
Connectome Analysis
Characterization, Methods, and Analysis
- 1st Edition - June 28, 2023
- Imprint: Academic Press
- Editors: Markus D. Schirmer, Tomoki Arichi, Ai Wern Chung
- Language: English
- Paperback ISBN:9 7 8 - 0 - 3 2 3 - 8 5 2 8 0 - 7
- eBook ISBN:9 7 8 - 0 - 3 2 3 - 8 5 2 8 1 - 4
Connectome Analysis: Characterization, Methods, and Analysis is a comprehensive companion for the analysis of brain networks, or connectomes. The book provides sources of constitue… Read more

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Request a sales quoteConnectome Analysis: Characterization, Methods, and Analysis is a comprehensive companion for the analysis of brain networks, or connectomes. The book provides sources of constituent structural and functional MRI signals, network construction and practices for analysis, cutting-edge methods that address the latest challenges in neuroscience, and the fundamentals of network theory in the context of giving practical methods for building connectomes for analysis. Emphasis is placed on quality control of the individual analysis steps. Subsequent chapters discuss networks in neuroscience in clinical and general populations, including how findings are related to underlying neurophysiology and neuropsychology.
This book is aimed at students and early-career researchers in brain connectomics and neuroimaging who have a background in computer science, mathematics and physics, as well as more broadly to neuroscientists and psychologists who want to start incorporating connectomics into their research.
- Provides practical recommendations on how to construct, assess and analyze brain networks
- Gives an understanding of all the technical methods for connectome analysis
- Presents the basic network theoretical principles typically used in neuroscience
- Covers the latest tools and data repositories that are freely available for the reader to carry out connectomic analyses
- Cover image
- Title page
- Table of Contents
- Copyright
- Dedication
- List of contributors
- About the editors
- Preface
- Acknowledgments
- Introduction
- Section I: Fundamentals of connectomics
- Chapter 1. Neurobiology and the connectome
- Abstract
- 1.1 Introduction
- 1.2 A brief history of what preceded the connectome era
- 1.3 Microscale neurobiology
- 1.4 Mesoscale columns and circuits
- 1.5 Assembling the brain from microscale to macroscale connectivity
- 1.6 Conclusion—what can we answer with the connectome?
- Dos and don’ts
- References
- Chapter 2. Structural network construction using diffusion MRI
- Abstract
- 2.1 Introduction
- 2.2 Diffusion-weighted MRI
- 2.3 Image processing
- 2.4 Connectome construction
- 2.5 Conclusion
- Dos and don’ts
- Acknowledgments
- References
- Chapter 3. Functional network construction using functional MRI
- Abstract
- 3.1 Introduction
- 3.2 Biology and physics of the Blood Oxygen Level Dependent signal
- 3.3 BOLD contrast fMRI acquisition
- 3.4 fMRI preprocessing
- 3.5 Functional network matrix construction
- 3.6 Conclusion
- Dos and don’ts
- Additional resources
- Acknowledgments
- References
- Chapter 4. Network nodes in the brain
- Abstract
- 4.1 What is a network node?
- 4.2 How have nodes been defined previously in human brain networks?
- 4.3 Strengths and limitations of current node definitions
- 4.4 What is the ideal definition of a brain node?
- 4.5 Conclusion
- Dos and don’ts
- References
- Chapter 5. Network measures and null models
- Abstract
- 5.1 Introduction
- 5.2 Background
- 5.3 Network measures
- 5.4 Network topology and null models
- 5.5 Network measures and null models
- 5.6 Future directions
- 5.7 Conclusion
- Dos and don'ts
- References
- Chapter 6. Hubs and rich clubs
- Abstract
- 6.1 Introduction
- 6.2 Network theoretical principles of hubs and rich clubs
- 6.3 Hubs and rich clubs in brain networks
- 6.4 Future directions
- 6.5 Conclusions
- Dos and don’ts
- Additional resources
- References
- Chapter 7. Community detection in network neuroscience
- Abstract
- 7.1 Introduction
- 7.2 Background
- 7.3 Community detection: methods
- 7.4 Limitations
- 7.5 Future directions and alternative approaches
- 7.6 Outlook and conclusion
- Dos and don’ts
- Additional resources
- Acknowledgments
- References
- Chapter 8. Network comparisons and their applications in connectomics
- Abstract
- 8.1 Introduction
- 8.2 Preliminaries
- 8.3 Graph theory for population studies
- 8.4 Mechanistic network models
- 8.5 Data-driven approaches
- 8.6 Recommendations and warnings
- 8.7 Future directions and conclusion
- Dos and don’ts
- References
- Section II: Advanced concepts and methods
- Chapter 9. Beyond the shortest path—diffusion-based routing strategies
- Abstract
- 9.1 Introduction
- 9.2 Methods
- 9.3 Limitations
- 9.4 Future directions and conclusion
- Dos and don’ts
- References
- Chapter 10. Dynamic functional connectivity
- Abstract
- 10.1 Introduction
- 10.2 Background
- 10.3 Methods
- 10.4 Limitations and considerations
- 10.5 Future directions and conclusion
- Dos and don’ts
- Additional resources
- References
- Chapter 11. The synergy of structural and functional connectivity
- Abstract
- 11.1 Introduction
- 11.2 Background
- 11.3 Methods
- 11.4 Limitations, practical choices, and recommendations
- 11.5 Conclusion
- Dos and don’ts
- Acknowledgments
- References
- Chapter 12. Machine learning in connectomics: from representation learning to model fitting
- Abstract
- 12.1 Introduction
- 12.2 Background
- 12.3 Methods
- 12.4 Limitations
- 12.5 Recommendations
- 12.6 Future directions and conclusions
- Dos and don’ts
- References
- Chapter 13. Deep learning with connectomes
- Abstract
- 13.1 Introduction
- 13.2 Background
- 13.3 Model training
- 13.4 Limitations
- 13.5 Recommendations and warnings
- 13.6 Future directions
- 13.7 Conclusions
- Dos and don'ts
- References
- Chapter 14. Uncovering the genetics of the human connectome
- Abstract
- 14.1 Introduction
- 14.2 Heritability analyses
- 14.3 Association analyses
- 14.4 Transcriptional analyses
- 14.5 Conclusions and future directions
- Dos and don’ts
- Additional resources
- References
- Section III: Applications in the human brain
- Chapter 15. The developmental connectome
- Abstract
- 15.1 Introduction
- 15.2 A brief description of the connectome
- 15.3 Development of the functional connectome
- 15.4 Development of the structural connectome
- 15.5 Coupling between structural and functional connectomes
- 15.6 Methodological considerations
- 15.7 Conclusions and future directions
- Dos and don’ts
- Additional resources
- Acknowledgment
- References
- Chapter 16. Connectomics in aging and cognition
- Abstract
- 16.1 Introduction
- 16.2 Connectomic changes with aging and association with cognition
- 16.3 Questions of interest in aging
- 16.4 Methodological challenges in aging connectome construction and analysis
- 16.5 Going further—how to inform connectomics with other clinical data
- 16.6 Summary, caveats, and future directions in aging connectome research
- 16.7 Conclusions
- Dos and don’ts
- Additional resources
- References
- Chapter 17. Networks with lesions
- Abstract
- 17.1 Introduction
- 17.2 Background
- 17.3 Methods
- 17.4 Limitations
- 17.5 Future directions and conclusion
- Dos and don’ts
- References
- Chapter 18. Clinical application of connectomics to disorders of consciousness
- Abstract
- 18.1 Introduction
- 18.2 Background
- 18.3 Methods and limitations
- 18.4 Future directions and conclusion
- Dos and don’ts
- References
- Chapter 19. Connectome analysis and psychiatric disorders
- Abstract
- 19.1 Studying the brain in psychiatric disorders
- 19.2 Advantages of connectomic approaches
- 19.3 Psychiatric disorders as pathological processes of global network organization
- 19.4 Psychiatric disorders as pathological processes within a network
- 19.5 Summary and recommendations
- Dos and don’ts
- Additional resources
- References
- Afterword: The road ahead for connectomics
- 1 From brain structure to function
- 2 Network science
- 3 Clinical and translational connectomics
- 4 Network neuroscience
- Index
- Edition: 1
- Published: June 28, 2023
- Imprint: Academic Press
- No. of pages: 486
- Language: English
- Paperback ISBN: 9780323852807
- eBook ISBN: 9780323852814
MS
Markus D. Schirmer
TA
Tomoki Arichi
AC