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ksgfan edited this page Feb 8, 2024 · 15 revisions

User Manual - Automagic 3.0.

Introduction

Automagic is a MATLAB based toolbox for preprocessing of EEG-datasets. It has been developed with the intention to offer a user-friendly pre-processing software for big (and small) EEG datasets. The software can be used by command line and with a graphical user interface (GUI) and does not require any knowledge about programming. It runs on Matlab (R2016b and newer releases). Due to the fact that the application is compiled of several Matlab functions that are compatible with EEGLAB (Delorme and Makeig 2004), one of the most used opens-source frameworks for EEG analysis), more experienced users can extend Automagic to their specific needs. Automagic is licensed under the GNU General Public License v3.0. You may freely modify and redistribute it under certain conditions.

System Requirements

You need Matlab installed and activated on your system to use Automagic. Automagic was developed and tested with Matlab R2016b and newer releases on Windows, Linux and Mac computers. In order to run preprocessing steps you need two MATLAB toolboxes:

  • Statistics and Machine Learning Toolbox
  • Signal Processing Toolbox

In addition to the above toolboxes, Parallel Computing Toolbox is recommended to speed up PREP preprocessing step.

Installation

Download and unzip the code from the GitHub repository to your favorite place on your hard drive.

Workflow

A typical workflow of using Automagic is to

  1. First create a project with your raw data and desired configurations.
  2. Then by clicking on Run in the preprocessing section you can start the preprocessing of the data. This action may take considerable amount of time depending on the size of your dataset and preprocessing steps that you have chosen.
  3. After preprocessing has finished you will be notified with a pop-up message. Now you can either review the data and inspect which channels have been detected as bad channels and how the artifact removal and filtering has changed your raw data using the Data Viewer button or you can interpolate the bad channels straight away by clicking Interpolate All.
  4. Finally, you can start the quality assessment of the preprocessing and interpolation. This is explained extensively in Quality Assessment

Automagic as an EEGLab extension (plugin)

Automagic can be started from within the EEGLab GUI. From there you could also import your preprocessing results easily to the EEGLab GUI for further analysis. Here is how.

Using Automagic within the Matlab commandline without any GUI

Sometimes it is more convenient to run Automagic from the command line. Here is how.

Using the preprocessing code independently for your own project

You could also use only the preprocessing code for your own projects or modify it. Here is how

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