Installation

The simplest way to get Apéro installed is to clone the repository

$ git clone https://github.com/juancarlosfarah/apero.git

You can then add the /src/matlab folder from the directory to which you cloned Apéro to your MATLAB path.

External Dependencies

Apéro is currently written using MATLAB R2021a (or above) and requires external neuroimaging tools to run. What these tools are depends on the type of operations that are executed.

By default, we include the following MATLAB toolboxes within the /src/matlab/external directory, which can be added to the MATLAB path alongside Apéro.

However, the following tools need to be installed separately:

Environment Setup

In order to run Apéro you need to specify certain variables to your path. You can easily do this by including the following in your startup.m file. For more information, please have a look at the MATLAB startup documentation.

% if fsl is installed somewhere other than `/usr/local/fsl/`,
% change this first line accordingly
fsldir = '/usr/local/fsl/';
fsldirmpath = sprintf('%s/etc/matlab',fsldir);
setenv('FSLDIR', fsldir);
setenv('FSLOUTPUTTYPE', 'NIFTI_GZ');
path(path, fsldirmpath);
setenv('PATH', [getenv('PATH') ':/usr/local/fsl/bin']);
clear fsldir fsldirmpath;

This code is included in the /src/matlab/utils/PrepareEnvironment.m function, which you can copy, modify, and execute before running your Apéro script.