BIDS-Apps/aa

Name: aa

Owner: BIDS Apps

Description: BIDS App containing an instance of the Automatic Analysis

Created: 2016-08-02 15:51:12.0

Updated: 2016-10-28 11:07:38.0

Pushed: 2017-07-21 16:51:21.0

Homepage: http://automaticanalysis.org

Size: 51

Language: Shell

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README

aa

BIDS App containing an instance of the Automatic Analysis.

Automatic Analysis 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.

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

aa is a pipeline system for neuroimaging written primarily in Matlab. It robustly supports recent versions of SPM, as well as selected functions from other software packages. The goal is to facilitate automatic, flexible, and replicable neuroimaging analyses through a comprehensive pipeline system.

License

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

Documentations

More information can be found on the official aa webpage

Error Reporting

Experiencing problems? Please open an issue and explain what's happening so we can help.

Acknowledgement

For any papers that report data analyzed with aa, please include the website (http://www.automaticanalysis.org) 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.

Instructions

The bids/aa Docker container enables users to run Automatic Analysis right from container launch. The pipeline requires that data be organized in accordance with the BIDS spec.

To get your container ready to run just follow these steps:

• In your terminal, type:

  cker pull bids/aa
  

Now we're ready to launch our instances and process some data!

Like a normal docker container, you can startup your container with a single line.

usage: aa {participant|group} [–participant_label ]

positional arguments:

                  The directory with the input dataset formatted
                    according to the BIDS standard.

                  The directory where the output files should be stored.
                    If you are running group level analysis this folder
                    should be prepopulated with the results of the
                    participant level analysis.

{participant|group}

                  Level of the analysis that will be performed. Multiple
                    participant level analyses can be run independently
                    (in parallel) using the same output_dir.

optional arguments: –participant_label

                  The label(s) of the participant(s) that should be
                    analyzed. The label corresponds to
                    sub-<participant_label> from the BIDS spec (so it does
                    not include "sub-"). If this parameter is not provided
                    all subjects should be analyzed. Multiple participants
                    can be specified with a space separated list.