Principles of fMRI
Principles of fMRI
About the Book
Functional Magnetic Resonance Imaging (fMRI) is the most widely used technique for investigating the living, functioning human brain as people perform tasks and experience mental states. It is a convergence point for multidisciplinary work from many disciplines. Psychologists, statisticians, physicists, computer scientists, neuroscientists, medical researchers, behavioral scientists, engineers, public health researchers, biologists, and others are coming together to advance our understanding of the human mind and brain. In this book we provide an introduction to fMRI, including physics and acquisition, experimental design, analysis, and inferences about brain and mind. We discuss both theoretical considerations and practical aspects of conducting fMRI studies. The book is appropriate for readers who want to learn more about fMRI, and for researchers engaged in fMRI studies.
- What’s in this book?
About the Authors
- Martin Lindquist
- Tor Wager
Part 1: Motivation
Chapter 1 - Introduction
- MRI, PET, and beyond: A quick tour
Chapter 2 - Why fMRI? Neuroimaging and the movement toward multidisciplinary science
- Neuroimaging and the `common language’ of the brain
- Multiple roles, multiple fields: An example
- Challenges and motivation for multidisciplinary science
Chapter 3 - Types of imaging: What PET and fMRI can measure
- MRI: Multiple measures, multiple modalities
- Structural MRI imaging
- Functional imaging with fMRI and PET
Chapter 4 - Brain mapping: A conceptual overview
- What is a brain map?
- Fundamental assumptions and principles
- Types of inference: What brain maps can and cannot tell us
Chapter 5 - Limitations in inferences from brain maps
- Seven caveats in brain map inferences
- A non-imaging example
Chapter 6 - How to lie with brain imaging
- How to tell a story about the ``one brain region’’
- How to make your results look really strong
- Overlapping processes: How to make two maps look the same
- How to make two maps look really different
- Chapter 1 - Introduction
Part 2: Fundamentals: The origins of PET and fMRI signals in the brain
Chapter 7 - fMRI basics: Processing stages, terminology, and data structure
- fMRI basics
- Data structure in fMRI experiments
Chapter 8 - The MRI environment and human factors
- MR basics and safety
- Physical limitations on data collection
Chapter 9 - A head-to-head comparison of PET and MRI
- Acquisition options and fidelity
- Available signal types and their interpretability
- Spatial and temporal resolution
- Accessibility to a broad community
- Chapter 10 - Fundamentals of MRI Physics
- Chapter 11 - Physiological basis of fMRI signals
Chapter 12 - Constraints on fMRI spatial and temporal resolution
- Spatial Limitations
- Temporal Limitations
- Chapter 7 - fMRI basics: Processing stages, terminology, and data structure
Part 3: Basics of fMRI signal processing and analysis
Chapter 14 - Experimental Design
- Block designs
- Event-related fMRI
- Optimized experimental designs
Chapter 15 - Resting state, natural viewing, and non-experimental designs
- Resting state
- Natural viewing and non-experimental designs
Chapter 16 - Essentials of fMRI signal processing
- BOLD signal
- Noise and nuisance signal
Chapter 17 - Preprocessing
- Slice-timing correction
- Motion correction
- Spatial smoothing
Chapter 18 - The General Linear Model and Foundations of Analysis
- Setting up the GLM
- GLM Estimation
- Chapter 19 - Conditions and Contrasts
- Chapter 20 - Design Specification: Flexible Hemodynamics and Mis-modeling
- Chapter 21 - Design Specification: Dealing with Artifacts and Noise
- Chapter 22 - Group Analysis
Chapter 23 - Multiple Comparisons
- FWE correction
- FDR control
Chapter 24 - Assessing Brain Connectivity
- Functional connectivity
- Effective connectivity
- Network analysis
- Chapter 14 - Experimental Design
Part 4: Predictive Mapping
Chapter 25 - Multivariate brain analysis: From maps to models
- From univariate mapping to multivariate brain models
- Basic criteria for a good model
Chapter 26 - Advantages of MVPA from a neuroscientific perspective
- MPVA analysis choices: Spatial scope and flexibility
- Sensitivity to neural topography
- Sensitivity to distributed representations
- Benefits in testing generalizability across individuals and studies
Resources and further reading
- Other books about fMRI
- Chapter 25 - Multivariate brain analysis: From maps to models
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