Magnetoencephalography (MEG)
Support for MEG 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:
Niso Galan, J.G., Gorgolewski, K.J., Bock, E., Brooks, T.L., Flandin, G., Gramfort, A., Henson, R.N., Jas, M., Litvak, V., Moreau, J., Oostenveld, R., Schoffelen, J.-M., Tadel, F., Wexler, J., Baillet, S., 2018. MEG-BIDS, the brain imaging data structure extended to magnetoencephalography. Scientific Data volume 5, Article number: 180110 (2018)
MEG recording data
Template:
sub-<label>/
[ses-<label>]/
meg/
sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_run-<index>][_proc-<label>]_meg.<manufacturer_specific_extension>
[sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_run-<index>][_proc-<label>]_meg.json]
Unprocessed MEG data MUST be stored in the native file format of the MEG instrument with which the data was collected. With MEG-BIDS, we wish to promote the adoption of good practices in the management of scientific data. Hence, the emphasis of MEG-BIDS is not to impose a new, generic data format for the modality, but rather to standardize the way data is stored in repositories. Further, there is currently no widely accepted standard file format for MEG, but major software applications, including free and open-source solutions for MEG data analysis provide readers of such raw files.
Some software reader may skip important metadata that is specific to MEG system manufacturers. It is therefore RECOMMENDED that users provide additional meta information extracted from the manufacturer raw data files in a sidecar JSON file. This allows for easy searching and indexing of key metadata elements without the need to parse files in proprietary data format. Other relevant files MAY be included alongside the MEG data; examples are provided below.
This template is for MEG data of any kind, including but not limited to
task-based, resting-state, and noise recordings. If multiple Tasks were
performed within a single Run, the task description can be set to
task-multitask
. The _meg.json SHOULD contain details on the Tasks. Some
manufacturers data storage conventions use folders which contain data files of
various nature: e.g., CTF’s .ds format, or 4D/BTi. Please refer to
Appendix VI for examples from a
selection of MEG manufacturers.
The proc
label is analogous to rec
for MR and denotes a variant of a file
that was a result of particular processing performed on the device. This is
useful for files produced in particular by Elekta’s MaxFilter (e.g. sss, tsss,
trans, quat, mc, etc.), which some installations impose to be run on raw data
because of active shielding software corrections before the MEG data can
actually be exploited.
Sidecar JSON document (*_meg.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 MEG system (CTF , Elekta/Neuromag , 4D/BTi , KIT/Yokogawa , ITAB , KRISS , Other ). See Appendix VII with preferred names |
ManufacturersModelName | RECOMMENDED. Manufacturer’s designation of the MEG scanner model (e.g. CTF-275 ). See Appendix VII with preferred names |
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 behavioural 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 MEG fields MUST be present:
Field name | Definition |
---|---|
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 MEG instrument (i.e. 50 or 60) |
DewarPosition | REQUIRED. Position of the dewar during the MEG scan: upright , supine or degrees of angle from vertical: for example on CTF systems, upright=15°, supine = 90°. |
SoftwareFilters | REQUIRED. List of temporal and/or spatial software filters applied, or ideally key:value pairs of pre-applied software filters and their parameter values: e.g., {"SSS": {"frame": "head", "badlimit": 7}}, {"SpatialCompensation": {"GradientOrder": Order of the gradient compensation}}. Write n/a if no software filters applied. |
DigitizedLandmarks | REQUIRED. Boolean ("true" or "false") value indicating whether anatomical landmark points (i.e. fiducials) are contained within this recording. |
DigitizedHeadPoints | REQUIRED. Boolean (true or false ) value indicating whether head points outlining the scalp/face surface are contained within this recording. |
SHOULD be present
Field name | Definition |
---|---|
MEGChannelCount | RECOMMENDED. Number of MEG channels (e.g. 275) |
MEGREFChannelCount | RECOMMENDED. Number of MEG reference channels (e.g. 23). For systems without such channels (e.g. Neuromag Vectorview), MEGREFChannelCount =0 |
EEGChannelCount | RECOMMENDED. Number of EEG channels recorded simultaneously (e.g. 21) |
ECOGChannelCount | RECOMMENDED. Number of ECoG channels |
SEEGChannelCount | RECOMMENDED. Number of SEEG channels |
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 |
ContinuousHeadLocalization | RECOMMENDED. Boolean (true or false ) value indicating whether continuous head localisation was performed. |
HeadCoilFrequency | RECOMMENDED. List of frequencies (in Hz) used by the head localisation coils (‘HLC’ in CTF systems, ‘HPI’ in Elekta, ‘COH’ in 4D/BTi) that track the subject’s head position in the MEG helmet (e.g. [293, 307, 314, 321] ) |
MaxMovement | RECOMMENDED. Maximum head movement (in mm) detected during the recording, as measured by the head localisation coils (e.g., 4.8) |
SubjectArtefactDescription | RECOMMENDED. Freeform description of the observed subject artefact 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. |
AssociatedEmptyRoom | RECOMMENDED. Relative path in BIDS folder structure to empty-room file associated with the subject’s MEG recording. The path needs to use forward slashes instead of backward slashes (e.g. sub-emptyroom/ses-/meg/sub-emptyroom_ses-_task-noise_run-_meg.ds ). |
Specific EEG fields (if recorded with MEG) SHOULD be present:
Field name | Definition |
---|---|
EEGPlacementScheme | OPTIONAL. Placement scheme of EEG electrodes. Either the name of a standardised placement system (e.g., "10-20") or a list of standardised electrode names (e.g. ["Cz", "Pz"] ). |
ManufacturersAmplifierModelName | OPTIONAL. Manufacturer’s designation of the EEG amplifier model (e.g., Biosemi-ActiveTwo ). |
CapManufacturer | OPTIONAL. Manufacturer of the EEG cap (e.g. EasyCap ) |
CapManufacturersModelName | OPTIONAL. Manufacturer’s designation of the EEG cap model (e.g., M10 ) |
EEGReference | OPTIONAL. Description of the type of EEG reference used (e.g., M1 for left mastoid, average , or longitudinal bipolar ). |
By construct, EEG when recorded simultaneously with the same MEG system , should
have the same SamplingFrequency
as MEG. Note that if EEG is recorded with a
separate amplifier, it should be stored separately under a new /eeg data type
(see
BEP006).
Example:
{
"InstitutionName": "Stanford University",
"InstitutionAddress": "450 Serra Mall, Stanford, CA 94305-2004, USA",
"Manufacturer": "CTF",
"ManufacturersModelName": "CTF-275",
"DeviceSerialNumber": "11035",
"SoftwareVersions": "Acq 5.4.2-linux-20070507",
"PowerLineFrequency": 60,
"SamplingFrequency": 2400,
"MEGChannelCount": 270,
"MEGREFChannelCount": 26,
"EEGChannelCount": 0,
"EOGChannelCount": 2,
"ECGChannelCount": 1,
"EMGChannelCount": 0,
"DewarPosition": "upright",
"SoftwareFilters": {
"SpatialCompensation": {"GradientOrder": "3rd"}
},
"RecordingDuration": 600,
"RecordingType": "continuous",
"EpochLength": 0,
"TaskName": "rest",
"ContinuousHeadLocalization": true,
"HeadCoilFrequency": [1470,1530,1590],
"DigitizedLandmarks": true,
"DigitizedHeadPoints": true
}
Note that the date and time information SHOULD be stored in the Study key file
(scans.tsv
), see 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 table (*_channels.tsv
)
Template:
sub-<label>/
[ses-<label>]/
meg/
[sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_run-<index>][_proc-<label>]_channels.tsv]
This file is RECOMMENDED as it provides easily searchable information across
MEG-BIDS datasets for e.g., general curation, response to queries or batch
analysis. To avoid confusion, the channels SHOULD be listed in the order they
appear in the MEG data file. Missing values MUST be indicated with n/a
.
The columns of the Channels description table stored in *_channels.tsv
are:
MUST be present:
Field name | Definition |
---|---|
name | REQUIRED. Channel name (e.g., MRT012, MEG023) |
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 (see Appendix V: Units for allowed symbols). |
SHOULD be present:
Field name | Definition |
---|---|
description | OPTIONAL. Brief free-text description of the channel, or other information of interest. See examples below. |
sampling_frequency | OPTIONAL. Sampling rate of the channel in Hz. |
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 MEG/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 . |
software_filters | OPTIONAL. List of temporal and/or spatial software filters applied (e.g. "SSS", "SpatialCompensation" ). Note that parameters should be defined in the general MEG sidecar .json file. Indicate n/a in the absence of software filters applied. |
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:
name type units description sampling_frequency low_cutoff high_cutoff notch software_filters status
UDIO001 TRIG V analogue trigger 1200 0.1 300 0 n/a good
MLC11 MEGGRADAXIAL T sensor 1st-order grad 1200 0 n/a 50 SSS bad
Restricted keyword list for field type
Keyword | Definition |
---|---|
MEGMAG | MEG magnetometer |
MEGGRADAXIAL | MEG axial gradiometer |
MEGGRADPLANAR | MEG planargradiometer |
MEGREFMAG | MEG reference magnetometer |
MEGREFGRADAXIAL | MEG reference axial gradiometer |
MEGREFGRADPLANAR | MEG reference planar gradiometer |
MEGOTHER | Any other type of MEG sensor |
EEG | Electrode channel |
ECOG | Electrode channel |
SEEG | Electrode channel |
DBS | Electrode channel |
VEOG | Vertical EOG (electrooculogram) |
HEOG | Horizontal EOG |
EOG | Generic EOG channel |
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 |
HLU | Measured position of head and head coils |
FITERR | Fit error signal from each head localization coil |
OTHER | Any other type of channel |
Example of free text for field description
- stimulus, response, vertical EOG, horizontal EOG, skin conductance, sats, intracranial, eyetracker
Example:
name type units description
VEOG VEOG V vertical EOG
FDI EMG V left first dorsal interosseous
UDIO001 TRIG V analog trigger signal
UADC001 AUDIO V envelope of audio signal presented to participant
Coordinate System JSON document (*_coordsystem.json
)
Template:
sub-<label>/
[ses-<label>]/
meg/
[sub-<label>[_ses-<label>][_acq-<label>]_coordsystem.json]
OPTIONAL. A JSON document specifying the coordinate system(s) used for the MEG, EEG, head localization coils, and anatomical landmarks.
MEG and EEG sensors:
Field name | Description |
---|---|
MEGCoordinateSystem | REQUIRED. Defines the coordinate system for the MEG sensors. See Appendix VIII: preferred names of Coordinate systems. If Other , provide definition of the coordinate system in [MEGCoordinateSystemDescription] . |
MEGCoordinateUnits | REQUIRED. Units of the coordinates of MEGCoordinateSystem . MUST be m , cm , or mm . |
MEGCoordinateSystemDescription | OPTIONAL. Freeform text description or link to document describing the MEG coordinate system system in detail. |
EEGCoordinateSystem | OPTIONAL. Describes how the coordinates of the EEG sensors are to be interpreted. |
EEGCoordinateUnits | OPTIONAL. Units of the coordinates of EEGCoordinateSystem . MUST be m , cm , or mm . |
EEGCoordinateSystemDescription | OPTIONAL. Freeform text description or link to document describing the EEG coordinate system system in detail. |
Head localization coils:
Field name | Description |
---|---|
HeadCoilCoordinates | OPTIONAL. Key:value pairs describing head localization coil labels and their coordinates, interpreted following the HeadCoilCoordinateSystem , e.g., {NAS : [12.7,21.3,13.9] , LPA : [5.2,11.3,9.6] , RPA : [20.2,11.3,9.1] }. Note that coils are not always placed at locations that have a known anatomical name (e.g. for Elekta, Yokogawa systems); in that case generic labels can be used (e.g. {coil1 : [12.2,21.3,12.3] , coil2 : [6.7,12.3,8.6] , coil3 : [21.9,11.0,8.1] } ). |
HeadCoilCoordinateSystem | OPTIONAL. Defines the coordinate system for the coils. See Appendix VIII: preferred names of Coordinate systems. If "Other", provide definition of the coordinate system in HeadCoilCoordinateSystemDescription . |
HeadCoilCoordinateUnits | OPTIONAL. Units of the coordinates of HeadCoilCoordinateSystem . MUST be m , cm , or mm . |
HeadCoilCoordinateSystemDescription | OPTIONAL. Freeform text description or link to document describing the Head Coil coordinate system system in detail. |
Digitized head points:
Field name | Description |
---|---|
DigitizedHeadPoints | OPTIONAL. Relative path to the file containing the locations of digitized head points collected during the session (e.g., sub-01_headshape.pos ). RECOMMENDED for all MEG systems, especially for CTF and 4D/BTi. For Elekta/Neuromag the head points will be stored in the fif file. |
DigitizedHeadPointsCoordinateSystem | OPTIONAL. Defines the coordinate system for the digitized head points. See Appendix VIII: preferred names of Coordinate systems. If Other , provide definition of the coordinate system in DigitizedHeadPointsCoordinateSystemDescription . |
DigitizedHeadPointsCoordinateUnits | OPTIONAL. Units of the coordinates of DigitizedHeadPointsCoordinateSystem . MUST be m , cm , or mm . |
DigitizedHeadPointsCoordinateSystemDescription | OPTIONAL. Freeform text description or link to document describing the Digitized head Points coordinate system system in detail. |
Anatomical MRI:
Field name | Description |
---|---|
IntendedFor | OPTIONAL. Path or list of path relative to the subject subfolder pointing to the structural MRI, possibly of different types if a list is specified, to be used with the MEG recording. The path(s) need(s) to use forward slashes instead of backward slashes (e.g. ses-/anat/sub-01_T1w.nii.gz ). |
Anatomical landmarks:
Field name | Description |
---|---|
AnatomicalLandmarkCoordinates | OPTIONAL. Key:value pairs of the labels and 3-D digitized locations 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 | OPTIONAL. Defines the coordinate system for the anatomical landmarks. See Appendix VIII: preferred names of Coordinate systems. If Other , provide definition of the coordinate system in AnatomicalLandmarkCoordinateSystemDescription . |
AnatomicalLandmarkCoordinateUnits | OPTIONAL. Units of the coordinates of AnatomicalLandmarkCoordinateSystem . MUST be m , cm , or mm . |
AnatomicalLandmarkCoordinateSystemDescription | OPTIONAL. Freeform text description or link to document describing the Head Coil coordinate system system in detail. |
It is also RECOMMENDED that the MRI voxel coordinates of the actual anatomical
landmarks for co-registration of MEG with structural MRI are stored in the
AnatomicalLandmarkCoordinates
field in the JSON sidecar of the corresponding
T1w MRI anatomical data of the subject seen in the MEG session (see
here ) - for
example: sub-01/ses-mri/anat/sub-01_ses-mri_acq-mprage_T1w.json
In principle, these locations are those of absolute anatomical markers. However,
the marking of NAS, LPA and RPA is more ambiguous than that of e.g., AC and PC.
This may result in some variability in their 3-D digitization from session to
session, even for the same participant. The solution would be to use only one
T1w file and populate the AnatomicalLandmarkCoordinates
field with
session-specific labels e.g., "NAS-session1": [127,213,139]
,"NAS-session2":
[123,220,142]
, etc.
Fiducials information:
Field name | Description |
---|---|
FiducialsDescription | OPTIONAL. A freeform text field documenting the anatomical landmarks that were used and how the head localization coils were placed relative to these. This field can describe, for instance, whether the true anatomical locations of the left and right pre-auricular points were used and digitized, or rather whether they were defined as the intersection between the tragus and the helix (the entry of the ear canal), or any other anatomical description of selected points in the vicinity of the ears. |
For more information on the definition of anatomical landmarks, please visit: http://www.fieldtriptoolbox.org/faq/how_are_the_lpa_and_rpa_points_define
For more information on typical coordinate systems for MEG-MRI coregistration: http://www.fieldtriptoolbox.org/faq/how_are_the_different_head_and_mri_coordinate_systems_defined, or: http://neuroimage.usc.edu/brainstorm/CoordinateSystems
Landmark photos (*_photo.jpg
)
Photos of the anatomical landmarks and/or head localization coils
(*_photo.jpg
)
Template:
sub-<label>/
[ses-<label>]/
meg/
[sub-<label>[_ses-<label>][_acq-<label>]_photo.jpg]
Photos of the anatomical landmarks and/or head localization coils on the subject’s head are RECOMMENDED. If the coils are not placed at the location of actual anatomical landmarks, these latter may be marked with a piece of felt-tip taped to the skin. 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 form signed by the participant.
Example of the NAS fiducial placed between the eyebrows, rather than at the
actual anatomical nasion: sub-0001_ses-001_acq-NAS_photo.jpg
3-D head point /electrode locations file
Template:
sub-<label>/
[ses-<label>]/
meg/
[sub-<label>[_ses-<label>][_acq-<label>]_headshape.<manufacturer_specific_extension>]
This file is RECOMMENDED.
The 3-D locations of head points and/or EEG electrode locations can be digitized
and stored in separate files. The *_acq-<label>
can be used when more than one
type of digitization in done for a session, for example when the head points are
in a separate file from the EEG locations. These files are stored in the
specific format of the 3-D digitizer’s manufacturer (see
Appendix VI).
Example:
sub-control01
ses-01
sub-control01_ses-01_acq-HEAD_headshape.pos
sub-control01_ses-01_acq-ECG_headshape.pos
Note that the *_headshape
file(s) is shared by all the runs and tasks in a
session. If the subject needs to be taken out of the scanner and the head-shape
has to be updated, then for MEG it could be considered to be a new session.
Empty-room files (sub-emptyroom
)
Empty-room MEG files capture the environment and system noise. Their collection
is RECOMMENDED, before/during/after each session. This data is stored inside a
subject folder named sub-emptyroom
. The session label
SHOULD be that of the
date of the empty-room recording (e.g. ses-YYYYMMDD
). The scans.tsv
file
containing the date/time of the acquisition SHOULD also be included. Hence,
users will be able to retrieve the empty-room recording that best matches a
particular session with a participant, based on date/time of recording.
Example:
sub-control01/
sub-control02/
sub-emptyroom/
ses-20170801/
sub-emptyroom_ses-20170801_scans.tsv
meg/
sub-emptyroom_ses-20170801_task-noise_meg.ds
sub-emptyroom_ses-20170801_task-noise_meg.json
TaskName
in the *_meg.json
file should be set to "noise".