The best source is the official AFNI web-page maintained at NIMH.
- Hillary Schaefer created a thorough introduction to AFNI, available as a PDF file. This intro does a nice job of demonstrating the GUI.
- Tom Johnstone has a tutorial using a single subject block-design.
- Aaron Olson has a set of instructions summarizing the demo he gave for the LfAN's Brain Imaging Workshop on AFNI.
- Wil Irwin wrote a nice description of the various file-formats we use in the lab and how to get these various files into AFNI. This document also discusses how we find anatomical landmarks and apply a Talairach transform to image data.