4. 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.
- 4.1. Overview
- 4.2. FMRI Codex
- 4.2.1. Steinhauser et al. (2022). Functional dissection of neural connectivity in generalized anxiety disorder
- 4.2.2. Yang et al. (2021). Different activation signatures in the primary sensorimotor and higher-level regions for haptic three-dimensional curved surface exploration
- 4.2.3. Chen et al. (2018b). Handling Multiplicity in Neuroimaging Through Bayesian Lenses with Multilevel Modeling
- 4.2.4. Chen et al. (2018a). A tail of two sides: Artificially doubled false positive rates in neuroimaging due to the sidedness choice with t-tests
- 4.2.5. Taylor et al. (2018). FMRI processing with AFNI: Some comments and corrections on “Exploring the Impact of Analysis Software on Task fMRI Results”
- 4.2.6. Chen et al. (2016). Untangling the Relatedness among Correlations, Part II: Inter-Subject Correlation Group Analysis through Linear Mixed-Effects Modeling