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EEG-BIDS

EEG-BIDS

The EEG-BIDS (formerly known as BIDS-MATLAB-tools) repository contains a collection of functions that import and export BIDS-formated experiments. The code is tailored for use as an EEGLAB plugin but may also be used independently of EEGLAB. Conversion of data format from non-supported BIDS binary format requires that EEGLAB be installed (supported formats are EEGLAB .set files, EDF files, BDF files, and Brain Vision Exchange Format files).

Documentation

Refer to the wiki documentation or the submenus of this plugin if you are on the EEGLAB website.

EEG-BIDS vs other BIDS software

BIDS-MATLAB is a project to import BIDS data. BIDS-MATLAB maps the BIDS directory architectures to MATLAB structures but does not import or convert data like EEG-BIDS. In theory, EEG-BIDS could use BIDS-MATLAB to get the BIDS directory architectures into MATLAB and then convert it to an EEGLAB STUDY. However, in 2021, BIDS-MATLAB could not yet import all the relevant EEG, MEG, and iEEG files.

EEG2BIDS is a Python-based executable that formatted a collection of EDF files in BIDS format. EEG2BIDS requires users to create JSON files for meta-data. It is a tool designed to archive data as part of a lab protocol where JSON files have been prepared in advance and are suited for technicians organizing data. EEG-BIDS export capabilities are more suited for researchers managing their data and are agnostic regarding the original data format.

ezBIDS is a data export tool for MRI and fMRI data. It does not allow to export EEG data to our knowledge.

data2bids.m is a Fieldtrip function to export BIDS data. This includes EEG and maybe fMRI. This function can only be used from the command line.

EEG-BIDS (this program) is the most popular tool to export EEG data using both a graphical interface and/or command line (more than half of the BIDS datasets on OpenNeuro were exported using EEG-BIDS and it has more than 2200 installs in EEGLAB). A compiled stand-alone version will also be released soon.

Standalone version

A standalone version of the plugin is available when downloading EEGLAB. The standalone plugin version is distributed with EEGLAB because it uses EEGLAB resources. After download EEGLAB, use the executable named EEGBIDS (Mac) or EEGBIDS.bat (Windows).

EEG-BIDS export capabilities

Accepted EEG input formats are all files that EEGLAB can read.

  • EEG export: ✔ (as .set, .edf, .bdf, or .vhmk files)
  • iEEG export: ✔ (as .set, .edf or .nwb)
  • Eye-tracking export: ✔ (beta)
  • HED export: ✔
  • BEH export: ✔
  • MRI export: ✔ (no conversion)
  • fMRI export: ✖
  • Motion-cap export: ✖ (upcoming)
  • EMG export: ✖ (upcoming)
  • MEG export: ✖ (upcoming)

EEG-BIDS import capabilities for EEGLAB

EEG-BIDS allows importing BIDS datasets into EEGLAB. This is the type of information that can be imported.

  • EEG import: ✔ (all formats)
  • iEEG import: ✔ (all formats)
  • MEG import: ✔ (.ds and .fif files supported, more formats upcoming)
  • Eye-tracking import: ✖ (upcoming)
  • HED import: ✔
  • BEH import: ✔
  • MRI import: n/a
  • fMRI import: n/a
  • Motion-cap import: ✔ (beta)
  • EMG import: ✖ (upcoming)

Cloning

Make sure you clone with submodules

git clone --recurse-submodules https://github.com/sccn/EEG-BIDS

Use with EEGLAB

Simply place the code in the EEGLAB plugin folder, and EEGLAB will automatically detect it. See documentation at https://github.com/sccn/EEG-BIDS/wiki.

zip command to release plugin

zip -r EEG-BIDS8.0.zip EEG-BIDS/* -x /EEG-BIDS/testing/additionaltests/* /EEG-BIDS/testing/ds004117/* /EEG-BIDS/testing/hbn_eye_tracking_data/* /EEG-BIDS/testing/data/*

Version history

v1.0 - initial version

v2.0 - add support for external channel location and fix minor bugs

v3.0 - better export for multiple runs and allowing importing BIDS folder with multiple runs

v3.1 - fix multiple issues at export time, including subject numbering

v3.2 - fix menu conflict in EEGLAB with bids validator; check channel types; add option to choose EEG event field; minor bugs

v3.3 - fix an issue for Windows and work on GUI

v3.4 - fix the issue with saving datasets in memory. Allowing to anonymize participant ID or not. Fixed issue with looking up channel locations.

v3.5 - fix issue with choosing event type in graphic interface; various fixes for GUI edit of BIDS info

v4.0 - fix GUI and many minor export issues

v4.1 - fix the issue with JSON

v5.0 - major fixes to import all OpenNeuro EEG datasets

v5.1 - allow calculating dataset meta-data quality

v5.2 - fix the issue with history

v5.3 - adding the capability to export stimuli

v5.3.1 - update documentation for tInfo.HardwareFilters; fix bug defaults fields not filled for eInfo

v5.4 - fix the issue with reading BIDS information when importing BIDS data to STUDY

v6.0 - new examples and fixes for HED

v6.1 - allow data with no events. Fix HED import/export. Fix history.

v7.0 - split code into different functions. Support for behavioral data. Various bug fixes.

v7.2 - fix the issue with the missing file.

v7.3 - various minor fixes (EEG reference as string; add duration if not present; resave datasets)

v7.4 - fix version issues for HED and BIDS. Export subjects in order. Remove unused columns in participants.tsv file

v7.5 - adding support for coordsystem files, for loading specific runs, support for motion files

v7.6 - adding export to non-EEGLAB formats, refactoring export

v7.7 - fix importing MEG and MEF files. Better handling of runs. Now tracks tool version in BIDS.

v8.0 - renamed files, separate file for task info, adding BIDS statistic output, handling EGI & BVA file better, channel types and units, adding eye-tracking and behavioral support

v9.0 - update json import to conform to BIDS key-level inheritance principle. Support iEEG and MEG export. Support exporting multiple tasks. Fix issues with exporting channel locations. BIDS export wizard.