Getting started

Installing dependencies

This project uses the mpm MATLAB package manager whihc is included in the mpm/ folder in the root directory. To install dependencies follow these steps:

1. In MATLAB add the mpm/ folder to paths.
2. From the MATLAB command line, run mpm_install.

The dependencies are now automatically installed into the mpm/mpm-packages/ directory and automatically added to your MATLAB paths.

Setup paths for your machine

A data folder is required for the pipeline to run on data. This folder must only be saved locally due to the data access law. Ask Emil about this.

The project is divided into two analysis: ERP (Event-related potentials), and default mode network (steady-state). There is a corresponding folder for each analysis. The following instructions work for both.

1. Create a copy of config_sample.m in the same directory and name it my_config.m.
2. my_config.m contains absolute paths and could look like this:

my_root = '/Users/emiljohansen/Documents/Laosdirg/Roskilde'; % Path to root folder
my_output_folder = '/Users/emiljohansen/Documents/Roskilde/steadystate'; % Path to processed data output
my_fieldtrip_path = '/Users/emiljohansen/Documents/Laosdirg/Roskilde/roskilde-eeg-pipeline/fieldtrip'; % Path to fieldtrip

Run the analysis

Run the file run_pipeline_steadystate.m