Open-Source Tool

The following is a list of tools used to analyze data (.MFF files) from the Magstim EGI Geodesic EEG System (GES). Most of the toolboxes on the list require no exporting and can natively open MFF files (recorded in Net Station version 4.5.7 or newer) using the MFFmatlabIO plugin or other methods. While Magstim EGI works with many of these developers, all of the software below is open- source and not tested by Magstim EGI. Contact the software developers directly or on the software wiki site to report issues. Contact the Magstim EGI support team if your data is in an older Net Station format (for conversion) or you encounter other technical issues related to your data files.

While some users of the Geodesic EEG System (GES) use it as a cleared medical device, all of the following tools are for research use only and fall under the Magstim EGI research end use statement: “This instrument is not intended for use in diagnosis or treatment of any disease or condition. Magstim makes no representation of the suitability of the instrument for any particular research study. It will be used as a scientific research instrument designed for performing measurements and acquiring data for neurophysiological research.”

EEGLAB and other Matlab and Python based toolboxes using the MFFmatlabIO extension

• Documentation Wiki / Download: https://github.com/arnodelorme/mffmatlabio/wiki
• Export EGI MFF data to BIDS: https://github.com/arnodelorme/mffmatlabio/wiki/4.-Exporting-to-BIDS
• Using EGI MFF data in MNE & Python: https://github.com/arnodelorme/mffmatlabio/wiki/6.-Use-with-Python-&-MNE
• Commonly Used EEGLAB Extensions
  • Cwleegfmri – EEG-MRI analysis tools for carbon wire loops
    • Paper: https://sciencedirect.com/science/article/pii/S1053811915009787
  • EYE-EEG – Co-Registration of Eye Movements and EEG
• Paper: http://www.dimigen.de/docs/Dimigen.et.al.JEPGEN.2011.Eyetracking+EEG.Review.pdf
• Download: http://www2.hu-berlin.de/eyetracking-eeg/
  • ICLabel – automatic independent component (IC) classification
    • Documentation: https://sccn.ucsd.edu/wiki/ICLabel
    • Artifact Review Training: https://labeling.ucsd.edu/tutorial/practice

Fieldtrip

FieldTrip is the MATLAB software toolbox for MEG, EEG and iEEG analysis. It offers preprocessing and advanced analysis methods, such as time-frequency analysis, source reconstruction using dipoles, distributed sources and beamformers and non-parametric statistical testing.

• Paper: https://hindawi.com/journals/cin/2011/156869/
• Using Fieldtrip with MFF data: https://fieldtriptoolbox.org/getting_started/egi/
• Download: https://fieldtriptoolbox.org/download/

Brainstorm

Brainstorm is a collaborative, open-source application dedicated to the analysis of brain recordings: MEG, EEG, fNIRS, ECoG, depth electrodes and multiunit electrophysiology.

• Download: https://neuroimage.usc.edu/brainstorm/Installation
• Paper: https://neuroimage.usc.edu/brainstorm/CiteBrainstorm

Harvard Automated Processing Pipeline for Electroencephalography (HAPPE)

A standardized, automated pipeline compatible with EEG recordings of variable lengths and artifact contamination levels, including high-artifact and short EEG recordings from young children or those with neurodevelopmental disorders

• Paper: https://frontiersin.org/articles/10.3389/fnins.2018.00097/full
• Download: https://github.com/lcnhappe/happe

The Batch Electroencephalography Automated Processing Platform (BEAPP)

an automated, flexible EEG processing platform incorporating freely available software tools for batch processing of multiple EEG files across multiple processing steps

• Paper: https://frontiersin.org/articles/10.3389/fnins.2018.00513/full
• Download: https://github.com/lcnbeapp/beapp

Maryland Analysis of Developmental EEG (MADE) Pipeline

An automated preprocessing pipeline compatible with EEG data recorded with different hardware systems, different populations, levels of artifact contamination, and length of recordings

• Paper: https://onlinelibrary.wiley.com/doi/abs/10.1111/psyp.13580
• Download: https://github.com/ChildDevLab/MADE-EEG-preprocessing-pipeline

Mohawk

MOHAWK is a software prototype that brings together state of the art computational analysis of brain activity to benefit patients with severe brain injury at their bedside. This prototype includes algorithms to visualize and measure networks of brain activity in such patients

• Paper: https://academic.oup.com/brain/article/140/8/2120/3896394?guestAccessKey=37194adc-cf03-49fd-a505-5df2afce0b79
• Download: https://github.com/srivaschennu/MOHAWK/wiki

HyPyP

The HyPyP library provides a suite of Python tools to manipulate hyperscanning data and inter-brain connectivity measures

• Paper: https://academic.oup.com/scan/advance-article/doi/10.1093/scan/nsaa141/5919711
• Download: https://github.com/GHFC/HyPyP

Cartool

Cartool is an EEG analysis software developed at the Functional Brain Mapping Lab (FBMLab), in Geneva, Switzerland.

• Paper: https://hindawi.com/journals/cin/2011/813870
• Download: https://sites.google.com/site/cartoolcommunity/

ERP / PCA Toolkit

A Matlab toolkit for all aspects of EEG/ERP analysis, especially PCA.

• Paper: https://sciencedirect.com/science/article/abs/pii/S0165027009006736
• Download: https://sourceforge.net/projects/erppcatoolkit/

BCI 2000

A general-purpose Brain Computer Interface research and development platform called BCI2000

• Documentation for Brain Computer Interface + GTEN 200 Functionality: https://www.bci2000.org/mediawiki/index.php/Contributions:AmpServerProADC
• Paper: http://www.bci2000.org/downloads/doc/paper.pdf
• Note regarding functionality with EGI hardware: AmpServer Pro SDK must be enabled for BCI 2000 to work for the GES 300 (enabled on HASP), GES 400 (enabled on amplifier) or GTEN 200.

Default Electrode / Sensor Location Files for EGI Hydrocel Geodesic Sensor Nets (256, 128, 64, 32 Channel Nets)

Download 3D Sensor Locations (SFP) Files:

• https://egi.com/knowledge-center/item/71-sensor-position-files-for-visualizing-data-in-third-party- software?highlight=WyJzZW5zb3IiLCJzZW5zb3JzIiwic2Vuc29yJ3MiLCJzZW5zb3JlcyIsImxvY2F0aW9ucyIsImxvY2F0aW9uIiwib G9jYXRlIiwibG9jYXRlZCIsImxvY2F0aW5nIiwibG9jYXRvciIsInNlbnNvciBsb2NhdGlvbnMiXQ==

Relating the HCGSN sensor positions to the 10-10 International electrode placement system

• https://egi.com/knowledge-center/item/62-relating-the-hcgsn-sensor-positions-to-the-10-10-international-electrode-placement- system?highlight=WyIxMC0xMCJd