Introduction to Neuroimaging Analysis

Title Page
Copyright Page
Dedication
Contents
1 Introduction
	1.1 Main MRI modalities and analysis techniques
	1.2 Walk-through of a typical study
		Example Box: Look at your data!
		Example Box: Keep looking at your data!
		Example Box: Think through your analysis early
	1.3 MR physics and scanner hardware
		Box 1.1: B0 field inhomogeneities
		Box 1.2: Resonance frequency
		Box 1.3: RF inhomogeneity and bias fields
		Box 1.4: Head coils and accelerated imaging
		Box 1.5: Gradient fields
	1.4 Overview
		Summary
		Further reading
2 MRI Modalities for Neuroimaging
	2.1 Image fundamentals
		Box 2.1: Image formats
	2.2 Structural MRI
		Example Box: SNR, resolution, and acquisition time trade-offs
		Example Box: MRI artifacts
		Summary
		Further reading
	2.3 Diffusion MRI
		Example Box: Diffusion signal in different tissues
		Box 2.2: HARDI
		Example Box: Diffusion signal in different tissues (revisited)
		Example Box: Viewing diffusion images
		Summary
		Further reading
	2.4 Functional MRI
		Box 2.3: T2* Relaxation and BOLD
		Summary
		Further reading
	2.5 Perfusion MRI
		Summary
		Further reading
	2.6 Spectroscopy (MRS)
		Summary
		Further reading
	2.7 Complementary techniques
		Summary
		Further reading
3 Overview of MRI Analysis
	Group Analysis Box
	3.1 Early stages
		Box 3.1: Voxel and world coordinates
		Summary
	3.2 Structural pipeline
		Example Box: Tissue-type segmentation
		Box 3.2: Segmentation of pathological tissue
		Example Box: Deep gray matter structure segmentation
		Summary
		Further reading
	3.3 Diffusion pipeline
		Box 3.3: Fieldmap acquisitions
		Example Box: Correcting for distortions and artifacts in diffusion images
		Box 3.4: Diffusion tensor model
		Example Box: DTI
		Example Box: TBSS
		Example Box: Tractography
		Summary
		Further reading
	3.4 Functional pipeline (task and resting state fMRI)
		Box 3.5: Motion artifacts
		Example Box: Slice timing effects and corrections
		Example Box: Aliasing of physiological signals
		Example Box: Physiological noise modeling
		Example Box: Independent component classification
		Example Box: Task fMRI data
		Example Box: Resting state fMRI networks
		Summary
		Further reading
	3.5 Perfusion pipeline
		Summary
		Further reading
4 Brain Extraction
	4.1 When it is needed
	4.2 Skull stripping versus cortical modeling
		Example Box:Brain extraction
	4.3 Brain masks
		Example Box: Brain masks
	4.4 Skull estimation
	4.5 Difficulties and troubleshooting
		Example Box: Troubleshooting brain extraction
		Summary
		Further reading
5 Registration
	5.1 Spatial transformations
		Box 5.1: Transformation parameters, coordinates, and conventions
		Example Box: Spatial Transformations
	5.2 Cost functions
		Box 5.2: Similarity functions
		Box 5.3: Intensity models for cost functions
		Example Box: Registration
	5.3 Resampling and interpolation
		Box 5.4: Symmetric registration and halfway spaces
	5.4 Case studies
		Example Box: Evaluating registrations
		Example Box: Registration case studies
	5.5 Standard space and templates
	5.6 Atlases
		Example Box: Probabilistic atlas construction
	5.7 Atlas-based segmentation
		Summary
		Further reading
6 Motion and Distortion Correction
	6.1 Motion correction
	6.2 Distortion correction
		Box 6.1: Gradient-echo fieldmap acquisitions
		Box 6.2: Calculating distortion from gradient-echo fieldmaps
		Box 6.3: Intensity model for BBR
		Box 6.4: Low contrast EPI and registration
		Box 6.5: Combining fieldmap-based distortion correction and registration
		Example Box: Distortion correction with fieldmaps
		Example Box: Distortion correction with blip-up–blip-down data
		Summary
		Further reading
7 Surface-Based Analysis
	7.1 Cortical surface extraction
	7.2 Inflated, spherical, and flattened surfaces
	7.3 Registration of surface data
	7.4 Surface-based fMRI analysis
		Summary
		Further reading
8 Epilogue
	8.1 Planning
	8.2 Analysis
	8.3 Interpretation
	8.4 Next steps
Appendix A: Short Introduction to Brain Anatomy for Neuroimaging
	A.1 Brain cells and tissues
	A.2 Navigating around brain images
	A.3 Brain structures
		Example Box: Learning anatomy with digital atlases
		Summary
		Further reading
Index