Skip to content

intracranial Electroencephalography (iEEG)

Support for iEEG 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:

Holdgraf, C., Appelhoff, S., Bickel, S., Bouchard, K., D'Ambrosio, S., David, O., Devinsky, O., Dichter, B., Flinker, A., Foster, B. L., Gorgolewski, K. J., Groen, I., Groppe, D., Gunduz, A., Hamilton, L., Honey, C. J., Jas, M., Knight, R., Lauchaux, J.-P., Lau, J. C., Lundstrom, B. N., Lee-Messer, C., Miller, K. J., Ojemann, J. G., Oostenveld, R., Petridou, N., Piantoni, G., Pigorini, A., Pouratian, N., Ramsey, N. F., Stolk, A., Swann, N. C., Tadel, F., Voytek, B., Wandell, B. A., Winawer, J., Zehl, L., Hermes, D. (2018, December 13). BIDS-iEEG: an extension to the brain imaging data structure (BIDS) specification for human intracranial electrophysiology. https://doi.org/10.31234/osf.io/r7vc2

iEEG recording data

Template:

sub-<label>/
  [ses-<label>]/
    ieeg/
      sub-<label>[_ses-<label>]_task-<task_label>[_run-<index>]_ieeg.<manufacturer_specific_extension>
      sub-<label>[_ses-<label>]_task-<task_label>[_run-<index>]_ieeg.json

The iEEG community uses a variety of formats for storing raw data, and there is no single standard that all researchers agree on. For BIDS, iEEG 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.

Future versions of BIDS may extend this list of supported file formats. File formats for future consideration MUST have open access documentation, MUST have open source implementation for both reading and writing in at least two programming languages and SHOULD be widely supported in multiple software packages. Other formats that may be considered in the future should have a clear added advantage over the existing formats and should have wide adoption in the BIDS community.

The data format in which the data was originally stored is especially valuable in case conversion elicits the loss of crucial metadata specific to manufacturers and specific iEEG 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 iEEG data in the /sourcedata directory.

Terminology: Electrodes vs. Channels

For proper documentation of iEEG recording metadata it is important to understand the difference between electrode and channel: An iEEG electrode is placed on or in the brain, 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 iEEG 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 arrays, grids, leads, strips, probes, shafts, caps (for EEG), 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 iEEG 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 (*_ieeg.json)

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

Generic fields MUST be present:

Field name Definition
TaskName REQUIRED. Name of the task (for resting state use the "rest" prefix). No two tasks should have the same name. Task label is derived from this field by removing all non alphanumeric ([a-zA-Z0-9]) characters. Note this does not have to be a "behavioral task" that subjects perform, but can reflect some information about the conditions present when the data was acquired (e.g., "rest", "sleep", or "seizure").

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 amplifier system (e.g., "TDT, Blackrock").
ManufacturersModelName RECOMMENDED. Manufacturer's designation of the iEEG amplifier model.
SoftwareVersions RECOMMENDED. Manufacturer's designation of the acquisition software.
TaskDescription RECOMMENDED. Longer description of the task.
Instructions RECOMMENDED. Text of the instructions given to participants before the recording. This is especially important in context of resting state and distinguishing between eyes open and eyes closed paradigms.
CogAtlasID RECOMMENDED. URL of the corresponding Cognitive Atlas Task term.
CogPOID RECOMMENDED. URL of the corresponding CogPO term.
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 iEEG fields MUST be present:

Field name Definition
iEEGReference 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", "bipolar", "T01" for electrode with name T01, "intracranial electrode on top of a grid, not included with data", "upside down electrode"). 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 iEEG channels in the recording (e.g., 2400). All other channels should have frequency specified as well in the channels.tsv file.
PowerLineFrequency REQUIRED. Frequency (in Hz) of the power grid where the iEEG recording was done (i.e., 50 or 60).
SoftwareFilters REQUIRED. List of temporal software filters applied or ideally key:value pairs of pre-applied filters and their parameter values. (n/a if none). E.g., "{'HighPass': {'HalfAmplitudeCutOffHz': 1, 'RollOff: '6dB/Octave'}}".

Specific iEEG fields SHOULD be present:

Field name Definition
DCOffsetCorrection RECOMMENDED. A description of the method (if any) used to correct for a DC offset. If the method used was subtracting the mean value for each channel, use "mean".
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.
ElectrodeManufacturer RECOMMENDED. can be used if all electrodes are of the same manufacturer (e.g., AD-TECH, DIXI). If electrodes of different manufacturers are used, please use the corresponding table in the _electrodes.tsv file.
ElectrodeManufacturersModelName RECOMMENDED. If different electrode types are used, please use the corresponding table in the _electrodes.tsv file.
ECOGChannelCount RECOMMENDED. Number of iEEG surface channels included in the recording (e.g., 120).
SEEGChannelCount RECOMMENDED. Number of iEEG depth channels included in the recording (e.g., 8).
EEGChannelCount RECOMMENDED. Number of scalp EEG channels recorded simultaneously (e.g., 21).
EOGChannelCount RECOMMENDED. Number of EOG channels.
ECGChannelCount RECOMMENDED. Number of ECG channels.
EMGChannelCount RECOMMENDED. Number of EMG channels.
MiscChannelCount RECOMMENDED. Number of miscellaneous analog channels for auxiliary signals.
TriggerChannelCount RECOMMENDED. Number of channels for digital (TTL bit level) triggers.
RecordingDuration RECOMMENDED. Length of the recording in seconds (e.g., 3600).
RecordingType RECOMMENDED. Defines whether the recording is "continuous" or "epoched"; this latter limited to time windows about events of interest (e.g., stimulus presentations, subject responses etc.)
EpochLength RECOMMENDED. Duration of individual epochs in seconds (e.g., 1) in case of epoched data. If recording was continuous, leave out the field.
iEEGGround RECOMMENDED. Description of the location of the ground electrode ("placed on right mastoid (M2)").
iEEGPlacementScheme RECOMMENDED. Freeform description of the placement of the iEEG electrodes. Left/right/bilateral/depth/surface (e.g., "left frontal grid and bilateral hippocampal depth" or "surface strip and STN depth" or "clinical indication bitemporal, bilateral temporal strips and left grid").
iEEGElectrodeGroups RECOMMENDED. Field to describe the way electrodes are grouped into strips, grids or depth probes e.g., {'grid1': "10x8 grid on left temporal pole", 'strip2': "1x8 electrode strip on xxx"}.
SubjectArtefactDescription RECOMMENDED. Freeform description of the observed subject artefact and its possible cause (e.g., "door open", "nurse walked into room at 2 min", "seizure at 10 min"). If this field is left empty, it will be interpreted as absence of artifacts.

Specific iEEG fields MAY be present:

Field name Definition
ElectricalStimulation OPTIONAL. Boolean field to specify if electrical stimulation was done during the recording (options are "true" or "false"). Parameters for event-like stimulation should be specified in the _events.tsv file (see example below).
ElectricalStimulationParameters OPTIONAL. Free form description of stimulation parameters, such as frequency, shape etc. Specific onsets can be specified in the _events.tsv file. Specific shapes can be described here in freeform text.

Example:

{
  "TaskName":"visual",
  "InstitutionName":"Stanford Hospital and Clinics",
  "InstitutionAddress":"300 Pasteur Dr, Stanford, CA 94305",
  "Manufacturer":"Tucker Davis Technologies",
  "ManufacturersModelName":"n/a",
  "TaskDescription":"visual gratings and noise patterns",
  "Instructions":"look at the dot in the center of the screen and press the button when it changes color",
  "iEEGReference":"left mastoid",
  "SamplingFrequency":1000,
  "PowerLineFrequency":60,
  "SoftwareFilters":"n/a",
  "DCOffsetCorrection":0,
  "HardwareFilters":{"Highpass RC filter": {"Half amplitude cutoff (Hz)": 0.0159, "Roll-off": "6dBOctave"}},
  "ElectrodeManufacturer":"AdTech",
  "ECOGChannelCount":120,
  "SEEGChannelCount":0,
  "EEGChannelCount":0,
  "EOGChannelCount":0,
  "ECGChannelCount":0,
  "EMGChannelCount":0,
  "MiscChannelCount":0,
  "TriggerChannelCount":0,
  "RecordingDuration":233.639,
  "RecordingType":"continuous",
  "iEEGGround":"placed on the right mastoid",
  "iEEGPlacementScheme":"right occipital temporal surface",
  "ElectricalStimulation":false
}

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

A channel represents one time series recorded with the recording system (for example, there can be a bipolar channel, recorded from two electrodes or contact points on the tissue). Although this information can often be extracted from the iEEG recording, listing it in a simple .tsv document makes it easy to browse or search (e.g., searching for recordings with a sampling frequency of >=1000 Hz). The two required columns are channel name and type. Channels should appear in the table in the same order they do in the iEEG 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. Label of the channel. The label must correspond to _electrodes.tsv name and all ieeg type channels are required to have a position. The reference channel name MAY be provided in the reference column.
type REQUIRED. Type of channel, see below for adequate keywords in this field.
units REQUIRED. Physical unit of the value represented in this channel, e.g., V for Volt, specified according to the SI unit symbol and possibly prefix symbol (e.g., mV, μV). For guidelines for Units and Prefixes see Appendix V.
low_cutoff REQUIRED. Frequencies used for the low pass filter applied to the channel in Hz. If no low pass filter was applied, use n/a. Note that anti-alias is a low pass filter, specify its frequencies here if applicable.
high_cutoff REQUIRED. Frequencies used for the high pass filter applied to the channel in Hz. If no high pass filter applied, use n/a.

SHOULD be present:

Column name Definition
reference OPTIONAL. Specification of the reference (e.g., 'mastoid', 'ElectrodeName01', 'intracranial', 'CAR', 'other', 'n/a'). If the channel is not an electrode channel (e.g., a microphone channel) use n/a.
group OPTIONAL. Which group of channels (grid/strip/seeg/depth) this channel belongs to. This is relevant because one group has one cable-bundle and noise can be shared. This can be a name or number. Note that any groups specified in _electrodes.tsv must match those present here.
sampling_frequency OPTIONAL. Sampling rate of the channel in Hz.
description OPTIONAL. Brief free-text description of the channel, or other information of interest (e.g., position (e.g., "left lateral temporal surface", etc.).
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. Freeform 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].

Example sub-01_channels.tsv:

name  type  units low_cutoff  high_cutoff status  status_description
LT01  ECOG  μV    300         0.11        good    n/a
LT02  ECOG  μV    300         0.11        bad     broken
H01   SEEG  μV    300         0.11        bad     line_noise
ECG1  ECG   μV    n/a         0.11        good    n/a
TR1   TRIG  n/a   n/a         n/a         good    n/a
Restricted keyword list for field type in alphabetic order (shared with the MEG and EEG modality; however, only types that are common in iEEG data are listed here):

Keyword Description
EEG Electrode channel from electroencephalogram
ECOG Electrode channel from electrocorticogram (intracranial)
SEEG Electrode channel from stereo-electroencephalogram (intracranial)
DBS Electrode channel from deep brain stimulation electrode (intracranial)
VEOG Vertical EOG (electrooculogram)
HEOG Horizontal EOG
EOG Generic EOG channel if HEOG or VEOG information not available
ECG ElectroCardioGram (heart)
EMG ElectroMyoGram (muscle)
TRIG System Triggers
AUDIO Audio signal
PD Photodiode
EYEGAZE Eye Tracker gaze
PUPIL Eye Tracker pupil diameter
MISC Miscellaneous
SYSCLOCK System time showing elapsed time since trial started
ADC Analog to Digital input
DAC Digital to Analog output
REF Reference channel
OTHER Any other type of channel

The free text field for the channel description can for example be specified as intracranial, stimulus, response, vertical EOG, horizontal EOG, skin conductance, eyetracker, etc.

Electrode description (*_electrodes.tsv)

Template:

sub-<label>/
    [ses-<label>]/
      ieeg/
         sub-<label>[_ses-<label>][_space-<label>]_electrodes.tsv

File that gives the location, size and other properties of iEEG electrodes. Note that coordinates are expected in cartesian coordinates according to the iEEGCoordinateSystem and iEEGCoordinateSystemUnits fields in *_coordsystem.json. If an *_electrodes.tsv file is specified, a *_coordsystem.json file MUST be specified as well.

The optional space label (*[_space-<label>]_electrodes.tsv) can be used to indicate the way in which electrode positions are interpreted. The space label needs to be taken from the list in Appendix VIII

For examples:

  • _space-MNI152Lin (electrodes are coregistred and scaled to a specific MNI template)

  • _space-Talairach (electrodes are coregistred and scaled to Talairach space)

When referring to the *_electrodes.tsv file in a certain space as defined above, the space-<label> of the accompanying *_coordsystem.json MUST correspond.

For example:

  • sub-01_space-Talairach_electrodes.tsv
  • sub-01_space-Talairach_coordsystem.json

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 contact point.
x REQUIRED. X position. The positions of the center of each electrode in xyz space. Units are in millimeters or pixels and are specified in _*space-
y REQUIRED. Y position.
z REQUIRED. Z position. If electrodes are in 2D space this should be a column of n/a values.
size REQUIRED. Surface area of the electrode, in mm^2.

SHOULD be present:

Column name Definition
material OPTIONAL. Material of the electrodes.
manufacturer OPTIONAL. Recommended field to specify the manufacturer for each electrode. Can be used if electrodes were manufactured by more than one company.
group OPTIONAL. Optional field to specify the group that the electrode is a part of. Note that any group specified here should match a group specified in _channels.tsv.
hemisphere OPTIONAL. Optional field to specify the hemisphere in which the electrode is placed, one of ['L' or 'R'] (use capital).

MAY be present:

Column name Definition
type OPTIONAL. Optional type of the electrode, e.g., cup, ring, clip-on, wire, needle, ...
impedance OPTIONAL. Impedance of the electrode in kOhm.
dimension OPTIONAL. Size of the group (grid/strip/probe) that this electrode belongs to. Must be of form [AxB] with the smallest dimension first (e.g., [1x8]).

Example:

name  x   y    z    size   manufacturer
LT01  19  -39  -16  2.3    Integra
LT02  23  -40  -19  2.3    Integra
H01   27  -42  -21  5      AdTech

Coordinate System JSON (*_coordsystem.json)

Template:

sub-<label>/
    [ses-<label>]/
      ieeg/
         sub-<label>[_ses-<label>][_space-<label>]_coordsystem.json

This _coordsystem.json file contains the coordinate system in which electrode positions are expressed. The associated MRI, CT, X-Ray, or operative photo can also be specified.

General fields:

Field name Definition
IntendedFor RECOMMENDED. This can be an MRI/CT or a file containing the operative photo, x-ray or drawing with path relative to the project folder. If only a surface reconstruction is available, this should point to the surface reconstruction file. Note that this file should have the same coordinate system specified in iEEGCoordinateSystem. For example, T1: sub-<label>/ses-<label>/anat/sub-01_T1w.nii.gz Surface: /derivatives/surfaces/sub-<label>/ses-<label>/anat/sub-01_T1w_pial.R.surf.gii Operative photo: /sub-<label>/ses-<label>/ieeg/sub-0001_ses-01_acq-photo1_photo.jpg Talairach: /derivatives/surfaces/sub-Talairach/ses-01/anat/sub-Talairach_T1w_pial.R.surf.gii

Fields relating to the iEEG electrode positions:

Field name Definition
iEEGCoordinateSystem REQUIRED. Defines the coordinate system for the iEEG electrodes. See Appendix VIII for a list of restricted keywords. If positions correspond to pixel indices in a 2D image (of either a volume-rendering, surface-rendering, operative photo, or operative drawing), this must be "Pixels". For more information, see the section on 2D coordinate systems.
iEEGCoordinateUnits REQUIRED. Units of the _electrodes.tsv, MUST be "m", "mm", "cm" or "pixels".
iEEGCoordinateSystemDescription RECOMMENDED. Freeform text description or link to document describing the iEEG coordinate system system in detail (e.g., "Coordinate system with the origin at anterior commissure (AC), negative y-axis going through the posterior commissure (PC), z-axis going to a mid-hemisperic point which lies superior to the AC-PC line, x-axis going to the right").
iEEGCoordinateProcessingDescription RECOMMENDED. Has any post-processing (such as projection) been done on the electrode positions (e.g., "surface_projection", "none").
iEEGCoordinateProcessingReference RECOMMENDED. A reference to a paper that defines in more detail the method used to localize the electrodes and to post-process the electrode positions. .

It is preferred that electrodes are localized in a 3D coordinate system (with respect to a pre- and/or post-operative anatomical MRI or CT scans or in a standard space as specified in BIDS Appendix VIII about preferred names of coordinate systems, such as ACPC).

Allowed 2D coordinate systems

If electrodes are localized in 2D space (only x and y are specified and z is n/a), then the positions in this file must correspond to the locations expressed in pixels on the photo/drawing/rendering of the electrodes on the brain. In this case, coordinates must be (row,column) pairs, with (0,0) corresponding to the upper left pixel and (N,0) corresponding to the lower left pixel.

Multiple coordinate systems

If electrode positions are known in multiple coordinate systems (e.g., MRI, CT and MNI), these spaces can be distinguished by the optional [_space-<label>] field, see the *_electrodes.tsv-section for more information. Note that the [_space-<label>] fields must correspond between *_electrodes.tsv and *_coordsystem.json if they refer to the same data.

Example:

{
    "IntendedFor": "/sub-01/ses-01/anat/sub-01_T1w.nii.gz",
    "iEEGCoordinateSystem": "ACPC",
    "iEEGCoordinateUnits": "mm",
    "iEEGCoordinateSystemDescription": "Coordinate system with the origin at anterior commissure (AC), negative y-axis going through the posterior commissure (PC), z-axis going to a mid-hemisperic point which lies superior to the AC-PC line, x-axis going to the right",
    "iEEGCoordinateProcessingDescription": "surface_projection",
    "iEEGCoordinateProcessingReference": "Hermes et al., 2010 JNeuroMeth"
}

Photos of the electrode positions (*_photo.jpg)

Template:

sub-<label>/
    [ses-<label>]/
      ieeg/
         sub-<label>[_ses-<label>][_acq-<label]_photo.json

These can include photos of the electrodes on the brain surface, photos of anatomical features or landmarks (such as sulcal structure), and fiducials. Photos can also include an X-ray picture, a flatbed scan of a schematic drawing made during surgery, or screenshots of a brain rendering with electrode positions. The photos may need to be cropped and/or blurred to conceal identifying features or entirely omitted prior to sharing, depending on obtained consent.

If there are photos of the electrodes, the acquisition field should be specified with:

  • *_photo.jpg in case of an operative photo

  • *_acq-xray#_photo.jpg in case of an x-ray picture

  • *_acq-drawing#_photo.jpg in case of a drawing or sketch of electrode placements

  • *_acq-render#_photo.jpg in case of a rendering

The session label may be used to specify when the photo was taken.

Example of the operative photo of ECoG electrodes (here is an annotated example in which electrodes and vasculature are marked, taken from Hermes et al., JNeuroMeth 2010).

    sub-0001_ses-01_acq-photo1_photo.jpg
    sub-0001_ses-01_acq-photo2_photo.jpg

operative photo of ECoG electrodes

Below is an example of a volume rendering of the cortical surface with a superimposed subdural electrode implantation. This map is often provided by the EEG technician and provided to the epileptologists (e.g., see Burneo JG et al. 2014 https://doi.org/10.1016/j.clineuro.2014.03.020).

    sub-0002_ses-01_acq-render_photo.jpg

volume rendering of the cortical surface

Electrical stimulation

In case of electrical stimulation of brain tissue by passing current through the iEEG electrodes, and the electrical stimulation has an event structure (on-off, onset, duration), the _events.tsv file can contain the electrical stimulation parameters in addition to other events. Note that these can be intermixed with other task events. Electrical stimulation parameters can be described in columns called electrical_stimulation_<label>, with labels chosen by the researcher and optionally defined in more detail in an accompanying _events.json file (as per the main BIDS spec). Functions for complex stimulation patterns can, similar as when a video is presented, be stored in a folder in the /stimuli/ folder. For example: /stimuli/electrical_stimulation_functions/biphasic.tsv

Example:

onset duration trial_type             electrical_stimulation_type electrical_stimulation_site electrical_stimulation_current
1.2   0.001    electrical_stimulation biphasic                    LT01-LT02                   0.005
1.3   0.001    electrical_stimulation biphasic                    LT01-LT02                   0.005
2.2   0.001    electrical_stimulation biphasic                    LT02-LT03                   0.005
4.2   1        electrical_stimulation complex                     LT02-LT03                   n/a
15.2  3        auditory_stimulus      n/a                         n/a                         n/a