FUNCTIONAL Magnetic Resonance Imaging - sinauer.com

1 FUNCTIONALM agnetic Resonance ImagingSECOND EDITIONS cott A. HuettelBrain Imaging and Analysis Center, Duke UniversityAllen W. SongBrain Imaging and Analysis Center, Duke UniversityGregory McCarthyYale UniversitySinauer Associates, Inc PublishersSunderland, Massachusetts 12/19/08 1:30 PM Page iii Sinauer Associates, Inc. This material cannot be copied, reproduced, manufactured or disseminated in any form without express written permission from the Introduction to fMRI12 MRI Scanners313 Basic Principles of MR Signal Generation574 Basic Principles of MR Image Formation895MR Contrast Mechanisms and Pulse Sequences1216 From Neuronal to Hemodynamic Activity1597 BOLD fMRI: Origins and Properties1938 Signal, Noise, and Preprocessing of fMRI Data2439 Experimental Design29310 Statistical Analysis: Basic Analyses33111 Statistical Analysis II: Advanced Approaches37712 Advanced fMRI Methods41913 Combining fMRI with other Techniques44314 The Future of fMRI: Practical and Ethical Issues485 Brief ContentsFM 12/19/08 1:30 PM Page vi Sinauer Associates, Inc.

2 This material cannot be copied, reproduced, manufactured or disseminated in any form without express written permission from the Introduction to fMRI1 What Is fMRI?3 Measurement versus manipulation techniques WHATISFMRI USEDFOR?6 Key concept: contrast 9 Key concept: resolution 11 History of fMRI15 Early studies of Magnetic Resonance 15 NMR in bulk matter: Bloch and Purcell 17 The first MR images 18 Growth of MRI THENOBELCONTROVERSY: SCANNERS ORIMAGES?22 Organization of the Textbook24 Physical bases of fMRI 25 Principles of BOLD fMRI 25 Design and analysis of fMRI experiments 26 Applications and future directions 27 Summary28 Suggested Reading28 Chapter References292 MRI Scanners31 How MRI Scanners Work31 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 Safety44 Effects of static Magnetic fields on humanphysiology OUTLINE OF AN FMRI EXPERIMENT45 Translation and torsion 49 Gradient Magnetic field effects 50 Radiofrequency field effects 52 Claustrophobia 53 Acoustic noise 54 Summary54 Suggested Reading55 Chapter

3 References55 ContentsPrefacexiiiFM 12/22/08 3:10 PM Page vii Sinauer Associates, Inc. This material cannot be copied, reproduced, manufactured or disseminated in any form without express written permission from the Principles of MR SignalGeneration57 CONCEPTUAL PATH57 Nuclear Spins59 Spins in an External Magnetic Field60 Magnetization of a Spin System62 Excitation of a Spin System and SignalReception64 Relaxation Mechanisms of the MR Signal65 Conceptual Summary of MR SignalGeneration67 QUANTITATIVE PATH68 Common Terms and Notations68 Nuclear Spins69 Magnetic Moment69 Angular Momentum70 Spins in an External Magnetic Field71 Spin precession 71 Energy Difference between Parallel and Antiparallel States74 Magnetization of a Spin System75 Excitation of a Spin System and SignalReception77 Spin excitation A QUANTITATIVECONSIDERATION OFTHEROTATINGREFERENCEFRAME80 Signal reception

4 83 Relaxation Mechanisms of a Spin System85 The Bloch Equation for MR signal generation87 Summary87 Suggested Reading884 Basic Principles of MR ImageFormation89 CONCEPTUAL PATH90 Slice Selection91 Frequency Encoding93 Phase Encoding95 Conceptual Path: Summary of ImageFormation96 QUANTITATIVE PATH97 Analysis of the MR ANEXAMPLE OFSPATIALENCODING98 Longitudinal magnetization (Mz) 101 Solution for transverse magnetization (Mxy) 102 The MR signal equation 105 Slice Selection, Spatial Encoding, andImage Reconstruction106 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 1143-D Imaging 117 Potential Problems in Image Formation117 Summary120 Suggested Reading1205MR Contrast Mechanisms andPulse Sequences121 Static Contrasts and Related PulseSequences122 Proton-density contrast 123T1contrast 126T2contrast 129T2* contrast 131 Chemical contrast 132 Macromolecular contrast 133 Motion Contrasts 135MR angiography 135 Diffusion-weighted contrast DIFFUSIONTENSORIMAGING140 Perfusion-weighted contrast 142FM 12/19/08 1:30 PM Page viii Sinauer Associates, Inc.

5 This material cannot be copied, reproduced, manufactured or disseminated in any form without express written permission from the Imaging Sequences for fMRI 147 Echo-planar Imaging 147 Spiral Imaging 148 Signal recovery and distortion correction for EPI and spiral images 152 Summary154 Suggested Reading156 Chapter References1576 From Neuronal toHemodynamic Activity159 Neuronal Activity160 Ion channels in neurons 162 Neurotransmitters and action potentials 163 Cerebral Metabolism: Neuronal EnergyConsumption165 Adenosine triphosphate (ATP) 166 The Vascular System of the Brain168 Arteries, capillaries, and veins 170 Arterial and venous anatomy of the humanbrain 171 Microcirculation 172 Blood Flow174 Control of blood flow NEUROVASCULARCOUPLING ANDCONTROL OFBLOODFLOW176 Effects of increased blood flow on capillaries PRIMER ONNEUROANATOMY182 Summary190 Suggested Reading190 Chapter References1917 BOLD fMRI.

6 Origins andProperties193 History of BOLD fMRI193 Discovery of BOLD contrast 194 The coupling of metabolism and blood flow PET IMAGING197 The Growth of BOLD fMRI201 Contributing factors 201 Early fMRI studies FUNCTIONALSTUDIESUSINGCONTRASTAGENTS204 The BOLD Hemodynamic NEURONALACTIVITY ANDBOLD FMRI 209 The initial dip 211 Spatial Resolution214 Spatial specificity in the vascular system 216 What spatial resolution is needed? 219 Temporal Resolution of fMRI220 What temporal resolution is needed? 223 Effects of stimulus duration and timing 225 Linearity of the Hemodynamic Response229 Properties of a linear system 230 Evidence for rough linearity 231 Challenges to linearity 233fMRI-adaptation 235 Summary237 Suggested Reading238 Chapter References2398 Signal, Noise, andPreprocessing of fMRI Data243 Understanding Signal and Noise245 Signal and noise defined TERMINOLOGY OF FMRI 246 FUNCTIONAL SNR 248 Effects of Field Strength on fMRI Data250 Field strength and raw SNR 251 Field strength and spatial properties of activation 252 Challenges of high-field fMRI 254FM 12/19/08 1:30 PM Page ix Sinauer Associates, Inc.

7 This material cannot be copied, reproduced, manufactured or disseminated in any form without express written permission from the of Noise in fMRI255 Thermal noise 256 System noise 258 Motion and physiological noise 259 Non-task-related neural variability 262 Behavioral and cognitive variability in taskperformance VARIABILITY IN THEHEMODYNAMICRESPONSE OVERSUBJECTS ANDSESSIONS264 Preprocessing267 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 Normalization280 FUNCTIONAL structural coregistration 280 Spatial normalization 281 Temporal and Spatial Filtering284 Temporal filtering 285 Spatial filtering 287 Summary289 Suggested Reading289 Chapter References2909 Experimental Design293 Basic Principles of Experimental Design294 Setting Up a Good Research Hypothesis296 Are fMRI data correlational?

8 298 Confounding factors 299 Good Practices in fMRI ExperimentalDesign302 Blocked Designs303 Setting up a blocked design BASELINEACTIVATION IN FMRI 306 Advantages and disadvantages of blockeddesigns 310 Event-Related Designs313 Principles of event-related fMRI 316 Advantages of event-related designs EFFICIENT FMRI EXPERIMENTALDESIGN320 Mixed Designs325 Summary327 Suggested Reading327 Chapter References32810 Statistical Analysis: BasicAnalyses331 Basic Statistical Tests333 Contrasting experimental conditions: the t-test 334 Comparing experimental and predictedresponses: correlation analyses : FOURIERANALYSES341 Regression Analyses343 The general linear model: an overview 343 Constructing a design matrix: regressors ofinterest 345 Constructing a design matrix: nuisanceregressors 349 Modeling neuronal activity 351 Modeling hemodynamic convolution 352 Contrasts 354 Assumptions of the general linear model 356 Corrections for Multiple Comparisons357 Calculating the significance threshold 358 Thresholding based on clusters of activation 360 Estimating the number of independent tests 361 Region-of-Interest Analyses362 Intersubject Analyses365 Group and parametric effects 367 Displaying Statistical Results369 Summary373 Suggested Reading373 Chapter References374FM 12/19/08 1:30 PM Page x Sinauer Associates, Inc.

9 This material cannot be copied, reproduced, manufactured or disseminated in any form without express written permission from the Analysis II: Advanced Approaches377 Data Exploration Approaches378 Principal components analysis (PCA) 378 Independent components analysis (ICA) 380 Partial least squares (PLS) 382 Between-Subjects Correlations:Hyperscanning384 FUNCTIONAL Connectivity Approaches386 From coactivation to connectivity:a conceptual overview INFREEVIEWING387 Resting-state connectivity 391 Psychophysiological interactions 393 Inferring causality from fMRI data 394 Combining fMRI and DTI 399 Prediction Approaches401 Predicting variation among individuals REAL-TIME FMRI 403 Predicting variation in behavior 407 Pattern classification using machine learningalgorithms 408 Capabilities and challenges of fMRI patternclassification 412 Summary415 Suggested Reading416 Chapter References41612 Advanced fMRI Methods419 Improved Spatial Resolution420MR microscopy 420 Parallel Imaging 423 Parallel Imaging with massive coil arrays 425 Improved Temporal Resolution426 Multiple-channel acquisition 427 Partial k-space Imaging 427 Efficient

10 K-space trajectories 430 Improved experimental designs 432 Improved FUNCTIONAL Resolution throughNew Contrast Mechanisms433 Temperature-dependent contrast 434pH-dependent contrast 435 Ion-gated contrast 437 Neuronal Magnetic field contrast 438 Lorentz effect contrast 439 Summary440 Suggested Reading441 Chapter References44113 Combining fMRI with otherTechniques443 Cognitive Neuroscience443 Strategies for research in cognitive neuroscience 445 Manipulating Brain Function446 Direct cortical stimulation 446 FUNCTIONAL consequences of direct corticalstimulation 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 Function458 Single-unit recording ELECTROGENESIS459 Limitations of single-unit recording 462 Properties of electrical field potentials 464 Localizing the neural generators of fieldpotentials 465FM 12/19/08 1:30 PM Page xi Sinauer Associates, Inc.