This manual is for aa parallel version 2.2 and earlier. You might prefer the new aa wiki for aa version 3.0 and above or information on cloud execution
Contents
Contents
Summary
The system automates the analysis of neuroimaging data using SPM.
Two versions are available: one for Siemens data (e.g., CBU 3T Tim Trio), SPM 5 and NIFTI; and one for Bruker data (e.g., WBIC Medspec 3T), SPM 2 and Analyze. It is written in Matlab.
Main Features
Automatic. Almost completely automatic analysis, currently up to the end of normalisation with minimal coding, and the end of second level statistics with a little customisation to specify your first level model.
Flexible control. Users that are new to neuroimaging don't get bombarded with options, but are directed to what is essential, while all other settings take sensible defaults. More experienced users can easily change a range of settings, and advanced users can add or replace modules to the system to change any behaviour
Restartable. If the users stops the script, or if it crashes (e.g., because of a machine fault, or because the right data aren't there) then when restarted it will begin at the stage where it left off.
Parallel processing. Where multiple machines are available, aa jobs can seamlessly be distributed across them
Well behaved. Field maps and structurals are automatically detected. Structurals are copied to /imaging/local/structurals/cbu automatically by default.
Easy to maintain. The code components are stored in a central repository (/imaging/local/spm/aa) which means that new components can be made available, or existing ones changed in new releases
Record keeping. Unlike SPM used from the GUI, the system records exactly which parameters were used, and allows easy recreation of a dataset from the raw data at a later date.
Modular, with simple interface. It is easy for Matlab programmers to write new modules and incorporate them into the processing stream.