4. Code examples from publications

Below is an archive of “larger” AFNI commands that have been used in published work, largely grouped by category of processing. 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.

For each set of examples, there is a “brief” description, that is meant to be scannable and searchable by keyword; links to the papers and scripts are provided. Each entry also a link to the “detailed” description, where the codes can be viewed directly.

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.

We fully expect that developments in the field will continue to push processing techniques forward, and therefore preferred processing steps will assuredly change over time. We will try to note these cases and their rationales when possible.

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