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Automatic Analysis (aa) is a pipeline system for neuroimaging written primarily in Matlab. It supports SPM 12, as well as selected functions from other software packages (e.g., FSL, Freesurfer). The goal is to facilitate automatic, flexible, and replicable neuroimaging analyses through a comprehensive pipeline system.

The software was originally developed by Dr Rhodri Cusack for supporting research at the MRC Cognition and Brain Science Unit. It is made available to the academic community in the hope that it may prove useful.

CI Docker image available! manuscript resource DOI View Automatic Analysis (aa) on File Exchange

Definitions: aa means the Automatic Analysis software package and any associated documentation whether electronic or printed.


Use of this software is subject to the terms of the license, found in the license.txt file distributed with this software.


The best source for aa documentation is the github wiki at:

A second website at provides recent aa news and current events, as well as discussion of topics that might be of interest to aa developers.

Help and support

Please feel free to open a discusion thread or an issue here on GitHub if you want to make comment or suggestions or are having trouble getting aa to work.

Software updates

The master branch on github is only updated after testing, so this version is the one to use. Developer versions are maintained in each developer's aa fork on GitHub.

References and citation

For any papers that report data analyzed with aa, please include the GitHub repo URL and cite the aa paper:

Cusack R, Vicente-Grabovetsky A, Mitchell DJ, Wild CJ, Auer T, Linke AC, Peelle JE (2015) Automatic analysis (aa): Efficient neuroimaging workflows and parallel processing using Matlab and XML. Frontiers in Neuroinformatics 8:90.