Handbook of Neuroimaging Data Analysis

666 Pages·2017·21.065 MB·English

by  Hernando Ombao, Martin Lindquist, Wesley Thompson, John Aston (eds.)

Handbook of
Neuroimaging
Data Analysis
Chapman & Hall/CRC
Handbooks of Modern Statistical Methods
Series Editor
Garrett Fitzmaurice
Department of Biostatistics
Harvard School of Public Health
Boston, MA, U.S.A.
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Handbook of Neuroimaging Data Analysis
Edited by Hernando Ombao, Martin Lindquist,
Wesley Thompson, and John Aston

Chapman & Hall/CRC
Handbooks of Modern
Statistical Methods
Handbook of
Neuroimaging
Data Analysis
Edited by
Hernando Ombao
University of California
Irvine, USA
Martin Lindquist
Johns Hopkins University
Baltimore, Maryland, USA
Wesley Thompson
Institute of Biological Psychiatry, Denmark
University of California, San Diego, La Jolla, USA

John Aston
University of Cambridge, UK
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Contents
List of Figures xix
List of Tables xxxiii
Preface xxxv
Contributors xxxvii
I Overview 1
1 Overview of the Handbook 3
1.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
1.2 A Brief History of Neuroimaging . . . . . . . . . . . . . . . . . . . . . . . . 4
1.3 Modalities . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
1.4 Statistical Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
1.4.1 Preprocessing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
1.4.2 Methods in Structural Neuroimaging . . . . . . . . . . . . . . . . . . 8
1.4.3 Localizing Areas of Activation . . . . . . . . . . . . . . . . . . . . . 9
1.4.4 Brain Connectivity . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
1.4.5 Analysis of Electroencephalograms . . . . . . . . . . . . . . . . . . . 10
1.4.6 Multi-Modal Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . 10
1.5 Additional Topics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
1.5.1 Meta-Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
1.5.2 Experimental Design in fMRI . . . . . . . . . . . . . . . . . . . . . . 11
1.5.3 Experimental Design in EEG . . . . . . . . . . . . . . . . . . . . . . 11
1.5.4 Imaging Genetics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
1.6 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
Bibliography . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
II Imaging Modalities 15

2 Positron Emission Tomography: Some Analysis Methods 17
John Aston
2.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
2.2 Background . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
2.3 Tracer Kinetic Modelling: Compartmental Approaches . . . . . . . . . . . . 20
2.3.1 Plasma Input Functions Models. . . . . . . . . . . . . . . . . . . . . 20
2.3.2 Reference Tissue Models . . . . . . . . . . . . . . . . . . . . . . . . . 23
2.4 Estimation and Statistical Methods . . . . . . . . . . . . . . . . . . . . . . 24
2.4.1 Non-Linear Least Squares . . . . . . . . . . . . . . . . . . . . . . . . 24
2.4.2 Basis Function Methods . . . . . . . . . . . . . . . . . . . . . . . . . 25
2.4.3 Model Selection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
vii
viii Contents
2.5 Other Modelling Approaches . . . . . . . . . . . . . . . . . . . . . . . . . . 27
2.5.1 Graphical Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
2.5.2 Bayesian Approaches . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
2.5.3 Non-Parametric Approaches . . . . . . . . . . . . . . . . . . . . . . . 28
2.6 Further Modelling Considerations . . . . . . . . . . . . . . . . . . . . . . . 29
Bibliography . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
3 Structural Magnetic Resonance Imaging 35
Wesley K. Thompson, Hauke Bartsch, and Martin A. Lindquist
3.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
3.2 Image Acquisition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
3.2.1 MRI Physics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
3.2.2 Image Reconstruction . . . . . . . . . . . . . . . . . . . . . . . . . . 38
3.2.3 MRI Sequences . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
3.2.4 MRI Artifacts. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
3.3 Multi-Subject MRI . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
3.3.1 Registration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
3.3.1.1 Volumetric Registration . . . . . . . . . . . . . . . . . . . . 41
3.3.1.2 Surface-Based Registration . . . . . . . . . . . . . . . . . . 41
3.3.2 Segmentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
3.3.2.1 Foreground from Background Segmentation . . . . . . . . . 43
3.3.2.2 Brain Tissue Segmentation . . . . . . . . . . . . . . . . . . 44
3.3.3 Templates and Atlases . . . . . . . . . . . . . . . . . . . . . . . . . . 45
3.3.4 Morphometry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
3.3.4.1 Subcortical Volumes . . . . . . . . . . . . . . . . . . . . . . 46
3.3.4.2 Voxel-Based Morphometry . . . . . . . . . . . . . . . . . . 47
3.3.4.3 Deformation- and Tensor-Based Morphometry . . . . . . . 47
3.3.4.4 Surface-Based Measures . . . . . . . . . . . . . . . . . . . . 48
3.3.4.5 Other Morphometric Measures . . . . . . . . . . . . . . . . 49
3.3.5 Statistical Analyses . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
3.3.5.1 Statistical Parametric Maps . . . . . . . . . . . . . . . . . 51
3.4 Miscellaneous Topics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
3.4.1 Structural Integrity and Tumor Detection . . . . . . . . . . . . . . . 51
3.4.2 Anatomical References for Functional Imaging . . . . . . . . . . . . 52
3.4.3 Multi-Center Studies . . . . . . . . . . . . . . . . . . . . . . . . . . . 52
3.4.4 Imaging Genetics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
3.5 Glossary of MRI Terms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
Bibliography . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
4 Diffusion Magnetic Resonance Imaging (dMRI) 65
Jian Cheng and Hongtu Zhu
4.1 Introduction to Diffusion MRI . . . . . . . . . . . . . . . . . . . . . . . . . 66
4.1.1 Diffusion Weighted Imaging (DWI) . . . . . . . . . . . . . . . . . . . 66
4.1.1.1 Diffusion Gradient Sequence . . . . . . . . . . . . . . . . . 66
4.1.1.2 Free Diffusion . . . . . . . . . . . . . . . . . . . . . . . . . 67
4.1.1.3 Restricted Diffusion . . . . . . . . . . . . . . . . . . . . . . 67
4.1.2 Diffusion Tensor Imaging (DTI). . . . . . . . . . . . . . . . . . . . . 69
4.1.2.1 Scalar Indices and Eigenvectors of Diffusion Tensor . . . . 69
4.2 High Angular Resolution Diffusion Imaging (HARDI) . . . . . . . . . . . . 70
4.2.1 Generalization of Diffusion Tensor Imaging . . . . . . . . . . . . . . 70
4.2.1.1 Mixture of Tensor Model . . . . . . . . . . . . . . . . . . . 70
Contents ix
4.2.1.2 Generalized DTI (GDTI) . . . . . . . . . . . . . . . . . . . 71
4.2.1.3 High-Order Tensor Model, ADC-Based Model . . . . . . . 72
4.2.2 Diffusion Spectrum Imaging (DSI) . . . . . . . . . . . . . . . . . . . 73
4.2.3 Hybrid Diffusion Imaging (HYDI) . . . . . . . . . . . . . . . . . . . 74
4.2.4 Q-Ball Imaging (QBI) . . . . . . . . . . . . . . . . . . . . . . . . . . 75
4.2.4.1 Original Q-Ball Imaging. . . . . . . . . . . . . . . . . . . . 75
4.2.4.2 Exact Q-Ball Imaging . . . . . . . . . . . . . . . . . . . . . 76
4.2.5 Diffusion Orientation Transform (DOT) . . . . . . . . . . . . . . . . 77
4.2.6 Spherical Deconvolution (SD) . . . . . . . . . . . . . . . . . . . . . . 77
4.2.7 Diffusion Propagator Imaging (DPI) . . . . . . . . . . . . . . . . . . 77
4.2.8 Simple Harmonic Oscillator Reconstruction and Estimation (SHORE) 78
4.2.9 Spherical Polar Fourier Imaging (SPFI) . . . . . . . . . . . . . . . . 78
4.3 Reconstruction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
4.3.1 Noise Components and Voxelwise Estimation Methods . . . . . . . . 79
4.3.2 Spatial-Adaptive Estimation Methods . . . . . . . . . . . . . . . . . 80
4.4 Tractography Algorithms . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
4.5 Uncertainty in Estimated Diffusion Quantities . . . . . . . . . . . . . . . . 86
4.6 Sampling Mechanisms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
4.7 Registration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
4.8 Group Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
4.9 Public Resources . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
4.9.1 Datasets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
4.9.2 Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94
4.10 Glossary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
Bibliography . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96
5 A Tutorial for Multisequence Clinical Structural Brain MRI 109
Ciprian Crainiceanu, Elizabeth M. Sweeney, Ani Eloyan, and
Russell T. Shinohara
5.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
5.1.1 What Are These Images? . . . . . . . . . . . . . . . . . . . . . . . . 112
5.1.2 How Can We Handle sMRI?. . . . . . . . . . . . . . . . . . . . . . . 113
5.1.3 What Are Some Major Pitfalls When Starting Working on sMRI? . 114
5.2 Data Structure and Intuitive Description of Associated Problems . . . . . . 114
5.3 Acquisition and Reconstruction . . . . . . . . . . . . . . . . . . . . . . . . 115
5.4 Preprocessing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116
5.4.1 Inhomogeneity Correction . . . . . . . . . . . . . . . . . . . . . . . . 117
5.4.1.1 Concepts . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118
5.4.1.2 Practical Approaches, Software, and Application to Data . 118
5.4.2 Skull Stripping . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119
5.4.2.1 Concepts . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119
5.4.2.2 Practical Approaches, Software, and Application to Data . 119
5.4.3 Interpolation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119
5.4.3.1 Concepts . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120
5.4.3.2 Practical Approaches, Software, and Application to Data . 121
5.4.4 Spatial Registration . . . . . . . . . . . . . . . . . . . . . . . . . . . 121
5.4.4.1 Concepts . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121
5.4.4.2 Practical Approaches, Software, and Application to Data . 123
5.4.5 Intensity Normalization . . . . . . . . . . . . . . . . . . . . . . . . . 126
5.4.5.1 Concepts . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127
5.4.5.2 Practical Approaches, Software, and Application to Data . 127
x Contents
5.5 Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129
5.5.1 Lesion Segmentation . . . . . . . . . . . . . . . . . . . . . . . . . . . 129
5.5.2 Lesion Mapping. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130
5.5.3 Longitudinal and Cross Sectional Intensity Analysis . . . . . . . . . 131
5.6 Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133
Bibliography . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133
6 Principles of Functional Magnetic Resonance Imaging 139
Martin A. Lindquist and Tor D. Wager
6.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 139
6.2 The Basics of fMRI Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141
6.2.1 Principles of Magnetic Resonance Signal Generation . . . . . . . . . 141
6.2.1.1 The MRI Scanner . . . . . . . . . . . . . . . . . . . . . . . 141
6.2.1.2 Basic MR Physics . . . . . . . . . . . . . . . . . . . . . . . 142
6.2.1.3 Image Contrast. . . . . . . . . . . . . . . . . . . . . . . . . 143
6.2.2 Image Formation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144
6.2.3 From MRI to fMRI. . . . . . . . . . . . . . . . . . . . . . . . . . . . 146
6.3 BOLD fMRI . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 148
6.3.1 Understanding BOLD fMRI . . . . . . . . . . . . . . . . . . . . . . . 148
6.3.2 Spatial Limitations . . . . . . . . . . . . . . . . . . . . . . . . . . . . 150
6.3.3 Temporal Limitations . . . . . . . . . . . . . . . . . . . . . . . . . . 151
6.3.4 Acquisition Artifacts . . . . . . . . . . . . . . . . . . . . . . . . . . . 152
6.4 Modeling Signal and Noise in fMRI . . . . . . . . . . . . . . . . . . . . . . 153
6.4.1 BOLD Signal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153
6.4.2 Noise and Nuisance Signal . . . . . . . . . . . . . . . . . . . . . . . . 155
6.5 Experimental Design . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 157
6.6 Preprocessing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 158
6.7 Data Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 160
6.7.1 Localization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 160
6.7.2 Connectivity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 162
6.7.3 Prediction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 164
6.8 Resting-State fMRI . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165
6.9 Data Format, Databases, and Software . . . . . . . . . . . . . . . . . . . . 166
6.10 Future Developments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 168
Bibliography . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169
7 Electroencephalography (EEG): Neurophysics, Experimental Methods,
and Signal Processing 175
Michael D. Nunez, Paul L. Nunez, and Ramesh Srinivasan
7.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 175
7.2 The Neurophysics of EEG . . . . . . . . . . . . . . . . . . . . . . . . . . . 177
7.3 Synchronization and EEG . . . . . . . . . . . . . . . . . . . . . . . . . . . 180
7.4 Recording EEG . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 182
7.5 Preprocessing EEG . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 183
7.6 Artifact Removal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 184
7.7 Stationary Data Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . 187
7.8 Nonstationary Data Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . 194
7.9 Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 197
Bibliography . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 197