Getting started

Downloading and installing aa

There are two ways to install aa. If you have git installed on your local machine, simply clone the aa repository:

$ git clone https://github.com/automaticanalysis/automaticanalysis

If you do not have git installed, visit https://github.com/automaticanalysis/automaticanalysis and use the green (as of this writing) button to access a pull down menu that will allow you to download the code as a zip file. Unzip the file and put it somewhere convenient on your machine.

Other required software

Basic analysis using aa only requires MATLAB, the Image Processing, the Parallel Computing and the Statistics and Machine Learning toolboxes, and SPM.

Some types of aa analysis requires other packages such as FSL, Freesurfer, or a third-party SPM toolbox such as CONN or WDS. You will need to install these packages separately to use this functionality.

Matlab paths

Once you have downloaded aa and SPM, add their respective top level directories to your Matlab path. The easiest way to do this is to use the Set Path dialog box. Click Set Path on the Home tab in the Environment section. You then click "Add Folder" and select the top-level aa and SPM folders. Alternatively, you can use the addpath command in Matlab -- for instructions, type "help addpath" into the Matlab command prompt.

Type SPM at the Matlab command prompt to check if SPM is properly installed. The command should bring up the main SPM window. Exit, and then type aa_ver5 at the Matlab command prompt (or whatever version of aa you are using). You should see a welcome message and a notification aa has added a few required directories to your Matlab path. You are good to go.

If Matlab cannot find SPM or aa, check that your Matlab path was modified and saved correctly.

For a guided first experience using aa, see the Tutorial listed in the sidebar.