Brain Mapping: The Methods (eBook)

Front Cover 1
Brain Mapping: The Methods 4
Copyright Page 5
Contents 6
Contributors 12
Preface 16
Acknowledgments 18
Part I: Introduction 20
Chapter 1. Introduction to Cartography of the Brain 22
I. Introduction to Cartography 22
II. The Dimensions of a Brain Map 25
III. The Full Scope of Brain Mapping 30
IV. Relationships to Other Biological Maps 33
V. Stereotaxy 34
VI. Nomenclature 36
VII. Detection Devices 37
VIII. Brain Maps: Content and Format 40
IX. Summary 44
References 45
Chapter 2. Time and Space 52
I. Introduction 52
II. Critical Variables in Brain Mapping Techniques 53
III. The Concept of Resolution 55
IV. Sampling 59
V. Sites Accessed 62
VI. Invasiveness 63
VII. Conclusions 63
References 64
Part II: Surface-Based Data Acquisition 66
Chapter 3. Optical Imaging of Neural Structure and Physiology: Confocal Fluorescence Microscopy in Live Brain Slices 68
I. Introduction 68
II. Live Brain Slice Preparation and Culture 70
III. Labeling Neuronal and Glial Cells in Brain Tissue Slices 71
IV. Imaging Methodology 76
V. Application: Mapping Neural Structure and Physiology in Developing Brain Slices 80
VI. Conclusions and Future Prospects 90
References 92
Chapter 4. Voltage and Calcium Imaging of Brain Activity: Examples from the Turtle and the Mouse 96
I. Why (and Why Not) Voltage and Calcium Imaging 96
II. Signal Type 97
III. Dyes 97
IV. Amplitude of the Voltage or Calcium Change 100
V. Noise in the Optical Measurements 100
VI. Light Sources 102
VII. Optics 102
VIII. Cameras 103
IX. Comparison of Local Field Potential and Voltage-Sensitive Dye Recording 104
X. Voltage-Sensitive Dye Recording in the Turtle Olfactory Bulb 104
XI. Calcium Dye Recording in the Mouse Olfactory Bulb 108
XII. Intrinsic Imaging and Fluorescence Signals from In Vivo Mammalian Brain 112
XIII. Summary and Future Directions 112
References 113
Chapter 5. Optical Imaging Based on Intrinsic Signals 116
I. Introduction 116
II. Sources of Intrinsic Signals and Wavelength Dependency 117
III. Preparation of an Animal for Optical Imaging 122
IV. The Apparatus 126
V. Data Acquisition 131
VI. Data Analysis for Mapping Functional Architecture 133
VII. Chronic Optical Imaging 140
VIII. Optical Imaging of the Human Neocortex 142
IX. Combining Optical Imaging with Other Techniques 144
X. Applications 149
XI. Comparison of Intrinsic Optical Imaging with Other Imaging Techniques 154
XII. Conclusions and Outlook 155
References 156
Chapter 6. Near-Infrared Spectroscopy and Imaging 160
I. Introduction 160
II. Optical Window for Noninvasive Studies 161
III. Other Optical Parameters Relevant for Near-Infrared Studies 162
IV. Technical Approaches for Near-Infrared Spectroscopy and Imaging 162
V. Physiological Parameters of NIRS Measurements 163
VI. Near-Infrared Spectroscopy and Imaging: Applications 168
VII. Practical Aspects of NIRS Measurements 170
VIII. Problems and Perspectives 174
References 175
Chapter 7. Dynamic Measurements of Local Cerebral Blood Flow: Examples from Rodent Whisker Barrel Cortex 178
I. Why Measure Local Cerebral Blood Flow? 178
II. Function and Structural Contexts 179
III. Global Tracers 180
IV. Volatile Tracers 181
V. Doppler Flowmetry 182
VI. Video Microscopy 182
VII. Localization of Activity Changes 183
VIII. Diameter 184
IX. Intravascular Dyes 185
X. Intravascular Particles 186
XI. Localization of Flow Changes 188
XII. Conclusions and Prospects 188
References 189
Chapter 8. Electrophysiological Imaging of Brain Function 194
I. Introduction 194
II. The Electroencephalogram and Averaged Event-Related Potentials 195
III. Improving the Spatial Resolution of the Electroencephalogram 198
IV. Analysis of Functional Networks 202
V. The EEG as a Monitoring (vs Imaging) Modality 204
VI. Summary and Conclusions 205
References 205
Chapter 9. Electrophysiological Methods for Mapping Brain Motor and Sensory Circuits 208
I. Introduction and Historical Perspective 209
II. Structural versus Functional Brain Maps 210
III. Strengths of Electrophysiological Mapping Methods Compared to Other Brain Mapping Methods 210
IV. Contrasts between Sensory versus Motor System Mapping 211
V. Output Measures for Mapping Motor System Organization 213
VI. Electrical Stimulation and Other Input Measures for Mapping Motor System Organization 214
VII. Mapping Motor Output with Transcranial Stimulation of Cortex 216
VIII. Mapping Motor Output with Electrical Stimulation of the Cortical Surface 224
IX. Mapping Motor Output with Intracortical Microstimulation (ICMS) 228
X. Mapping Motor Output with High-Density Microelectrode Arrays 230
XI. Mapping Motor Output with Spike-Triggered Averaging of EMG Activity from Single Neurons 232
XII. Mapping Motor Output with Stimulus-Triggered Averaging of EMG Activity (Single-Pulse ICMS) 235
XIII. Comparison of Results from Spike-Triggered Averaging, Stimulus-Triggered Averaging, and Repetitive ICMS 238
XIV. Mapping the Output Terminations of Single Neurons Electrophysiologically 240
XV. The Future of Electrophysiological Mapping 241
References 242
Chapter 10. Magnetoencephalographic Characterization of Dynamic Brain Activation: Basic Principles and Methods of Data Collection and Source Analysis 246
I. Introduction 246
II. Generation of Neuromagnetic Fields 247
III. Instrumentation and Data Acquisition 252
IV. Source Analysis 257
V. Neuromagnetic Studies 263
VI. Conclusions and Future Directions 267
References 269
Chapter 11. Transcranial Magnetic Stimulation 274
I. Introduction 274
II. Basic Principles of Magnetic Brain Stimulation 275
III. TMS in Clinical Neurophysiology 282
IV. TMS in Cognitive Neuroscience 289
V. TMS Limitations 298
References 304
Part III: Tomographic-Based Data Acquisition 310
Chapter 12. High-Field Magnetic Resonance 312
I. Introduction 312
II. Signal-to-Noise Ratio 313
III. Functional Brain Imaging 314
IV. Spectroscopy at High Magnetic Fields 327
References 332
Chapter 13. Functional MRI 336
I. Introduction 336
II. MRI: A Brief Primer 337
III. From MRI to fMRI 341
IV. Physics and Physiology 343
V. Sensitivity 351
VI. Resolution 357
VII. Structure-Function Integration 364
VII. Future 365
References 365
Chapter 14. Magnetic Resonance Spectroscopic Imaging 372
I. Introduction 372
II. Basics of in Vivo MR Spectroscopy 373
III. MRSI Data Acquisition Methods 378
IV. Data Processing Methods 382
V. MRSI Data Analysis 387
VI. Applications 392
VII. Emerging Technologies 394
VIII. Conclusion 394
References 395
Chapter 15. Principles, Methods, and Applications of Diffusion Tensor Imaging 400
I. Diffusion Measurement by NMR 400
II. Diffusion Tensor Imaging 405
III. Data Visualization and Analysis of DTI 409
IV. Application Studies 412
V. Summary 416
References 416
Chapter 16. Neuroanatomical Micromagnetic Resonance Imaging 420
I. Introduction 420
II. Magnetic Resonance Basics 421
III. Magnetic Resonance Imaging Basics 424
IV. k Space and MR Images 426
V. Signal-to-Noise Ratio (SNR) and Contrast-to-Noise Ratio (CNR) 427
VI. T1- and T2-Induced Contrasts 428
VII. Diffusion-Weighted, Perfusion, and Water Displacement Imaging 430
VIII. Microscopic MRI 432
IX. Micromagnetic Resonance Imaging of the Nervous System 434
X. Concluding Remarks 440
References 442
Chapter 17. CT Angiography and CT Perfusion Imaging 448
I. Introduction 448
II. Technical Background 452
III. Scanning Protocols: Acquisition, Postprocessing, Analysis, and Interpretation 477
IV. Clinical Utility 483
V. Conclusions 497
References 499
Chapter 18. Imaging Brain Function with Positron Emission Tomography 506
I. Introduction 506
II. Basic Overview and Principles of PET 507
III. Preparation of Positron-Labeled Compounds 508
IV. PET Scanners 510
V. PET Data Correction and Image Reconstruction 515
VI. Tracer Kinetic Models 519
VII. Task-Specific Mapping of the Human Brain 522
VIII. Mapping Brain Function in Development and Disease 525
IX. High-Resolution PET Studies in Animal Models 527
X. Summary 529
References 529
Chapter 19. SPECT Functional Brain Imaging 534
I. Introduction 534
II. Instrumentation 535
III. Radiopharmaceuticals 541
IV. Factors That Affect Image Appearance 546
V. Intercomparison of Neuroimaging Techniques for the Quantification of rCBF 549
VI. Radiation Risk Issues 553
VII. Conclusions 554
References 554
Part IV: Postmortem 558
Chapter 20. Postmortem Anatomy 560
I. Introduction 560
II. The Representation of Anatomy 561
III. The Specimen 562
IV. Preservation of Anatomical Information 564
V. Preparing the Specimen for Cutting 566
VI. Histological Slides 567
VII. Histological Methods 569
VIII. Anatomical Visualization 576
IX. Quantification 580
X. 3D Reconstruction 581
XI. Epilogue 585
References 587
Chapter 21. Quantitative Analysis of Cyto- and Receptor Architecture of the Human Brain 596
I. Introduction 596
II. Principles of Cytoarchitectonic Analysis 598
III. Observer-Independent Mapping of the Human Cerebral Cortex 602
IV. Quantitative Autoradiography of Different Receptor Binding Sites 610
V. Perspectives of Architectonic Mapping 621
References 622
Part V: Analysis 626
Chapter 22. Statistics I: Experimental Design and Statistical Parametric Mapping 628
I. Introduction 628
II. Functional Specialization and Integration 629
III. Spatial Realignment and Normalization 630
IV. Statistical Parametric Mapping 633
V. Experimental Design 639
VI. Designing fMRI Studies 641
VII. Inferences about Subjects and Populations 647
VIII. Effective Connectivity 650
References 653
Chapter 23. Statistics II: Correlation of Brain Structure and Function 656
I. Introduction 656
II. Intrasubject Multimodal Integration 658
III. Clinical Examples of Intrasubject Multimodal Registration 663
IV. Intersubject Multimodal Integration 672
V. Conclusion 680
References 680
Chapter 24. Advanced Nonrigid Registration Algorithms for Image Fusion 684
I. Introduction 684
II. Intermodality and Multicontrast Images 685
III. Image Fusion during Neurosurgery with a Biomechanical Model of Brain Deformation 691
IV. Physics-Based Regularization with an Empirical Model of Anatomical Variability 697
V. Registration of Diffusion Tensor Images 700
VI. The Monge-Kantorovich Problem and Image Registration 706
References 710
Chapter 25. Combination of Transcranial Magnetic Stimulation and Brain Mapping 714
I. Introduction 714
II. Neurophysiological Underpinnings of the Signal 714
III. Combination of TMS and Brain Mapping 716
IV. Conclusion 725
References 726
Chapter 26. Volume Visualization 730
I. Introduction 730
II. Segmentation 732
III. Surface Extraction 734
IV. Direct Volume Visualization 735
V. Visualization of Transformed Data 740
VI. Image Fusion 740
VII. Intelligent Visualization 741
VIII. Image Quality 743
IX. Conclusions 743
References 744
Part VI: Databases and Atlases 748
Chapter 27. The International Consortium for Brain Mapping: A Probabilistic Atlas and Reference System for the Human Brain 750
I. Introduction 750
II. Motivation for Developing a Probabilistic Human Brain Atlas 751
III. Strategy and Rationale 752
IV. Methods and Results 764
V. Other Issues 772
VI. Limitations and Deliverables 772
VII. Conclusions 773
References 774
Chapter 28. Subpopulation Brain Atlases 780
I. Population-Based Brain Imaging 780
II. Atlases in Brain Mapping 782
III. Anatomical Modeling 784
IV. Population Maps of the Cortex 789
V. Brain Averaging 796
VI. Atlas Statistics: Probabilistic Atlases 798
VII. Applications to Development and Disease 802
VIII. Dynamic Brain Maps 803
IX. Genetic Brain Maps 807
X. Subpopulation Selections 809
XI. Conclusions 811
References 811
Part VII: Emerging Concepts 820
Chapter 29. Radionuclide Imaging of Reporter Gene Expression 822
I. Overview of Molecular Imaging 822
II. Instrumentation for Molecular Imaging 823
III. Reporter Genes 823
IV. Adapting the Reporter Gene Concept for Radionuclide Imaging 824
V. Application of in Vivo Reporter Gene Imaging to Monitor Gene Therapy Regimens 829
VI. Indirect Imaging of Endogenous Gene Expression through Coupling Endogenous Promoters with Reporter Genes 832
VII. Antisense Reporter Probes for Imaging Endogenous Gene Expression in Vivo 835
VIII. Nonradionuclide Approaches to Reporter Gene Imaging 835
IX. Specific Issues for Neuroscience Applications 836
X. Human Gene Therapy of Brain Tumors and Imaging Studies 836
XI. Conclusion 838
References 838
Chapter 30. Mapping Gene Expression by MRI 842
I. Introduction 842
II. MRI Contrast Agents 842
III. Biochemically Activated MR Contrast Agents 844
IV. Targeted MR Contrast Agents 846
V. Magnetic Resonance Spectroscopy and Gene Expression 848
VI. Conclusion 850
References 850
Chapter 31. Speculations about the Future 852
I. Introduction 852
II. Previous Predictions and Their Outcomes 852
III. New Predictions 861
IV. Conclusion 874
References 874
Index 880