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Copyright, iv
Preface, xiii
1. An Introduction to fMRI, 1
What Is fMRI?, 3
Measurement versus manipulation techniques, 4
BOX 1.1 WHAT IS FMRI USED FOR?, 6
Key concept: contrast, 9
Key concept: resolution, 11
History of fMRI, 15
Early studies of magnetic resonance, 15
NMR in bulk matter: Bloch and Purcell, 17
The first MR images, 18
Growth of MRI, 21
BOX 1.2 THE NOBEL CONTROVERSY: SCANNERS OR IMAGES?, 22
Organization of the Textbook, 24
Physical bases of fMRI, 25
Principles of BOLD fMRI, 25
Design and analysis of fMRI experiments, 26
Applications and future directions, 27
Summary, 28
Suggested Reading, 28
Chapter References, 29
2. MRI Scanners, 31
How MRI Scanners Work, 31
Static magnetic field, 32
Radiofrequency coils, 35
Gradient coils, 38
Shimming coils, 41
Computer hardware and software, 41
Experimental control system, 43
Physiological monitoring equipment, 43
MRI Safety, 44
Effects of static magnetic fields on human physiology, 44
BOX 2.1 Outline of an fMRI EXPERIMENT, 45
Translation and torsion, 49
Gradient magnetic field effects, 50
Radiofrequency field effects, 52
Claustrophobia, 53
Acoustic noise, 54
Summary, 54
Suggested Reading, 55
Chapter References, 55
3. Basic Principles of MR Signal Generation, 57
CONCEPTUAL PATH, 57
Nuclear Spins, 59
Spins in an External Magnetic Field, 60
Magnetization of a Spin System, 62
Excitation of a Spin System and Signal Reception, 64
Relaxation Mechanisms of the MR Signal, 65
Conceptual Summary of MR Signal Generation, 67
QUANTITATIVE PATH, 68
Common Terms and Notations, 68
Nuclear Spins, 69
Magnetic Moment, 69
Angular Momentum, 70
Spins in an External Magnetic Field, 71
Spin precession, 71
Energy Difference between Parallel and Antiparallel States, 74
Magnetization of a Spin System, 75
Excitation of a Spin System and Signal Reception, 77
Spin excitation, 78
BOX 3.1 AQUANTITATIVE CONSIDERATION OF THE ROTATING REFERENCE FRAME, 80
Signal reception, 83
Relaxation Mechanisms of a Spin System, 85
The Bloch Equation for MR signal generation, 87
Summary, 87
Suggested Reading, 88
4. Basic Principles of MR Image Formation, 89
CONCEPTUAL PATH, 90
Slice Selection, 91
Frequency Encoding, 93
Phase Encoding, 95
Conceptual Path: Summary of Image Formation, 96
QUANTITATIVE PATH, 97
Analysis of the MR Signal, 97
BOX 4.1 AN EXAMPLE OF SPATIAL ENCODING, 98
Longitudinal magnetization (M_z), 101
Solution for transverse magnetization (M_xy), 102
The MR signal equation, 105
Slice Selection, Spatial Encoding, and Image Reconstruction, 106
Slice selection, 106
Two-dimensional spatial encoding (frequency and phase encoding), 109
Relationship between image space and k-space, 113
Converting from k-space to image space, 114
3-D Imaging, 117
Potential Problems in Image Formation, 117
Summary, 120
Suggested Reading, 120
5. MR Contrast Mechanisms and Pulse Sequences, 121
Static Contrasts and Related Pulse Sequences, 122
Proton-density contrast, 123
T₁ contrast, 126
T₂ contrast, 129
T₂* contrast, 131
Chemical contrast, 132
Macromolecular contrast, 133
Motion Contrasts, 135
MR angiography, 135
Diffusion-weighted contrast, 138
BOX 5.1 DIFFUSION TENSOR IMAGING, 140
Perfusion-weighted contrast, 142
Fast Imaging Sequences for fMRI, 147
Echo-planar imaging, 147
Spiral imaging, 148
Signal recovery and distortion correction for EPI and spiral images, 152
Summary, 154
Suggested Reading, 156
Chapter References, 157
6. From Neuronal to Hemodynamic Activity, 159
Neuronal Activity, 160
Ion channels in neurons, 162
Neurotransmitters and action potentials, 163
Cerebral Metabolism: Neuronal Energy Consumption, 165
Adenosine triphosphate (ATP), 166
The Vascular System of the Brain, 168
Arteries, capillaries, and veins, 170
Arterial and venous anatomy of the human brain, 171
Microcirculation, 172
Blood Flow, 174
Control of blood flow, 175
BOX 6.1 NEUROVASCULAR COUPLING AND CONTROL OF BLOOD FLOW, 176
Effects of increased blood flow on capillaries, 179
BOX 6.2 PRIMER ON NEUROANATOMY, 182
Summary, 190
Suggested Reading, 190
Chapter References, 191
7. BOLD fMRI: Origins and Properties, 193
History of BOLD fMRI, 193
Discovery of BOLD contrast, 194
The coupling of metabolism and blood flow, 196
BOX 7.1 PET IMAGING, 197
The Growth of BOLD fMRI, 201
Contributing factors, 201
Early fMRI studies, 203
BOX 7.2 FUNCTIONAL STUDIES USING CONTRAST AGENTS, 204
The BOLD Hemodynamic Response, 208
BOX 7.3 NEURONAL ACTIVITY AND BOLD FMRI, 209
The initial dip, 211
Spatial Resolution, 214
Spatial specificity in the vascular system, 216
What spatial resolution is needed?, 219
Temporal Resolution of fMRI, 220
What temporal resolution is needed?, 223
Effects of stimulus duration and timing, 225
Linearity of the Hemodynamic Response, 229
Properties of a linear system, 230
Evidence for rough linearity, 231
Challenges to linearity, 233
fMRI-adaptation, 235
Summary, 237
Suggested Reading, 238
Chapter References, 239
8. Signal, Noise, and Preprocessing of fMRI Data, 243
Understanding Signal and Noise, 245
Signal and noise defined, 245
BOX 8.1 TERMINOLOGY OF FMRI, 246
Functional SNR, 248
Effects of Field Strength on fMRI Data, 250
Field strength and raw SNR, 251
Field strength and spatial properties of activation, 252
Challenges of high-field fMRI, 254
Sources of Noise in fMRI, 255
Thermal noise, 256
System noise, 258
Motion and physiological noise, 259
Non-task-related neural variability, 262
Behavioral and cognitive variability in task performance, 262
BOX 8.2 VARIABILITY IN THE HEMODYNAMIC RESPONSE OVER SUBJECTS AND SESSIONS, 264
Preprocessing, 267
Quality assurance, 267
Slice acquisition time correction, 269
Head motion: an overview, 271
Prevention of head motion, 274
Correction of head motion, 276
Distortion correction, 277
Functional–Structural Coregistration and Normalization, 280
Functional–structural coregistration, 280
Spatial normalization, 281
Temporal and Spatial Filtering, 284
Temporal filtering, 285
Spatial filtering, 287
Summary, 289
Suggested Reading, 289
Chapter References, 290
9. Experimental Design, 293
Basic Principles of Experimental Design, 294
Setting Up a Good Research Hypothesis, 296
Are fMRI data correlational?, 298
Confounding factors, 299
Good Practices in fMRI Experimental Design, 302
Blocked Designs, 303
Setting up a blocked design, 304
BOX 9.1 BASELINE ACTIVATION IN FMRI, 306
Advantages and disadvantages of blocked designs, 310
Event-Related Designs, 313
Principles of event-related fMRI, 316
Advantages of event-related designs, 319
BOX 9.2 EFFICIENT FMRI EXPERIMENTAL DESIGN, 320
Mixed Designs, 325
Summary, 327
Suggested Reading, 327
Chapter References, 328
10. Statistical Analysis: Basic Analyses, 331
Basic Statistical Tests, 333
Contrasting experimental conditions: the t-test, 334
Comparing experimental and predicted responses: correlation analyses, 338
BOX 10.1 IDENTIFYING TASK-RELATED PERIODICITY: FOURIER ANALYSES, 341
Regression Analyses, 343
The general linear model: an overview, 343
Constructing a design matrix: regressors of interest, 345
Constructing a design matrix: nuisance regressors, 349
Modeling neuronal activity, 351
Modeling hemodynamic convolution, 352
Contrasts, 354
Assumptions of the general linear model, 356
Corrections for Multiple Comparisons, 357
Calculating the significance threshold, 358
Thresholding based on clusters of activation, 360
Estimating the number of independent tests, 361
Region-of-Interest Analyses, 362
Intersubject Analyses, 365
Group and parametric effects, 367
Displaying Statistical Results, 369
Summary, 373
Suggested Reading, 373
Chapter References, 374
11. Statistical Analysis II: Advanced Approaches, 377
Data Exploration Approaches, 378
Principal components analysis (PCA), 378
Independent components analysis (ICA), 380
Partial least squares (PLS), 382
Between-Subjects Correlations: Hyperscanning, 384
Functional Connectivity Approaches, 386
From coactivation to connectivity: a conceptual overview, 386
BOX 11.1 INTERSUBJECT CORRELATIONS IN FREE VIEWING, 387
Resting-state connectivity, 391
Psychophysiological interactions, 393
Inferring causality from fMRI data, 394
Combining fMRI and DTI, 399
Prediction Approaches, 401
Predicting variation among individuals, 402
BOX 11.2 REAL-TIME FMRI, 403
Predicting variation in behavior, 407
Pattern classification using machine learning algorithms, 408
Capabilities and challenges of fMRI pattern classification, 412
Summary, 415
Suggested Reading, 416
Chapter References, 416
12. Advanced fMRI Methods, 419
Improved Spatial Resolution, 420
MR microscopy, 420
Parallel imaging, 423
Parallel imaging with massive coil arrays, 425
Improved Temporal Resolution, 426
Multiple-channel acquisition, 427
Partial k-space imaging, 427
Efficient k-space trajectories, 430
Improved experimental designs, 432
Improved Functional Resolution through New Contrast Mechanisms, 433
Temperature-dependent contrast, 434
pH-dependent contrast, 435
Ion-gated contrast, 437
Neuronal magnetic field contrast, 438
Lorentz effect contrast, 439
Summary, 440
Suggested Reading, 441
Chapter References, 441
13. Combining fMRI with other Techniques, 443
Cognitive Neuroscience, 443
Strategies for research in cognitive neuroscience, 445
Manipulating Brain Function, 446
Direct cortical stimulation, 446
Functional consequences of direct cortical stimulation, 448
Transcranial magnetic stimulation (TMS), 450
Brain lesions, 452
Combined lesion and fMRI studies, 454
Probabilistic brain atlases, 455
Brain imaging and genomics, 457
Measuring Brain Function, 458
Single-unit recording, 458
BOX 13.1 ELECTROGENESIS, 459
Limitations of single-unit recording, 462
Properties of electrical field potentials, 464
Localizing the neural generators of field potentials, 465
Intracranially recorded field potentials, 466
BOX 13.2 LOCALIZATION OF FUNCTION USING FIELD POTENTIAL RECORDINGS, 468
Scalp-recorded field potentials, 470
BOX 13.3 COMBINING FMRI AND EEG/ERP TECHNIQUES, 472
Magnetoencephalography, 474
Using fMRI with non-human primates, 476
Summary, 480
Suggested Reading, 480
Chapter References, 481
14. The Future of fMRI: Practical and Ethical Issues, 485
Introduction, 485
Interpreting and Presenting fMRI Data, 486
Coverage of fMRI research in the popular media, 487
Core principles for presenting fMRI research, 489
BOX 14.1 REVERSE INFERENCE, 490
Conducting fMRI Research, 494
Proposing and approving fMRI research, 495
Ensuring the confidentiality of fMRI data, 497
BOX 14.2 INCIDENTAL FINDINGS IN FMRI RESEARCH, 498
Safe conduct of fMRI studies, 502
Pregnancy testing in fMRI research, 504
Applying fMRI to New and Controversial Topics, 505
Reading minds, 506
Identifying traits, 509
The Future of fMRI Research (and your role in it), 511
Summary, 513
Suggested Reading, 514
Chapter References, 514
Glossary, 517
Index, 533

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