Automatic analysis

Automatic analysis
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Uses : Automatic Analysis (aa) is a unique comprehensive framework for designing, executing, and sharing neuroimaging workflows. By tightly integrating major open-source neuroimaging packages (and specialized methods) via a single point of configuration, aa strongly focuses on lowering the technical debt, while its detailed data diagnostic facilities ensure quality control.

Features :

  • comprehensive pipeline
  • tight integration of tools (SPM, EEGLAB, FieldTrip, FreeSurfer, FSL, etc.)
  • multi-modal (xMRI, M/EEG)
  • scalable in most MTC environment (SLURM, Torque, SoGE, IBM LSF)
  • quality control

Platform : Linux, Mac, Docker

File formats : DICOM, NIfTI, ANALYZE, BIDS

Language/API : MATLAB

Documentation : Detailed documentation on the website and the GitHub repo wiki

Users : Advanced, Developer

Access : Free, Open source

Links :

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Hi Tibor,

Automatic analysis looks really useful. I was wondering if it can process large DICOM volumes (fMRI, diffusion etc.) in the Siemens Mosaic format? Or does the data have to be reformatted first?



Hi James,

Sure. aa uses the SPM converter for Siemens images, which can also handle mosaic. I routinely use 3D Mosaic (i.e. one DICOM file per volume). Based on a limited number of use cases, it can also handle 4D Mosaic (i.e. one DICOM file per run), but this functionality is experimental only, so you should always check the data.


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