5. AFNI Codex: Code Examples from publications

Below is an archive of “larger” AFNI commands that have been used in published work. We thank the authors who have kindly agreed to put their AFNI processing commands and/or scripts onto the interweb for public reference and use. These take the guess work out of translating a paper’s Methods section into a command and provide a good starting point for building your own scripts with AFNI.

Scripts and commands may be provided in simplified/basic form. One can also expect that file names or any other identifying information has been removed, relabelled, recoded, etc. We will try to make such instances obvious.

As the field develops, preferred processing steps will surely change over time. We will try to note these cases and their rationales when possible, but please reach out to discuss any possible improvements or modernizations.

We are always (well, usually) happy to answer questions via the AFNI Message Board, and hopefully these scripts further the discussion.