Intracranial Electroencephalography

Support for Intracranial Electroencephalography (iEEG) was developed as a BIDS Extension Proposal. Please see Citing BIDS on how to appropriately credit this extension when referring to it in the context of the academic literature.

Example datasets

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

iEEG recording data

Template:

sub-<label>/
    [ses-<label>/]
        ieeg/
            sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_run-<index>]_ieeg.<extension>
            sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_run-<index>]_ieeg.json
            sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_run-<index>]_events.json
            sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_run-<index>]_events.tsv
            sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_run-<index>][_recording-<label>]_physio.json
            sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_run-<index>][_recording-<label>]_physio.tsv.gz
            sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_run-<index>][_recording-<label>]_stim.json
            sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_run-<index>][_recording-<label>]_stim.tsv.gz

Legend:

• For more information about filename elements (for example, entities, suffixes, extensions), follow the links embedded in the filename template.

• Filename entities or directories between square brackets (for example, [_ses-<label>]) are OPTIONAL.

• Some entities may only allow specific values, in which case those values are listed in <>, separated by |.

• _<suffix> means that there are several (>6) valid suffixes for this filename pattern.

• .<extension> means that there are several (>6) valid extensions for this file type.

• [.gz] means that both the unzipped and gzipped versions of the extension are valid.

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:

Format	Extension(s)	Description
European data format	.edf	Each recording consists of a .edf single file. edf+ files are permitted. The capital .EDF extension MUST NOT be used.
BrainVision Core Data Format	.vhdr, .vmrk, .eeg	Each recording consists of a .vhdr, .vmrk, .eeg file triplet.
EEGLAB	.set, .fdt	The format used by the MATLAB toolbox EEGLAB. Each recording consists of a .set file with an OPTIONAL .fdt file.
Neurodata Without Borders	.nwb	Each recording consists of a single .nwb file.
MEF3	.mefd	Each recording consists of a .mefd directory.

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.

We encourage users to provide additional metadata extracted from the manufacturer-specific data files in the sidecar JSON file.

Note the RecordingType, which depends on whether the data stream on disk is interrupted or not. Continuous data is by definition 1 segment without interruption. Epoched data consists of multiple segments that all have the same length (for example, corresponding to trials) and that have gaps in between. Discontinuous data consists of multiple segments of different length, for example due to a pause in the acquisition.

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 (for example, scalp, neural tissue, ...). Multiple electrodes can be organized as arrays, grids, leads, strips, probes, shafts, caps (for EEG), and so forth.

• 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, and so forth.

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.

Those fields MUST be present:

Key name	Requirement Level	Data type	Description
iEEGReference	REQUIRED	string	General description of the reference scheme used and (when applicable) of location of the reference electrode in the raw recordings (for example, "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	number	Sampling frequency (in Hz) of all the data in the recording, regardless of their type (for example, 2400). The sampling frequency of data channels that deviate from the main sampling frequency SHOULD be specified in the channels.tsv file.
PowerLineFrequency	REQUIRED	number or "n/a"	Frequency (in Hz) of the power grid at the geographical location of the instrument (for example, 50 or 60).
SoftwareFilters	REQUIRED	object of objects or "n/a"	Object of temporal software filters applied, or "n/a" if the data is not available. Each key-value pair in the JSON object is a name of the filter and an object in which its parameters are defined as key-value pairs (for example, {"Anti-aliasing filter": {"half-amplitude cutoff (Hz)": 500, "Roll-off": "6dB/Octave"}}).

Those fields SHOULD be present:

Key name	Requirement Level	Data type	Description
DCOffsetCorrection	DEPRECATED	string	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	object of objects or "n/a"	Object of temporal hardware filters applied, or "n/a" if the data is not available. Each key-value pair in the JSON object is a name of the filter and an object in which its parameters are defined as key-value pairs. For example, {"Highpass RC filter": {"Half amplitude cutoff (Hz)": 0.0159, "Roll-off": "6dB/Octave"}}.
ElectrodeManufacturer	RECOMMENDED	string	Can be used if all electrodes are of the same manufacturer (for example, "AD-TECH", "DIXI"). If electrodes of different manufacturers are used, please use the corresponding table in the _electrodes.tsv file.
ElectrodeManufacturersModelName	RECOMMENDED	string	If different electrode types are used, please use the corresponding table in the _electrodes.tsv file.
ECOGChannelCount	RECOMMENDED	integer	Number of ECoG channels. Must be a number greater than or equal to 0.
SEEGChannelCount	RECOMMENDED	integer	Number of SEEG channels. Must be a number greater than or equal to 0.
EEGChannelCount	RECOMMENDED	integer	Number of EEG channels recorded simultaneously (for example, 21). Must be a number greater than or equal to 0.
EOGChannelCount	RECOMMENDED	integer	Number of EOG channels. Must be a number greater than or equal to 0.
ECGChannelCount	RECOMMENDED	integer	Number of ECG channels. Must be a number greater than or equal to 0.
EMGChannelCount	RECOMMENDED	integer	Number of EMG channels. Must be a number greater than or equal to 0.
MiscChannelCount	RECOMMENDED	integer	Number of miscellaneous analog channels for auxiliary signals. Must be a number greater than or equal to 0.
TriggerChannelCount	RECOMMENDED	integer	Number of channels for digital (binary TTL) triggers or analog equivalents (TTL in volt). Corresponds to the TRIG channel type. Must be a number greater than or equal to 0.
RecordingDuration	RECOMMENDED	number	Length of the recording in seconds (for example, 3600).
RecordingType	RECOMMENDED	string	Defines whether the recording is "continuous", "discontinuous", or "epoched", where "epoched" is limited to time windows about events of interest (for example, stimulus presentations or subject responses). Must be one of: "continuous", "epoched", "discontinuous".
EpochLength	RECOMMENDED	number	Duration of individual epochs in seconds (for example, 1) in case of epoched data. If recording was continuous or discontinuous, leave out the field. Must be a number greater than or equal to 0.
iEEGGround	RECOMMENDED	string	Description of the location of the ground electrode ("placed on right mastoid (M2)").
iEEGPlacementScheme	RECOMMENDED	string	Freeform description of the placement of the iEEG electrodes. Left/right/bilateral/depth/surface (for example, "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	string	Field to describe the way electrodes are grouped into strips, grids or depth probes. For example, "grid1: 10x8 grid on left temporal pole, strip2: 1x8 electrode strip on xxx".
SubjectArtefactDescription	RECOMMENDED	string	Freeform description of the observed subject artifact and its possible cause (for example, "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.

These fields MAY be present:

Key name	Requirement Level	Data type	Description
ElectricalStimulation	OPTIONAL	boolean	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. Must be one of: "true", "false".
ElectricalStimulationParameters	OPTIONAL	string	Free form description of stimulation parameters, such as frequency or shape. Specific onsets can be specified in the events.tsv file. Specific shapes can be described here in freeform text.

Note that the date and time information SHOULD be stored in the study key file (scans.tsv). Date time information MUST be expressed as indicated in Units

Hardware information

Key name	Requirement Level	Data type	Description
Manufacturer	RECOMMENDED	string	Manufacturer of the equipment that produced the measurements. For example, "TDT", "Blackrock".
ManufacturersModelName	RECOMMENDED	string	Manufacturer's model name of the equipment that produced the measurements.
SoftwareVersions	RECOMMENDED	string	Manufacturer's designation of software version of the equipment that produced the measurements.
DeviceSerialNumber	RECOMMENDED	string	The serial number of the equipment that produced the measurements. A pseudonym can also be used to prevent the equipment from being identifiable, so long as each pseudonym is unique within the dataset.

Task information

Key name	Requirement Level	Data type	Description
TaskName	REQUIRED	string	Name of the task. No two tasks should have the same name. The task label included in the filename is derived from this "TaskName" field by removing all non-alphanumeric characters (that is, all except those matching [0-9a-zA-Z]). For example "TaskName" "faces n-back" or "head nodding" will correspond to task labels facesnback and headnodding, respectively. A RECOMMENDED convention is to name resting state task using labels beginning with rest.
TaskDescription	RECOMMENDED	string	Longer description of the task.
Instructions	RECOMMENDED	string	Text of the instructions given to subjects before the recording. This is especially important in context of resting state recordings and distinguishing between eyes open and eyes closed paradigms.
CogAtlasID	RECOMMENDED	string	URI of the corresponding Cognitive Atlas Task term.
CogPOID	RECOMMENDED	string	URI of the corresponding CogPO term.

Note that the TaskName field 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 (for example, "rest", "sleep", or "seizure").

Institution information

Key name	Requirement Level	Data type	Description
InstitutionName	RECOMMENDED	string	The name of the institution in charge of the equipment that produced the measurements.
InstitutionAddress	RECOMMENDED	string	The address of the institution in charge of the equipment that produced the measurements.
InstitutionalDepartmentName	RECOMMENDED	string	The department in the institution in charge of the equipment that produced the measurements.

Example *_ieeg.json

{
  "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",
  "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
}

Channels description (*_channels.tsv)

Template:

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

Legend:

• For more information about filename elements (for example, entities, suffixes, extensions), follow the links embedded in the filename template.

• Filename entities or directories between square brackets (for example, [_ses-<label>]) are OPTIONAL.

• Some entities may only allow specific values, in which case those values are listed in <>, separated by |.

• _<suffix> means that there are several (>6) valid suffixes for this filename pattern.

• .<extension> means that there are several (>6) valid extensions for this file type.

• [.gz] means that both the unzipped and gzipped versions of the extension are valid.

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 (for example, searching for recordings with a sampling frequency of >=1000 Hz). Hence, the channels.tsv file is RECOMMENDED. 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:

Column name	Requirement Level	Data type	Description
name	REQUIRED	string	Label of the channel. When a corresponding electrode is specified in _electrodes.tsv, the name of that electrode MAY be specified here and the reference electrode name MAY be provided in the reference column. Values in name MUST be unique. This column must appear first in the file.
type	REQUIRED	string	Type of channel; MUST use the channel types listed below. Note that the type MUST be in upper-case. This column must appear second in the file. For a list of valid values for this column, see the associated glossary entry.
units	REQUIRED	string	Physical unit of the value represented in this channel, for example, V for Volt, or fT/cm for femto Tesla per centimeter (see Units). This column must appear third in the file.
low_cutoff	REQUIRED	number or "n/a"	Frequencies used for the high-pass filter applied to the channel in Hz. If no high-pass filter applied, use n/a. This column must appear fourth in the file.
high_cutoff	REQUIRED	number or "n/a"	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 MEG/EEG electronics applies a low-pass filter; specify its frequency here if applicable. This column must appear fifth in the file.
reference	OPTIONAL	string or "n/a"	Specification of the reference (for example, mastoid, ElectrodeName01, intracranial, CAR, other, n/a). If the channel is not an electrode channel (for example, a microphone channel) use n/a. This column may appear anywhere in the file.
group	OPTIONAL	string or number	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. This column may appear anywhere in the file.
sampling_frequency	OPTIONAL	number	Sampling rate of the channel in Hz. This column may appear anywhere in the file.
description	OPTIONAL	string	Brief free-text description of the channel, or other information of interest. This column may appear anywhere in the file.
notch	OPTIONAL	string	Frequencies used for the notch filter applied to the channel, in Hz. If notch filters are applied at multiple frequencies, these frequencies MAY be specified as a list, for example, [60, 120, 180]. If no notch filter was applied, use n/a. This column may appear anywhere in the file.
status	OPTIONAL	string	Data quality observed on the channel. A channel is considered bad if its data quality is compromised by excessive noise. If quality is unknown, then a value of n/a may be used. Description of noise type SHOULD be provided in [status_description]. This column may appear anywhere in the file. Must be one of: "good", "bad", "n/a".
status_description	OPTIONAL	string	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 the status column. This column may appear anywhere in the file.
Additional Columns	OPTIONAL	n/a	Additional columns are allowed if they are defined in the associated metadata file.

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). Note that upper-case is REQUIRED:

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	Analog (TTL in Volt) or digital (binary TTL) trigger channel
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

Examples of free-form text for field description:

• intracranial
• stimulus
• response
• vertical EOG
• skin conductance

Example *_channels.tsv

name  type  units low_cutoff  high_cutoff status  status_description
LT01  ECOG  uV    300         0.11        good    n/a
LT02  ECOG  uV    300         0.11        bad     broken
H01   SEEG  uV    300         0.11        bad     line_noise
ECG1  ECG   uV    n/a         0.11        good    n/a
TR1   TRIG  n/a   n/a         n/a         good    n/a

Electrode description (*_electrodes.tsv)

Template:

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

Legend:

• For more information about filename elements (for example, entities, suffixes, extensions), follow the links embedded in the filename template.

• Filename entities or directories between square brackets (for example, [_ses-<label>]) are OPTIONAL.

• Some entities may only allow specific values, in which case those values are listed in <>, separated by |.

• _<suffix> means that there are several (>6) valid suffixes for this filename pattern.

• .<extension> means that there are several (>6) valid extensions for this file type.

• [.gz] means that both the unzipped and gzipped versions of the extension are valid.

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 iEEGCoordinateUnits fields in *_coordsystem.json. If an *_electrodes.tsv file is specified, a *_coordsystem.json file MUST be specified as well.

The optional space-<label> entity (*[_space-<label>]_electrodes.tsv) can be used to indicate the way in which electrode positions are interpreted. The space <label> MUST be taken from one of the modality specific lists in the Coordinate Systems Appendix. For example for iEEG data, the restricted keywords listed under iEEG Specific Coordinate Systems are acceptable for <label>.

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/
   ├─ 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. The x, y, and z columns indicate the positions of the center of each electrode in Cartesian coordinates. Units are specified in space-<label>_coordsystem.json.

Column name	Requirement Level	Data type	Description
name	REQUIRED	string	Name of the electrode contact point. Values in name MUST be unique. This column must appear first in the file.
x	REQUIRED	number	Recorded position along the x-axis. This column must appear second in the file.
y	REQUIRED	number	Recorded position along the y-axis. This column must appear third in the file.
z	REQUIRED	number or "n/a"	Recorded position along the z-axis. If electrodes are in 2D space this should be a column of n/a values. This column must appear fourth in the file.
size	REQUIRED	number	Surface area of the electrode, units MUST be in mm^2. This column must appear fifth in the file.
material	RECOMMENDED	string	Material of the electrode (for example, Tin, Ag/AgCl, Gold). This column may appear anywhere in the file.
manufacturer	RECOMMENDED	string	The manufacturer for each electrode. Can be used if electrodes were manufactured by more than one company. This column may appear anywhere in the file.
group	RECOMMENDED	string or number	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 group specified here should match a group specified in _channels.tsv. This column may appear anywhere in the file.
hemisphere	RECOMMENDED	string	The hemisphere in which the electrode is placed. This column may appear anywhere in the file. Must be one of: "L", "R".
type	OPTIONAL	string	Type of the electrode (for example, cup, ring, clip-on, wire, needle). This column may appear anywhere in the file.
impedance	OPTIONAL	number	Impedance of the electrode, units MUST be in kOhm. This column may appear anywhere in the file.
dimension	OPTIONAL	string	Size of the group (grid/strip/probe) that this electrode belongs to. Must be of form [AxB] with the smallest dimension first (for example, [1x8]). This column may appear anywhere in the file.
Additional Columns	OPTIONAL	n/a	Additional columns are allowed if they are defined in the associated metadata file.

*_electrodes.tsv files SHOULD NOT be duplicated for each data file, for example, during multiple runs of a task. The inheritance principle MUST be used to find the appropriate electrode positions for a given data file. If electrodes are repositioned, it is RECOMMENDED to use multiple sessions to indicate this.

Example *_electrodes.tsv

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>][_acq-<label>][_space-<label>]_coordsystem.json

Legend:

• For more information about filename elements (for example, entities, suffixes, extensions), follow the links embedded in the filename template.

• Filename entities or directories between square brackets (for example, [_ses-<label>]) are OPTIONAL.

• Some entities may only allow specific values, in which case those values are listed in <>, separated by |.

• _<suffix> means that there are several (>6) valid suffixes for this filename pattern.

• .<extension> means that there are several (>6) valid extensions for this file type.

• [.gz] means that both the unzipped and gzipped versions of the extension are valid.

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:

Key name	Requirement Level	Data type	Description
IntendedFor	OPTIONAL	string or array	The paths to files for which the associated file is intended to be used. Contains one or more BIDS URIs. Using forward-slash separated paths relative to the dataset root is DEPRECATED. 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: 'bids::sub-<label>/ses-<label>/anat/sub-01_T1w.nii.gz' Surface: 'bids::derivatives/surfaces/sub-<label>/ses-<label>/anat/ sub-01_hemi-R_desc-T1w_pial.surf.gii' Operative photo: 'bids::sub-<label>/ses-<label>/ieeg/ sub-0001_ses-01_acq-photo1_photo.jpg' Talairach: 'bids::derivatives/surfaces/sub-Talairach/ses-01/anat/ sub-Talairach_hemi-R_pial.surf.gii'

Fields relating to the iEEG electrode positions:

Key name	Requirement Level	Data type	Description
iEEGCoordinateSystem	REQUIRED	string	Defines the coordinate system for the iEEG sensors. See the Coordinate Systems Appendix for a list of restricted keywords for coordinate systems. If "Other", provide definition of the coordinate system in iEEGCoordinateSystemDescription. 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. For a list of valid values for this field, see the associated glossary entry.
iEEGCoordinateUnits	REQUIRED	string	Units of the *_electrodes.tsv. MUST be "pixels" if iEEGCoordinateSystem is Pixels. Must be one of: "pixels", "m", "mm", "cm", "n/a".
iEEGCoordinateSystemDescription	RECOMMENDED, but REQUIRED if iEEGCoordinateSystem is "Other"	string	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.
iEEGCoordinateProcessingDescription	RECOMMENDED	string	Has any post-processing (such as projection) been done on the electrode positions (for example, "surface_projection", "none").
iEEGCoordinateProcessingReference	RECOMMENDED	string	A reference to a paper that defines in more detail the method used to localize the electrodes and to post-process the electrode positions.

Recommended 3D coordinate systems

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 the BIDS Coordinate Systems Appendix 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, iEEGCoordinateSystem MUST be defined as "Pixels", and iEEGCoordinateUnits MUST be defined as "pixels" (note the difference in capitalization). Furthermore, the 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 (for example, 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 *_coordsystem.json

{
    "IntendedFor": "bids::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.<extension>)

Template:

sub-<label>/
    [ses-<label>/]
        ieeg/
            sub-<label>[_ses-<label>][_acq-<label>]_photo.jpg
            sub-<label>[_ses-<label>][_acq-<label>]_photo.png
            sub-<label>[_ses-<label>][_acq-<label>]_photo.tif

Legend:

• For more information about filename elements (for example, entities, suffixes, extensions), follow the links embedded in the filename template.

• Filename entities or directories between square brackets (for example, [_ses-<label>]) are OPTIONAL.

• Some entities may only allow specific values, in which case those values are listed in <>, separated by |.

• _<suffix> means that there are several (>6) valid suffixes for this filename pattern.

• .<extension> means that there are several (>6) valid extensions for this file type.

• [.gz] means that both the unzipped and gzipped versions of the extension are valid.

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 acq-<label> entity should be specified with:

• *_photo.<extension> in case of an operative photo

• *_acq-xray#_photo.<extension> in case of an x-ray picture

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

• *_acq-render#_photo.<extension> in case of a rendering

The ses-<label> entity may be used to specify when the photo was taken.

Example *_photo.<extension>

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-01/
   └─ ses-0001/
      ├─ sub-0001_ses-01_acq-photo1_photo.jpg 
      ├─ sub-0001_ses-01_acq-photo2_photo.jpg 
      └─ ... 

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 (for example, see Burneo JG et al. 2014. doi:10.1016/j.clineuro.2014.03.020).

    sub-0002_ses-01_acq-render_photo.jpg

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 directory in the /stimuli/ directory. For example: /stimuli/electrical_stimulation_functions/biphasic.tsv

Example *_events.tsv

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