This accessible primer gives an introduction to the wide array of MRI-based neuroimaging methods that are used in research. It provides an overview of the fundamentals of what different MRI modalities measure, what artifacts commonly occur, the essentials of the analysis, and common 'pipelines'.

• 1: Introduction


• 2: MRI modalities for neuroimaging


• 3: Overview of MRI analysis


• 4: Brain Extraction


• 5: Registration


• 6: Motion and Distortion Correction


• 7: Surface-based Analysis


• 8: Epilogue

Mark Jenkinson is a co-founder and the principal developer of FSL (FMRIB Software Library) and has written numerous tools for analysis of structural, diffusion and functional data. He has been a part of the FMRIB centre, University of Oxford, since 1998, working on analysis methodology for MRI-based neuroimaging research and is included in Thomson Reuters' list of Highly Cited Researchers. From 2002 he has been teaching neuroimaging analysis to students and researchers from a wide variety of backgrounds (medicine, psychology, physiology, engineering, physics, and philosophy) through both annual FSL Courses and the FMRIB Graduate Programme. He has won teaching awards from the University of Oxford and the International Society of Magnetic Resonance in Medicine (ISMRM) and authored over 150 journal papers and book chapters covering a wide range of methodology and applications in MRI-based neuroimaging.
Michael Chappell is an Associate Professor of Engineering Science in the Institute of Biomedical Engineering, University of Oxford. He remains a member of the Oxford Centre for Functional MRI of the Brain (FMRIB) where he started his work on the quantification and analysis of Arterial Spin Labelling perfusion MRI data. He is an active developer on the FMIRB Software Library, providing tools for the analysis of perfusion MRI. Since 2014 he has been the Director of Training for the EPSRC-MRC Centre for Doctoral Training in Biomedical Imaging. He has taught undergraduate and postgraduate students on a wide variety of imaging and quantitative physiology topics as part of the FSL course, FMRIB Graduate Programme, the undergraduate degree in Engineering Science and in various doctoral training centres. He has also won teaching awards from the International Society of Magnetic Resonance in Medicine. He has published over 50 journal papers and is the co-author of Physiology for Engineers.