Brain Mapping: The Methods: The Methods
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Table of contents
- Cover
- Brain Mapping: The Methodsiii
- Copyright Pageiv
- Contentsv
- Contributorsxi
- Prefacexv
- Acknowledgmentsxvii
- Part I: Introduction1
- Chapter 1. Introduction to Cartography of the Brain3
- I. Introduction to Cartography3
- II. The Dimensions of a Brain Map6
- III. The Full Scope of Brain Mapping11
- IV. Relationships to Other Biological Maps14
- V. Stereotaxy15
- VI. Nomenclature17
- VII. Detection Devices18
- VIII. Brain Maps: Content and Format21
- IX. Summary25
- References26
- Chapter 2. Time and Space33
- I. Introduction33
- II. Critical Variables in Brain Mapping Techniques34
- III. The Concept of Resolution36
- IV. Sampling40
- V. Sites Accessed43
- VI. Invasiveness44
- VII. Conclusions44
- References45
- Part II: Surface-Based Data Acquisition47
- Chapter 3. Optical Imaging of Neural Structure and Physiology: Confocal Fluorescence Microscopy in L49
- I. Introduction49
- II. Live Brain Slice Preparation and Culture51
- III. Labeling Neuronal and Glial Cells in Brain Tissue Slices52
- IV. Imaging Methodology57
- V. Application: Mapping Neural Structure and Physiology in Developing Brain Slices61
- VI. Conclusions and Future Prospects71
- References73
- Chapter 4. Voltage and Calcium Imaging of Brain Activity: Examples from the Turtle and the Mouse77
- I. Why (and Why Not) Voltage and Calcium Imaging77
- II. Signal Type78
- III. Dyes78
- IV. Amplitude of the Voltage or Calcium Change81
- V. Noise in the Optical Measurements81
- VI. Light Sources83
- VII. Optics83
- VIII. Cameras84
- IX. Comparison of Local Field Potential and Voltage-Sensitive Dye Recording85
- X. Voltage-Sensitive Dye Recording in the Turtle Olfactory Bulb85
- XI. Calcium Dye Recording in the Mouse Olfactory Bulb89
- XII. Intrinsic Imaging and Fluorescence Signals from In Vivo Mammalian Brain93
- XIII. Summary and Future Directions93
- References94
- Chapter 5. Optical Imaging Based on Intrinsic Signals97
- I. Introduction97
- II. Sources of Intrinsic Signals and Wavelength Dependency98
- III. Preparation of an Animal for Optical Imaging103
- IV. The Apparatus107
- V. Data Acquisition112
- VI. Data Analysis for Mapping Functional Architecture114
- VII. Chronic Optical Imaging121
- VIII. Optical Imaging of the Human Neocortex123
- IX. Combining Optical Imaging with Other Techniques125
- X. Applications130
- XI. Comparison of Intrinsic Optical Imaging with Other Imaging Techniques135
- XII. Conclusions and Outlook136
- References137
- Chapter 6. Near-Infrared Spectroscopy and Imaging141
- I. Introduction141
- II. Optical Window for Noninvasive Studies142
- III. Other Optical Parameters Relevant for Near-Infrared Studies143
- IV. Technical Approaches for Near-Infrared Spectroscopy and Imaging143
- V. Physiological Parameters of NIRS Measurements144
- VI. Near-Infrared Spectroscopy and Imaging: Applications149
- VII. Practical Aspects of NIRS Measurements151
- VIII. Problems and Perspectives155
- References156
- Chapter 7. Dynamic Measurements of Local Cerebral Blood Flow: Examples from Rodent Whisker Barrel Co159
- I. Why Measure Local Cerebral Blood Flow?159
- II. Function and Structural Contexts160
- III. Global Tracers161
- IV. Volatile Tracers162
- V. Doppler Flowmetry163
- VI. Video Microscopy163
- VII. Localization of Activity Changes164
- VIII. Diameter165
- IX. Intravascular Dyes166
- X. Intravascular Particles167
- XI. Localization of Flow Changes169
- XII. Conclusions and Prospects169
- References170
- Chapter 8. Electrophysiological Imaging of Brain Function175
- I. Introduction175
- II. The Electroencephalogram and Averaged Event-Related Potentials176
- III. Improving the Spatial Resolution of the Electroencephalogram179
- IV. Analysis of Functional Networks183
- V. The EEG as a Monitoring (vs Imaging) Modality185
- VI. Summary and Conclusions186
- References186
- Chapter 9. Electrophysiological Methods for Mapping Brain Motor and Sensory Circuits189
- I. Introduction and Historical Perspective190
- II. Structural versus Functional Brain Maps191
- III. Strengths of Electrophysiological Mapping Methods Compared to Other Brain Mapping Methods191
- IV. Contrasts between Sensory versus Motor System Mapping192
- V. Output Measures for Mapping Motor System Organization194
- VI. Electrical Stimulation and Other Input Measures for Mapping Motor System Organization195
- VII. Mapping Motor Output with Transcranial Stimulation of Cortex197
- VIII. Mapping Motor Output with Electrical Stimulation of the Cortical Surface205
- IX. Mapping Motor Output with Intracortical Microstimulation (ICMS)209
- X. Mapping Motor Output with High-Density Microelectrode Arrays211
- XI. Mapping Motor Output with Spike-Triggered Averaging of EMG Activity from Single Neurons213
- XII. Mapping Motor Output with Stimulus-Triggered Averaging of EMG Activity (Single-Pulse ICMS)216
- XIII. Comparison of Results from Spike-Triggered Averaging, Stimulus-Triggered Averaging, and Repeti219
- XIV. Mapping the Output Terminations of Single Neurons Electrophysiologically221
- XV. The Future of Electrophysiological Mapping222
- References223
- Chapter 10. Magnetoencephalographic Characterization of Dynamic Brain Activation: Basic Principles a227
- I. Introduction227
- II. Generation of Neuromagnetic Fields228
- III. Instrumentation and Data Acquisition233
- IV. Source Analysis238
- V. Neuromagnetic Studies244
- VI. Conclusions and Future Directions248
- References250
- Chapter 11. Transcranial Magnetic Stimulation255
- I. Introduction255
- II. Basic Principles of Magnetic Brain Stimulation256
- III. TMS in Clinical Neurophysiology263
- IV. TMS in Cognitive Neuroscience270
- V. TMS Limitations279
- References285
- Part III: Tomographic-Based Data Acquisitiona
- Chapter 12. High-Field Magnetic Resonance291
- I. Introduction291
- II. Signal-to-Noise Ratio292
- III. Functional Brain Imaging293
- IV. Spectroscopy at High Magnetic Fields306
- References311
- Chapter 13. Functional MRI315
- I. Introduction315
- II. MRI: A Brief Primer316
- III. From MRI to fMRI320
- IV. Physics and Physiology322
- V. Sensitivity330
- VI. Resolution336
- VII. Structure-Function Integration343
- VII. Future344
- References344
- Chapter 14. Magnetic Resonance Spectroscopic Imaging351
- I. Introduction351
- II. Basics of in Vivo MR Spectroscopy352
- III. MRSI Data Acquisition Methods357
- IV. Data Processing Methods361
- V. MRSI Data Analysis366
- VI. Applications371
- VII. Emerging Technologies373
- VIII. Conclusion373
- References374
- Chapter 15. Principles, Methods, and Applications of Diffusion Tensor Imaging379
- I. Diffusion Measurement by NMR379
- II. Diffusion Tensor Imaging384
- III. Data Visualization and Analysis of DTI388
- IV. Application Studies391
- V. Summary395
- References395
- Chapter 16. Neuroanatomical Micromagnetic Resonance Imaging399
- I. Introduction399
- II. Magnetic Resonance Basics400
- III. Magnetic Resonance Imaging Basics403
- IV. k Space and MR Images405
- V. Signal-to-Noise Ratio (SNR) and Contrast-to-Noise Ratio (CNR)406
- VI. T1- and T2-Induced Contrasts407
- VII. Diffusion-Weighted, Perfusion, and Water Displacement Imaging409
- VIII. Microscopic MRI411
- IX. Micromagnetic Resonance Imaging of the Nervous System413
- X. Concluding Remarks419
- References421
- Chapter 17. CT Angiography and CT Perfusion Imaging427
- I. Introduction427
- II. Technical Background431
- III. Scanning Protocols: Acquisition, Postprocessing, Analysis, and Interpretation456
- IV. Clinical Utility462
- V. Conclusions476
- References478
- Chapter 18. Imaging Brain Function with Positron Emission Tomography485
- I. Introduction485
- II. Basic Overview and Principles of PET486
- III. Preparation of Positron-Labeled Compounds487
- IV. PET Scanners489
- V. PET Data Correction and Image Reconstruction494
- VI. Tracer Kinetic Models498
- VII. Task-Specific Mapping of the Human Brain501
- VIII. Mapping Brain Function in Development and Disease504
- IX. High-Resolution PET Studies in Animal Models506
- X. Summary508
- References508
- Chapter 19. SPECT Functional Brain Imaging513
- I. Introduction513
- II. Instrumentation514
- III. Radiopharmaceuticals520
- IV. Factors That Affect Image Appearance525
- V. Intercomparison of Neuroimaging Techniques for the Quantification of rCBF528
- VI. Radiation Risk Issues532
- VII. Conclusions533
- References533
- Part IV: Postmortemc
- Chapter 20. Postmortem Anatomy537
- I. Introduction537
- II. The Representation of Anatomy538
- III. The Specimen539
- IV. Preservation of Anatomical Information541
- V. Preparing the Specimen for Cutting543
- VI. Histological Slides544
- VII. Histological Methods546
- VIII. Anatomical Visualization553
- IX. Quantification557
- X. 3D Reconstruction558
- XI. Epilogue562
- References564
- Chapter 21. Quantitative Analysis of Cyto- and Receptor Architecture of the Human Brain573
- I. Introduction573
- II. Principles of Cytoarchitectonic Analysis575
- III. Observer-Independent Mapping of the Human Cerebral Cortex579
- IV. Quantitative Autoradiography of Different Receptor Binding Sites587
- V. Perspectives of Architectonic Mapping598
- References599
- Part V: Analysis603
- Chapter 22. Statistics I: Experimental Design and Statistical Parametric Mapping605
- I. Introduction605
- II. Functional Specialization and Integration606
- III. Spatial Realignment and Normalization607
- IV. Statistical Parametric Mapping610
- V. Experimental Design616
- VI. Designing fMRI Studies618
- VII. Inferences about Subjects and Populations624
- VIII. Effective Connectivity627
- References630
- Chapter 23. Statistics II: Correlation of Brain Structure and Function633
- I. Introduction633
- II. Intrasubject Multimodal Integration635
- III. Clinical Examples of Intrasubject Multimodal Registration640
- IV. Intersubject Multimodal Integration649
- V. Conclusion657
- References657
- Chapter 24. Advanced Nonrigid Registration Algorithms for Image Fusion661
- I. Introduction661
- II. Intermodality and Multicontrast Images662
- III. Image Fusion during Neurosurgery with a Biomechanical Model of Brain Deformation668
- IV. Physics-Based Regularization with an Empirical Model of Anatomical Variability674
- V. Registration of Diffusion Tensor Images677
- VI. The Monge-Kantorovich Problem and Image Registration683
- References687
- Chapter 25. Combination of Transcranial Magnetic Stimulation and Brain Mapping691
- I. Introduction691
- II. Neurophysiological Underpinnings of the Signal691
- III. Combination of TMS and Brain Mapping693
- IV. Conclusion702
- References703
- Chapter 26. Volume Visualization707
- I. Introduction707
- II. Segmentation709
- III. Surface Extraction711
- IV. Direct Volume Visualization712
- V. Visualization of Transformed Data717
- VI. Image Fusion717
- VII. Intelligent Visualization718
- VIII. Image Quality720
- IX. Conclusions720
- References721
- Part VI: Databases and Atlases725
- Chapter 27. The International Consortium for Brain Mapping: A Probabilistic Atlas and Reference Syst727
- I. Introduction727
- II. Motivation for Developing a Probabilistic Human Brain Atlas728
- III. Strategy and Rationale729
- IV. Methods and Results741
- V. Other Issues749
- VI. Limitations and Deliverables749
- VII. Conclusions750
- References751
- Chapter 28. Subpopulation Brain Atlases757
- I. Population-Based Brain Imaging757
- II. Atlases in Brain Mapping759
- III. Anatomical Modeling761
- IV. Population Maps of the Cortex766
- V. Brain Averaging773
- VI. Atlas Statistics: Probabilistic Atlases775
- VII. Applications to Development and Disease779
- VIII. Dynamic Brain Maps780
- IX. Genetic Brain Maps784
- X. Subpopulation Selections786
- XI. Conclusions788
- References788
- Part VII: Emerging Concepts797
- Chapter 29. Radionuclide Imaging of Reporter Gene Expression799
- I. Overview of Molecular Imaging799
- II. Instrumentation for Molecular Imaging800
- III. Reporter Genes800
- IV. Adapting the Reporter Gene Concept for Radionuclide Imaging801
- V. Application of in Vivo Reporter Gene Imaging to Monitor Gene Therapy Regimens806
- VI. Indirect Imaging of Endogenous Gene Expression through Coupling Endogenous Promoters with Report809
- VII. Antisense Reporter Probes for Imaging Endogenous Gene Expression in Vivo812
- VIII. Nonradionuclide Approaches to Reporter Gene Imaging812
- IX. Specific Issues for Neuroscience Applications813
- X. Human Gene Therapy of Brain Tumors and Imaging Studies813
- XI. Conclusion815
- References815
- Chapter 30. Mapping Gene Expression by MRI819
- I. Introduction819
- II. MRI Contrast Agents819
- III. Biochemically Activated MR Contrast Agents821
- IV. Targeted MR Contrast Agents823
- V. Magnetic Resonance Spectroscopy and Gene Expression825
- VI. Conclusion827
- References827
- Chapter 31. Speculations about the Future829
- I. Introduction829
- II. Previous Predictions and Their Outcomes829
- III. New Predictions838
- IV. Conclusion851
- References851
- Index857
Investigation of the functional architecture of the human brain using modern noninvasive imaging techniques is a rapidly expanding area of research. A proper knowledge of methodology is needed to appreciate the burgeoning literature in the field. This timely publication provides an excellent catalogue of the main techniques.
The authors offer an invaluable analysis of mapping strategies and techniques, providing everything from the foundations to the major pitfalls and practical applications of the modern techniques used in neuroimaging. Contains over 1000 full color pages with more than 200 color figures.
Spanning the methodological gamut from the molecular level to the whole brain while discussing anatomy, physiology, and pathology, as well as their integration, Brain Mapping: The Methods, 2e, brings the reader a comprehensive, well-illustrated and entirely readable description of the methods for brain mapping. Drs. Toga and Mazziotta provide everything from the foundations to the major pitfalls and practical applications of the technique by assembling an impressive group of experts, all widely known in their field, who contribute an outstanding set of chapters.
The authors offer an invaluable analysis of mapping strategies and techniques, providing everything from the foundations to the major pitfalls and practical applications of the modern techniques used in neuroimaging. Contains over 1000 full color pages with more than 200 color figures.
Spanning the methodological gamut from the molecular level to the whole brain while discussing anatomy, physiology, and pathology, as well as their integration, Brain Mapping: The Methods, 2e, brings the reader a comprehensive, well-illustrated and entirely readable description of the methods for brain mapping. Drs. Toga and Mazziotta provide everything from the foundations to the major pitfalls and practical applications of the technique by assembling an impressive group of experts, all widely known in their field, who contribute an outstanding set of chapters.