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Preface | |
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Introduction | |
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A brief overview of fMRI | |
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The emergence of cognitive neuroscience | |
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A brief history of fMRI analysis | |
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Major components of fMRI analysis | |
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Software packages for fMRI analysis | |
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Choosing a software package | |
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Overview of processing streams | |
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Prerequisites for fMRI analysis | |
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Image processing basics | |
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What is an image? | |
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Coordinate systems | |
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Spatial transformations | |
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Filtering and Fourier analysis | |
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Preprocessing fMRI data | |
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Introduction | |
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An overview of fMRI preprocessing | |
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Quality control techniques | |
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Distortion correction | |
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Slice timing correction | |
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Motion correction | |
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Spatial smoothing | |
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Spatial normalization | |
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Introduction | |
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Anatomical variability | |
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Coordinate spaces for neuroimaging | |
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Atlases and templates | |
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Preprocessing of anatomical images | |
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Processing streams for fMRI normalization | |
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Spatial normalization methods | |
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Surface-based methods | |
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Choosing a spatial normalization method | |
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Quality control for spatial normalization | |
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Troubleshooting normalization problems | |
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Normalizing data from special populations | |
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Statistical modeling: Single subject analysis | |
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The BOLD signal | |
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The BOLD noise | |
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Study design and modeling strategies | |
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Statistical modeling: Group analysis | |
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The mixed effects model | |
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Mean centering continuous covariates | |
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Statistical inference on images | |
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Basics of statistical inference | |
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Features of interest in images | |
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The multiple testing problem and solutions | |
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Combining inferences: masking and conjunctions | |
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Use of region of interest masks | |
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Computing statistical power | |
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Modeling brain connectivity | |
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Introduction | |
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Functional connectivity | |
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Effective connectivity | |
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Network analysis and graph theory | |
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Multivoxel pattern analysis and machine learning | |
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Introduction to pattern classification | |
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Applying classifiers to fMRI data | |
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Data extraction | |
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Feature selection | |
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Training and testing the classifier | |
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Characterizing the classifier | |
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Visualizing, localizing, and reporting fMRI data | |
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Visualizing activation data | |
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Localizing activation | |
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Localizing and reporting activation | |
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Region of interest analysis | |
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Review of the General Linear Model | |
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Estimating GLM parameters | |
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Hypothesis testing | |
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Correlation and heterogeneous variances | |
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Why "general" linear model? | |
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Data organization and management | |
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Computing for fMRI analysis | |
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Data organization | |
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Project management | |
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Scripting for data analysis | |
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Image formats | |
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Data storage | |
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File formats | |
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Bibliography | |
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Index | |