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Electroencephalography (EEG)

Support for EEG was developed as a BIDS Extension Proposal. Please cite the following paper when referring to this part of the standard in context of the academic literature:

Pernet, C. R., Appelhoff, S., Flandin, G., Phillips, C., Delorme, A., & Oostenveld, R. (2018, December 6). BIDS-EEG: an extension to the Brain Imaging Data Structure (BIDS) Specification for electroencephalography. https://doi.org/10.31234/osf.io/63a4y

The following example EEG datasets have been formatted using this specification and can be used for practical guidance when curating a new dataset.

Further datasets are available from the BIDS examples repository.

EEG recording data

Template:

sub-<label>/
    [ses-<label>]/
      eeg/
        sub-<label>[_ses-<label>]_task-<label>[_run-<index>]_eeg.<manufacturer_specific_extension>
        sub-<label>[_ses-<label>]_task-<label>[_run-<index>]_eeg.json

The EEG community uses a variety of formats for storing raw data, and there is no single standard that all researchers agree on. For BIDS, EEG data MUST be stored in one of the following formats:

It is RECOMMENDED to use the European data format, or the BrainVision data format. It is furthermore discouraged to use the other accepted formats over these RECOMMENDED formats, particularly because there are conversion scripts available in most commonly used programming languages to convert data into the RECOMMENDED formats. The data in their original format, if different from the supported formats, can be stored in the /sourcedata directory.

The original data format is especially valuable in case conversion elicits the loss of crucial metadata specific to manufacturers and specific EEG systems. We also encourage users to provide additional meta information extracted from the manufacturer specific data files in the sidecar JSON file. Other relevant files MAY be included alongside the original EEG data in /sourcedata.

Note that for proper documentation of EEG recording metadata it is important to understand the difference between electrode and channel: An EEG electrode is attached to the skin, whereas a channel is the combination of the analog differential amplifier and analog-to-digital converter that result in a potential (voltage) difference that is stored in the EEG dataset. We employ the following short definitions:

  • Electrode = A single point of contact between the acquisition system and the recording site (e.g., scalp, neural tissue, ...). Multiple electrodes can be organized as caps (for EEG), arrays, grids, leads, strips, probes, shafts, etc.

  • Channel = A single analog-to-digital converter in the recording system that regularly samples the value of a transducer, which results in the signal being represented as a time series in the digitized data. This can be connected to two electrodes (to measure the potential difference between them), a magnetic field or magnetic gradient sensor, temperature sensor, accelerometer, etc.

Although the reference and ground electrodes are often referred to as channels, they are in most common EEG systems not recorded by themselves. Therefore they are not represented as channels in the data. The type of referencing for all channels and optionally the location of the reference electrode and the location of the ground electrode MAY be specified.

Sidecar JSON (*_eeg.json)

Generic fields MUST be present:

Field name Definition
TaskName REQUIRED. Name of the task (for resting state use the rest prefix). Different Tasks SHOULD NOT have the same name. The Task label is derived from this field by removing all non alphanumeric ([a-zA-Z0-9]) characters.

SHOULD be present: For consistency between studies and institutions, we encourage users to extract the values of these fields from the actual raw data. Whenever possible, please avoid using ad hoc wording.

Field name Definition
InstitutionName RECOMMENDED. The name of the institution in charge of the equipment that produced the composite instances.
InstitutionAddress RECOMMENDED. The address of the institution in charge of the equipment that produced the composite instances.
Manufacturer RECOMMENDED. Manufacturer of the EEG system (e.g., Biosemi, Brain Products, Neuroscan).
ManufacturersModelName RECOMMENDED. Manufacturer's designation of the EEG system model (e.g., BrainAmp DC).
SoftwareVersions RECOMMENDED. Manufacturer's designation of the acquisition software.
TaskDescription RECOMMENDED. Description of the task.
Instructions RECOMMENDED. Text of the instructions given to participants before the scan. This is not only important for behavioral or cognitive tasks but also in resting state paradigms (e.g., to distinguish between eyes open and eyes closed).
CogAtlasID RECOMMENDED. URL of the corresponding Cognitive Atlas term that describes the task (e.g., Resting State with eyes closed "http://www.cognitiveatlas.org/term/id/trm_54e69c642d89b").
CogPOID RECOMMENDED. URL of the corresponding CogPO term that describes the task (e.g., Rest "http://wiki.cogpo.org/index.php?title=Rest") .
DeviceSerialNumber RECOMMENDED. The serial number of the equipment that produced the composite instances. A pseudonym can also be used to prevent the equipment from being identifiable, as long as each pseudonym is unique within the dataset.

Specific EEG fields MUST be present:

Field name Definition
EEGReference REQUIRED. General description of the reference scheme used and (when applicable) of location of the reference electrode in the raw recordings (e.g., "left mastoid", "Cz", "CMS"). If different channels have a different reference, this field should have a general description and the channel specific reference should be defined in the _channels.tsv file.
SamplingFrequency REQUIRED. Sampling frequency (in Hz) of all the data in the recording, regardless of their type (e.g., 2400).
PowerLineFrequency REQUIRED. Frequency (in Hz) of the power grid at the geographical location of the EEG instrument (i.e., 50 or 60).
SoftwareFilters REQUIRED. List of temporal software filters applied. Ideally key:value pairs of pre-applied software filters and their parameter values: e.g., {"Anti-aliasing filter": {"half-amplitude cutoff (Hz)": 500, "Roll-off": "6dB/Octave"}}. Write n/a if no software filters applied.

SHOULD be present:

Field name Definition
CapManufacturer RECOMMENDED. Name of the cap manufacturer (e.g., "EasyCap").
CapManufacturersModelName RECOMMENDED. Manufacturer's designation of the EEG cap model (e.g., "actiCAP 64 Ch Standard-2").
EEGChannelCount RECOMMENDED. Number of EEG channels included in the recording (e.g., 128).
ECGChannelCount RECOMMENDED. Number of ECG channels.
EMGChannelCount RECOMMENDED. Number of EMG channels.
EOGChannelCount RECOMMENDED. Number of EOG channels.
MiscChannelCount RECOMMENDED. Number of miscellaneous analog channels for auxiliary signals.
TriggerChannelCount RECOMMENDED. Number of channels for digital (TTL bit level) trigger.
RecordingDuration RECOMMENDED. Length of the recording in seconds (e.g., 3600).
RecordingType RECOMMENDED. Defines whether the recording is continuous or epoched.
EpochLength RECOMMENDED. Duration of individual epochs in seconds (e.g., 1) in case of epoched data.
HeadCircumference RECOMMENDED. Circumference of the participants head, expressed in cm (e.g., 58).
EEGPlacementScheme RECOMMENDED. Placement scheme of EEG electrodes. Either the name of a standardized placement system (e.g., "10-20") or a list of standardized electrode names (e.g., ["Cz", "Pz"]).
EEGGround RECOMMENDED. Description of the location of the ground electrode (e.g., "placed on right mastoid (M2)").
HardwareFilters RECOMMENDED. List of temporal hardware filters applied. Ideally key:value pairs of pre-applied hardware filters and their parameter values: e.g., {"HardwareFilters": {"Highpass RC filter": {"Half amplitude cutoff (Hz)": 0.0159, "Roll-off": "6dB/Octave"}}}. Write n/a if no hardware filters applied.
SubjectArtefactDescription RECOMMENDED. Free-form description of the observed subject artifact and its possible cause (e.g., "Vagus Nerve Stimulator", "non-removable implant"). If this field is set to n/a, it will be interpreted as absence of major source of artifacts except cardiac and blinks.

Example:

{
  "TaskName":"Seeing stuff",
  "TaskDescription":"Subjects see various images for which phase, amplitude spectrum, and color vary continuously",
  "Instructions":"Your task is to detect images when they appear for the 2nd time, only then press the response button with your right/left hand (counterbalanced across subjects)",
  "InstitutionName":"The world best university, 10 Beachfront Avenue, Papeete",
  "SamplingFrequency":2400,
  "Manufacturer":"Brain Products",
  "ManufacturersModelName":"BrainAmp DC",
  "CapManufacturer":"EasyCap",
  "CapManufacturersModelName":"M1-ext",
  "EEGChannelCount":87,
  "EOGChannelCount":2,
  "ECGChannelCount":1,
  "EMGChannelCount":0,
  "MiscChannelCount":0,
  "TriggerChannelCount":1,
  "PowerLineFrequency":50,
  "EEGPlacementScheme":"10 percent system",
  "EEGReference":"single electrode placed on FCz",
  "EEGGround":"placed on AFz",
  "HardwareFilters":{
    "ADC's decimation filter (hardware bandwidth limit)":{
      "-3dB cutoff point (Hz)":480,
      "Filter order sinc response":5
    }
  },
  "RecordingDuration":600,
  "RecordingType":"continuous"
}

Note that the date and time information SHOULD be stored in the Study key file (scans.tsv). As it is indicated there, date time information MUST be expressed in the following format YYYY-MM-DDThh:mm:ss (ISO8601 date-time format). For example: 2009-06-15T13:45:30. It does not need to be fully detailed, depending on local REB/IRB ethics board policy.

Channels description (*_channels.tsv)

Template:

sub-<label>/
    [ses-<label>]/
      eeg/
        [sub-<label>[_ses-<label>]_task-<label>[_run-<index>]_channels.tsv]

Although this information can often be extracted from the EEG recording, listing it in a simple .tsv document makes it easy to browse or search. The required columns are channel name, type and units in this specific order. Channel names should furthermore appear in the table in the same order they do in the EEG data file. Any number of additional columns may be provided to provide additional information about the channels. Note that electrode positions should not be added to this file, but to *_electrodes.tsv.

The columns of the Channels description table stored in *_channels.tsv are:

MUST be present:

Column name Definition
name REQUIRED. Channel name (e.g., FC1, Cz)
type REQUIRED. Type of channel; MUST use the channel types listed below.
units REQUIRED. Physical unit of the data values recorded by this channel in SI units (see Appendix V: Units for allowed symbols).

SHOULD be present:

Column name Definition
description OPTIONAL. Free-form text description of the channel, or other information of interest. See examples below.
sampling_frequency OPTIONAL. Sampling rate of the channel in Hz.
reference OPTIONAL. Name of the reference electrode(s) (not needed when it is common to all channels, in that case it can be specified in *_eeg.json as EEGReference).
low_cutoff OPTIONAL. Frequencies used for the high-pass filter applied to the channel in Hz. If no high-pass filter applied, use n/a.
high_cutoff OPTIONAL. Frequencies used for the low-pass filter applied to the channel in Hz. If no low-pass filter applied, use n/a. Note that hardware anti-aliasing in A/D conversion of all EEG electronics applies a low-pass filter; specify its frequency here if applicable.
notch OPTIONAL. Frequencies used for the notch filter applied to the channel, in Hz. If no notch filter applied, use n/a.
status OPTIONAL. Data quality observed on the channel (good/bad). A channel is considered bad if its data quality is compromised by excessive noise. Description of noise type SHOULD be provided in [status_description].
status_description OPTIONAL. Free-form text description of noise or artifact affecting data quality on the channel. It is meant to explain why the channel was declared bad in [status].

Restricted keyword list for field type in alphabetic order (shared with the MEG and iEEG modality; however, only the types that are common in EEG data are listed here):

Keyword Description
AUDIO Audio signal
EEG Electroencephalogram channel
EOG Generic electrooculogram (eye), different from HEOG and VEOG
ECG Electrocardiogram (heart)
EMG Electromyogram (muscle)
EYEGAZE Eye tracker gaze
GSR Galvanic skin response
HEOG Horizontal EOG (eye)
MISC Miscellaneous
PUPIL Eye tracker pupil diameter
REF Reference channel
RESP Respiration
SYSCLOCK System time showing elapsed time since trial started
TEMP Temperature
TRIG System triggers
VEOG Vertical EOG (eye)

Example of free-form text for field description

  • n/a, stimulus, response, skin conductance, battery status

Example:

name     type   units   description                     status  status_description
VEOG     VEOG   microV  n/a                             good    n/a
FDI      EMG    microV  left first dorsal interosseous  good    n/a
Cz       EEG    microV  n/a                             bad     high frequency noise
UADC001  MISC   n/a     enevelope of audio signal       good    n/a

Electrodes description (*_electrodes.tsv)

Template:

sub-<label>/
    [ses-<label>]/
      eeg/
        [sub-<label>[_ses-<label>][_acq-<label>][_run-<index>]_electrodes.tsv]

File that gives the location of EEG electrodes. Note that coordinates are expected in cartesian coordinates according to the EEGCoordinateSystem and EEGCoordinateSystemUnits fields in *_coordsystem.json. If an *_electrodes.tsv file is specified, a *_coordsystem.json file MUST be specified as well. The order of the required columns in the *_electrodes.tsv file MUST be as listed below.

MUST be present:

Column name Definition
name REQUIRED. Name of the electrode
x REQUIRED. Recorded position along the x-axis
y REQUIRED. Recorded position along the y-axis
z REQUIRED. Recorded position along the z-axis

SHOULD be present:

Column name Definition
type RECOMMENDED. Type of the electrode (e.g., cup, ring, clip-on, wire, needle)
material RECOMMENDED. Material of the electrode, e.g., Tin, Ag/AgCl, Gold
impedance RECOMMENDED. Impedance of the electrode in kOhm

Example:

name  x         y        z         type      material
A1    -0.0707   0.0000   -0.0707   clip-on   Ag/AgCl
F3    -0.0567   0.0677   0.0469    cup       Ag/AgCl
Fz    0.0000    0.0714   0.0699    cup       Ag/AgCl
REF   -0.0742   -0.0200  -0.0100   cup       Ag/AgCl
GND   0.0742    -0.0200  -0.0100   cup       Ag/AgCl

The acq parameter can be used to indicate acquisition of the same data. For example, this could be the recording of electrode positions with a different electrode position recording device, or repeated digitization before and after the recording.

Coordinate System JSON (*_coordsystem.json)

Template:

sub-<label>/
    [ses-<label>]/
      eeg/
        [sub-<label>[_ses-<label>][_acq-<label>]_coordsystem.json]

A *_coordsystem.json file is used to specify the fiducials, the location of anatomical landmarks, and the coordinate system and units in which the position of electrodes and landmarks is expressed. The *_coordsystem.json is REQUIRED if the optional *_electrodes.tsv is specified. If a corresponding anatomical MRI is available, the locations of landmarks and fiducials according to that scan should also be stored in the *_T1w.json file which goes alongside the MRI data.

For disambiguation, we employ the following definitions for fiducials and anatomical landmarks respectively:

  • Fiducials = objects with a well defined location used to facilitate the localization of electrodes and co-registration with other geometric data such as the participant's own T1 weighted magnetic resonance head image, a T1 weighted template head image, or a spherical head model. Commonly used fiducials are vitamin-E pills, which show clearly in an MRI, or reflective spheres that are localized with an infrared optical tracking system.

  • Anatomical landmarks = locations on a research subject such as the nasion, which is the intersection of the frontal bone and two nasal bones of the human skull.

Fiducials are typically used in conjunction with anatomical landmarks. An example would be the placement of vitamin-E pills on top of anatomical landmarks, or the placement of LEDs on the nasion and preauricular points to triangulate the position of other LED-lit electrodes on a research subject's head.

General fields:

Keyword Description
IntendedFor OPTIONAL. Relative path to associate the electrodes, landmarks and fiducials to an MRI/CT.

Fields relating to the EEG electrode positions:

Keyword Description
EEGCoordinateSystem REQUIRED. Refers to the coordinate system in which the EEG electrode positions are to be interpreted (see Appendix VIII).
EEGCoordinateUnits REQUIRED. Units in which the coordinates that are listed in the field EEGCoordinateSystem are represented (e.g., "mm", "cm").
EEGCoordinateSystemDescription RECOMMENDED. Free-form text description of the coordinate system. May also include a link to a documentation page or paper describing the system in greater detail.

Fields relating to the position of fiducials measured during an EEG session/run:

Keyword Description
FiducialsDescription OPTIONAL. Free-form text description of how the fiducials such as vitamin-E capsules were placed relative to anatomical landmarks, and how the position of the fiducials were measured (e.g., both with Polhemus and with T1w MRI).
FiducialsCoordinates RECOMMENDED. Key:value pairs of the labels and 3-D digitized position of anatomical landmarks, interpreted following the FiducialsCoordinateSystem (e.g., {"NAS": [12.7,21.3,13.9], "LPA": [5.2,11.3,9.6], "RPA": [20.2,11.3,9.1]}).
FiducialsCoordinateSystem RECOMMENDED. Refers to the coordinate space to which the landmarks positions are to be interpreted - preferably the same as the EEGCoordinateSystem.
FiducialsCoordinateUnits RECOMMENDED. Units in which the coordinates that are listed in the field AnatomicalLandmarkCoordinateSystem are represented (e.g., "mm", "cm").
FiducialsCoordinateSystemDescription RECOMMENDED. Free-form text description of the coordinate system. May also include a link to a documentation page or paper describing the system in greater detail.

Fields relating to the position of anatomical landmark measured during an EEG session/run:

Keyword Description
AnatomicalLandmarkCoordinates RECOMMENDED. Key:value pairs of the labels and 3-D digitized position of anatomical landmarks, interpreted following the AnatomicalLandmarkCoordinateSystem (e.g., {"NAS": [12.7,21.3,13.9], "LPA": [5.2,11.3,9.6], "RPA": [20.2,11.3,9.1]}).
AnatomicalLandmarkCoordinateSystem RECOMMENDED. Refers to the coordinate space to which the landmarks positions are to be interpreted - preferably the same as the EEGCoordinateSystem.
AnatomicalLandmarkCoordinateUnits RECOMMENDED. Units in which the coordinates that are listed in the field AnatomicalLandmarkCoordinateSystem are represented (e.g., "mm", "cm").
AnatomicalLandmarkCoordinateSystemDescription RECOMMENDED. Free-form text description of the coordinate system. May also include a link to a documentation page or paper describing the system in greater detail.

If the position of anatomical landmarks is measured using the same system or device used to measure electrode positions, and if thereby the anatomical landmarks are expressed in the same coordinates, the coordinates of the anatomical landmarks can be specified in electrodes.tsv. The same applies to the coordinates of the fiducials.

Anatomical landmarks or fiducials measured on an anatomical MRI that match the landmarks or fiducials during an EEG session/run, must be stored separately in the corresponding *_T1w.json or *_T2w.json file and should be expressed in voxels (starting from [0, 0, 0]).

Example:

{
  "IntendedFor":"/sub-01/ses-01/anat/sub-01_T1w.nii",
  "EEGCoordinateSystem":"Other",
  "EEGCoordinateUnits":"mm",
  "EEGCoordinateSystemDescription":"RAS orientation: Origin halfway between LPA and RPA, positive x-axis towards RPA, positive y-axis orthogonal to x-axis through Nasion,  z-axis orthogonal to xy-plane, pointing in superior direction.",
  "FiducialsDescription":"Electrodes and fiducials were digitized with Polhemus, fiducials were recorded as the centre of vitamin E capsules sticked on the left/right pre-auricular and on the nasion, these are also visible on the T1w MRI"
}

Landmark photos (*_photo.jpg)

Photos of the anatomical landmarks and/or fiducials.

Template:

sub-<label>/
    [ses-<label>]/
      eeg/
        [sub-<label>[_ses-<label>][_acq-<label>]_photo.jpg]

Photos of the anatomical landmarks and/or fiducials are OPTIONAL. Please note that the photos may need to be cropped or blurred to conceal identifying features prior to sharing, depending on the terms of the consent given by the participant.

The acq parameter can be used to indicate acquisition of different photos of the same face (or other body part in different angles to show, for example, the location of the nasion (NAS) as opposed to the right periauricular point (RPA).

Example:

Picture of a NAS fiducial placed between the eyebrows, rather than at the actual anatomical nasion: sub-0001_ses-001_acq-NAS_photo.jpg

placement of NAS fiducial