Handbook of Diffusion MR Tractography

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. 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). 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

PART I: From Anatomy to Tractography 1. The Brain and its Pathways 2. Neurobiology of Connections 3. Past and Present of Mapping Brain Connections 4. From Brownian motion to the brain connectome: My perspective and historical view of Diffusion MRI PART II: Diffusion MRI 5. Physics of Diffusion Imaging: Fundamentals 6. Diffusion MRI acquisition for tractography: diffusion encoding 7. Diffusion MRI acquisition for tractography: Diffusion sequences 8. Diffusion MRI acquisition for tractography: Beyond the in vivo adult human brain 9. Artifacts and Diffusion MRI Processing 10. Single Shell Models: from DTI to HARDI 11. Multi-shell Models 12. From Diffusion Models to Fiber Orientations PART III: Tractography Algorithms 13. Deterministic Tractography 14. Probabilistic Tractography 15. Shortest Path Tractography 16. Global Tractography 17. Machine Learning in Tractography 18. Improving Tractography with Multimodal Integration & Anatomical Priors 19. Tractography in normal and pathological anatomy : practical considerations 20. Tractography Visualization PART IV: From Streamlines to Tracts 21. Dissecting White Matter Pathways : A Neuroanatomical Approach 22. Dissecting White Matter Pathways : Automatic Approaches 23. Methods and statistics for diffusion MRI tractometry 24. Connectivity and Connectomics 25. Tractography Validation Part 1: what needs validation, numerical simulations, and phantoms 26. Tractography Validation Part 2: The use of anatomical model systems and measures for validation 27. Tractography Validation Part 3: Lessons Learned through validation studies 28. Current challenges and opportunities for tractography PART V: Tractography Applications 29. Tractography: Applications to Neurodevelopment, Ageing and Plasticity 30. Tractography: Linking Behavior with White Matter Networks 31. Tractography as a Clinical Tool 32. Ex-vivo and Preclinical Tractography: Techniques and Applications at High Field 33. "Multicenter Studies and Harmonization: Problems, Solutions, and Open Challenges" PART VI: Appendix A. Vectors and Tensors B. Numerical Integration C. Interpolation, Splines and Smoothing D. Spherical Harmonics