Handbook of Tractography presents methods and applications of MR diffusion tractography, providing deep insights into the theory and implementation of existing tractography techniques and offering practical advice on how to apply diffusion tractography to research projects and clinical applications. Starting from the design of MR acquisition protocols optimized for tractography, the book follows a pipeline approach to explain the main methods behind diffusion modelling and tractography, including advanced analysis of tractography data and connectomics. An extensive section of the book is devoted to the description of tractography applications in research and clinical settings to give a complete picture of tractography practice today. By focusing on technology, models and applications, this handbook will be an indispensable reference for researchers and students with backgrounds in computer science, mathematics, physics, neuroscience and medical science.
Provides a unique reference covering the whole field of MRI diffusion tractography
Includes in-depth descriptions of the latest research and current state-of-the-art of methods available in the field of diffusion tractography
Present a step-by-step pipeline approach, from setting up MRI data acquisition to the analysis of large-scale tractography datasets
Researchers and graduate students working in diffusion MRI Trachtography with a background in computer science, biomedical engineering, Physics and mathematics, neuroscientists and clinicians
Table of Contents
PART I: From Anatomy to Tractography 1. The Brain 2. White Matter Pathways 3. Brain Connectivity and Neuroimaging.
PART II: MR Physics of Diffusion Imaging 4. Principles of Magnetic Resonance Imaging 5. Principles of Diffusion Imaging 6. Diffusion Imaging Pulse Sequences 7. Artefacts and Data preprocessing
PART III: Diffusion Models for Tractography 8. From Diffusion Weighted Imaging to Diffusion Tensor Imaging 9. Diffusion Tensor Imaging 10. High Angular Resolution Diffusion Imaging (HARDI) models 11. Beyond HARDI Models 12. Extractions of fiber orientations and ODF
PART V: From Streamlines to Tracts 18. Dissecting White Matter Pathways 19. Tract Specific Metrics and Along Tracts Metrics 20. Analysis of Tractography Data 21. Connectivity and Connectomics Analysis 22. Current Limitations and Challenges of Tractography
PART VI: Tractography Applications 23. Tractography as a Research Tool 24. Tractography as a Clinical Tool 25. Validation of Diffusion Tractography 26. Preclinical animal models and ex-vivo Tractography
PART VII: Tools / Appendix 27. Vectors and Tensors 28. Numerical Integration 29. Interpolation and Splines 32. Fourier Transform and Spherical Harmonics 33. Tractography Data Formats 34. Tractography Visualisation
Flavio Dell’Acqua (FDA), King’s College London, is Senior Lecturer in Translational Neuroimaging at the Department of Forensics and Neurodevelopmental Sciences and the Sackler Institute for Translational Neurodevelopment, Institute of Psychiatry, Psychology and Neuroscience. FDA's research focuses on the development and application of new diffusion imaging and tractography methods for neuroscience, psychiatric and clinical research as well as preclinical applications.
FDA is coauthor of more than 60 papers and his methods have been successfully applied in a broad range of tractography studies ranging from the first visualisation of the superior longitudinal fasciculus in humans (Thiebaut De Schotten*, Dell'Acqua* et al., Nat. Neuroscience. 2011) to application on autism (Catani et al. Brain 2016), stroke (Forkel et al. Brain 2014) and neurosurgery (Vergani et al. Neurosurgery 2016). His methods have been fundamental also in major debates on new neuroanatomical theories (Catani, Body & Dell’Acqua, Science 2013) and, more recently, FDA contributed in the critical evaluation of the current challenges of modern tractography and structural connectivity methods (Maier-Hein et al. Nature Communications 2017).
FDA is currently the lead of the diffusion imaging analysis team for the largest European multi-centre study on autism (EU-AIMS) and is collaborating with research institutes across Europe and US. He is a member and co-founder of the NATBRAINLAB (www.natbrainlab.com) an interdepartmental laboratory dedicated to the study of human neuroanatomy and tractography research. Since 2014, he has been the organiser of the educational courses on Diffusion Imaging for the Organisation for Human Brain Mapping (OHBM) conferences. He is also an active member of the International Society of Magnetic Resonance in Medicine (ISMRM) where he has lectured at the morning educational courses and past international workshops (Lisbon 2016 and Ljubljana 2017) on tractography methods.
Affiliations and Expertise
Senior Lecturer in Translational Neuroimaging, Department of Forensics and Neurodevelopmental Sciences, King's College, London, UK
Alexander Leemans is a physicist who received his Ph.D. in 2006 at the University of Antwerp, Belgium. From 2007 to 2009, he worked as a postdoctoral researcher at the Cardiff University Brain Research Imaging Center (CUBRIC), Cardiff University, Wales, United Kingdom. In 2009, he joined the Image Sciences Institute (ISI), University Medical Center Utrecht, the Netherlands, where he currently holds a tenured faculty position as Associate Professor. His current research interests include modeling, processing, visualizing and analyzing diffusion MRI data for investigating microstructural and architectural tissue organization. He heads the PROVIDI Lab and is the developer of ExploreDTI, which is a graphical toolbox for investigating diffusion MRI data
Affiliations and Expertise
UMC Utrecht, Utecht, The Netherlands
The investigator Maxime Descôteaux is a member of the Medical Imaging Axis of the Centre de recherche du CHUS, professor of the Computer Science Department, Faculty of Science, Université de Sherbrooke, Director of the Imaging and Visualization Platform (PAVI, pavi.dinf.usherbrooke.ca) and Director of the Sherbrooke Connectivity Imaging Laboratory (SCIL, scil.dinf.usherbrooke.ca). He is a leader in diffusion Magnetic Resonance Imaging (MRI) acquisition, processing and visualization to infer white matter connectivity of the brain.
The goal of his research is to develop state-of-the-art fiber tractography tools to better understand functional coupling between cortical and sub-cortical regions of the brain and study connectivity properties of white matter to characterize fiber integrity. This field is now named ‘’connectomics’’. His most important contributions are in the fields of fundamental diffusion MRI processing and white matter fiber tract reconstruction and visualization. Recently, his tools have made the transfer to clinical applications for neurosurgical planning and interventions. He is a member of the editorial board of several important journals in neuroscience and co-founder of the company Imeka Solution Inc (www.imeka.ca).
Affiliations and Expertise
Professor, Department of Computer Science, Faculty of Science, Université de Sherbrooke, Sherbrooke, Canada; Director, Imaging and Visualization Platform; Director, Sherbrooke Connectivity Imaging Laboratory