دانلود کتاب Introduction to Neuroimaging Analysis (Oxford Neuroimaging Primers)

فهرست مطالب :

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