Automatic analysis (aa)

Automatic analysis (aa) is a pipeline system for neuroimaging, written in Matlab. It supports SPM 5/8 and some functions from FSL.

As of December 2020, AA is deprecated at CBU. The last update that was deployed at CBU is release 5.4.0_202008, which is available on the imaging system under /imaging/local/software/AA/release-5.4.0_202008. For critical errors in existing pipelines, please contact Johan Carlin for support. For new projects, please investigate alternatives such as nipype, which is available at CBU as part of the Neuroconda environment.

AA continues to be developed outside of CBU, and its developers can be reached on the project Github page.

The documentation below is outdated and should be read with caution.

For more information see:

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Paths to aa

Different versions live in:

Installing aa


Using aa

For a comprehensive summary, please read the latest manuscript. Please, do not forget to cite it when using!


Before running aa you need to add the corresponding path to MATLAB Path:

(!) To avoid version conflicts make sure that it is added to the top of the Path. It is even more important that path_to_aa/extrafunctions/spm_mods is on the top (of SPM's paths), so modification to the spm may have effect.


You need a

Optionally, you can also specify your own parameter settings loaded by aarecipe. E.g.: User-specific parameter settings (you may need to change the path pointing to the "parent" xml)


Parallel computing

Handling multiple DICOM sources

Support for NIFTI-4D images

Multi-level interlinked reporting

Garbage collection

(!) From v4.2, it is automatically performed at the end of the analysis according to aap.options.garbagecollection

"Inheritable" parameter settings

There is an option to have site-, user-, and/or study-specific parameter settings containing only the parameters to be overridden (see example).

Non-Standard Modules

Advanced Features

Input file

It is possible to specify Subjects, Sessions and Events based on a text file. Required options in aap.acq_details.input (see also aap_parameters_defaults_CBSU.xml):

Citing aa

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.