetic Resonance Imaging: Principles and Techniques. Cambridge University Press (2002).

  • Chap. 1: "Energy Metabolism in the Brain," 4-21.
  • Chap. 2: "Cerebral Blood Flow," 22-40.
  • Chap. 3: "Brain Activation," 41-62.

Edvinsson, L., and D. N. Krause. Chapters from Cerebral Blood Flow and Metabolism.

  • Chap. 1: "General and Comparative Anatomy of the Cerebral Circulation." L. Edvinsson and E. T. MacKenzie, 71-87.
  • Chap. 9: "Neurotransmitters." P. J. Magistretti, L. Pellerin, and G. Bonvento, 162-171.
  • Chap. 10: "Neurovascular Control of the Cerebral Circulation." P. J. Goadsby and L. Edvinsson, 172-189.
8

Buxton, R., ed. Chapters from Introduction to Functional Magnetic Resonance Imaging: Principles and Techniques. Cambridge University Press (2002).

  • Chap. 1: "Energy Metabolism in the Brain," 4-21.
  • Chap. 2: "Cerebral Blood Flow," 22-40.
  • Chap. 3: "Brain Activation," 41-62.

Edvinsson, L., and D. N. Krause. Chapters from Cerebral Blood Flow and Metabolism.

  • Chap. 1: General and Comparative Anatomy of the Cerebral Circulation. L Edvinsson and E. T. MacKenzie, 71-87.
  • Chap. 9: "Neurotransmitters." P. J. Magistretti, L. Pellerin, and G. Bonvento, 162-171.
  • Chap. 10: "Neurovascular Control of the Cerebral Circulation." P. J. Goadsby and L. Edvinsson, 172-189.
Physics of Image Acquisition
9

Buxton, R. Chapters from Introduction to Functional Magnetic Resonance Imaging: Principles and Techniques.

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

Buxton, R. Chapters from Introduction to Functional Magnetic Resonance Imaging: Principles and Techniques.

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

Buxton, R. Chapters from Introduction to Functional Magnetic Resonance Imaging: Principles and Techniques.

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

Buxton, R. Chapters from Introduction to Functional Magnetic Resonance Imaging: Principles and Techniques.

  • Chap. 4: "Nuclear Magnetic Resonance," 64-85.
  • Chap. 5: "Magnetic Resonance Imaging," 86-103.
  • Chap. 6: "Imaging Functional Activity," 104-120.
  • Chap. 7: "Basic Physics of Magnetism and NMR," 124-154.
  • Chap. 8: "Relaxation and Contrast in MRI," 155-184.
  • Chap. 10: "Mapping the MR Signal," 218-248.
  • Chap. 11: "MRI Techniques," 249-273.
  • Chap. 12: "Noise and Artifacts in MR Images," 274-303.
  • Chap. 16: "The Nature of the Blood Oxygenation Level Dependent Effect," 390-416.
  • Chap. 17: "Mapping Brain Activation with BOLD-fMRI," 417-444.
13

Buxton, R. Chapters from Introduction to Functional Magnetic Resonance Imaging: Principles and Techniques.

  • Chap. 4: "Nuclear Magnetic Resonance," 64-85.
  • Chap. 5: "Magnetic Resonance Imaging," 86-103.
  • Chap. 6: "Imaging Functional Activity," 104-120.
  • Chap. 7: "Basic Physics of Magnetism and NMR," 124-154.
  • Chap. 8: "Relaxation and Contrast in MRI," 155-184.
  • Chap. 10: "Mapping the MR Signal," 218-248.
  • Chap. 11: "MRI Techniques," 249-273.
  • Chap. 12: "Noise and Artifacts in MR Images," 274-303.
  • Chap. 16: "The Nature of the Blood Oxygenation Level Dependent Effect," 390-416.
  • Chap. 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.
14

Buxton, R. Chapters from Introduction to Functional Magnetic Resonance Imaging: Principles and Techniques.

  • Chap. 4: "Nuclear Magnetic Resonance," 64-85.
  • Chap. 5: "Magnetic Resonance Imaging," 86-103.
  • Chap. 6: "Imaging Functional Activity," 104-120.
  • Chap. 7: "Basic Physics of Magnetism and NMR," 124-154.
  • Chap. 8: "Relaxation and Contrast in MRI," 155-184.
  • Chap. 10: "Mapping the MR Signal," 218-248.
  • Chap. 11: "MRI Techniques," 249-273.
  • Chap. 12: "Noise and Artifacts in MR Images," 274-303.
  • Chap. 16: "The Nature of the Blood Oxygenation Level Dependent Effect," 390-416.
  • Chap. 17: "Mapping Brain Activation with BOLD-fMRI," 417-444.
15

Bihan, D. Le, et al. "Diffusion Tensor Imaging: Concepts and Applications." J Mag Res Imaging12, 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.
16

Jezzard, P., P. M. Matthews, and S. M. Smith, eds. Chapter from Functional MRI: An Introduction to Methods. Oxford University Press (2001).

  • Chap. 8: "Quantitative Measurement Using fMRI." R. D. Hoge, G. B. Pike, 159-174.

Buxton, R. Chapter from Introduction to Functional Magnetic Resonance Imaging: Principles and Techniques.

  • Chap. 15: "Arterial Spin Labeling Techniques," 351-388.
17
Experiment Design
18

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.

  • Chap. 9: "Effective Paradigm Design." D. I. Donaldson and R. L. Buckner, 177-195.
19

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.

  • Chap. 9: "Effective Paradigm Design." D. I. Donaldson and R. L. Buckner, 177-195.
Statistical Analysis
20

Jezzard, P., P. M. Matthews, and S. M. Smith. Chapters from Functional MRI: An Introduction to Methods.

  • Chap. 11: "Overview of fMRI Analysis." S. M. Smith, 215-228.
21

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.

  • Chap. 12: "Preparing fMRI Data for Statistical Analysis." S. M. Smith, 229-242.
  • Chap. 13: "Head Motion and its Correction." M. J. Brammer, 243-250.
22

Jezzard, P., P. M. Matthews, and S. M. Smith. Chapters from Functional MRI: An Introduction to Methods.

  • Chap. 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.
23
24

Makris, N. et al. "Diffusion Tensor Imaging." Chap. 27 in Neuropsychopharmacology. Lippincott Williams & Wilkins, 2002.

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 Analysis
25 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.
26

Dale, A. M. et al. "Dynamic Statistical Parametric Mapping: Combining fMRI and MEG for High-resolution Imaging of Cortical Activity." Neuron26, no. 1 (2000): 55-67.
27

Supplementary Reading

Suggested for students with no prior neuroscience background:

Nolte, J. Chapters from The Human Brain: An Introduction to Its Functional Anatomy.

  • Chap. 1: "Introduction to the Nervous System."
  • Chap. 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.

  • Chap. 1: "Introduction to Probability."
  • Chap. 2: "Conditional Probability."

Texts to supplement physiology lectures:

West, John B. Pulmonary Physiology and Pathophysiology: An Integrated, Case-Based Approach. 1st ed. Lippincott Williams & Wilkins Publishers, 15 Jan. 2001. (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. 15 Jan., 1998. (Paperback) - 353 pages.
This book not known to me, but Dexter Speck is a good respiratory neurophysiologist.

Levitzky, Michael G. Pulmonary Physiology. 5th ed. McGraw-Hill Professional Publishing, 1999 - 320 pages.
I'm 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. McGraw-Hill Higher Education, 2000 - 864 pages.
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.

 
Creative Commons - some rights reserved

Your use of the MIT OpenCourseWare site and course materials is subject to the conditions and terms of use in our Legal Notices section.