AFNI Essentials: Analyzing fMRI and Anatomical Data

Understanding brain function through neuroimaging requires powerful, flexible computational tools. The AFNI software suite is an industry standard for processing and analyzing functional MRI (fMRI) data, but getting started with command-line neuroimaging can feel overwhelming. This text-only course guides you from absolute beginner to confidently running your first neuroimaging pipelines. You will learn how to structure your imaging files, execute preprocessing commands, and perform basic statistical analyses to extract meaningful insights from brain scans. What you'll learn: - Understand foundational neuroimaging terminology, coordinate systems, and fMRI data formats - Configure your command-line environment to run AFNI programs and shell scripts - Perform essential preprocessing steps including motion correction, slice timing alignment, and spatial smoothing - Align anatomical scans to functional data and standardize them to template spaces - Execute basic statistical analyses to identify brain activation patterns - Apply modern reproducible practices, including script-based workflows and containerized environments The course starts with essential neuroimaging concepts and AFNI installation fundamentals before moving step-by-step through preprocessing, alignment, and statistical modeling. You will work through written examples and command-line snippets designed to build practical, repeatable analysis habits. This course is designed for aspiring neuroscientists, researchers, and data enthusiasts who are new to AFNI. No prior experience with neuroimaging software or command-line scripting is required. Start your journey into computational neuroimaging today.