FUNCTIONAL Magnetic Resonance Imaging
FM Huettel.qxd12/19/081:30 PMPage iiiFUNCTIONALMagnetic Resonance ImagingSECOND EDITIONScott A. HuettelBrain Imaging and Analysis Center, Duke UniversityAllen W. SongBrain Imaging and Analysis Center, Duke UniversityGregory McCarthyYale UniversitySinauer Associates, Inc PublishersSunderland, Massachusetts U.S.A. Sinauer Associates, Inc. This material cannot be copied, reproduced, manufacturedor disseminated in any form without express written permission from the publisher.
FM Huettel.qxd12/19/081:30 PMPage viBrief Contents12345An Introduction to fMRI 1MRI Scanners 31Basic Principles of MR Signal Generation 57Basic Principles of MR Image Formation 89MR Contrast Mechanismsand Pulse Sequences 1216 From Neuronal to Hemodynamic Activity 1597 BOLD fMRI: Origins and Properties 1938 Signal, Noise, and Preprocessingof fMRI Data 24391011121314Experimental Design 293Statistical Analysis: Basic Analyses 331Statistical Analysis II: Advanced Approaches 377Advanced fMRI Methods 419Combining fMRI with other Techniques 443The Future of fMRI: Practicaland Ethical Issues 485 Sinauer Associates, Inc. This material cannot be copied, reproduced, manufacturedor disseminated in any form without express written permission from the publisher.
FM Huettel.qxd12/22/083:10 PMPage viiContents2Preface xiii1MRI Scanners31How MRI Scanners WorkAn Introduction to fMRIWhat Is fMRI?1History of fMRIStatic magnetic field 32Radiofrequency coils 35Gradient coils 38Shimming coils 41Computer hardware and software 41Experimental control system 43Physiological monitoring equipment 433Measurement versus manipulationtechniques 4BOX 1.1 WHAT IS FMRI USED FOR?Key concept: contrast 9Key concept: resolution 116MRI Safety15Early studies of magnetic resonance 15NMR in bulk matter: Bloch and Purcell 17The first MR images 18Growth of MRI 21BOX 1.2 THE NOBEL CONTROVERSY:SCANNERS OR IMAGES? 22Organization of the Textbook24Physical bases of fMRI 25Principles of BOLD fMRI 25Design and analysis of fMRI experimentsApplications and future directions 27Summary 28Suggested ReadingChapter References312644Effects of static magnetic fields on humanphysiology 44BOX 2.1 OUTLINE OF AN FMRIEXPERIMENT 45Translation and torsion 49Gradient magnetic field effects 50Radiofrequency field effects 52Claustrophobia 53Acoustic noise 54Summary 54Suggested ReadingChapter References2829 Sinauer Associates, Inc. This material cannot be copied, reproduced, manufacturedor disseminated in any form without express written permission from the publisher.5555
FM Huettel.qxdviii12/19/081:30 PMPage viiiContents43Basic Principles of MR SignalGeneration 57CONCEPTUAL PATH 57Nuclear Spins 59Spins in an External Magnetic Field 60Magnetization of a Spin System 62Excitation of a Spin System and SignalReception 64Relaxation Mechanisms of theMR Signal 65Conceptual Summary of MR SignalGeneration 67CONCEPTUAL PATH 90Slice Selection 91Frequency Encoding 93Phase Encoding 95Conceptual Path: Summary of ImageFormation 96QUANTITATIVE PATH 97Analysis of the MR SignalSlice Selection, Spatial Encoding, andImage Reconstruction 106Slice selection 106Two-dimensional spatial encoding(frequency and phase encoding) 109Relationship between image space andk-space 113Converting from k-space to image space 1143-D Imaging 117Potential Problems in ImageFormation 117Summary 120Suggested Reading 12071Energy Difference between Paralleland Antiparallel States 74Magnetization of a Spin System 75Excitation of a Spin System and SignalReception 77Spin excitation 78BOX 3.1 A QUANTITATIVE CONSIDERATION OFTHE ROTATING REFERENCE FRAME 80Signal reception 83Relaxation Mechanisms of a SpinSystem 85The Bloch Equation for MR signalgeneration 87Summary 87Suggested Reading 8897BOX 4.1 AN EXAMPLE OF SPATIALENCODING 98Longitudinal magnetization (Mz) 101Solution for transverse magnetization(Mxy ) 102The MR signal equation 105QUANTITATIVE PATH 68Common Terms and Notations 68Nuclear Spins 69Magnetic Moment 69Angular Momentum 70Spins in an External Magnetic Field 71Spin precessionBasic Principles of MR ImageFormation 895MR Contrast Mechanisms andPulse Sequences 121Static Contrasts and Related PulseSequences 122Proton-density contrast 123T1 contrast 126T2 contrast 129T2* contrast 131Chemical contrast 132Macromolecular contrast 133Motion Contrasts135MR angiography 135Diffusion-weighted contrast 138BOX 5.1 DIFFUSION TENSOR IMAGING 140Perfusion-weighted contrast 142 Sinauer Associates, Inc. This material cannot be copied, reproduced, manufacturedor disseminated in any form without express written permission from the publisher.
FM Huettel.qxd12/19/081:30 PMPage ixContentsFast Imaging Sequences for fMRI147Echo-planar imaging 147Spiral imaging 148Signal recovery and distortion correctionfor EPI and spiral images 152Summary 154Suggested ReadingChapter References7BOLD fMRI: Origins andProperties 193History of BOLD fMRI193Discovery of BOLD contrast 194The coupling of metabolism andblood flow 196BOX 7.1 PET IMAGING 197156157The Growth of BOLD fMRI6From Neuronal toHemodynamic ActivityNeuronal Activity160The BOLD Hemodynamic Response163Spatial Resolution166The Vascular System of the Brain214Spatial specificity in the vascular systemWhat spatial resolution is needed? 219168Arteries, capillaries, and veins 170Arterial and venous anatomy of the humanbrain 171Microcirculation 172Temporal Resolution of fMRI216220What temporal resolution is needed? 223Effects of stimulus duration and timing 225Linearity of the HemodynamicResponse 229174Control of blood flow 175BOX 6.1 NEUROVASCULAR COUPLING ANDCONTROL OF BLOOD FLOW 176Effects of increased blood flow oncapillaries 179BOX 6.2 PRIMER ON NEUROANATOMY 182Summary 190Suggested ReadingChapter References208BOX 7.3 NEURONAL ACTIVITY AND BOLDFMRI 209The initial dip 211Cerebral Metabolism: Neuronal EnergyConsumption 165Blood Flow201Contributing factors 201Early fMRI studies 203BOX 7.2 FUNCTIONAL STUDIES USINGCONTRAST AGENTS 204159Ion channels in neurons 162Neurotransmitters and action potentialsAdenosine triphosphate (ATP)ixProperties of a linear system 230Evidence for rough linearity 231Challenges to linearity 233fMRI-adaptation 235Summary 237Suggested ReadingChapter References1901918238239Signal, Noise, andPreprocessing of fMRIData 243Understanding Signal and NoiseSignal and noise defined 245BOX 8.1 TERMINOLOGY OF FMRIFunctional SNR 248245246Effects of Field Strength on fMRIData 250Field strength and raw SNR 251Field strength and spatial properties ofactivation 252Challenges of high-field fMRI 254 Sinauer Associates, Inc. This material cannot be copied, reproduced, manufacturedor disseminated in any form without express written permission from the publisher.
FM Huettel.qxdx12/19/081:30 PMPage xContentsSources of Noise in fMRI255Thermal noise 256System noise 258Motion and physiological noise 259Non-task-related neural variability 262Behavioral and cognitive variability in taskperformance 262BOX 8.2 VARIABILITY IN THE HEMODYNAMICRESPONSE OVER SUBJECTS ANDSESSIONS 264Preprocessing267280284Temporal filtering 285Spatial filtering 287Summary 289Suggested ReadingChapter References9289290Experimental Design293Basic Principles of ExperimentalDesign 294Setting Up a Good ResearchHypothesis 296Are fMRI data correlational?Confounding factors 299298Good Practices in fMRI ExperimentalDesign 302Blocked Designs 303Setting up a blocked design 304BOX 9.1 BASELINE ACTIVATION IN FMRI 306Advantages and disadvantages of blockeddesigns 310Event-Related Designs313Statistical Analysis: BasicAnalyses 331Basic Statistical TestsFunctional–Structural Coregistrationand Normalization 280Temporal and Spatial FilteringMixed Designs 325Summary 327Suggested Reading 327Chapter References 32810Quality assurance 267Slice acquisition time correction 269Head motion: an overview 271Prevention of head motion 274Correction of head motion 276Distortion correction 277Functional–structural coregistrationSpatial normalization 281Principles of event-related fMRI 316Advantages of event-related designs 319BOX 9.2 EFFICIENT FMRI EXPERIMENTALDESIGN 320333Contrasting experimental conditions:the t-test 334Comparing experimental and predictedresponses: correlation analyses 338BOX 10.1 IDENTIFYING TASK-RELATEDPERIODICITY: FOURIER ANALYSES 341Regression Analyses343The general linear model: an overview 343Constructing a design matrix: regressors ofinterest 345Constructing a design matrix: nuisanceregressors 349Modeling neuronal activity 351Modeling hemodynamic convolution 352Contrasts 354Assumptions of the general linearmodel 356Corrections for MultipleComparisons 357Calculating the significance threshold 358Thresholding based on clusters ofactivation 360Estimating the number of independenttests 361Region-of-Interest AnalysesIntersubject Analyses 365Group and parametric effectsDisplaying Statistical ResultsSummary 373Suggested Reading 373Chapter References 374 Sinauer Associates, Inc. This material cannot be copied, reproduced, manufacturedor disseminated in any form without express written permission from the publisher.362367369
FM Huettel.qxd12/19/081:30 PMPage xiContents11Statistical Analysis II:Advanced ApproachesData Exploration Approaches377378Principal components analysis (PCA) 378Independent components analysis (ICA) 380Partial least squares (PLS) 382Between-Subjects Correlations:Hyperscanning 384Functional Connectivity Approaches386From coactivation to connectivity:a conceptual overview 386BOX 11.1 INTERSUBJECT CORRELATIONS IN FREEVIEWING 387Resting-state connectivity 391Psychophysiological interactions 393Inferring causality from fMRI data 394Combining fMRI and DTI 399Prediction Approaches401Predicting variation among individuals 402BOX 11.2 REAL-TIME FMRI 403Predicting variation in behavior 407Pattern classification using machine learningalgorithms 408Capabilities and challenges of fMRI patternclassification 412Summary 415Suggested ReadingChapter References41641612xiAdvanced fMRIMethods 419Improved Spatial Resolution420MR microscopy 420Parallel imaging 423Parallel imaging with massivecoil arrays 425Improved Temporal Resolution426Multiple-channel acquisition 427Partial k-space imaging 427Efficient k-space trajectories 430Improved experimental designs 432Improved Functional Resolution throughNew Contrast Mechanisms 433Temperature-dependent contrast 434pH-dependent contrast 435Ion-gated contrast 437Neuronal magnetic field contrast 438Lorentz effect contrast 439Summary 440Suggested ReadingChapter References13441441Combining fMRI with otherTechniques 443Cognitive Neuroscience443Strategies for research in cognitiveneuroscience 445Manipulating Brain Function446Direct cortical stimulation 446Functional consequences of direct corticalstimulation 448Transcranial magnetic stimulation (TMS) 450Brain lesions 452Combined lesion and fMRI studies 454Probabilistic brain atlases 455Brain imaging and genomics 457Measuring Brain Function458Single-unit recording 458BOX 13.1 ELECTROGENESIS 459Limitations of single-unit recording 462Properties of electrical field potentials 464Localizing the neural generators of fieldpotentials 465 Sinauer Associates, Inc. This material cannot be copied, reproduced, manufacturedor disseminated in any form without express written permission from the publisher.
FM Huettel.qxdxii12/19/081:30 PMPage xiiContents14The Future of fMRI: Practicaland Ethical Issues 485Introduction 485Interpreting and PresentingfMRI Data 486Coverage of fMRI research in the popularmedia 487Core principles for presenting fMRIresearch 489BOX 14.1 REVERSE INFERENCE 490Conducting fMRI ResearchIntracranially recorded field potentials 466BOX 13.2 LOCALIZATION OF FUNCTION USINGFIELD POTENTIAL RECORDINGS 468Scalp-recorded field potentials 470BOX 13.3 COMBINING FMRI AND EEG/ERPTECHNIQUES 472Magnetoencephalography 474Using fMRI with non-human primates 476Summary 480Suggested ReadingChapter References480481494Proposing and approving fMRI research 495Ensuring the confidentiality offMRI data 497BOX 14.2 INCIDENTAL FINDINGS IN FMRIRESEARCH 498Safe conduct of fMRI studies 502Pregnancy testing in fMRI research 504Applying fMRI to New and ControversialTopics 505Reading minds 506Identifying traits 509The Future of fMRI Research (and yourrole in it) 511Summary 513Suggested Reading 515Chapter References 515Glossary 517Index 533 Sinauer Associates, Inc. This material cannot be copied, reproduced, manufacturedor disseminated in any form without express written permission from the publisher.
1 An Introduction to fMRI 1 2 MRI Scanners 31 3 Basic Principles of MR Signal Generation 57 4 Basic Principles of MR Image Formation 89 5 MR Contrast Mechanisms and Pulse Sequences 121 6 From Neuronal to Hemodynamic Activity 159 7 BOLD fMRI: Origins and Properties 193 8 Signal, Noise, and Preprocessing of fMRI Data 243 9 Experiment
Functional magnetic resonance imaging (fMRI) has quickly become the preferred technique for imaging normal brain activity, especially in the typically developing child. This technique takes advantage of specific magnetic properties and phys
Safety Guidelines for Magnetic Resonance Imaging Equipment in Clinical Use 5/86 1 Introduction 1.1 Background This is the 4th edition of the safety guidelines and aims to provide relevant safety information for users of magnetic resonance imaging (MRI) eq
“Clinical Magnetic Resonance Imaging” by Edelman, Hesselink and Zlatkin. Three volumes featuring a good mixture of technique and use. Not an intro, but a good follow-up (according to people who have read it. I haven’t). ‘Magnetic Resonance Imaging – Physical Principles and Seq
Magnetic resonance imaging (MRI) is a spectroscopic imaging technique used in medical settings to produce images of the inside of the human body. ! MRI is based on the principles of nuclear magnetic resonance (NMR), which is a spectroscopic technique used to
Safety Guidelines for Magnetic Resonance Imaging Equipment in Clinical Use 5/85 1 Introduction 1.1 Background This is the 4th edition of the safety guidelines and aims to provide relevant safety information for users of magnetic resonance imaging (MRI) equipment in clinical use but will have some relevance in academic
1. Medical imaging coordinate naming 2. X-ray medical imaging Projected X-ray imaging Computed tomography (CT) with X-rays 3. Nuclear medical imaging 4. Magnetic resonance imaging (MRI) 5. (Ultrasound imaging covered in previous lecture) Slide 3: Medical imaging coordinates The anatomical terms of location Superior / inferior, left .
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