2. Starting with AFNI

2.1. Overview

Welcome to the AFNI software toolbox. AFNI (Analysis of Functional NeuroImages) is a suite of programs for looking at and analyzing MRI brain images at all stages of analysis (planning, setting up acquisiton, preprocessing, analysis, quality control and statistical analysis). It contains C, Python and R programs, as well as shell scripts.

The philosophy driving AFNI development is simple: help keep users close to their data.

AFNI is primarily developed for the processing, analysis and display of multiple MRI modalities:

• anatomical/structural MRI

  • at various field strengths

• diffusion weighted imaging (DWI)

  • for DTI or HARDI modeling and tractography (using the FATCAT programs)

• functional MRI (FMRI)

  • resting state, task-based or naturalistic paradigms

  • single- or multi-echo acquisitions

  • voxelwise or ROI-based analyses, volumetric or surface-based

  • convenient+efficient pipeline design with afni_proc.py

Many AFNI programs have also been applied and adapted to other modalities, such as ECoG, EEG, MEG, and more.

AFNI can be used for volumetric or surface analyses, as well as their combination, and has been applied widely across studies of humans, NHP and other species.

2.2. Where to begin

Below we provide a quick roadmap through the AFNI toolbox, including educational resources, reference links, demo examples (with data+scripts) and more. Note: these are just subsets of the material here, which we encourage exploring.

Installation instructions

• Installation instructions per OS
• Docker container notes

Bootcamp and video lectures

• AFNI Academy series: lectures based on the AFNI Bootcamp, combining theory and hands-on examples

• Additional Bootcamp recordings

• Links to AFNI handouts (part of Bootcamp), GUI keyboard shortcuts and startup tips (and more)

• Quick Unix tutorial

Program listings and helps

• “Classified” program guide: list of AFNI programs grouped thematically

• Mega-page linking to all program helps

Code, command, script and functionality examples

• Tutorial examples, scripts and demos

• Publication-based code examples (AFNI Codex)

• Statistics notes on various programs

Additional resources

• Methods publications (read the backstory of various code pieces) and reference list

• Nonhuman projects and processing (with demos)

• Templates and atlases

Code-centric

• AFNI github page

• Notes on making a pull request (PR)

2.3. Asking questions and following updates

We are happy to answer questions, receive suggestions, and generally discuss data analysis on the AFNI Message Board.

Additionally, please consider signing up for the AFNI Digest. This approximately weekly (or so) emailer contains developments or changes within the AFNI realm that we deem large enough for wide dissemination. We will also broadcast things like Bootcamp info; installation and build instruction changes; processing commentary; and perhaps dollops of humor.