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Glossary of schema objects

This section compiles the object definitions in the schema.

ACCELChannelCount (metadata)

Name: Accelerometer channel count

Type: Metadata

Description: Number of accelerometer channels.

Schema information:

minimum: 0
type: integer

Acknowledgements (metadata)

Name: Acknowledgements

Type: Metadata

Description: Text acknowledging contributions of individuals or institutions beyond those listed in Authors or Funding.

Schema information:

type: string

AcquisitionDuration (metadata)

Name: Acquisition Duration

Type: Metadata

Description: Duration (in seconds) of volume acquisition. Corresponds to DICOM Tag 0018, 9073 Acquisition Duration. This field is mutually exclusive with "RepetitionTime".

Schema information:

exclusiveMinimum: 0
type: number
unit: s

AcquisitionMode (metadata)

Name: Acquisition Mode

Type: Metadata

Description: Type of acquisition of the PET data (for example, "list mode").

Schema information:

type: string

AcquisitionVoxelSize (metadata)

Name: Acquisition Voxel Size

Type: Metadata

Description: An array of numbers with a length of 3, in millimeters. This parameter denotes the original acquisition voxel size, excluding any inter-slice gaps and before any interpolation or resampling within reconstruction or image processing. Any point spread function effects, for example due to T2-blurring, that would decrease the effective resolution are not considered here.

Schema information:

items:
  exclusiveMinimum: 0
  type: number
  unit: mm
maxItems: 3
minItems: 3
type: array

Anaesthesia (metadata)

Name: Anaesthesia

Type: Metadata

Description: Details of anaesthesia used, if any.

Schema information:

type: string

AnalyticalApproach (metadata)

Name: Analytical Approach

Type: Metadata

Description: Methodology or methodologies used to analyse the "GeneticLevel". Values MUST be taken from the database of Genotypes and Phenotypes (dbGaP) under /Study/Molecular Data Type (for example, SNP Genotypes (Array) or Methylation (CpG).

Schema information:

anyOf:
- type: string
- items:
    type: string
  type: array

AnatomicalLandmarkCoordinateSystem (metadata)

Name: Anatomical Landmark Coordinate System

Type: Metadata

Allowed values: CTF, ElektaNeuromag, 4DBti, KitYokogawa, ChietiItab, Other, CapTrak, EEGLAB, EEGLAB-HJ, Other, ICBM452AirSpace, ICBM452Warp5Space, IXI549Space, fsaverage, fsaverageSym, fsLR, MNIColin27, MNI152Lin, MNI152NLin2009aSym, MNI152NLin2009bSym, MNI152NLin2009cSym, MNI152NLin2009aAsym, MNI152NLin2009bAsym, MNI152NLin2009cAsym, MNI152NLin6Sym, MNI152NLin6ASym, MNI305, NIHPD, OASIS30AntsOASISAnts, OASIS30Atropos, Talairach, UNCInfant, fsaverage3, fsaverage4, fsaverage5, fsaverage6, fsaveragesym, UNCInfant0V21, UNCInfant1V21, UNCInfant2V21, UNCInfant0V22, UNCInfant1V22, UNCInfant2V22, UNCInfant0V23, UNCInfant1V23, UNCInfant2V23

Description: Defines the coordinate system for the anatomical landmarks. See the Coordinate Systems Appendix for a list of restricted keywords for coordinate systems. If "Other", provide definition of the coordinate system in "AnatomicalLandmarkCoordinateSystemDescription".

Schema information:

type: string

AnatomicalLandmarkCoordinateSystemDescription (metadata)

Name: Anatomical Landmark Coordinate System Description

Type: Metadata

Description: 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.

Schema information:

type: string

AnatomicalLandmarkCoordinateUnits (metadata)

Name: Anatomical Landmark Coordinate Units

Type: Metadata

Allowed values: m, mm, cm, n/a

Description: Units of the coordinates of "AnatomicalLandmarkCoordinateSystem".

Schema information:

type: string

AnatomicalLandmarkCoordinates sense 1 (metadata)

Name: Anatomical Landmark Coordinates

Type: Metadata

Description: Key-value pairs of the labels and 3-D digitized locations of anatomical landmarks, interpreted following the "AnatomicalLandmarkCoordinateSystem" (for example, {"NAS": [12.7,21.3,13.9], "LPA": [5.2,11.3,9.6], "RPA": [20.2,11.3,9.1]}. Each array MUST contain three numeric values corresponding to x, y, and z axis of the coordinate system in that exact order.

Schema information:

additionalProperties:
  items:
    type: number
  maxItems: 3
  minItems: 3
  type: array
type: object

AnatomicalLandmarkCoordinates sense 2 (metadata)

Name: Anatomical Landmark Coordinates

Type: Metadata

Description: Key-value pairs of any number of additional anatomical landmarks and their coordinates in voxel units (where first voxel has index 0,0,0) relative to the associated anatomical MRI (for example, {"AC": [127,119,149], "PC": [128,93,141], "IH": [131,114,206]}, or {"NAS": [127,213,139], "LPA": [52,113,96], "RPA": [202,113,91]}). Each array MUST contain three numeric values corresponding to x, y, and z axis of the coordinate system in that exact order.

Schema information:

additionalProperties:
  items:
    type: number
  maxItems: 3
  minItems: 3
  type: array
type: object

Any (extensions)

Name: Any Extension

Type: Extension

Format: <entities>_<suffix>.*

Description: Any extension is allowed.

ArterialSpinLabelingType (metadata)

Name: Arterial Spin Labeling Type

Type: Metadata

Allowed values: CASL, PCASL, PASL

Description: The arterial spin labeling type.

Schema information:

type: string

AssociatedEmptyRoom (metadata)

Name: Associated Empty Room

Type: Metadata

Description: One or more BIDS URIs pointing to empty-room file(s) associated with the subject's MEG recording. Using forward-slash separated paths relative to the dataset root is DEPRECATED.

Schema information:

anyOf:
- items:
    anyOf:
    - format: dataset_relative
      type: string
    - format: bids_uri
      type: string
  type: array
- format: dataset_relative
  type: string
- format: bids_uri
  type: string

Atlas (metadata)

Name: Atlas

Type: Metadata

Description: Which atlas (if any) was used to generate the mask.

Schema information:

type: string

AttenuationCorrection (metadata)

Name: Attenuation Correction

Type: Metadata

Description: Short description of the attenuation correction method used.

Schema information:

type: string

AttenuationCorrectionMethodReference (metadata)

Name: Attenuation Correction Method Reference

Type: Metadata

Description: Reference paper for the attenuation correction method used.

Schema information:

type: string

Authors (metadata)

Name: Authors

Type: Metadata

Description: List of individuals who contributed to the creation/curation of the dataset.

Schema information:

items:
  type: string
type: array

B0FieldIdentifier (metadata)

Name: B0 Field Identifier

Type: Metadata

Description: The presence of this key states that this particular 3D or 4D image MAY be used for fieldmap estimation purposes. Each "B0FieldIdentifier" MUST be a unique string within one participant's tree, shared only by the images meant to be used as inputs for the estimation of a particular instance of the B0 field estimation. It is RECOMMENDED to derive this identifier from DICOM Tags, for example, DICOM tag 0018, 1030 Protocol Name, or DICOM tag 0018, 0024 Sequence Name when the former is not defined (for example, in GE devices.)

Schema information:

anyOf:
- type: string
- items:
    type: string
  type: array

B0FieldSource (metadata)

Name: B0 Field Source

Type: Metadata

Description: At least one existing "B0FieldIdentifier" defined by images in the participant's tree. This field states the B0 field estimation designated by the "B0FieldIdentifier" that may be used to correct the dataset for distortions caused by B0 inhomogeneities. "B0FieldSource" and "B0FieldIdentifier" MAY both be present for images that are used to estimate their own B0 field, for example, in "pepolar" acquisitions.

Schema information:

anyOf:
- type: string
- items:
    type: string
  type: array

BF (suffixes)

Name: Bright-field microscopy

Type: Suffix

Format: <entities>_BF.<extension>

Description: Bright-field microscopy imaging data

BIDSVersion (metadata)

Name: BIDS Version

Type: Metadata

Description: The version of the BIDS standard that was used.

Schema information:

type: string

BackgroundSuppression (metadata)

Name: Background Suppression

Type: Metadata

Description: Boolean indicating if background suppression is used.

Schema information:

type: boolean

BackgroundSuppressionNumberPulses (metadata)

Name: Background Suppression Number Pulses

Type: Metadata

Description: The number of background suppression pulses used. Note that this excludes any effect of background suppression pulses applied before the labeling.

Schema information:

minimum: 0
type: number

BackgroundSuppressionPulseTime (metadata)

Name: Background Suppression Pulse Time

Type: Metadata

Description: Array of numbers containing timing, in seconds, of the background suppression pulses with respect to the start of the labeling. In case of multi-PLD with different background suppression pulse times, only the pulse time of the first PLD should be defined.

Schema information:

items:
  minimum: 0
  type: number
  unit: s
type: array

BasedOn (metadata)

Name: Based On

Type: Metadata

Description: List of files in a file collection to generate the map. Fieldmaps are also listed, if involved in the processing. This field is DEPRECATED, and this metadata SHOULD be recorded in the Sources field using BIDS URIs to distinguish sources from different datasets.

Schema information:

anyOf:
- format: participant_relative
  type: string
- items:
    format: participant_relative
    type: string
  type: array

BloodDensity (metadata)

Name: Blood Density

Type: Metadata

Description: Measured blood density. Unit of blood density should be in "g/mL".

Schema information:

type: number
unit: g/mL

BodyPart (metadata)

Name: Body Part

Type: Metadata

Description: Body part of the organ / body region scanned.

Schema information:

type: string

BodyPartDetails (metadata)

Name: Body Part Details

Type: Metadata

Description: Additional details about body part or location (for example: "corpus callosum").

Schema information:

type: string

BodyPartDetailsOntology (metadata)

Name: Body Part Details Ontology

Type: Metadata

Description: URI of ontology used for BodyPartDetails (for example: "https://www.ebi.ac.uk/ols/ontologies/uberon").

Schema information:

format: uri
type: string

BolusCutOffDelayTime (metadata)

Name: Bolus Cut Off Delay Time

Type: Metadata

Description: Duration between the end of the labeling and the start of the bolus cut-off saturation pulse(s), in seconds. This can be a number or array of numbers, of which the values must be non-negative and monotonically increasing, depending on the number of bolus cut-off saturation pulses. For Q2TIPS, only the values for the first and last bolus cut-off saturation pulses are provided. Based on DICOM Tag 0018, 925F ASL Bolus Cut-off Delay Time.

Schema information:

anyOf:
- minimum: 0
  type: number
  unit: s
- items:
    minimum: 0
    type: number
    unit: s
  type: array

BolusCutOffFlag (metadata)

Name: Bolus Cut Off Flag

Type: Metadata

Description: Boolean indicating if a bolus cut-off technique is used. Corresponds to DICOM Tag 0018, 925C ASL Bolus Cut-off Flag.

Schema information:

type: boolean

BolusCutOffTechnique (metadata)

Name: Bolus Cut Off Technique

Type: Metadata

Description: Name of the technique used, for example "Q2TIPS", "QUIPSS", "QUIPSSII". Corresponds to DICOM Tag 0018, 925E ASL Bolus Cut-off Technique.

Schema information:

type: string

BrainLocation (metadata)

Name: Brain Location

Type: Metadata

Description: Refers to the location in space of the "TissueOrigin". Values may be an MNI coordinate, a label taken from the Allen Brain Atlas, or layer to refer to layer-specific gene expression, which can also tie up with laminar fMRI.

Schema information:

type: string

CARS (suffixes)

Name: Coherent anti-Stokes Raman spectroscopy

Type: Suffix

Format: <entities>_CARS.<extension>

Description: Coherent anti-Stokes Raman spectroscopy imaging data

CASLType (metadata)

Name: CASL Type

Type: Metadata

Allowed values: single-coil, double-coil

Description: Describes if a separate coil is used for labeling.

Schema information:

type: string

CHANGES (files)

Name: Changelog

Type: Files And Directories

Description: Version history of the dataset (describing changes, updates and corrections) MAY be provided in the form of a CHANGES text file. This file MUST follow the CPAN Changelog convention. The CHANGES file MUST be either in ASCII or UTF-8 encoding.

Schema information:

file_type: regular

CONF (suffixes)

Name: Confocal microscopy

Type: Suffix

Format: <entities>_CONF.<extension>

Description: Confocal microscopy imaging data

CTF (extensions)

Name: CTF MEG Dataset Directory

Type: Extension

Format: <entities>_<suffix>.ds/

Description: A directory for MEG data, typically containing a .meg4 file for the data and a .res4 file for the resources.

CapManufacturer (metadata)

Name: Cap Manufacturer

Type: Metadata

Description: Name of the cap manufacturer (for example, "EasyCap").

Schema information:

type: string

CapManufacturersModelName (metadata)

Name: Cap Manufacturers Model Name

Type: Metadata

Description: Manufacturer's designation of the cap model (for example, "actiCAP 64 Ch Standard-2").

Schema information:

type: string

CellType (metadata)

Name: Cell Type

Type: Metadata

Description: Describes the type of cell analyzed. Values SHOULD come from the cell ontology.

Schema information:

type: string

Chimap (suffixes)

Name: Quantitative susceptibility map (QSM)

Type: Suffix

Format: <entities>_Chimap.<extension>

Description: In parts per million (ppm). QSM allows for determining the underlying magnetic susceptibility of tissue (Chi) (Wang & Liu, 2014). Chi maps are REQUIRED to use this suffix regardless of the method used to generate them.

Schema information:

unit: ppm

ChunkTransformationMatrix (metadata)

Name: Chunk Transformation Matrix

Type: Metadata

Description: 3x3 or 4x4 affine transformation matrix describing spatial chunk transformation, for 2D and 3D respectively (for examples: [[2, 0, 0], [0, 3, 0], [0, 0, 1]] in 2D for 2x and 3x scaling along the first and second axis respectively; or [[1, 0, 0, 0], [0, 2, 0, 0], [0, 0, 3, 0], [0, 0, 0, 1]] in 3D for 2x and 3x scaling along the second and third axis respectively). Note that non-spatial dimensions like time and channel are not included in the transformation matrix.

Schema information:

anyOf:
- items:
    items:
      type: number
    maxItems: 3
    minItems: 3
    type: array
  maxItems: 3
  minItems: 3
  type: array
- items:
    items:
      type: number
    maxItems: 4
    minItems: 4
    type: array
  maxItems: 4
  minItems: 4
  type: array

ChunkTransformationMatrixAxis (metadata)

Name: Chunk Transformation Matrix Axis

Type: Metadata

Description: Describe the axis of the ChunkTransformationMatrix (for examples: ["X", "Y"] or ["Z", "Y", "X"]).

Schema information:

items:
  type: string
maxItems: 3
minItems: 2
type: array

Code (metadata)

Name: Code

Type: Metadata

Description: URI of the code used to present the stimuli. Persistent identifiers such as DOIs are preferred. If multiple versions of code may be hosted at the same location, revision-specific URIs are recommended.

Schema information:

format: uri
type: string

CogAtlasID (metadata)

Name: Cognitive Atlas ID

Type: Metadata

Description: URI of the corresponding Cognitive Atlas Task term.

Schema information:

format: uri
type: string

CogPOID (metadata)

Name: Cognitive Paradigm Ontology ID

Type: Metadata

Description: URI of the corresponding CogPO term.

Schema information:

format: uri
type: string

CoilCombinationMethod (metadata)

Name: Coil Combination Method

Type: Metadata

Description: Almost all fMRI studies using phased-array coils use root-sum-of-squares (rSOS) combination, but other methods exist. The image reconstruction is changed by the coil combination method (as for the matrix coil mode above), so anything non-standard should be reported.

Schema information:

type: string

Columns (metadata)

Name: Columns

Type: Metadata

Description: Names of columns in file.

Schema information:

items:
  type: string
type: array

ContinuousHeadLocalization (metadata)

Name: Continuous Head Localization

Type: Metadata

Description: true or false value indicating whether continuous head localisation was performed.

Schema information:

type: boolean

ContrastBolusIngredient (metadata)

Name: Contrast Bolus Ingredient

Type: Metadata

Allowed values: IODINE, GADOLINIUM, CARBON DIOXIDE, BARIUM, XENON

Description: Active ingredient of agent. Corresponds to DICOM Tag 0018, 1048 Contrast/Bolus Ingredient.

Schema information:

type: string

DCOffsetCorrection (metadata)

Name: DC Offset Correction

Type: Metadata

Description: 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".

Schema information:

type: string

DF (suffixes)

Name: Dark-field microscopy

Type: Suffix

Format: <entities>_DF.<extension>

Description: Dark-field microscopy imaging data

DIC (suffixes)

Name: Differential interference contrast microscopy

Type: Suffix

Format: <entities>_DIC.<extension>

Description: Differential interference contrast microscopy imaging data

DatasetDOI (metadata)

Name: DatasetDOI

Type: Metadata

Description: The Digital Object Identifier of the dataset (not the corresponding paper). DOIs SHOULD be expressed as a valid URI; bare DOIs such as 10.0.2.3/dfjj.10 are DEPRECATED.

Schema information:

format: uri
type: string

Name: Dataset Links

Type: Metadata

Description: Used to map a given <dataset-name> from a BIDS URI of the form bids:<dataset-name>:path/within/dataset to a local or remote location. The <dataset-name>: "" (an empty string) is a reserved keyword that MUST NOT be a key in DatasetLinks (example: bids::path/within/dataset).

Schema information:

additionalProperties:
  format: uri
  type: string
type: object

DatasetType (metadata)

Name: Dataset Type

Type: Metadata

Allowed values: raw, derivative

Description: The interpretation of the dataset. For backwards compatibility, the default value is "raw".

Schema information:

type: string

DecayCorrectionFactor (metadata)

Name: Decay Correction Factor

Type: Metadata

Description: Decay correction factor for each frame.

Schema information:

items:
  type: number
type: array

DelayAfterTrigger (metadata)

Name: Delay After Trigger

Type: Metadata

Description: Duration (in seconds) from trigger delivery to scan onset. This delay is commonly caused by adjustments and loading times. This specification is entirely independent of "NumberOfVolumesDiscardedByScanner" or "NumberOfVolumesDiscardedByUser", as the delay precedes the acquisition.

Schema information:

type: number
unit: s

DelayTime (metadata)

Name: Delay Time

Type: Metadata

Description: User specified time (in seconds) to delay the acquisition of data for the following volume. If the field is not present it is assumed to be set to zero. Corresponds to Siemens CSA header field lDelayTimeInTR. This field is REQUIRED for sparse sequences using the "RepetitionTime" field that do not have the "SliceTiming" field set to allowed for accurate calculation of "acquisition time". This field is mutually exclusive with "VolumeTiming".

Schema information:

type: number
unit: s

Density (metadata)

Name: Density

Type: Metadata

Description: Specifies the interpretation of the density keyword. If an object is used, then the keys should be values for the den entity and values should be descriptions of those den values.

Schema information:

anyOf:
- type: string
- additionalProperties:
    type: string
  type: object

Derivative (metadata)

Name: Derivative

Type: Metadata

Description: Indicates that values in the corresponding column are transformations of values from other columns (for example a summary score based on a subset of items in a questionnaire).

Schema information:

type: boolean

Description (metadata)

Name: Description

Type: Metadata

Description: Free-form natural language description.

Schema information:

type: string

DetectorType (metadata)

Name: Detector Type

Type: Metadata

Description: Type of detector. This is a free form description with the following suggested terms: "SiPD", "APD". Preferably a specific model/part number is supplied. If individual channels have different DetectorType, then the field here should be specified as "mixed" and this column should be included in optodes.tsv.

Schema information:

anyOf:
- format: unit
  type: string
- enum:
  - mixed
  type: string

DeviceSerialNumber (metadata)

Name: Device Serial Number

Type: Metadata

Description: 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.

Schema information:

type: string

DewarPosition (metadata)

Name: Dewar Position

Type: Metadata

Description: 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°".

Schema information:

type: string

DigitizedHeadPoints sense 1 (metadata)

Name: Digitized Head Points

Type: Metadata

Description: true or false value indicating whether head points outlining the scalp/face surface are contained within this recording.

Schema information:

type: boolean

DigitizedHeadPoints sense 2 (metadata)

Name: Digitized Head Points

Type: Metadata

Description: Relative path to the file containing the locations of digitized head points collected during the session (for example, "sub-01_headshape.pos"). RECOMMENDED for all MEG systems, especially for CTF and BTi/4D. For Neuromag/Elekta/MEGIN, the head points will be stored in the .fif file.

Schema information:

format: file_relative
type: string

DigitizedHeadPointsCoordinateSystem (metadata)

Name: Digitized Head Points Coordinate System

Type: Metadata

Allowed values: CTF, ElektaNeuromag, 4DBti, KitYokogawa, ChietiItab, Other, CapTrak, EEGLAB, EEGLAB-HJ, Other, ICBM452AirSpace, ICBM452Warp5Space, IXI549Space, fsaverage, fsaverageSym, fsLR, MNIColin27, MNI152Lin, MNI152NLin2009aSym, MNI152NLin2009bSym, MNI152NLin2009cSym, MNI152NLin2009aAsym, MNI152NLin2009bAsym, MNI152NLin2009cAsym, MNI152NLin6Sym, MNI152NLin6ASym, MNI305, NIHPD, OASIS30AntsOASISAnts, OASIS30Atropos, Talairach, UNCInfant, fsaverage3, fsaverage4, fsaverage5, fsaverage6, fsaveragesym, UNCInfant0V21, UNCInfant1V21, UNCInfant2V21, UNCInfant0V22, UNCInfant1V22, UNCInfant2V22, UNCInfant0V23, UNCInfant1V23, UNCInfant2V23

Description: Defines the coordinate system for the digitized head points. See the Coordinate Systems Appendix for a list of restricted keywords for coordinate systems. If "Other", provide definition of the coordinate system in "DigitizedHeadPointsCoordinateSystemDescription".

Schema information:

type: string

DigitizedHeadPointsCoordinateSystemDescription (metadata)

Name: Digitized Head Points Coordinate System Description

Type: Metadata

Description: 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.

Schema information:

type: string

DigitizedHeadPointsCoordinateUnits (metadata)

Name: Digitized Head Points Coordinate Units

Type: Metadata

Allowed values: m, mm, cm, n/a

Description: Units of the coordinates of "DigitizedHeadPointsCoordinateSystem".

Schema information:

type: string

DigitizedLandmarks (metadata)

Name: Digitized Landmarks

Type: Metadata

Description: true or false value indicating whether anatomical landmark points (fiducials) are contained within this recording.

Schema information:

type: boolean

Directory (extensions)

Name: Directory

Type: Extension

Format: <entities>_<suffix>/

Description: A directory with no extension. Corresponds to BTi/4D data.

DispersionConstant (metadata)

Name: Dispersion Constant

Type: Metadata

Description: External dispersion time constant resulting from tubing in default unit seconds.

Schema information:

type: number
unit: s

DispersionCorrected (metadata)

Name: Dispersion Corrected

Type: Metadata

Description: Boolean flag specifying whether the blood data have been dispersion-corrected. NOTE: not customary for manual samples, and hence should be set to false.

Schema information:

type: boolean

DoseCalibrationFactor (metadata)

Name: Dose Calibration Factor

Type: Metadata

Description: Multiplication factor used to transform raw data (in counts/sec) to meaningful unit (Bq/ml). Corresponds to DICOM Tag 0054, 1322 Dose Calibration Factor.

Schema information:

type: number

DwellTime (metadata)

Name: Dwell Time

Type: Metadata

Description: Actual dwell time (in seconds) of the receiver per point in the readout direction, including any oversampling. For Siemens, this corresponds to DICOM field 0019, 1018 (in ns). This value is necessary for the optional readout distortion correction of anatomicals in the HCP Pipelines. It also usefully provides a handle on the readout bandwidth, which isn't captured in the other metadata tags. Not to be confused with "EffectiveEchoSpacing", and the frequent mislabeling of echo spacing (which is spacing in the phase encoding direction) as "dwell time" (which is spacing in the readout direction).

Schema information:

type: number
unit: s

ECGChannelCount (metadata)

Name: ECG Channel Count

Type: Metadata

Description: Number of ECG channels.

Schema information:

minimum: 0
type: integer

ECOGChannelCount (metadata)

Name: ECOG Channel Count

Type: Metadata

Description: Number of ECoG channels.

Schema information:

minimum: 0
type: integer

EEGChannelCount (metadata)

Name: EEG Channel Count

Type: Metadata

Description: Number of EEG channels recorded simultaneously (for example, 21).

Schema information:

minimum: 0
type: integer

EEGCoordinateSystem (metadata)

Name: EEG Coordinate System

Type: Metadata

Allowed values: CTF, ElektaNeuromag, 4DBti, KitYokogawa, ChietiItab, Other, CapTrak, EEGLAB, EEGLAB-HJ, Other, ICBM452AirSpace, ICBM452Warp5Space, IXI549Space, fsaverage, fsaverageSym, fsLR, MNIColin27, MNI152Lin, MNI152NLin2009aSym, MNI152NLin2009bSym, MNI152NLin2009cSym, MNI152NLin2009aAsym, MNI152NLin2009bAsym, MNI152NLin2009cAsym, MNI152NLin6Sym, MNI152NLin6ASym, MNI305, NIHPD, OASIS30AntsOASISAnts, OASIS30Atropos, Talairach, UNCInfant, fsaverage3, fsaverage4, fsaverage5, fsaverage6, fsaveragesym, UNCInfant0V21, UNCInfant1V21, UNCInfant2V21, UNCInfant0V22, UNCInfant1V22, UNCInfant2V22, UNCInfant0V23, UNCInfant1V23, UNCInfant2V23

Description: Defines the coordinate system for the EEG sensors.
See the Coordinate Systems Appendix for a list of restricted keywords for coordinate systems. If "Other", provide definition of the coordinate system in EEGCoordinateSystemDescription.

Schema information:

type: string

EEGCoordinateSystemDescription (metadata)

Name: EEG Coordinate System Description

Type: Metadata

Description: 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.

Schema information:

type: string

EEGCoordinateUnits (metadata)

Name: EEG Coordinate Units

Type: Metadata

Allowed values: m, mm, cm, n/a

Description: Units of the coordinates of EEGCoordinateSystem.

Schema information:

type: string

EEGGround (metadata)

Name: EEG Ground

Type: Metadata

Description: Description of the location of the ground electrode (for example, "placed on right mastoid (M2)").

Schema information:

type: string

EEGPlacementScheme (metadata)

Name: EEG Placement Scheme

Type: Metadata

Description: Placement scheme of EEG electrodes. Either the name of a standardized placement system (for example, "10-20") or a list of standardized electrode names (for example, ["Cz", "Pz"]).

Schema information:

type: string

EEGReference (metadata)

Name: EEG Reference

Type: Metadata

Description: General description of the reference scheme used and (when applicable) of location of the reference electrode in the raw recordings (for example, "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.

Schema information:

type: string

EMGChannelCount (metadata)

Name: EMG Channel Count

Type: Metadata

Description: Number of EMG channels.

Schema information:

minimum: 0
type: integer

EOGChannelCount (metadata)

Name: EOG Channel Count

Type: Metadata

Description: Number of EOG channels.

Schema information:

minimum: 0
type: integer

EchoTime sense 1 (metadata)

Name: Echo Time

Type: Metadata

Description: The echo time (TE) for the acquisition, specified in seconds. Corresponds to DICOM Tag 0018, 0081 Echo Time (please note that the DICOM term is in milliseconds not seconds). The data type number may apply to files from any MRI modality concerned with a single value for this field, or to the files in a file collection where the value of this field is iterated using the echo entity. The data type array provides a value for each volume in a 4D dataset and should only be used when the volume timing is critical for interpretation of the data, such as in ASL or variable echo time fMRI sequences.

Schema information:

anyOf:
- exclusiveMinimum: 0
  type: number
  unit: s
- items:
    exclusiveMinimum: 0
    type: number
    unit: s
  type: array

EchoTime sense 2 (metadata)

Name: Echo Time

Type: Metadata

Description: The time (in seconds) when the echo corresponding to this map was acquired.

Schema information:

exclusiveMinimum: 0
type: number
unit: s

EchoTime1 (metadata)

Name: Echo Time1

Type: Metadata

Description: The time (in seconds) when the first (shorter) echo occurs.

Schema information:

exclusiveMinimum: 0
type: number
unit: s

EchoTime2 (metadata)

Name: Echo Time2

Type: Metadata

Description: The time (in seconds) when the second (longer) echo occurs.

Schema information:

exclusiveMinimum: 0
type: number
unit: s

EffectiveEchoSpacing (metadata)

Name: Effective Echo Spacing

Type: Metadata

Description: The "effective" sampling interval, specified in seconds, between lines in the phase-encoding direction, defined based on the size of the reconstructed image in the phase direction. It is frequently, but incorrectly, referred to as "dwell time" (see the "DwellTime" parameter for actual dwell time). It is required for unwarping distortions using field maps. Note that beyond just in-plane acceleration, a variety of other manipulations to the phase encoding need to be accounted for properly, including partial fourier, phase oversampling, phase resolution, phase field-of-view and interpolation.

Schema information:

exclusiveMinimum: 0
type: number
unit: s

ElectricalStimulation (metadata)

Name: Electrical Stimulation

Type: Metadata

Description: 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.

Schema information:

type: boolean

ElectricalStimulationParameters (metadata)

Name: Electrical Stimulation Parameters

Type: Metadata

Description: 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.

Schema information:

type: string

ElectrodeManufacturer (metadata)

Name: Electrode Manufacturer

Type: Metadata

Description: 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.

Schema information:

type: string

ElectrodeManufacturersModelName (metadata)

Name: Electrode Manufacturers Model Name

Type: Metadata

Description: If different electrode types are used, please use the corresponding table in the _electrodes.tsv file.

Schema information:

type: string

EpochLength (metadata)

Name: Epoch Length

Type: Metadata

Description: Duration of individual epochs in seconds (for example, 1) in case of epoched data. If recording was continuous or discontinuous, leave out the field.

Schema information:

minimum: 0
type: number

EstimationAlgorithm (metadata)

Name: Estimation Algorithm

Type: Metadata

Description: Type of algorithm used to perform fitting (for example, "linear", "non-linear", "LM" and such).

Schema information:

type: string

EstimationReference (metadata)

Name: Estimation Reference

Type: Metadata

Description: Reference to the study/studies on which the implementation is based.

Schema information:

type: string

EthicsApprovals (metadata)

Name: Ethics Approvals

Type: Metadata

Description: List of ethics committee approvals of the research protocols and/or protocol identifiers.

Schema information:

items:
  type: string
type: array

FLAIR (suffixes)

Name: Fluid attenuated inversion recovery image

Type: Suffix

Format: <entities>_FLAIR.<extension>

Description: In arbitrary units (arbitrary). Structural images with predominant T2 contribution (also known as T2-FLAIR), in which signal from fluids (for example, CSF) is nulled out by adjusting inversion time, coupled with notably long repetition and echo times.

Schema information:

unit: arbitrary

FLASH (suffixes)

Name: Fast-Low-Angle-Shot image

Type: Suffix

Format: <entities>_FLASH.<extension>

Description: FLASH (Fast-Low-Angle-Shot) is a vendor-specific implementation for spoiled gradient echo acquisition. It is commonly used for rapid anatomical imaging and also for many different qMRI applications. When used for a single file, it does not convey any information about the image contrast. When used in a file collection, it may result in conflicts across filenames of different applications. Change: Removed from suffixes.

FLUO (suffixes)

Name: Fluorescence microscopy

Type: Suffix

Format: <entities>_FLUO.<extension>

Description: Fluorescence microscopy imaging data

FiducialsCoordinateSystem (metadata)

Name: Fiducials Coordinate System

Type: Metadata

Allowed values: CTF, ElektaNeuromag, 4DBti, KitYokogawa, ChietiItab, Other, CapTrak, EEGLAB, EEGLAB-HJ, Other, ICBM452AirSpace, ICBM452Warp5Space, IXI549Space, fsaverage, fsaverageSym, fsLR, MNIColin27, MNI152Lin, MNI152NLin2009aSym, MNI152NLin2009bSym, MNI152NLin2009cSym, MNI152NLin2009aAsym, MNI152NLin2009bAsym, MNI152NLin2009cAsym, MNI152NLin6Sym, MNI152NLin6ASym, MNI305, NIHPD, OASIS30AntsOASISAnts, OASIS30Atropos, Talairach, UNCInfant, fsaverage3, fsaverage4, fsaverage5, fsaverage6, fsaveragesym, UNCInfant0V21, UNCInfant1V21, UNCInfant2V21, UNCInfant0V22, UNCInfant1V22, UNCInfant2V22, UNCInfant0V23, UNCInfant1V23, UNCInfant2V23

Description: Defines the coordinate system for the fiducials. Preferably the same as the "EEGCoordinateSystem". See the Coordinate Systems Appendix for a list of restricted keywords for coordinate systems. If "Other", provide definition of the coordinate system in "FiducialsCoordinateSystemDescription".

Schema information:

type: string

FiducialsCoordinateSystemDescription (metadata)

Name: Fiducials Coordinate System Description

Type: Metadata

Description: 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.

Schema information:

type: string

FiducialsCoordinateUnits (metadata)

Name: Fiducials Coordinate Units

Type: Metadata

Allowed values: m, mm, cm, n/a

Description: Units in which the coordinates that are listed in the field "FiducialsCoordinateSystem" are represented.

Schema information:

type: string

FiducialsCoordinates (metadata)

Name: Fiducials Coordinates

Type: Metadata

Description: Key-value pairs of the labels and 3-D digitized position of anatomical landmarks, interpreted following the "FiducialsCoordinateSystem" (for example, {"NAS": [12.7,21.3,13.9], "LPA": [5.2,11.3,9.6], "RPA": [20.2,11.3,9.1]}). Each array MUST contain three numeric values corresponding to x, y, and z axis of the coordinate system in that exact order.

Schema information:

additionalProperties:
  items:
    type: number
  maxItems: 3
  minItems: 3
  type: array
type: object

FiducialsDescription (metadata)

Name: Fiducials Description

Type: Metadata

Description: 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 (for example, "both with Polhemus and with T1w MRI").

Schema information:

type: string

FlipAngle (metadata)

Name: Flip Angle

Type: Metadata

Description: Flip angle (FA) for the acquisition, specified in degrees. Corresponds to: DICOM Tag 0018, 1314 Flip Angle. The data type number may apply to files from any MRI modality concerned with a single value for this field, or to the files in a file collection where the value of this field is iterated using the flip entity. The data type array provides a value for each volume in a 4D dataset and should only be used when the volume timing is critical for interpretation of the data, such as in ASL or variable flip angle fMRI sequences.

Schema information:

anyOf:
- exclusiveMinimum: 0
  maximum: 360
  type: number
  unit: degree
- items:
    exclusiveMinimum: 0
    maximum: 360
    type: number
    unit: degree
  type: array

FrameDuration (metadata)

Name: Frame Duration

Type: Metadata

Description: Time duration of each frame in default unit seconds. This corresponds to DICOM Tag 0018, 1242 Actual Frame Duration converted to seconds.

Schema information:

items:
  type: number
type: array
unit: s

FrameTimesStart (metadata)

Name: Frame Times Start

Type: Metadata

Description: Start times for all frames relative to "TimeZero" in default unit seconds.

Schema information:

items:
  type: number
type: array
unit: s

Funding (metadata)

Name: Funding

Type: Metadata

Description: List of sources of funding (grant numbers).

Schema information:

items:
  type: string
type: array

GYROChannelCount (metadata)

Name: Gyrometer Channel Count

Type: Metadata

Description: Number of gyrometer channels.

Schema information:

minimum: 0
type: integer

GeneratedBy (metadata)

Name: Generated By

Type: Metadata

Description: Used to specify provenance of the dataset.

Schema information:

items:
  properties:
    CodeURL:
      description: URL where the code used to generate the dataset may be found.
      format: uri
      name: CodeURL
      type: string
    Container:
      description: 'Used to specify the location and relevant attributes of software
        container image

        used to produce the dataset. Valid keys in this object include `Type`, `Tag`
        and

        [`URI`][uri] with [string][] values.

        '
      name: Container
      properties:
        Tag:
          type: string
        Type:
          type: string
        URI:
          format: uri
          type: string
      recommended_fields:
      - Type
      - Tag
      - URI
      type: object
    Description:
      description: 'Plain-text description of the pipeline or process that generated
        the outputs.

        RECOMMENDED if `Name` is `"Manual"`.

        '
      name: Description
      type: string
    Name:
      description: 'Name of the pipeline or process that generated the outputs. Use
        `"Manual"` to

        indicate the derivatives were generated by hand, or adjusted manually after
        an

        initial run of an automated pipeline.

        '
      name: Name
      type: string
    Version:
      description: Version of the pipeline
      name: Version
      type: string
  recommended_fields:
  - Version
  required_fields:
  - Name
  type: object
minItems: 1
type: array

GeneticLevel (metadata)

Name: Genetic Level

Type: Metadata

Description: Describes the level of analysis. Values MUST be one of "Genetic", "Genomic", "Epigenomic", "Transcriptomic", "Metabolomic", or "Proteomic".

Schema information:

anyOf:
- enum: &id001
  - Genetic
  - Genomic
  - Epigenomic
  - Transcriptomic
  - Metabolomic
  - Proteomic
  type: string
- items:
    enum: *id001
    type: string
  type: array

Genetics (metadata)

Name: Genetics

Type: Metadata

Description: An object containing information about the genetics descriptor.

Schema information:

properties:
  Database:
    description: '[URI](./common-principles.md#uniform-resource-indicator)

      of database where the dataset is hosted.

      '
    format: uri
    name: Database
    type: string
  Dataset:
    description: '[URI](./common-principles.md#uniform-resource-indicator)

      where data can be retrieved.

      '
    format: uri
    name: Dataset
    type: string
  Descriptors:
    anyOf:
    - type: string
    - items:
        type: string
      type: array
    description: 'List of relevant descriptors (for example, journal articles) for
      dataset

      using a valid

      [URI](./common-principles.md#uniform-resource-indicator)

      when possible.

      '
    name: Descriptors
type: object

GradientSetType (metadata)

Name: Gradient Set Type

Type: Metadata

Description: It should be possible to infer the gradient coil from the scanner model. If not, for example because of a custom upgrade or use of a gradient insert set, then the specifications of the actual gradient coil should be reported independently.

Schema information:

type: string

HED (columns)

Name: HED Tag

Type: Column

Description: Hierarchical Event Descriptor (HED) Tag. See the HED Appendix for details.

Schema information:

type: string

HED (metadata)

Name: HED

Type: Metadata

Description: Hierarchical Event Descriptor (HED) information, see the HED Appendix for details.

Schema information:

anyOf:
- type: string
- additionalProperties:
    type: string
  type: object

HEDVersion (metadata)

Name: HED Version

Type: Metadata

Description: If HED tags are used: The version of the HED schema used to validate HED tags for study. May include a single schema or a base schema and one or more library schema.

Schema information:

anyOf:
- format: hed_version
  type: string
- items:
    format: hed_version
    type: string
  type: array

Haematocrit (metadata)

Name: Haematocrit

Type: Metadata

Description: Measured haematocrit, meaning the volume of erythrocytes divided by the volume of whole blood.

Schema information:

type: number

HardcopyDeviceSoftwareVersion (metadata)

Name: Hardcopy Device Software Version

Type: Metadata

Description: Manufacturer's designation of the software of the device that created this Hardcopy Image (the printer). Corresponds to DICOM Tag 0018, 101A Hardcopy Device Software Version.

Schema information:

type: string

HardwareFilters (metadata)

Name: Hardware Filters

Type: Metadata

Description: 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"}}.

Schema information:

anyOf:
- additionalProperties:
    type: object
  type: object
- enum:
  - n/a
  type: string

HeadCircumference (metadata)

Name: Head Circumference

Type: Metadata

Description: Circumference of the participant's head, expressed in cm (for example, 58).

Schema information:

exclusiveMinimum: 0
type: number
unit: cm

HeadCoilCoordinateSystem (metadata)

Name: Head Coil Coordinate System

Type: Metadata

Allowed values: CTF, ElektaNeuromag, 4DBti, KitYokogawa, ChietiItab, Other, CapTrak, EEGLAB, EEGLAB-HJ, Other, ICBM452AirSpace, ICBM452Warp5Space, IXI549Space, fsaverage, fsaverageSym, fsLR, MNIColin27, MNI152Lin, MNI152NLin2009aSym, MNI152NLin2009bSym, MNI152NLin2009cSym, MNI152NLin2009aAsym, MNI152NLin2009bAsym, MNI152NLin2009cAsym, MNI152NLin6Sym, MNI152NLin6ASym, MNI305, NIHPD, OASIS30AntsOASISAnts, OASIS30Atropos, Talairach, UNCInfant, fsaverage3, fsaverage4, fsaverage5, fsaverage6, fsaveragesym, UNCInfant0V21, UNCInfant1V21, UNCInfant2V21, UNCInfant0V22, UNCInfant1V22, UNCInfant2V22, UNCInfant0V23, UNCInfant1V23, UNCInfant2V23

Description: Defines the coordinate system for the head coils. See the Coordinate Systems Appendix for a list of restricted keywords for coordinate systems. If "Other", provide definition of the coordinate system in HeadCoilCoordinateSystemDescription.

Schema information:

type: string

HeadCoilCoordinateSystemDescription (metadata)

Name: Head Coil Coordinate System Description

Type: Metadata

Description: 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.

Schema information:

type: string

HeadCoilCoordinateUnits (metadata)

Name: Head Coil Coordinate Units

Type: Metadata

Allowed values: m, mm, cm, n/a

Description: Units of the coordinates of HeadCoilCoordinateSystem.

Schema information:

type: string

HeadCoilCoordinates (metadata)

Name: Head Coil Coordinates

Type: Metadata

Description: Key-value pairs describing head localization coil labels and their coordinates, interpreted following the HeadCoilCoordinateSystem (for example, {"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 (for example, for Neuromag/Elekta/MEGIN, Yokogawa systems); in that case generic labels can be used (for example, {"coil1": [12.2,21.3,12.3], "coil2": [6.7,12.3,8.6], "coil3": [21.9,11.0,8.1]}). Each array MUST contain three numeric values corresponding to x, y, and z axis of the coordinate system in that exact order.

Schema information:

additionalProperties:
  items:
    type: number
  maxItems: 3
  minItems: 3
  type: array
type: object

HeadCoilFrequency (metadata)

Name: Head Coil Frequency

Type: Metadata

Description: List of frequencies (in Hz) used by the head localisation coils ('HLC' in CTF systems, 'HPI' in Neuromag/Elekta/MEGIN, 'COH' in BTi/4D) that track the subject's head position in the MEG helmet (for example, [293, 307, 314, 321]).

Schema information:

anyOf:
- type: number
  unit: Hz
- items:
    type: number
    unit: Hz
  type: array

HowToAcknowledge (metadata)

Name: How To Acknowledge

Type: Metadata

Description: Text containing instructions on how researchers using this dataset should acknowledge the original authors. This field can also be used to define a publication that should be cited in publications that use the dataset.

Schema information:

type: string

IRT1 (suffixes)

Name: Inversion recovery T1 mapping

Type: Suffix

Format: <entities>_IRT1.<extension>

Description: The IRT1 method involves multiple inversion recovery spin-echo images acquired at different inversion times (Barral et al. 2010).

ImageAcquisitionProtocol (metadata)

Name: Image Acquisition Protocol

Type: Metadata

Description: Description of the image acquisition protocol or URI (for example from protocols.io).

Schema information:

type: string

ImageDecayCorrected (metadata)

Name: Image Decay Corrected

Type: Metadata

Description: Boolean flag specifying whether the image data have been decay-corrected.

Schema information:

type: boolean

ImageDecayCorrectionTime (metadata)

Name: Image Decay Correction Time

Type: Metadata

Description: Point in time from which the decay correction was applied with respect to "TimeZero" in the default unit seconds.

Schema information:

type: number
unit: s

Immersion (metadata)

Name: Immersion

Type: Metadata

Description: Lens immersion medium. If the file format is OME-TIFF, the value MUST be consistent with the Immersion OME metadata field.

Schema information:

type: string

InfusionRadioactivity (metadata)

Name: Infusion Radioactivity

Type: Metadata

Description: Amount of radioactivity infused into the patient. This value must be less than or equal to the total injected radioactivity ("InjectedRadioactivity"). Units should be the same as "InjectedRadioactivityUnits".

Schema information:

type: number

InfusionSpeed (metadata)

Name: Infusion Speed

Type: Metadata

Description: If given, infusion speed.

Schema information:

type: number

InfusionSpeedUnits (metadata)

Name: Infusion Speed Units

Type: Metadata

Description: Unit of infusion speed (for example, "mL/s").

Schema information:

format: unit
type: string

InfusionStart (metadata)

Name: Infusion Start

Type: Metadata

Description: Time of start of infusion with respect to "TimeZero" in the default unit seconds.

Schema information:

type: number
unit: s

InjectedMass (metadata)

Name: Injected Mass

Type: Metadata

Description: Total mass of radiolabeled compound injected into subject (for example, 10). This can be derived as the ratio of the "InjectedRadioactivity" and "MolarRadioactivity". For those tracers in which injected mass is not available (for example FDG) can be set to "n/a").

Schema information:

anyOf:
- type: number
- enum:
  - n/a
  type: string

InjectedMassPerWeight (metadata)

Name: Injected Mass Per Weight

Type: Metadata

Description: Injected mass per kilogram bodyweight.

Schema information:

type: number

InjectedMassPerWeightUnits (metadata)

Name: Injected Mass Per Weight Units

Type: Metadata

Description: Unit format of the injected mass per kilogram bodyweight (for example, "ug/kg").

Schema information:

format: unit
type: string

InjectedMassUnits (metadata)

Name: Injected Mass Units

Type: Metadata

Description: Unit format of the mass of compound injected (for example, "ug" or "umol"). Note this is not required for an FDG acquisition, since it is not available, and SHOULD be set to "n/a".

Schema information:

anyOf:
- format: unit
  type: string
- enum:
  - n/a
  type: string

InjectedRadioactivity (metadata)

Name: Injected Radioactivity

Type: Metadata

Description: Total amount of radioactivity injected into the patient (for example, 400). For bolus-infusion experiments, this value should be the sum of all injected radioactivity originating from both bolus and infusion. Corresponds to DICOM Tag 0018, 1074 Radionuclide Total Dose.

Schema information:

type: number

InjectedRadioactivityUnits (metadata)

Name: Injected Radioactivity Units

Type: Metadata

Description: Unit format of the specified injected radioactivity (for example, "MBq").

Schema information:

format: unit
type: string

InjectedVolume (metadata)

Name: Injected Volume

Type: Metadata

Description: Injected volume of the radiotracer in the unit "mL".

Schema information:

type: number
unit: mL

InjectionEnd (metadata)

Name: Injection End

Type: Metadata

Description: Time of end of injection with respect to "TimeZero" in the default unit seconds.

Schema information:

type: number
unit: s

InjectionStart (metadata)

Name: Injection Start

Type: Metadata

Description: Time of start of injection with respect to "TimeZero" in the default unit seconds. This corresponds to DICOM Tag 0018, 1072 Contrast/Bolus Start Time converted to seconds relative to "TimeZero".

Schema information:

type: number
unit: s

InstitutionAddress (metadata)

Name: Institution Address

Type: Metadata

Description: The address of the institution in charge of the equipment that produced the measurements.

Schema information:

type: string

InstitutionName (metadata)

Name: Institution Name

Type: Metadata

Description: The name of the institution in charge of the equipment that produced the measurements.

Schema information:

type: string

InstitutionalDepartmentName (metadata)

Name: Institutional Department Name

Type: Metadata

Description: The department in the institution in charge of the equipment that produced the measurements.

Schema information:

type: string

Instructions (metadata)

Name: Instructions

Type: Metadata

Description: Text of the instructions given to participants before the recording.

Schema information:

type: string

IntendedFor sense 1 (metadata)

Name: Intended For

Type: Metadata

Description: 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 participant subdirectory is DEPRECATED.

Schema information:

anyOf:
- format: bids_uri
  type: string
- format: participant_relative
  type: string
- items:
    anyOf:
    - format: bids_uri
      type: string
    - format: participant_relative
      type: string
  type: array

IntendedFor sense 2 (metadata)

Name: Intended For

Type: Metadata

Description: 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.

Schema information:

anyOf:
- format: bids_uri
  type: string
- format: dataset_relative
  type: string
- items:
    anyOf:
    - format: bids_uri
      type: string
    - format: dataset_relative
      type: string
  type: array

InversionTime (metadata)

Name: Inversion Time

Type: Metadata

Description: The inversion time (TI) for the acquisition, specified in seconds. Inversion time is the time after the middle of inverting RF pulse to middle of excitation pulse to detect the amount of longitudinal magnetization. Corresponds to DICOM Tag 0018, 0082 Inversion Time (please note that the DICOM term is in milliseconds not seconds).

Schema information:

exclusiveMinimum: 0
type: number
unit: s

LICENSE (files)

Name: License

Type: Files And Directories

Description: A LICENSE file MAY be provided in addition to the short specification of the used license in the dataset_description.json "License" field. The "License" field and LICENSE file MUST correspond. The LICENSE file MUST be either in ASCII or UTF-8 encoding.

Schema information:

file_type: regular

LabelingDistance (metadata)

Name: Labeling Distance

Type: Metadata

Description: Distance from the center of the imaging slab to the center of the labeling plane ((P)CASL) or the leading edge of the labeling slab (PASL), in millimeters. If the labeling is performed inferior to the isocenter, this number should be negative. Based on DICOM macro C.8.13.5.14.

Schema information:

type: number
unit: mm

LabelingDuration (metadata)

Name: Labeling Duration

Type: Metadata

Description: Total duration of the labeling pulse train, in seconds, corresponding to the temporal width of the labeling bolus for "PCASL" or "CASL". In case all control-label volumes (or deltam or CBF) have the same LabelingDuration, a scalar must be specified. In case the control-label volumes (or deltam or cbf) have a different "LabelingDuration", an array of numbers must be specified, for which any m0scan in the timeseries has a "LabelingDuration" of zero. In case an array of numbers is provided, its length should be equal to the number of volumes specified in *_aslcontext.tsv. Corresponds to DICOM Tag 0018, 9258 ASL Pulse Train Duration.

Schema information:

anyOf:
- minimum: 0
  type: number
  unit: s
- items:
    minimum: 0
    type: number
    unit: s
  type: array

LabelingEfficiency (metadata)

Name: Labeling Efficiency

Type: Metadata

Description: Labeling efficiency, specified as a number between zero and one, only if obtained externally (for example phase-contrast based).

Schema information:

exclusiveMinimum: 0
type: number

LabelingLocationDescription (metadata)

Name: Labeling Location Description

Type: Metadata

Description: Description of the location of the labeling plane ("CASL" or "PCASL") or the labeling slab ("PASL") that cannot be captured by fields LabelingOrientation or LabelingDistance. May include a link to an anonymized screenshot of the planning of the labeling slab/plane with respect to the imaging slab or slices *_asllabeling.jpg. Based on DICOM macro C.8.13.5.14.

Schema information:

type: string

LabelingOrientation (metadata)

Name: Labeling Orientation

Type: Metadata

Description: Orientation of the labeling plane ((P)CASL) or slab (PASL). The direction cosines of a normal vector perpendicular to the ASL labeling slab or plane with respect to the patient. Corresponds to DICOM Tag 0018, 9255 ASL Slab Orientation.

Schema information:

items:
  type: number
type: array

LabelingPulseAverageB1 (metadata)

Name: Labeling Pulse Average B1

Type: Metadata

Description: The average B1-field strength of the RF labeling pulses, in microteslas. As an alternative, "LabelingPulseFlipAngle" can be provided.

Schema information:

exclusiveMinimum: 0
type: number
unit: uT

LabelingPulseAverageGradient (metadata)

Name: Labeling Pulse Average Gradient

Type: Metadata

Description: The average labeling gradient, in milliteslas per meter.

Schema information:

exclusiveMinimum: 0
type: number
unit: mT/m

LabelingPulseDuration (metadata)

Name: Labeling Pulse Duration

Type: Metadata

Description: Duration of the individual labeling pulses, in milliseconds.

Schema information:

exclusiveMinimum: 0
type: number
unit: ms

LabelingPulseFlipAngle (metadata)

Name: Labeling Pulse Flip Angle

Type: Metadata

Description: The flip angle of a single labeling pulse, in degrees, which can be given as an alternative to "LabelingPulseAverageB1".

Schema information:

exclusiveMinimum: 0
maximum: 360
type: number
unit: degree

LabelingPulseInterval (metadata)

Name: Labeling Pulse Interval

Type: Metadata

Description: Delay between the peaks of the individual labeling pulses, in milliseconds.

Schema information:

exclusiveMinimum: 0
type: number
unit: ms

LabelingPulseMaximumGradient (metadata)

Name: Labeling Pulse Maximum Gradient

Type: Metadata

Description: The maximum amplitude of the gradient switched on during the application of the labeling RF pulse(s), in milliteslas per meter.

Schema information:

exclusiveMinimum: 0
type: number
unit: mT/m

LabelingSlabThickness (metadata)

Name: Labeling Slab Thickness

Type: Metadata

Description: Thickness of the labeling slab in millimeters. For non-selective FAIR a zero is entered. Corresponds to DICOM Tag 0018, 9254 ASL Slab Thickness.

Schema information:

exclusiveMinimum: 0
type: number
unit: mm

Levels (metadata)

Name: Levels

Type: Metadata

Description: For categorical variables: An object of possible values (keys) and their descriptions (values).

Schema information:

additionalProperties:
  type: string
type: object

License (metadata)

Name: License

Type: Metadata

Description: The license for the dataset. The use of license name abbreviations is RECOMMENDED for specifying a license (see Licenses). The corresponding full license text MAY be specified in an additional LICENSE file.

Schema information:

type: string

LongName (metadata)

Name: Long Name

Type: Metadata

Description: Long (unabbreviated) name of the column.

Schema information:

type: string

LookLocker (metadata)

Name: Look Locker

Type: Metadata

Description: Boolean indicating if a Look-Locker readout is used.

Schema information:

type: boolean

M0Estimate (metadata)

Name: M0Estimate

Type: Metadata

Description: A single numerical whole-brain M0 value (referring to the M0 of blood), only if obtained externally (for example retrieved from CSF in a separate measurement).

Schema information:

exclusiveMinimum: 0
type: number

M0Type (metadata)

Name: M0Type

Type: Metadata

Allowed values: Separate, Included, Estimate, Absent

Description: Describes the presence of M0 information. "Separate" means that a separate *_m0scan.nii[.gz] is present. "Included" means that an m0scan volume is contained within the current *_asl.nii[.gz]. "Estimate" means that a single whole-brain M0 value is provided. "Absent" means that no specific M0 information is present.

Schema information:

type: string

M0map (suffixes)

Name: Equilibrium magnetization (M0) map

Type: Suffix

Format: <entities>_M0map.<extension>

Description: In arbitrary units (arbitrary). A common quantitative MRI (qMRI) fitting variable that represents the amount of magnetization at thermal equilibrium. M0 maps are RECOMMENDED to use this suffix if generated by qMRI applications (for example, variable flip angle T1 mapping).

Schema information:

unit: arbitrary

MAGNChannelCount (metadata)

Name: Magnetometer Channel Count

Type: Metadata

Description: Number of magnetometer channels.

Schema information:

minimum: 0
type: integer

MEGChannelCount (metadata)

Name: MEG Channel Count

Type: Metadata

Description: Number of MEG channels (for example, 275).

Schema information:

minimum: 0
type: integer

MEGCoordinateSystem (metadata)

Name: MEG Coordinate System

Type: Metadata

Allowed values: CTF, ElektaNeuromag, 4DBti, KitYokogawa, ChietiItab, Other, CapTrak, EEGLAB, EEGLAB-HJ, Other, ICBM452AirSpace, ICBM452Warp5Space, IXI549Space, fsaverage, fsaverageSym, fsLR, MNIColin27, MNI152Lin, MNI152NLin2009aSym, MNI152NLin2009bSym, MNI152NLin2009cSym, MNI152NLin2009aAsym, MNI152NLin2009bAsym, MNI152NLin2009cAsym, MNI152NLin6Sym, MNI152NLin6ASym, MNI305, NIHPD, OASIS30AntsOASISAnts, OASIS30Atropos, Talairach, UNCInfant, fsaverage3, fsaverage4, fsaverage5, fsaverage6, fsaveragesym, UNCInfant0V21, UNCInfant1V21, UNCInfant2V21, UNCInfant0V22, UNCInfant1V22, UNCInfant2V22, UNCInfant0V23, UNCInfant1V23, UNCInfant2V23

Description: Defines the coordinate system for the MEG sensors. See the Coordinate Systems Appendix for a list of restricted keywords for coordinate systems. If "Other", provide definition of the coordinate system in "MEGCoordinateSystemDescription".

Schema information:

type: string

MEGCoordinateSystemDescription (metadata)

Name: MEG Coordinate System Description

Type: Metadata

Description: 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.

Schema information:

type: string

MEGCoordinateUnits (metadata)

Name: MEG Coordinate Units

Type: Metadata

Allowed values: m, mm, cm, n/a

Description: Units of the coordinates of "MEGCoordinateSystem".

Schema information:

type: string

MEGRE (suffixes)

Name: Multi-echo Gradient Recalled Echo

Type: Suffix

Format: <entities>_MEGRE.<extension>

Description: Anatomical gradient echo images acquired at different echo times. Please note that this suffix is not intended for the logical grouping of images acquired using an Echo Planar Imaging (EPI) readout.

MEGREFChannelCount (metadata)

Name: MEGREF Channel Count

Type: Metadata

Description: Number of MEG reference channels (for example, 23). For systems without such channels (for example, Neuromag Vectorview), MEGREFChannelCount should be set to 0.

Schema information:

minimum: 0
type: integer

MESE (suffixes)

Name: Multi-echo Spin Echo

Type: Suffix

Format: <entities>_MESE.<extension>

Description: The MESE method involves multiple spin echo images acquired at different echo times and is primarily used for T2 mapping. Please note that this suffix is not intended for the logical grouping of images acquired using an Echo Planar Imaging (EPI) readout.

MP2RAGE (suffixes)

Name: Magnetization Prepared Two Gradient Echoes

Type: Suffix

Format: <entities>_MP2RAGE.<extension>

Description: The MP2RAGE method is a special protocol that collects several images at different flip angles and inversion times to create a parametric T1map by combining the magnitude and phase images (Marques et al. 2010).

MPE (suffixes)

Name: Multi-photon excitation microscopy

Type: Suffix

Format: <entities>_MPE.<extension>

Description: Multi-photon excitation microscopy imaging data

MPM (suffixes)

Name: Multi-parametric Mapping

Type: Suffix

Format: <entities>_MPM.<extension>

Description: The MPM approaches (a.k.a hMRI) involves the acquisition of highly-similar anatomical images that differ in terms of application of a magnetization transfer RF pulse (MTon or MToff), flip angle and (optionally) echo time and magnitue/phase parts (Weiskopf et al. 2013). See here for suggested MPM acquisition protocols.

MRAcquisitionType (metadata)

Name: MR Acquisition Type

Type: Metadata

Allowed values: 2D, 3D

Description: Type of sequence readout. Corresponds to DICOM Tag 0018, 0023 MR Acquisition Type.

Schema information:

type: string

MRTransmitCoilSequence (metadata)

Name: MR Transmit Coil Sequence

Type: Metadata

Description: This is a relevant field if a non-standard transmit coil is used. Corresponds to DICOM Tag 0018, 9049 MR Transmit Coil Sequence.

Schema information:

type: string

MTNumberOfPulses (metadata)

Name: MT Number Of Pulses

Type: Metadata

Description: The number of magnetization transfer RF pulses applied before the readout.

Schema information:

type: number

MTOffsetFrequency (metadata)

Name: MT Offset Frequency

Type: Metadata

Description: The frequency offset of the magnetization transfer pulse with respect to the central H1 Larmor frequency in Hertz (Hz).

Schema information:

type: number
unit: Hz

MTPulseBandwidth (metadata)

Name: MT Pulse Bandwidth

Type: Metadata

Description: The excitation bandwidth of the magnetization transfer pulse in Hertz (Hz).

Schema information:

type: number
unit: Hz

MTPulseDuration (metadata)

Name: MT Pulse Duration

Type: Metadata

Description: Duration of the magnetization transfer RF pulse in seconds.

Schema information:

type: number
unit: s

MTPulseShape (metadata)

Name: MT Pulse Shape

Type: Metadata

Allowed values: HARD, GAUSSIAN, GAUSSHANN, SINC, SINCHANN, SINCGAUSS, FERMI

Description: Shape of the magnetization transfer RF pulse waveform. The value "GAUSSHANN" refers to a Gaussian pulse with a Hanning window. The value "SINCHANN" refers to a sinc pulse with a Hanning window. The value "SINCGAUSS" refers to a sinc pulse with a Gaussian window.

Schema information:

type: string

MTR (suffixes)

Name: Magnetization Transfer Ratio

Type: Suffix

Format: <entities>_MTR.<extension>

Description: This method is to calculate a semi-quantitative magnetization transfer ratio map.

MTRmap (suffixes)

Name: Magnetization transfer ratio image

Type: Suffix

Format: <entities>_MTRmap.<extension>

Description: In arbitrary units (arbitrary). MTR maps are REQUIRED to use this suffix regardless of the method used to generate them. MTRmap intensity values are RECOMMENDED to be represented in percentage in the range of 0-100%.

Schema information:

maxValue: 100
minValue: 0
unit: arbitrary

MTS (suffixes)

Name: Magnetization transfer saturation

Type: Suffix

Format: <entities>_MTS.<extension>

Description: This method is to calculate a semi-quantitative magnetization transfer saturation index map. The MTS method involves three sets of anatomical images that differ in terms of application of a magnetization transfer RF pulse (MTon or MToff) and flip angle (Helms et al. 2008).

MTState (metadata)

Name: MT State

Type: Metadata

Description: Boolean stating whether the magnetization transfer pulse is applied. Corresponds to DICOM Tag 0018, 9020 Magnetization Transfer.

Schema information:

type: boolean

MTVmap (suffixes)

Name: Macromolecular tissue volume (MTV) image

Type: Suffix

Format: <entities>_MTVmap.<extension>

Description: In arbitrary units (arbitrary). MTV maps are REQUIRED to use this suffix regardless of the method used to generate them.

Schema information:

unit: arbitrary

MTsat (suffixes)

Name: Magnetization transfer saturation image

Type: Suffix

Format: <entities>_MTsat.<extension>

Description: In arbitrary units (arbitrary). MTsat maps are REQUIRED to use this suffix regardless of the method used to generate them.

Schema information:

unit: arbitrary

MWFmap (suffixes)

Name: Myelin water fraction image

Type: Suffix

Format: <entities>_MWFmap.<extension>

Description: In arbitrary units (arbitrary). MWF maps are REQUIRED to use this suffix regardless of the method used to generate them. MWF intensity values are RECOMMENDED to be represented in percentage in the range of 0-100%.

Schema information:

maxValue: 100
minValue: 0
unit: arbitrary

MagneticFieldStrength (metadata)

Name: Magnetic Field Strength

Type: Metadata

Description: Nominal field strength of MR magnet in Tesla. Corresponds to DICOM Tag 0018, 0087 Magnetic Field Strength.

Schema information:

type: number

Magnification (metadata)

Name: Magnification

Type: Metadata

Description: Lens magnification (for example: 40). If the file format is OME-TIFF, the value MUST be consistent with the "NominalMagnification" OME metadata field.

Schema information:

exclusiveMinimum: 0
type: number

Manual (metadata)

Name: Manual

Type: Metadata

Description: Indicates if the segmentation was performed manually or via an automated process.

Schema information:

type: boolean

Manufacturer (metadata)

Name: Manufacturer

Type: Metadata

Description: Manufacturer of the equipment that produced the measurements.

Schema information:

type: string

ManufacturersModelName (metadata)

Name: Manufacturers Model Name

Type: Metadata

Description: Manufacturer's model name of the equipment that produced the measurements.

Schema information:

type: string

MatrixCoilMode (metadata)

Name: Matrix Coil Mode

Type: Metadata

Description: (If used) A method for reducing the number of independent channels by combining in analog the signals from multiple coil elements. There are typically different default modes when using un-accelerated or accelerated (for example, "GRAPPA", "SENSE") imaging.

Schema information:

type: string

MaxMovement (metadata)

Name: Max Movement

Type: Metadata

Description: Maximum head movement (in mm) detected during the recording, as measured by the head localisation coils (for example, 4.8).

Schema information:

type: number
unit: mm

MeasurementToolMetadata (metadata)

Name: Measurement Tool Metadata

Type: Metadata

Description: A description of the measurement tool as a whole. Contains two fields: "Description" and "TermURL". "Description" is a free text description of the measurement tool. "TermURL" is a URL to an entity in an ontology corresponding to this tool.

Schema information:

properties:
  Description:
    type: string
  TermURL:
    format: uri
    type: string
type: object

MetaboliteAvail (metadata)

Name: Metabolite Available

Type: Metadata

Description: Boolean that specifies if metabolite measurements are available. If true, the metabolite_parent_fraction column MUST be present in the corresponding *_blood.tsv file.

Schema information:

type: boolean

MetaboliteMethod (metadata)

Name: Metabolite Method

Type: Metadata

Description: Method used to measure metabolites.

Schema information:

type: string

MetaboliteRecoveryCorrectionApplied (metadata)

Name: Metabolite Recovery Correction Applied

Type: Metadata

Description: Metabolite recovery correction from the HPLC, for tracers where it changes with time postinjection. If true, the hplc_recovery_fractions column MUST be present in the corresponding *_blood.tsv file.

Schema information:

type: boolean

MiscChannelCount (metadata)

Name: Misc Channel Count

Type: Metadata

Description: Number of miscellaneous analog channels for auxiliary signals.

Schema information:

minimum: 0
type: integer

MixingTime (metadata)

Name: Mixing Time

Type: Metadata

Description: In the context of a stimulated- and spin-echo 3D EPI sequence for B1+ mapping, corresponds to the interval between spin- and stimulated-echo pulses. In the context of a diffusion-weighted double spin-echo sequence, corresponds to the interval between two successive diffusion sensitizing gradients, specified in seconds.

Schema information:

type: number
unit: s

ModeOfAdministration (metadata)

Name: Mode Of Administration

Type: Metadata

Description: Mode of administration of the injection (for example, "bolus", "infusion", or "bolus-infusion").

Schema information:

type: string

MolarActivity (metadata)

Name: Molar Activity

Type: Metadata

Description: Molar activity of compound injected. Corresponds to DICOM Tag 0018, 1077 Radiopharmaceutical Specific Activity.

Schema information:

type: number

MolarActivityMeasTime (metadata)

Name: Molar Activity Measurement Time

Type: Metadata

Description: Time to which molar radioactivity measurement above applies in the default unit "hh:mm:ss".

Schema information:

format: time
type: string

MolarActivityUnits (metadata)

Name: Molar Activity Units

Type: Metadata

Description: Unit of the specified molar radioactivity (for example, "GBq/umol").

Schema information:

format: unit
type: string

MultibandAccelerationFactor (metadata)

Name: Multiband Acceleration Factor

Type: Metadata

Description: The multiband factor, for multiband acquisitions.

Schema information:

type: number

MultipartID (metadata)

Name: MultipartID

Type: Metadata

Description: A unique (per participant) label tagging DWI runs that are part of a multipart scan.

Schema information:

type: string

NIRSChannelCount (metadata)

Name: NIRS Channel Count

Type: Metadata

Description: Total number of NIRS channels, including short channels. Corresponds to the number of rows in channels.tsv with any NIRS type.

Schema information:

minimum: 0
type: integer

NIRSCoordinateProcessingDescription (metadata)

Name: NIRS Coordinate Processing Description

Type: Metadata

Description: Has any post-processing (such as projection) been done on the optode positions (for example, "surface_projection", "n/a").

Schema information:

type: string

NIRSCoordinateSystem (metadata)

Name: NIRS Coordinate System

Type: Metadata

Allowed values: CTF, ElektaNeuromag, 4DBti, KitYokogawa, ChietiItab, Other, CapTrak, EEGLAB, EEGLAB-HJ, Other, ICBM452AirSpace, ICBM452Warp5Space, IXI549Space, fsaverage, fsaverageSym, fsLR, MNIColin27, MNI152Lin, MNI152NLin2009aSym, MNI152NLin2009bSym, MNI152NLin2009cSym, MNI152NLin2009aAsym, MNI152NLin2009bAsym, MNI152NLin2009cAsym, MNI152NLin6Sym, MNI152NLin6ASym, MNI305, NIHPD, OASIS30AntsOASISAnts, OASIS30Atropos, Talairach, UNCInfant, fsaverage3, fsaverage4, fsaverage5, fsaverage6, fsaveragesym, UNCInfant0V21, UNCInfant1V21, UNCInfant2V21, UNCInfant0V22, UNCInfant1V22, UNCInfant2V22, UNCInfant0V23, UNCInfant1V23, UNCInfant2V23

Description: Defines the coordinate system in which the optode positions are expressed.
See Appendix VIII for a list of restricted keywords for coordinate systems. If "Other", a definition of the coordinate system MUST be provided in NIRSCoordinateSystemDescription.

Schema information:

type: string

NIRSCoordinateSystemDescription (metadata)

Name: NIRS Coordinate System Description

Type: Metadata

Description: 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.

Schema information:

type: string

NIRSCoordinateUnits (metadata)

Name: NIRS Coordinate Units

Type: Metadata

Allowed values: m, mm, cm, n/a

Description: Units of the coordinates of NIRSCoordinateSystem.

Schema information:

type: string

NIRSDetectorOptodeCount (metadata)

Name: NIRS Detector Optode Channel Count

Type: Metadata

Description: Number of NIRS detectors. Corresponds to the number of rows in optodes.tsv with type "detector".

Schema information:

minimum: 1
type: integer

NIRSPlacementScheme (metadata)

Name: NIRS Placement Scheme

Type: Metadata

Description: Placement scheme of NIRS optodes. Either the name of a standardized placement system (for example, "10-20") or an array of standardized position names (for example, ["Cz", "Pz"]). This field should only be used if a cap was not used. If a standard cap was used, then it should be specified in CapManufacturer and CapManufacturersModelName and this field should be set to "n/a"

Schema information:

anyOf:
- type: string
- items:
    type: string
  type: array

NIRSSourceOptodeCount (metadata)

Name: NIRS Source Optode Count

Type: Metadata

Description: Number of NIRS sources. Corresponds to the number of rows in optodes.tsv with type "source".

Schema information:

minimum: 1
type: integer

NLO (suffixes)

Name: Nonlinear optical microscopy

Type: Suffix

Format: <entities>_NLO.<extension>

Description: Nonlinear optical microscopy imaging data

Name (metadata)

Name: Name

Type: Metadata

Description: Name of the dataset.

Schema information:

type: string

NegativeContrast (metadata)

Name: Negative Contrast

Type: Metadata

Description: true or false value specifying whether increasing voxel intensity (within sample voxels) denotes a decreased value with respect to the contrast suffix. This is commonly the case when Cerebral Blood Volume is estimated via usage of a contrast agent in conjunction with a T2* weighted acquisition protocol.

Schema information:

type: boolean

None (extensions)

Name: No extension

Type: Extension

Format: <entities>_<suffix>

Description: A file with no extension.

NonlinearGradientCorrection (metadata)

Name: Nonlinear Gradient Correction

Type: Metadata

Description: Boolean stating if the image saved has been corrected for gradient nonlinearities by the scanner sequence.

Schema information:

type: boolean

NumberOfVolumesDiscardedByScanner (metadata)

Name: Number Of Volumes Discarded By Scanner

Type: Metadata

Description: Number of volumes ("dummy scans") discarded by the scanner (as opposed to those discarded by the user post hoc) before saving the imaging file. For example, a sequence that automatically discards the first 4 volumes before saving would have this field as 4. A sequence that does not discard dummy scans would have this set to 0. Please note that the onsets recorded in the events.tsv file should always refer to the beginning of the acquisition of the first volume in the corresponding imaging file - independent of the value of "NumberOfVolumesDiscardedByScanner" field.

Schema information:

minimum: 0
type: integer

NumberOfVolumesDiscardedByUser (metadata)

Name: Number Of Volumes Discarded By User

Type: Metadata

Description: Number of volumes ("dummy scans") discarded by the user before including the file in the dataset. If possible, including all of the volumes is strongly recommended. Please note that the onsets recorded in the events.tsv file should always refer to the beginning of the acquisition of the first volume in the corresponding imaging file - independent of the value of "NumberOfVolumesDiscardedByUser" field.

Schema information:

minimum: 0
type: integer

NumberShots (metadata)

Name: Number Shots

Type: Metadata

Description: The number of RF excitations needed to reconstruct a slice or volume (may be referred to as partition). Please mind that this is not the same as Echo Train Length which denotes the number of k-space lines collected after excitation in a multi-echo readout. The data type array is applicable for specifying this parameter before and after the k-space center is sampled. Please see "NumberShots" metadata field in the qMRI appendix for corresponding calculations.

Schema information:

anyOf:
- type: number
- items:
    type: number
  type: array

NumericalAperture (metadata)

Name: Numerical Aperture

Type: Metadata

Description: Lens numerical aperture (for example: 1.4). If the file format is OME-TIFF, the value MUST be consistent with the LensNA OME metadata field.

Schema information:

exclusiveMinimum: 0
type: number

OCT (suffixes)

Name: Optical coherence tomography

Type: Suffix

Format: <entities>_OCT.<extension>

Description: Optical coherence tomography imaging data

OMEBigTiff (extensions)

Name: Open Microscopy Environment BigTIFF

Type: Extension

Format: <entities>_<suffix>.ome.btf

Description: A BigTIFF image file, for very large images.

OMETiff (extensions)

Name: Open Microscopy Environment Tag Image File Format

Type: Extension

Format: <entities>_<suffix>.ome.tif

Description: An OME-TIFF image file.

OMEZARR (extensions)

Name: OME Next Generation File Format

Type: Extension

Format: <entities>_<suffix>.ome.zarr/

Description: An OME-NGFF file.
OME-NGFF is a Zarr-based format, organizing data arrays in nested directories. This format was developed by the Open Microscopy Environment to provide data stream access to very large data.

OperatingSystem (metadata)

Name: Operating System

Type: Metadata

Description: Operating system used to run the stimuli presentation software (for formatting recommendations, see examples below this table).

Schema information:

type: string

OtherAcquisitionParameters (metadata)

Name: Other Acquisition Parameters

Type: Metadata

Description: Description of other relevant image acquisition parameters.

Schema information:

type: string

PASLType (metadata)

Name: PASL Type

Type: Metadata

Description: Type of the labeling pulse of the PASL labeling, for example "FAIR", "EPISTAR", or "PICORE".

Schema information:

type: string

PC (suffixes)

Name: Phase-contrast microscopy

Type: Suffix

Format: <entities>_PC.<extension>

Description: Phase-contrast microscopy imaging data

PCASLType (metadata)

Name: PCASL Type

Type: Metadata

Allowed values: balanced, unbalanced

Description: The type of gradient pulses used in the control condition.

Schema information:

type: string

PD (suffixes)

Name: Proton density image

Type: Suffix

Format: <entities>_PD.<extension>

Description: Ambiguous, may refer to a parametric image or to a conventional image. Change: Replaced by PDw or PDmap.

Schema information:

unit: arbitrary

PDT2 (suffixes)

Name: PD and T2 weighted image

Type: Suffix

Format: <entities>_PDT2.<extension>

Description: In arbitrary units (arbitrary). PDw and T2w images acquired using a dual echo FSE sequence through view sharing process (Johnson et al. 1994).

Schema information:

unit: arbitrary

PDT2map (suffixes)

Name: Combined PD/T2 image

Type: Suffix

Format: <entities>_PDT2map.<extension>

Description: In arbitrary units (arbitrary). Combined PD/T2 maps are REQUIRED to use this suffix regardless of the method used to generate them.

Schema information:

unit: arbitrary

PDmap (suffixes)

Name: Proton density image

Type: Suffix

Format: <entities>_PDmap.<extension>

Description: In arbitrary units (arbitrary). PD maps are REQUIRED to use this suffix regardless of the method used to generate them.

Schema information:

unit: arbitrary

PDw (suffixes)

Name: Proton density (PD) weighted image

Type: Suffix

Format: <entities>_PDw.<extension>

Description: In arbitrary units (arbitrary). The contrast of these images is mainly determined by spatial variations in the spin density (1H) of the imaged specimen. In spin-echo sequences this contrast is achieved at short repetition and long echo times. In a gradient-echo acquisition, PD weighting dominates the contrast at long repetition and short echo times, and at small flip angles.

Schema information:

unit: arbitrary

PLI (suffixes)

Name: Polarized-light microscopy

Type: Suffix

Format: <entities>_PLI.<extension>

Description: Polarized-light microscopy imaging data

ParallelAcquisitionTechnique (metadata)

Name: Parallel Acquisition Technique

Type: Metadata

Description: The type of parallel imaging used (for example "GRAPPA", "SENSE"). Corresponds to DICOM Tag 0018, 9078 Parallel Acquisition Technique.

Schema information:

type: string

ParallelReductionFactorInPlane (metadata)

Name: Parallel Reduction Factor In Plane

Type: Metadata

Description: The parallel imaging (for instance, GRAPPA) factor in plane. Use the denominator of the fraction of k-space encoded for each slice. For example, 2 means half of k-space is encoded. Corresponds to DICOM Tag 0018, 9069 Parallel Reduction Factor In-plane.

Schema information:

type: number

ParallelReductionFactorOutOfPlane (metadata)

Name: Parallel Reduction Factor Out of Plane

Type: Metadata

Description: The parallel imaging (for instance, GRAPPA) factor in the second phase encoding dimension of 3D sequences. Use the denominator of the fraction of k-space encoded in the second phase encoding dimension. For example, 2 means half of k-space is encoded. Will typically be 1 for 2D sequences, as each slice in a 2D acquisition is usually fully encoded. ParallelReductionFactorOutOfPlane should not be confused with MultibandAccelerationFactor, as they imply different methods of accelerating the acquisition. Corresponds to DICOM Tag 0018, 9155 Parallel Reduction Factor out-of-plane.

Schema information:

type: number

PartialFourier (metadata)

Name: Partial Fourier

Type: Metadata

Description: The fraction of partial Fourier information collected. Corresponds to DICOM Tag 0018, 9081 Partial Fourier.

Schema information:

type: number

PartialFourierDirection (metadata)

Name: Partial Fourier Direction

Type: Metadata

Description: The direction where only partial Fourier information was collected. Corresponds to DICOM Tag 0018, 9036 Partial Fourier Direction.

Schema information:

type: string

PharmaceuticalDoseAmount (metadata)

Name: Pharmaceutical Dose Amount

Type: Metadata

Description: Dose amount of pharmaceutical coadministered with tracer.

Schema information:

anyOf:
- type: number
- items:
    type: number
  type: array

PharmaceuticalDoseRegimen (metadata)

Name: Pharmaceutical Dose Regimen

Type: Metadata

Description: Details of the pharmaceutical dose regimen. Either adequate description or short-code relating to regimen documented elsewhere (for example, "single oral bolus").

Schema information:

type: string

PharmaceuticalDoseTime (metadata)

Name: Pharmaceutical Dose Time

Type: Metadata

Description: Time of administration of pharmaceutical dose, relative to time zero. For an infusion, this should be a vector with two elements specifying the start and end of the infusion period. For more complex dose regimens, the regimen description should be complete enough to enable unambiguous interpretation of "PharmaceuticalDoseTime". Unit format of the specified pharmaceutical dose time MUST be seconds.

Schema information:

anyOf:
- type: number
  unit: s
- items:
    type: number
    unit: s
  type: array

PharmaceuticalDoseUnits (metadata)

Name: Pharmaceutical Dose Units

Type: Metadata

Description: Unit format relating to pharmaceutical dose (for example, "mg" or "mg/kg").

Schema information:

format: unit
type: string

PharmaceuticalName (metadata)

Name: Pharmaceutical Name

Type: Metadata

Description: Name of pharmaceutical coadministered with tracer.

Schema information:

type: string

PhaseEncodingDirection (metadata)

Name: Phase Encoding Direction

Type: Metadata

Allowed values: i, j, k, i-, j-, k-

Description: The letters i, j, k correspond to the first, second and third axis of the data in the NIFTI file. The polarity of the phase encoding is assumed to go from zero index to maximum index unless - sign is present (then the order is reversed - starting from the highest index instead of zero). PhaseEncodingDirection is defined as the direction along which phase is was modulated which may result in visible distortions. Note that this is not the same as the DICOM term InPlanePhaseEncodingDirection which can have ROW or COL values.

Schema information:

type: string

PhotoDescription (metadata)

Name: Photo Description

Type: Metadata

Description: Description of the photo.

Schema information:

type: string

PixelSize (metadata)

Name: Pixel Size

Type: Metadata

Description: A 2- or 3-number array of the physical size of a pixel, either [PixelSizeX, PixelSizeY] or [PixelSizeX, PixelSizeY, PixelSizeZ], where X is the width, Y the height and Z the depth. If the file format is OME-TIFF, these values need to be consistent with PhysicalSizeX, PhysicalSizeY and PhysicalSizeZ OME metadata fields, after converting in PixelSizeUnits according to PhysicalSizeXunit, PhysicalSizeYunit and PhysicalSizeZunit OME fields.

Schema information:

items:
  minimum: 0
  type: number
maxItems: 3
minItems: 2
type: array

PixelSizeUnits (metadata)

Name: Pixel Size Units

Type: Metadata

Allowed values: mm, um, nm

Description: Unit format of the specified "PixelSize". MUST be one of: "mm" (millimeter), "um" (micrometer) or "nm" (nanometer).

Schema information:

type: string

PlasmaAvail (metadata)

Name: Plasma Avail

Type: Metadata

Description: Boolean that specifies if plasma measurements are available.

Schema information:

type: boolean

PlasmaFreeFraction (metadata)

Name: Plasma Free Fraction

Type: Metadata

Description: Measured free fraction in plasma, meaning the concentration of free compound in plasma divided by total concentration of compound in plasma (Units: 0-100%).

Schema information:

maximum: 100
minimum: 0
type: number

PlasmaFreeFractionMethod (metadata)

Name: Plasma Free Fraction Method

Type: Metadata

Description: Method used to estimate free fraction.

Schema information:

type: string

PostLabelingDelay (metadata)

Name: Post Labeling Delay

Type: Metadata

Description: This is the postlabeling delay (PLD) time, in seconds, after the end of the labeling (for "CASL" or "PCASL") or middle of the labeling pulse (for "PASL") until the middle of the excitation pulse applied to the imaging slab (for 3D acquisition) or first slice (for 2D acquisition). Can be a number (for a single-PLD time series) or an array of numbers (for multi-PLD and Look-Locker). In the latter case, the array of numbers contains the PLD of each volume, namely each control and label, in the acquisition order. Any image within the time-series without a PLD, for example an m0scan, is indicated by a zero. Based on DICOM Tags 0018, 9079 Inversion Times and 0018, 0082 InversionTime.

Schema information:

anyOf:
- exclusiveMinimum: 0
  type: number
  unit: s
- items:
    exclusiveMinimum: 0
    type: number
    unit: s
  type: array

PowerLineFrequency (metadata)

Name: Power Line Frequency

Type: Metadata

Description: Frequency (in Hz) of the power grid at the geographical location of the instrument (for example, 50 or 60).

Schema information:

anyOf:
- exclusiveMinimum: 0
  type: number
  unit: Hz
- enum:
  - n/a
  type: string

PromptRate (metadata)

Name: Prompt Rate

Type: Metadata

Description: Prompt rate for each frame (same units as Units, for example, "Bq/mL").

Schema information:

items:
  type: number
type: array

PulseSequenceDetails (metadata)

Name: Pulse Sequence Details

Type: Metadata

Description: Information beyond pulse sequence type that identifies the specific pulse sequence used (for example, "Standard Siemens Sequence distributed with the VB17 software", "Siemens WIP ### version #.##," or "Sequence written by X using a version compiled on MM/DD/YYYY").

Schema information:

type: string

PulseSequenceType (metadata)

Name: Pulse Sequence Type

Type: Metadata

Description: A general description of the pulse sequence used for the scan (for example, "MPRAGE", "Gradient Echo EPI", "Spin Echo EPI", "Multiband gradient echo EPI").

Schema information:

type: string

Purity (metadata)

Name: Purity

Type: Metadata

Description: Purity of the radiolabeled compound (between 0 and 100%).

Schema information:

maximum: 100
minimum: 0
type: number

R1map (suffixes)

Name: Longitudinal relaxation rate image

Type: Suffix

Format: <entities>_R1map.<extension>

Description: In seconds-1 (1/s). R1 maps (R1 = 1/T1) are REQUIRED to use this suffix regardless of the method used to generate them.

Schema information:

unit: 1/s

R2map (suffixes)

Name: True transverse relaxation rate image

Type: Suffix

Format: <entities>_R2map.<extension>

Description: In seconds-1 (1/s). R2 maps (R2 = 1/T2) are REQUIRED to use this suffix regardless of the method used to generate them.

Schema information:

unit: 1/s

R2starmap (suffixes)

Name: Observed transverse relaxation rate image

Type: Suffix

Format: <entities>_R2starmap.<extension>

Description: In seconds-1 (1/s). R2-star maps (R2star = 1/T2star) are REQUIRED to use this suffix regardless of the method used to generate them.

Schema information:

unit: 1/s

RB1COR (suffixes)

Name: RB1COR

Type: Suffix

Format: <entities>_RB1COR.<extension>

Description: Low resolution images acquired by the body coil (in the gantry of the scanner) and the head coil using identical acquisition parameters to generate a combined sensitivity map as described in Papp et al. (2016).

RB1map (suffixes)

Name: RF receive sensitivity map

Type: Suffix

Format: <entities>_RB1map.<extension>

Description: In arbitrary units (arbitrary). Radio frequency (RF) receive (B1-) sensitivity maps are REQUIRED to use this suffix regardless of the method used to generate them. RB1map intensity values are RECOMMENDED to be represented as percent multiplicative factors such that Amplitudeeffective = B1-intensity*Amplitudeideal.

Schema information:

unit: arbitrary

README (files)

Name: README

Type: Files And Directories

Description: A REQUIRED text file, README, SHOULD describe the dataset in more detail. The README file MUST be either in ASCII or UTF-8 encoding and MAY have one of the extensions: .md (Markdown), .rst (reStructuredText), or .txt. A BIDS dataset MUST NOT contain more than one README file (with or without extension) at its root directory. BIDS does not make any recommendations with regards to the Markdown flavor and does not validate the syntax of Markdown and reStructuredText. The README file SHOULD be structured such that its contents can be easily understood even if the used format is not rendered. A guideline for creating a good README file can be found in the bids-starter-kit.

Schema information:

file_type: regular

RandomRate (metadata)

Name: Random Rate

Type: Metadata

Description: Random rate for each frame (same units as "Units", for example, "Bq/mL").

Schema information:

items:
  type: number
type: array

RawSources (metadata)

Name: Raw Sources

Type: Metadata

Description: A list of paths relative to dataset root pointing to the BIDS-Raw file(s) that were used in the creation of this derivative. This field is DEPRECATED, and this metadata SHOULD be recorded in the Sources field using BIDS URIs to distinguish sources from different datasets.

Schema information:

items:
  format: dataset_relative
  type: string
type: array

ReceiveCoilActiveElements (metadata)

Name: Receive Coil Active Elements

Type: Metadata

Description: Information describing the active/selected elements of the receiver coil. This does not correspond to a tag in the DICOM ontology. The vendor-defined terminology for active coil elements can go in this field.

Schema information:

type: string

ReceiveCoilName (metadata)

Name: Receive Coil Name

Type: Metadata

Description: Information describing the receiver coil. Corresponds to DICOM Tag 0018, 1250 Receive Coil Name, although not all vendors populate that DICOM Tag, in which case this field can be derived from an appropriate private DICOM field.

Schema information:

type: string

ReconFilterSize (metadata)

Name: Recon Filter Size

Type: Metadata

Description: Kernel size of post-recon filter (FWHM) in default units "mm".

Schema information:

anyOf:
- type: number
  unit: mm
- items:
    type: number
    unit: mm
  type: array

ReconFilterType (metadata)

Name: Recon Filter Type

Type: Metadata

Description: Type of post-recon smoothing (for example, ["Shepp"]).

Schema information:

anyOf:
- type: string
- items:
    type: string
  type: array

ReconMethodImplementationVersion (metadata)

Name: Recon Method Implementation Version

Type: Metadata

Description: Identification for the software used, such as name and version.

Schema information:

type: string

ReconMethodName (metadata)

Name: Recon Method Name

Type: Metadata

Description: Reconstruction method or algorithm (for example, "3d-op-osem").

Schema information:

type: string

ReconMethodParameterLabels (metadata)

Name: Recon Method Parameter Labels

Type: Metadata

Description: Names of reconstruction parameters (for example, ["subsets", "iterations"]).

Schema information:

items:
  type: string
type: array

ReconMethodParameterUnits (metadata)

Name: Recon Method Parameter Units

Type: Metadata

Description: Unit of reconstruction parameters (for example, ["none", "none"]).

Schema information:

items:
  format: unit
  type: string
type: array

ReconMethodParameterValues (metadata)

Name: Recon Method Parameter Values

Type: Metadata

Description: Values of reconstruction parameters (for example, [21, 3]).

Schema information:

items:
  type: number
type: array

RecordingDuration (metadata)

Name: Recording Duration

Type: Metadata

Description: Length of the recording in seconds (for example, 3600).

Schema information:

type: number
unit: s

RecordingType (metadata)

Name: Recording Type

Type: Metadata

Allowed values: continuous, epoched, discontinuous

Description: 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).

Schema information:

type: string

Name: References And Links

Type: Metadata

Description: List of references to publications that contain information on the dataset. A reference may be textual or a URI.

Schema information:

items:
  type: string
type: array

RepetitionTime (metadata)

Name: Repetition Time

Type: Metadata

Description: The time in seconds between the beginning of an acquisition of one volume and the beginning of acquisition of the volume following it (TR). When used in the context of functional acquisitions this parameter best corresponds to DICOM Tag 0020, 0110: the "time delta between images in a dynamic of functional set of images" but may also be found in DICOM Tag 0018, 0080: "the period of time in msec between the beginning of a pulse sequence and the beginning of the succeeding (essentially identical) pulse sequence". This definition includes time between scans (when no data has been acquired) in case of sparse acquisition schemes. This value MUST be consistent with the 'pixdim[4]' field (after accounting for units stored in 'xyzt_units' field) in the NIfTI header. This field is mutually exclusive with VolumeTiming.

Schema information:

exclusiveMinimum: 0
type: number
unit: s

RepetitionTimeExcitation (metadata)

Name: Repetition Time Excitation

Type: Metadata

Description: The interval, in seconds, between two successive excitations. DICOM Tag 0018, 0080 best refers to this parameter. This field may be used together with the "RepetitionTimePreparation" for certain use cases, such as MP2RAGE. Use RepetitionTimeExcitation (in combination with "RepetitionTimePreparation" if needed) for anatomy imaging data rather than "RepetitionTime" as it is already defined as the amount of time that it takes to acquire a single volume in the task imaging data section.

Schema information:

minimum: 0
type: number
unit: s

RepetitionTimePreparation (metadata)

Name: Repetition Time Preparation

Type: Metadata

Description: The interval, in seconds, that it takes a preparation pulse block to re-appear at the beginning of the succeeding (essentially identical) pulse sequence block. The data type number may apply to files from any MRI modality concerned with a single value for this field. The data type array provides a value for each volume in a 4D dataset and should only be used when the volume timing is critical for interpretation of the data, such as in ASL.

Schema information:

anyOf:
- minimum: 0
  type: number
  unit: s
- items:
    minimum: 0
    type: number
    unit: s
  type: array

Resolution (metadata)

Name: Resolution

Type: Metadata

Description: Specifies the interpretation of the resolution keyword. If an object is used, then the keys should be values for the res entity and values should be descriptions of those res values.

Schema information:

anyOf:
- type: string
- additionalProperties:
    type: string
  type: object

S0map (suffixes)

Name: Observed signal amplitude (S0) image

Type: Suffix

Format: <entities>_S0map.<extension>

Description: In arbitrary units (arbitrary). For a multi-echo (typically fMRI) sequence, S0 maps index the baseline signal before exponential (T2-star) signal decay. In other words: the exponential of the intercept for a linear decay model across log-transformed echos. For more information, please see, for example, the tedana documentation. S0 maps are RECOMMENDED to use this suffix if derived from an ME-FMRI dataset.

SEEGChannelCount (metadata)

Name: SEEG Channel Count

Type: Metadata

Description: Number of SEEG channels.

Schema information:

minimum: 0
type: integer

SEM (suffixes)

Name: Scanning electron microscopy

Type: Suffix

Format: <entities>_SEM.<extension>

Description: Scanning electron microscopy imaging data

SPIM (suffixes)

Name: Selective plane illumination microscopy

Type: Suffix

Format: <entities>_SPIM.<extension>

Description: Selective plane illumination microscopy imaging data

SR (suffixes)

Name: Super-resolution microscopy

Type: Suffix

Format: <entities>_SR.<extension>

Description: Super-resolution microscopy imaging data

SampleEmbedding (metadata)

Name: Sample Embedding

Type: Metadata

Description: Description of the tissue sample embedding (for example: "Epoxy resin").

Schema information:

type: string

SampleEnvironment (metadata)

Name: Sample Environment

Type: Metadata

Allowed values: in vivo, ex vivo, in vitro

Description: Environment in which the sample was imaged. MUST be one of: "in vivo", "ex vivo" or "in vitro".

Schema information:

type: string

SampleExtractionInstitution (metadata)

Name: Sample Extraction Institution

Type: Metadata

Description: The name of the institution in charge of the extraction of the sample, if different from the institution in charge of the equipment that produced the image.

Schema information:

type: string

SampleExtractionProtocol (metadata)

Name: Sample Extraction Protocol

Type: Metadata

Description: Description of the sample extraction protocol or URI (for example from protocols.io).

Schema information:

type: string

SampleFixation (metadata)

Name: Sample Fixation

Type: Metadata

Description: Description of the tissue sample fixation (for example: "4% paraformaldehyde, 2% glutaraldehyde").

Schema information:

type: string

SampleOrigin (metadata)

Name: Sample Origin

Type: Metadata

Allowed values: blood, saliva, brain, csf, breast milk, bile, amniotic fluid, other biospecimen

Description: Describes from which tissue the genetic information was extracted.

Schema information:

type: string

SamplePrimaryAntibody (metadata)

Name: Sample Primary Antibody

Type: Metadata

Description: Description(s) of the primary antibody used for immunostaining. Either an RRID or the name, supplier and catalogue number of a commercial antibody. For non-commercial antibodies either an RRID or the host-animal and immunogen used (for examples: "RRID:AB_2122563" or "Rabbit anti-Human HTR5A Polyclonal Antibody, Invitrogen, Catalog # PA1-2453"). MAY be an array of strings if different antibodies are used in each channel of the file.

Schema information:

anyOf:
- type: string
- items:
    type: string
  type: array

SampleSecondaryAntibody (metadata)

Name: Sample Secondary Antibody

Type: Metadata

Description: Description(s) of the secondary antibody used for immunostaining. Either an RRID or the name, supplier and catalogue number of a commercial antibody. For non-commercial antibodies either an RRID or the host-animal and immunogen used (for examples: "RRID:AB_228322" or "Goat anti-Mouse IgM Secondary Antibody, Invitrogen, Catalog # 31172"). MAY be an array of strings if different antibodies are used in each channel of the file.

Schema information:

anyOf:
- type: string
- items:
    type: string
  type: array

SampleStaining (metadata)

Name: Sample Staining

Type: Metadata

Description: Description(s) of the tissue sample staining (for example: "Osmium"). MAY be an array of strings if different stains are used in each channel of the file (for example: ["LFB", "PLP"]).

Schema information:

anyOf:
- type: string
- items:
    type: string
  type: array

SamplingFrequency sense 1 (metadata)

Name: Sampling Frequency

Type: Metadata

Description: Sampling frequency (in Hz) of all the data in the recording, regardless of their type (for example, 2400).

Schema information:

type: number
unit: Hz

SamplingFrequency sense 2 (metadata)

Name: Sampling Frequency

Type: Metadata

Description: Sampling frequency (in Hz) of all the data in the recording, regardless of their type (for example, 2400).

Schema information:

anyOf:
- type: number
  unit: Hz
- enum:
  - n/a
  type: string

ScaleFactor (metadata)

Name: Scale Factor

Type: Metadata

Description: Scale factor for each frame. This field MUST be defined if the imaging data (.nii[.gz]) are scaled. If this field is not defined, then it is assumed that the scaling factor is 1. Defining this field when the scaling factor is 1 is RECOMMENDED, for the sake of clarity.

Schema information:

items:
  type: number
type: array

ScanDate (metadata)

Name: Scan Date

Type: Metadata

Description: Date of scan in the format "YYYY-MM-DD[Z]". This field is DEPRECATED, and this metadata SHOULD be recorded in the acq_time column of the corresponding Scans file.

Schema information:

format: date
type: string

ScanOptions (metadata)

Name: Scan Options

Type: Metadata

Description: Parameters of ScanningSequence. Corresponds to DICOM Tag 0018, 0022 Scan Options.

Schema information:

anyOf:
- type: string
- items:
    type: string
  type: array

ScanStart (metadata)

Name: Scan Start

Type: Metadata

Description: Time of start of scan with respect to TimeZero in the default unit seconds.

Schema information:

type: number
unit: s

ScanningSequence (metadata)

Name: Scanning Sequence

Type: Metadata

Description: Description of the type of data acquired. Corresponds to DICOM Tag 0018, 0020 Scanning Sequence.

Schema information:

anyOf:
- type: string
- items:
    type: string
  type: array

ScatterFraction (metadata)

Name: Scatter Fraction

Type: Metadata

Description: Scatter fraction for each frame (Units: 0-100%).

Schema information:

items:
  maximum: 100
  minimum: 0
  type: number
type: array

SequenceName (metadata)

Name: Sequence Name

Type: Metadata

Description: Manufacturer's designation of the sequence name. Corresponds to DICOM Tag 0018, 0024 Sequence Name.

Schema information:

type: string

SequenceVariant (metadata)

Name: Sequence Variant

Type: Metadata

Description: Variant of the ScanningSequence. Corresponds to DICOM Tag 0018, 0021 Sequence Variant.

Schema information:

anyOf:
- type: string
- items:
    type: string
  type: array

ShortChannelCount (metadata)

Name: Short Channel Count

Type: Metadata

Description: The number of short channels. 0 indicates no short channels.

Schema information:

minimum: 0
type: integer

SinglesRate (metadata)

Name: Singles Rate

Type: Metadata

Description: Singles rate for each frame (same units as Units, for example, "Bq/mL").

Schema information:

items:
  type: number
type: array

SkullStripped (metadata)

Name: Skull Stripped

Type: Metadata

Description: Whether the volume was skull stripped (non-brain voxels set to zero) or not.

Schema information:

type: boolean

SliceEncodingDirection (metadata)

Name: Slice Encoding Direction

Type: Metadata

Allowed values: i, j, k, i-, j-, k-

Description: The axis of the NIfTI data along which slices were acquired, and the direction in which "SliceTiming" is defined with respect to. i, j, k identifiers correspond to the first, second and third axis of the data in the NIfTI file. A - sign indicates that the contents of "SliceTiming" are defined in reverse order - that is, the first entry corresponds to the slice with the largest index, and the final entry corresponds to slice index zero. When present, the axis defined by "SliceEncodingDirection" needs to be consistent with the slice_dim field in the NIfTI header. When absent, the entries in "SliceTiming" must be in the order of increasing slice index as defined by the NIfTI header.

Schema information:

type: string

SliceThickness (metadata)

Name: Slice Thickness

Type: Metadata

Description: Slice thickness of the tissue sample in the unit micrometers ("um") (for example: 5).

Schema information:

exclusiveMinimum: 0
type: number
unit: um

SliceTiming (metadata)

Name: Slice Timing

Type: Metadata

Description: The time at which each slice was acquired within each volume (frame) of the acquisition. Slice timing is not slice order -- rather, it is a list of times containing the time (in seconds) of each slice acquisition in relation to the beginning of volume acquisition. The list goes through the slices along the slice axis in the slice encoding dimension (see below). Note that to ensure the proper interpretation of the "SliceTiming" field, it is important to check if the OPTIONAL SliceEncodingDirection exists. In particular, if "SliceEncodingDirection" is negative, the entries in "SliceTiming" are defined in reverse order with respect to the slice axis, such that the final entry in the "SliceTiming" list is the time of acquisition of slice 0. Without this parameter slice time correction will not be possible.

Schema information:

items:
  minimum: 0
  type: number
  unit: s
type: array

SoftwareFilters (metadata)

Name: Software Filters

Type: Metadata

Description: 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"}}).

Schema information:

anyOf:
- additionalProperties:
    type: object
  type: object
- enum:
  - n/a
  type: string

SoftwareName (metadata)

Name: Software Name

Type: Metadata

Description: Name of the software that was used to present the stimuli.

Schema information:

type: string

SoftwareRRID (metadata)

Name: SoftwareRRID

Type: Metadata

Description: Research Resource Identifier of the software that was used to present the stimuli. Examples: The RRID for Psychtoolbox is 'SCR_002881', and that of PsychoPy is 'SCR_006571'.

Schema information:

format: rrid
type: string

SoftwareVersion (metadata)

Name: Software Version

Type: Metadata

Description: Version of the software that was used to present the stimuli.

Schema information:

type: string

SoftwareVersions (metadata)

Name: Software Versions

Type: Metadata

Description: Manufacturer's designation of software version of the equipment that produced the measurements.

Schema information:

type: string

SourceDatasets (metadata)

Name: Source Datasets

Type: Metadata

Description: Used to specify the locations and relevant attributes of all source datasets. Valid keys in each object include "URL", "DOI" (see URI), and "Version" with string values.

Schema information:

items:
  properties:
    DOI:
      type: string
    URL:
      format: uri
      type: string
    Version:
      type: string
  type: object
type: array

SourceType (metadata)

Name: Source Type

Type: Metadata

Description: Type of source. Preferably a specific model/part number is supplied. This is a freeform description, but the following keywords are suggested: "LED", "LASER", "VCSEL". If individual channels have different SourceType, then the field here should be specified as "mixed" and this column should be included in optodes.tsv.

Schema information:

type: string

Sources (metadata)

Name: Sources

Type: Metadata

Description: A list of files with the paths specified using BIDS URIs; these files were directly used in the creation of this derivative data file. For example, if a derivative A is used in the creation of another derivative B, which is in turn used to generate C in a chain of A->B->C, C should only list B in "Sources", and B should only list A in "Sources". However, in case both X and Y are directly used in the creation of Z, then Z should list X and Y in "Sources", regardless of whether X was used to generate Y. Using paths specified relative to the dataset root is DEPRECATED.

Schema information:

items:
  format: dataset_relative
  type: string
type: array

SpatialReference (metadata)

Name: Spatial Reference

Type: Metadata

Description: For images with a single reference, the value MUST be a single string. For images with multiple references, such as surface and volume references, a JSON object MUST be used.

Schema information:

anyOf:
- enum:
  - orig
  type: string
- format: uri
  type: string
- format: dataset_relative
  type: string
- additionalProperties:
    anyOf:
    - enum:
      - orig
      type: string
    - format: uri
      type: string
    - format: dataset_relative
      type: string
  type: object

SpecificRadioactivity (metadata)

Name: Specific Radioactivity

Type: Metadata

Description: Specific activity of compound injected. Note this is not required for an FDG acquisition, since it is not available, and SHOULD be set to "n/a".

Schema information:

anyOf:
- type: number
- enum:
  - n/a
  type: string

SpecificRadioactivityMeasTime (metadata)

Name: Specific Radioactivity Measurement Time

Type: Metadata

Description: Time to which specific radioactivity measurement above applies in the default unit "hh:mm:ss".

Schema information:

format: time
type: string

SpecificRadioactivityUnits (metadata)

Name: Specific Radioactivity Units

Type: Metadata

Description: Unit format of specified specific radioactivity (for example, "Bq/g"). Note this is not required for an FDG acquisition, since it is not available, and SHOULD be set to "n/a".

Schema information:

anyOf:
- format: unit
  type: string
- enum:
  - n/a
  type: string

SpoilingGradientDuration (metadata)

Name: Spoiling Gradient Duration

Type: Metadata

Description: The duration of the spoiler gradient lobe in seconds. The duration of a trapezoidal lobe is defined as the summation of ramp-up and plateau times.

Schema information:

type: number
unit: s

SpoilingGradientMoment (metadata)

Name: Spoiling Gradient Moment

Type: Metadata

Description: Zeroth moment of the spoiler gradient lobe in millitesla times second per meter (mT.s/m).

Schema information:

type: number
unit: mT.s/m

SpoilingRFPhaseIncrement (metadata)

Name: Spoiling RF Phase Increment

Type: Metadata

Description: The amount of incrementation described in degrees, which is applied to the phase of the excitation pulse at each TR period for achieving RF spoiling.

Schema information:

type: number
unit: degrees

SpoilingState (metadata)

Name: Spoiling State

Type: Metadata

Description: Boolean stating whether the pulse sequence uses any type of spoiling strategy to suppress residual transverse magnetization.

Schema information:

type: boolean

SpoilingType (metadata)

Name: Spoiling Type

Type: Metadata

Allowed values: RF, GRADIENT, COMBINED

Description: Specifies which spoiling method(s) are used by a spoiled sequence.

Schema information:

type: string

StartTime (metadata)

Name: Start Time

Type: Metadata

Description: Start time in seconds in relation to the start of acquisition of the first data sample in the corresponding neural dataset (negative values are allowed).

Schema information:

type: number
unit: s

StationName (metadata)

Name: Station Name

Type: Metadata

Description: Institution defined name of the machine that produced the measurements.

Schema information:

type: string

StimulusPresentation (metadata)

Name: Stimulus Presentation

Type: Metadata

Description: Object containing key-value pairs related to the software used to present the stimuli during the experiment, specifically: "OperatingSystem", "SoftwareName", "SoftwareRRID", "SoftwareVersion" and "Code". See table below for more information.

Schema information:

properties:
  Code:
    description: '[URI](./common-principles.md#uniform-resource-indicator)

      of the code used to present the stimuli.

      Persistent identifiers such as DOIs are preferred.

      If multiple versions of code may be hosted at the same location,

      revision-specific URIs are recommended.

      '
    display_name: Code
    format: uri
    name: Code
    type: string
  OperatingSystem:
    description: 'Operating system used to run the stimuli presentation software

      (for formatting recommendations, see examples below this table).

      '
    display_name: Operating System
    name: OperatingSystem
    type: string
  SoftwareName:
    description: 'Name of the software that was used to present the stimuli.

      '
    display_name: Software Name
    name: SoftwareName
    type: string
  SoftwareRRID:
    description: '[Research Resource Identifier](https://scicrunch.org/resources)
      of the

      software that was used to present the stimuli.

      Examples: The RRID for Psychtoolbox is ''SCR_002881'',

      and that of PsychoPy is ''SCR_006571''.

      '
    display_name: SoftwareRRID
    format: rrid
    name: SoftwareRRID
    type: string
  SoftwareVersion:
    description: 'Version of the software that was used to present the stimuli.

      '
    display_name: Software Version
    name: SoftwareVersion
    type: string
recommended_fields:
- OperatingSystem
- SoftwareName
- SoftwareRRID
- SoftwareVersion
- Code
type: object

SubjectArtefactDescription (metadata)

Name: Subject Artefact Description

Type: Metadata

Description: Freeform description of the observed subject artefact 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.

Schema information:

type: string

T1map (suffixes)

Name: Longitudinal relaxation time image

Type: Suffix

Format: <entities>_T1map.<extension>

Description: In seconds (s). T1 maps are REQUIRED to use this suffix regardless of the method used to generate them. See this interactive book on T1 mapping for further reading on T1-mapping.

Schema information:

unit: s

T1rho (suffixes)

Name: T1 in rotating frame (T1 rho) image

Type: Suffix

Format: <entities>_T1rho.<extension>

Description: In seconds (s). T1-rho maps are REQUIRED to use this suffix regardless of the method used to generate them.

Schema information:

unit: s

T1w (suffixes)

Name: T1-weighted image

Type: Suffix

Format: <entities>_T1w.<extension>

Description: In arbitrary units (arbitrary). The contrast of these images is mainly determined by spatial variations in the longitudinal relaxation time of the imaged specimen. In spin-echo sequences this contrast is achieved at relatively short repetition and echo times. To achieve this weighting in gradient-echo images, again, short repetition and echo times are selected; however, at relatively large flip angles. Another common approach to increase T1 weighting in gradient-echo images is to add an inversion preparation block to the beginning of the imaging sequence (for example, TurboFLASH or MP-RAGE).

Schema information:

unit: arbitrary

T2map (suffixes)

Name: True transverse relaxation time image

Type: Suffix

Format: <entities>_T2map.<extension>

Description: In seconds (s). T2 maps are REQUIRED to use this suffix regardless of the method used to generate them.

Schema information:

unit: s

T2star (suffixes)

Name: T2* image

Type: Suffix

Format: <entities>_T2star.<extension>

Description: Ambiguous, may refer to a parametric image or to a conventional image. Change: Replaced by T2starw or T2starmap.

Schema information:

anyOf:
- unit: arbitrary
- unit: s

T2starmap (suffixes)

Name: Observed transverse relaxation time image

Type: Suffix

Format: <entities>_T2starmap.<extension>

Description: In seconds (s). T2-star maps are REQUIRED to use this suffix regardless of the method used to generate them.

Schema information:

unit: s

T2starw (suffixes)

Name: T2star weighted image

Type: Suffix

Format: <entities>_T2starw.<extension>

Description: In arbitrary units (arbitrary). The contrast of these images is mainly determined by spatial variations in the (observed) transverse relaxation time of the imaged specimen. In spin-echo sequences, this effect is negated as the excitation is followed by an inversion pulse. The contrast of gradient-echo images natively depends on T2-star effects. However, for T2-star variation to dominate the image contrast, gradient-echo acquisitions are carried out at long repetition and echo times, and at small flip angles.

Schema information:

unit: arbitrary

T2w (suffixes)

Name: T2-weighted image

Type: Suffix

Format: <entities>_T2w.<extension>

Description: In arbitrary units (arbitrary). The contrast of these images is mainly determined by spatial variations in the (true) transverse relaxation time of the imaged specimen. In spin-echo sequences this contrast is achieved at relatively long repetition and echo times. Generally, gradient echo sequences are not the most suitable option for achieving T2 weighting, as their contrast natively depends on T2-star rather than on T2.

Schema information:

unit: arbitrary

TB1AFI (suffixes)

Name: TB1AFI

Type: Suffix

Format: <entities>_TB1AFI.<extension>

Description: This method (Yarnykh 2007) calculates a B1+ map from two images acquired at interleaved (two) TRs with identical RF pulses using a steady-state sequence.

TB1DAM (suffixes)

Name: TB1DAM

Type: Suffix

Format: <entities>_TB1DAM.<extension>

Description: The double-angle B1+ method (Insko and Bolinger 1993) is based on the calculation of the actual angles from signal ratios, collected by two acquisitions at different nominal excitation flip angles. Common sequence types for this application include spin echo and echo planar imaging.

TB1EPI (suffixes)

Name: TB1EPI

Type: Suffix

Format: <entities>_TB1EPI.<extension>

Description: This B1+ mapping method (Jiru and Klose 2006) is based on two EPI readouts to acquire spin echo (SE) and stimulated echo (STE) images at multiple flip angles in one sequence, used in the calculation of deviations from the nominal flip angle.

TB1RFM (suffixes)

Name: TB1RFM

Type: Suffix

Format: <entities>_TB1RFM.<extension>

Description: The result of a Siemens rf_map product sequence. This sequence produces two images. The first image appears like an anatomical image and the second output is a scaled flip angle map.

TB1SRGE (suffixes)

Name: TB1SRGE

Type: Suffix

Format: <entities>_TB1SRGE.<extension>

Description: Saturation-prepared with 2 rapid gradient echoes (SA2RAGE) uses a ratio of two saturation recovery images with different time delays, and a simulated look-up table to estimate B1+ (Eggenschwiler et al. 2011). This sequence can also be used in conjunction with MP2RAGE T1 mapping to iteratively improve B1+ and T1 map estimation (Marques & Gruetter 2013).

TB1TFL (suffixes)

Name: TB1TFL

Type: Suffix

Format: <entities>_TB1TFL.<extension>

Description: The result of a Siemens tfl_b1_map product sequence. This sequence produces two images. The first image appears like an anatomical image and the second output is a scaled flip angle map.

TB1map (suffixes)

Name: RF transmit field image

Type: Suffix

Format: <entities>_TB1map.<extension>

Description: In arbitrary units (arbitrary). Radio frequency (RF) transmit (B1+) field maps are REQUIRED to use this suffix regardless of the method used to generate them. TB1map intensity values are RECOMMENDED to be represented as percent multiplicative factors such that FlipAngleeffective = B1+intensity*FlipAnglenominal .

Schema information:

unit: arbitrary

TEM (suffixes)

Name: Transmission electron microscopy

Type: Suffix

Format: <entities>_TEM.<extension>

Description: Transmission electron microscopy imaging data

TaskDescription (metadata)

Name: Task Description

Type: Metadata

Description: Longer description of the task.

Schema information:

type: string

TaskName (metadata)

Name: Task Name

Type: Metadata

Description: Name of the task. No two tasks should have the same name. The task label included in the file name 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 labelsfacesnbackandheadnodding`, respectively.

Schema information:

type: string

TermURL (metadata)

Name: TermURL

Type: Metadata

Description: URL pointing to a formal definition of this type of data in an ontology available on the web.

Schema information:

type: string

TimeZero (metadata)

Name: Time Zero

Type: Metadata

Description: Time zero to which all scan and/or blood measurements have been adjusted to, in the unit "hh:mm:ss". This should be equal to "InjectionStart" or "ScanStart".

Schema information:

format: time
type: string

TissueDeformationScaling (metadata)

Name: Tissue Deformation Scaling

Type: Metadata

Description: Estimated deformation of the tissue, given as a percentage of the original tissue size (for examples: for a shrinkage of 3%, the value is 97; and for an expansion of 100%, the value is 200).

Schema information:

exclusiveMinimum: 0
type: number

TissueOrigin (metadata)

Name: Tissue Origin

Type: Metadata

Allowed values: gray matter, white matter, csf, meninges, macrovascular, microvascular

Description: Describes the type of tissue analyzed for "SampleOrigin" brain.

Schema information:

type: string

TotalAcquiredPairs (metadata)

Name: Total Acquired Pairs

Type: Metadata

Description: The total number of acquired control-label pairs. A single pair consists of a single control and a single label image.

Schema information:

exclusiveMinimum: 0
type: number

TotalReadoutTime (metadata)

Name: Total Readout Time

Type: Metadata

Description: This is actually the "effective" total readout time, defined as the readout duration, specified in seconds, that would have generated data with the given level of distortion. It is NOT the actual, physical duration of the readout train. If "EffectiveEchoSpacing" has been properly computed, it is just EffectiveEchoSpacing * (ReconMatrixPE - 1).

Schema information:

type: number
unit: s

TracerMolecularWeight (metadata)

Name: Tracer Molecular Weight

Type: Metadata

Description: Accurate molecular weight of the tracer used.

Schema information:

type: number

TracerMolecularWeightUnits (metadata)

Name: Tracer Molecular Weight Units

Type: Metadata

Description: Unit of the molecular weights measurement (for example, "g/mol").

Schema information:

format: unit
type: string

TracerName (metadata)

Name: Tracer Name

Type: Metadata

Description: Name of the tracer compound used (for example, "CIMBI-36")

Schema information:

type: string

TracerRadLex (metadata)

Name: Tracer Rad Lex

Type: Metadata

Description: ID of the tracer compound from the RadLex Ontology.

Schema information:

type: string

TracerRadionuclide (metadata)

Name: Tracer Radionuclide

Type: Metadata

Description: Radioisotope labelling tracer (for example, "C11").

Schema information:

type: string

TracerSNOMED (metadata)

Name: TracerSNOMED

Type: Metadata

Description: ID of the tracer compound from the SNOMED Ontology (subclass of Radioactive isotope).

Schema information:

type: string

TriggerChannelCount (metadata)

Name: Trigger Channel Count

Type: Metadata

Description: Number of channels for digital (binary TTL) triggers or analog equivalents (TTL in volt). Corresponds to the TRIG channel type.

Schema information:

minimum: 0
type: integer

TubingLength (metadata)

Name: Tubing Length

Type: Metadata

Description: The length of the blood tubing, from the subject to the detector in meters.

Schema information:

type: number
unit: m

TubingType (metadata)

Name: Tubing Type

Type: Metadata

Description: Description of the type of tubing used, ideally including the material and (internal) diameter.

Schema information:

type: string

TwoPE (suffixes)

Name: 2-photon excitation microscopy

Type: Suffix

Format: <entities>_2PE.<extension>

Description: 2-photon excitation microscopy imaging data

Type (metadata)

Name: Type

Type: Metadata

Allowed values: Brain, Lesion, Face, ROI

Description: Short identifier of the mask. The value "Brain" refers to a brain mask. The value "Lesion" refers to a lesion mask. The value "Face" refers to a face mask. The value "ROI" refers to a region of interest mask.

Schema information:

type: string

UNIT1 (suffixes)

Name: Homogeneous (flat) T1-weighted MP2RAGE image

Type: Suffix

Format: <entities>_UNIT1.<extension>

Description: In arbitrary units (arbitrary). UNIT1 images are REQUIRED to use this suffix regardless of the method used to generate them. Note that although this image is T1-weighted, regions without MR signal will contain white salt-and-pepper noise that most segmentation algorithms will fail on. Therefore, it is important to dissociate it from T1w. Please see MP2RAGE specific notes in the qMRI appendix for further information.

Units (metadata)

Name: Units

Type: Metadata

Description: Measurement units for the associated file. SI units in CMIXF formatting are RECOMMENDED (see Units).

Schema information:

format: unit
type: string

VFA (suffixes)

Name: Variable flip angle

Type: Suffix

Format: <entities>_VFA.<extension>

Description: The VFA method involves at least two spoiled gradient echo (SPGR) of steady-state free precession (SSFP) images acquired at different flip angles. Depending on the provided metadata fields and the sequence type, data may be eligible for DESPOT1, DESPOT2 and their variants (Deoni et al. 2005).

VascularCrushing (metadata)

Name: Vascular Crushing

Type: Metadata

Description: Boolean indicating if Vascular Crushing is used. Corresponds to DICOM Tag 0018, 9259 ASL Crusher Flag.

Schema information:

type: boolean

VascularCrushingVENC (metadata)

Name: Vascular Crushing VENC

Type: Metadata

Description: The crusher gradient strength, in centimeters per second. Specify either one number for the total time-series, or provide an array of numbers, for example when using QUASAR, using the value zero to identify volumes for which VascularCrushing was turned off. Corresponds to DICOM Tag 0018, 925A ASL Crusher Flow Limit.

Schema information:

anyOf:
- type: number
  unit: cm/s
- items:
    type: number
    unit: cm/s
  type: array

VolumeTiming (metadata)

Name: Volume Timing

Type: Metadata

Description: The time at which each volume was acquired during the acquisition. It is described using a list of times referring to the onset of each volume in the BOLD series. The list must have the same length as the BOLD series, and the values must be non-negative and monotonically increasing. This field is mutually exclusive with "RepetitionTime" and "DelayTime". If defined, this requires acquisition time (TA) be defined via either "SliceTiming" or "AcquisitionDuration" be defined.

Schema information:

items:
  type: number
  unit: s
minItems: 1
type: array

WholeBloodAvail (metadata)

Name: Whole Blood Avail

Type: Metadata

Description: Boolean that specifies if whole blood measurements are available. If true, the whole_blood_radioactivity column MUST be present in the corresponding *_blood.tsv file.

Schema information:

type: boolean

WithdrawalRate (metadata)

Name: Withdrawal Rate

Type: Metadata

Description: The rate at which the blood was withdrawn from the subject. The unit of the specified withdrawal rate should be in "mL/s".

Schema information:

type: number
unit: mL/s

abbreviation (columns)

Name: Abbreviation

Type: Column

Description: The unique label abbreviation

Schema information:

type: string

acq_time sense 1 (columns)

Name: Scan acquisition time

Type: Column

Description: Acquisition time refers to when the first data point in each run was acquired. Furthermore, if this header is provided, the acquisition times of all files from the same recording MUST be identical. Datetime format and their anonymization are described in Units.

Schema information:

format: datetime
type: string

acq_time sense 2 (columns)

Name: Session acquisition time

Type: Column

Description: Acquisition time refers to when the first data point of the first run was acquired. Datetime format and their anonymization are described in Units.

Schema information:

format: datetime
type: string

acquisition (entities)

Name: Acquisition

Type: Entity

Description: The acq-<label> entity corresponds to a custom label the user MAY use to distinguish a different set of parameters used for acquiring the same modality.
For example, this should be used when a study includes two T1w images - one full brain low resolution and one restricted field of view but high resolution. In such case two files could have the following names: sub-01_acq-highres_T1w.nii.gz and sub-01_acq-lowres_T1w.nii.gz; however, the user is free to choose any other label than highres and lowres as long as they are consistent across subjects and sessions.
In case different sequences are used to record the same modality (for example, RARE and FLASH for T1w) this field can also be used to make that distinction. The level of detail at which the distinction is made (for example, just between RARE and FLASH, or between RARE, FLASH, and FLASHsubsampled) remains at the discretion of the researcher.

Schema information:

format: label
type: string

age (columns)

Name: Subject age

Type: Column

Description: Numeric value in years (float or integer value).

Schema information:

type: number
unit: year

anat (datatypes)

Name: Anatomical Magnetic Resonance Imaging

Type: Datatype

Description: Magnetic resonance imaging sequences designed to characterize static, anatomical features.

angio (suffixes)

Name: Angiogram

Type: Suffix

Format: <entities>_angio.<extension>

Description: Magnetic resonance angiography sequences focus on enhancing the contrast of blood vessels (generally arteries, but sometimes veins) against other tissue types.

asl (suffixes)

Name: Arterial Spin Labeling

Type: Suffix

Format: <entities>_asl.<extension>

Description: The complete ASL time series stored as a 4D NIfTI file in the original acquisition order, with possible volume types including: control, label, m0scan, deltam, cbf.

aslcontext (suffixes)

Name: Arterial Spin Labeling Context

Type: Suffix

Format: <entities>_aslcontext.<extension>

Description: A TSV file defining the image types for volumes in an associated ASL file.

asllabeling (suffixes)

Name: ASL Labeling Screenshot

Type: Suffix

Format: <entities>_asllabeling.<extension>

Description: An anonymized screenshot of the planning of the labeling slab/plane with respect to the imaging slab or slices *_asllabeling.jpg. Based on DICOM macro C.8.13.5.14.

atlas (entities)

Name: Atlas

Type: Entity

Description: The atlas-<label> key/value pair corresponds to a custom label the user MAY use to distinguish a different atlas used for similar type of data.
This entity is only applicable to derivative data.

Schema information:

format: label
type: string

ave (extensions)

Name: AVE

Type: Extension

Format: <entities>_<suffix>.ave

Description: File containing data averaged by segments of interest.
Used by KIT, Yokogawa, and Ricoh MEG systems.

bdf (extensions)

Name: Biosemi Data Format

Type: Extension

Format: <entities>_<suffix>.bdf

Description: A Biosemi Data Format file.
Each recording consists of a single .bdf file. bdf+ files are permitted. The capital .BDF extension MUST NOT be used.

beh (datatypes)

Name: Behavioral Data

Type: Datatype

Description: Behavioral data.

beh (modalities)

Name: Behavioral experiments

Type: Modalities

Description: Behavioral data acquired without accompanying neuroimaging data.

beh (suffixes)

Name: Behavioral recording

Type: Suffix

Format: <entities>_beh.<extension>

Description: Behavioral recordings from tasks. These files are similar to events files, but do not include the "onset" and "duration" columns that are mandatory for events files.

bids_uri (formats)

Name: BIDS uniform resource indicator

Type: Format

Regular expression: bids:[0-9a-zA-Z/#:\?\_\-\.]+

Description: A BIDS uniform resource indicator.
The validation for this format is minimal. It simply ensures that the value is a string with any characters that may appear in a valid URI, starting with "bids:".

blood (suffixes)

Name: Blood recording data

Type: Suffix

Format: <entities>_blood.<extension>

Description: Blood measurements of radioactivity stored in tabular files and located in the pet/ directory along with the corresponding PET data.

bold (suffixes)

Name: Blood-Oxygen-Level Dependent image

Type: Suffix

Format: <entities>_bold.<extension>

Description: Blood-Oxygen-Level Dependent contrast (specialized T2* weighting)

boolean (formats)

Name: Boolean

Type: Format

Regular expression: (true|false)

Description: A boolean. Must be either "true" or "false".

bval (extensions)

Name: FSL-Format Gradient Amplitudes

Type: Extension

Format: <entities>_<suffix>.bval

Description: A space-delimited file containing gradient directions (b-vectors) of diffusion measurement.
The bval file contains the b-values (in s/mm2) corresponding to the volumes in the relevant NIfTI file, with 0 designating b=0 volumes.

bvec (extensions)

Name: FSL-Format Gradient Directions

Type: Extension

Format: <entities>_<suffix>.bvec

Description: A space-delimited file containing gradient directions (b-vectors) of diffusion measurement.
This file contains 3 rows with N space-delimited floating-point numbers, corresponding to the N volumes in the corresponding NIfTI file.
The first row contains the x elements, the second row contains the y elements and the third row contains the z elements of a unit vector in the direction of the applied diffusion gradient, where the i-th elements in each row correspond together to the i-th volume, with [0,0,0] for non-diffusion-weighted (also called b=0 or low-b) volumes.
Following the FSL format for the bvec specification, the coordinate system of the b vectors MUST be defined with respect to the coordinate system defined by the header of the corresponding _dwi NIfTI file and not the scanner's device coordinate system (see Coordinate systems). The most relevant limitation imposed by this choice is that the gradient information cannot be directly stored in this format if the scanner generates b-vectors in scanner coordinates.

cardiac (columns)

Name: Cardiac measurement

Type: Column

Description: continuous pulse measurement

Schema information:

type: number

cbv (suffixes)

Name: Cerebral blood volume image

Type: Suffix

Format: <entities>_cbv.<extension>

Description: Cerebral Blood Volume contrast (specialized T2* weighting or difference between T1 weighted images)

ceagent (entities)

Name: Contrast Enhancing Agent

Type: Entity

Description: The ce-<label> entity can be used to distinguish sequences using different contrast enhanced images. The label is the name of the contrast agent.
This entity represents the "ContrastBolusIngredient" metadata field. Therefore, if the ce-<label> entity is present in a filename, "ContrastBolusIngredient" MAY also be added in the JSON file, with the same label.

Schema information:

format: label
type: string

channels (suffixes)

Name: Channels File

Type: Suffix

Format: <entities>_channels.<extension>

Description: Channel information.

chn (extensions)

Name: KRISS CHN

Type: Extension

Format: <entities>_<suffix>.chn

Description: A file generated by KRISS MEG systems containing the position of the center of the MEG coils.
Each experimental run on the KRISS system produces a file with extension .kdf. Additional files that may be available in the same directory include the digitized positions of the head points (\_digitizer.txt), the position of the center of the MEG coils (.chn), and the event markers (.trg).

chunk (entities)

Name: Chunk

Type: Entity

Description: The chunk-<index> key/value pair is used to distinguish between different regions, 2D images or 3D volumes files, of the same physical sample with different fields of view acquired in the same imaging experiment.

Schema information:

format: index
type: string

code (files)

Name: Code

Type: Files And Directories

Description: A directory in which to store any code (for example the one used to generate the derivatives from the raw data). See the Code section for more information.

Schema information:

file_type: directory

color (columns)

Name: Color label

Type: Column

Description: Hexadecimal. Label color for visualization.

Schema information:

type: string
unit: hexadecimal

con (extensions)

Name: KIT/Yokogawa/Ricoh Continuous Data

Type: Extension

Format: <entities>_<suffix>.con

Description: Raw continuous data from a KIT/Yokogawa/Ricoh MEG system.
Successor to the .sqd extension for raw continuous data.

coordsystem (suffixes)

Name: Coordinate System File

Type: Suffix

Format: <entities>_coordsystem.<extension>

Description: A JSON document specifying the coordinate system(s) used for the MEG, EEG, head localization coils, and anatomical landmarks.

dat (extensions)

Name: MEG Fine-Calibration Format

Type: Extension

Format: <entities>_<suffix>.dat

Description: A fine-calibration file used for Neuromag/Elekta/MEGIN MEG recording hardware.

data_acquisition (common_principles)

Name: Data acquisition

Type: Common Principle

Description: A continuous uninterrupted block of time during which a brain scanning instrument was acquiring data according to particular scanning sequence/protocol.

data_type (common_principles)

Name: Data type

Type: Common Principle

Description: A functional group of different types of data. Data files are contained in a directory named for the data type. In raw datasets, the data type directory is nested inside subject and (optionally) session directories. BIDS defines the following data types:
1. func (task based and resting state functional MRI)
2. dwi (diffusion weighted imaging)
3. fmap (field inhomogeneity mapping data such as field maps)
4. anat (structural imaging such as T1, T2, PD, and so on)
5. perf (perfusion)
6. meg (magnetoencephalography)
7. eeg (electroencephalography)
8. ieeg (intracranial electroencephalography)
9. beh (behavioral)
10. pet (positron emission tomography)
11. micr (microscopy)
12. nirs (near infrared spectroscopy)

dataset (common_principles)

Name: Dataset

Type: Common Principle

Description: A set of neuroimaging and behavioral data acquired for a purpose of a particular study. A dataset consists of data acquired from one or more subjects, possibly from multiple sessions.

dataset_description (files)

Name: Dataset Description

Type: Files And Directories

Description: The file dataset_description.json is a JSON file describing the dataset.

Schema information:

file_type: regular

dataset_relative (formats)

Name: Path relative to the BIDS dataset directory

Type: Format

Regular expression: (?!/)[0-9a-zA-Z/\_\-\.]+

Description: A path to a file, relative to the dataset directory.
The validation for this format is minimal. It simply ensures that the value is a string with any characters that may appear in a valid path, without starting with "/" (an absolute path).

date (formats)

Name: Date

Type: Format

Regular expression: [0-9]{4}-[0-9]{2}-[0-9]{2}([A-Z]{2,4})?

Description: A date in the form "YYYY-MM-DD[Z]", where [Z] is an optional, valid timezone code.

datetime (formats)

Name: Datetime

Type: Format

Regular expression: [0-9]{4}-[0-9]{2}-[0-9]{2}T(?:2[0-3]|[01][0-9]):[0-5][0-9]:[0-5][0-9](\.[0-9]{1,6})?([A-Z]{2,4})?

Description: A datetime in the form "YYYY-MM-DDThh:mm:ss[.000000][Z]", where [.000000] is an optional subsecond resolution between 1 and 6 decimal points, and [Z] is an optional, valid timezone code.

defacemask (suffixes)

Name: Defacing Mask

Type: Suffix

Format: <entities>_defacemask.<extension>

Description: A binary mask that was used to remove facial features from an anatomical MRI image.

density (entities)

Name: Density

Type: Entity

Description: Density of non-parametric surfaces.
This entity represents the "Density" metadata field. Therefore, if the den-<label> entity is present in a filename, "Density" MUST also be added in the JSON file, to provide interpretation.
This entity is only applicable to derivative data.

Schema information:

format: label
type: string

deprecated (common_principles)

Name: DEPRECATED

Type: Common Principle

Description: A "deprecated" entity or metadata field SHOULD NOT be used in the generation of new datasets. It remains in the standard in order to preserve the interpretability of existing datasets. Validating software SHOULD warn when deprecated practices are detected and provide a suggestion for updating the dataset to preserve the curator's intent.

derivatives (files)

Name: Derivative data

Type: Files And Directories

Description: Derivative data (for example preprocessed files). See the relevant section for more information.

Schema information:

file_type: directory

derived_from (columns)

Name: Derived from

Type: Column

Description: sample-<label> entity from which a sample is derived, for example a slice of tissue (sample-02) derived from a block of tissue (sample-01).

Schema information:

type: string

description (entities)

Name: Description

Type: Entity

Description: When necessary to distinguish two files that do not otherwise have a distinguishing entity, the desc-<label> entity SHOULD be used.
This entity is only applicable to derivative data.

Schema information:

format: label
type: string

description sense 1 (columns)

Name: Description

Type: Column

Description: Brief free-text description of the channel, or other information of interest.

Schema information:

type: string

description sense 2 (columns)

Name: Description

Type: Column

Description: Free-form text description of the optode, or other information of interest.

Schema information:

type: string

detector sense 1 (columns)

Name: Detector Name

Type: Column

Description: Name of the detector as specified in the *_optodes.tsv file. n/a for channels that do not contain NIRS signals (for example, acceleration).

Schema information:

anyOf:
- type: string
- enum:
  - n/a
  type: string

detector_type (columns)

Name: Detector Type

Type: Column

Description: The type of detector. Only to be used if the field DetectorType in *_nirs.json is set to mixed.

Schema information:

anyOf:
- type: string

dimension (columns)

Name: Dimension

Type: Column

Description: 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]).

Schema information:

type: string

direction (entities)

Name: Phase-Encoding Direction

Type: Entity

Description: The dir-<label> entity can be set to an arbitrary alphanumeric label (for example, dir-LR or dir-AP) to distinguish different phase-encoding directions.
This entity represents the "PhaseEncodingDirection" metadata field. Therefore, if the dir-<label> entity is present in a filename, "PhaseEncodingDirection" MUST be defined in the associated metadata. Please note that the <label> does not need to match the actual value of the field.

Schema information:

format: label
type: string

dlabelnii (extensions)

Name: CIFTI-2 Dense Label File

Type: Extension

Format: <entities>_<suffix>.dlabel.nii

Description: A CIFTI-2 dense label file.
This extension may only be used in derivative datasets.

dseg (suffixes)

Name: Discrete Segmentation

Type: Suffix

Format: <entities>_dseg.<extension>

Description: A discrete segmentation.
This suffix may only be used in derivative datasets.

duration (columns)

Name: Event duration

Type: Column

Description: Duration of the event (measured from onset) in seconds. Must always be either zero or positive (or n/a if unavailable). A "duration" value of zero implies that the delta function or event is so short as to be effectively modeled as an impulse.

Schema information:

anyOf:
- minimum: 0
  type: number
  unit: s
- enum:
  - n/a
  type: string

dwi (datatypes)

Name: Diffusion-Weighted Imaging

Type: Datatype

Description: Diffusion-weighted imaging (DWI).

dwi (suffixes)

Name: Diffusion-weighted image

Type: Suffix

Format: <entities>_dwi.<extension>

Description: Diffusion-weighted imaging contrast (specialized T2 weighting).

echo (entities)

Name: Echo

Type: Entity

Description: If files belonging to an entity-linked file collection are acquired at different echo times, the echo-<index> entity MUST be used to distinguish individual files.
This entity represents the "EchoTime" metadata field. Therefore, if the echo-<index> entity is present in a filename, "EchoTime" MUST be defined in the associated metadata. Please note that the <index> denotes the number/index (in the form of a nonnegative integer), not the "EchoTime" value of the separate JSON file.

Schema information:

format: index
type: string

edf (extensions)

Name: European Data Format

Type: Extension

Format: <entities>_<suffix>.edf

Description: A European data format file.
Each recording consists of a single .edf`` file. [edf+](https://www.edfplus.info/specs/edfplus.html) files are permitted. The capital.EDF` extension MUST NOT be used.

eeg (datatypes)

Name: Electroencephalography

Type: Datatype

Description: Electroencephalography

eeg (extensions)

Name: BrainVision Binary Data

Type: Extension

Format: <entities>_<suffix>.eeg

Description: A binary data file in the BrainVision Core Data Format. These files come in three-file sets, including a .vhdr, a .vmrk, and a .eeg file.

eeg (modalities)

Name: Electroencephalography

Type: Modalities

Description: Data acquired with EEG.

eeg (suffixes)

Name: Electroencephalography

Type: Suffix

Format: <entities>_eeg.<extension>

Description: Electroencephalography recording data.

electrodes (suffixes)

Name: Electrodes

Type: Suffix

Format: <entities>_electrodes.<extension>

Description: File that gives the location of (i)EEG electrodes.

epi (suffixes)

Name: EPI

Type: Suffix

Format: <entities>_epi.<extension>

Description: The phase-encoding polarity (PEpolar) technique combines two or more Spin Echo EPI scans with different phase encoding directions to estimate the underlying inhomogeneity/deformation map.

event (common_principles)

Name: Event

Type: Common Principle

Description: Something that happens or may be perceived by a test subject as happening at a particular instant during the recording. Events are most commonly associated with on- or offset of stimulus presentations, or with the distinct marker of on- or offset of a subject's response or motor action. Other events may include unplanned incidents (for example, sudden onset of noise and vibrations due to construction work, laboratory device malfunction), changes in task instructions (for example, switching the response hand), or experiment control parameters (for example, changing the stimulus presentation rate over experimental blocks), and noted data feature occurrences (for example, a recording electrode producing noise). In BIDS, each event has an onset time and duration. Note that not all tasks will have recorded events (for example, "resting state").

events (suffixes)

Name: Events

Type: Suffix

Format: <entities>_events.<extension>

Description: Event timing information from a behavioral task.

extension (common_principles)

Name: File extension

Type: Common Principle

Description: A portion of the file name after the left-most period (.) preceded by any other alphanumeric. For example, .gitignore does not have a file extension, but the file extension of test.nii.gz is .nii.gz. Note that the left-most period is included in the file extension.

fdt (extensions)

Name: EEGLAB FDT

Type: Extension

Format: <entities>_<suffix>.fdt

Description: An EEGLAB file.
The format used by the MATLAB toolbox EEGLAB. Each recording consists of a .set file with an optional .fdt file.

fieldmap (suffixes)

Name: Fieldmap

Type: Suffix

Format: <entities>_fieldmap.<extension>

Description: Some MR schemes such as spiral-echo imaging (SEI) sequences are able to directly provide maps of the B0 field inhomogeneity.

fif (extensions)

Name: Functional Imaging File Format

Type: Extension

Format: <entities>_<suffix>.fif

Description: An MEG file format used by Neuromag, Elekta, and MEGIN.

file_relative (formats)

Name: Path relative to the parent file

Type: Format

Regular expression: (?!/)[0-9a-zA-Z/\_\-\.]+

Description: A path to a file, relative to the file in which the field is defined.
The validation for this format is minimal. It simply ensures that the value is a string with any characters that may appear in a valid path, without starting with "/" (an absolute path).

filename (columns)

Name: Filename

Type: Column

Description: Relative paths to files.

Schema information:

format: participant_relative
type: string

flip (entities)

Name: Flip Angle

Type: Entity

Description: If files belonging to an entity-linked file collection are acquired at different flip angles, the _flip-<index> entity pair MUST be used to distinguish individual files.
This entity represents the "FlipAngle" metadata field. Therefore, if the flip-<index> entity is present in a filename, "FlipAngle" MUST be defined in the associated metadata. Please note that the <index> denotes the number/index (in the form of a nonnegative integer), not the "FlipAngle" value of the separate JSON file.

Schema information:

format: index
type: string

fmap (datatypes)

Name: Field maps

Type: Datatype

Description: MRI scans for estimating B0 inhomogeneity-induced distortions.

func (datatypes)

Name: Task-Based Magnetic Resonance Imaging

Type: Datatype

Description: Task (including resting state) imaging data

genetic_info (files)

Name: Genetic Information

Type: Files And Directories

Description: The genetic_info.json file describes the genetic information available in the participants.tsv file and/or the genetic database described in dataset_description.json. Datasets containing the Genetics field in dataset_description.json or the genetic_id column in participants.tsv MUST include this file.

Schema information:

file_type: regular

group sense 1 (columns)

Name: Channel group

Type: Column

Description: 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.

Schema information:

anyOf:
- type: string
- type: number

handedness (columns)

Name: Subject handedness

Type: Column

Allowed values: left, l, L, LEFT, Left, right, r, R, RIGHT, Right, ambidextrous, a, A, AMBIDEXTROUS, Ambidextrous, n/a

Description: String value indicating one of "left", "right", "ambidextrous".
For "left", use one of these values: left, l, L, LEFT, Left.
For "right", use one of these values: right, r, R, RIGHT, Right.
For "ambidextrous", use one of these values: ambidextrous, a, A, AMBIDEXTROUS, Ambidextrous.

Schema information:

type: string

headshape (suffixes)

Name: Headshape File

Type: Suffix

Format: <entities>_headshape.<extension>

Description: The 3-D locations of points that describe the head shape and/or electrode locations can be digitized and stored in separate files.

hed_version (formats)

Name: HED Version

Type: Format

Regular expression: ^(?:[a-zA-Z]+:)?(?:[a-zA-Z]+_)?(?:0|[1-9]\d*)\.(?:0|[1-9]\d*)\.(?:0|[1-9]\d*)\ (?:-(?:(?:0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\.(?:0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?\ (?:\+(?:[0-9a-zA-Z-]+(?:\.[0-9a-zA-Z-]+)*))?$

Description: The version string of the used HED schema.

hemisphere (columns)

Name: Electrode hemisphere

Type: Column

Allowed values: L, R

Description: The hemisphere in which the electrode is placed.

Schema information:

type: string

hemisphere (entities)

Name: Hemisphere

Type: Entity

Allowed values: L, R

Description: The hemi-<label> entity indicates which hemibrain is described by the file. Allowed label values for this entity are L and R, for the left and right hemibrains, respectively.

Schema information:

format: label
type: string

high_cutoff (columns)

Name: High cutoff

Type: Column

Description: 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.

Schema information:

anyOf:
- minimum: 0
  type: number
  unit: Hz
- enum:
  - n/a
  type: string

hplc_recovery_fractions (columns)

Name: HPLC recovery fractions

Type: Column

Description: HPLC recovery fractions (the fraction of activity that gets loaded onto the HPLC).

Schema information:

type: number
unit: arbitrary

iEEGCoordinateProcessingDescription (metadata)

Name: iEEG Coordinate Processing Description

Type: Metadata

Description: Has any post-processing (such as projection) been done on the electrode positions (for example, "surface_projection", "none").

Schema information:

type: string

iEEGCoordinateProcessingReference (metadata)

Name: iEEG Coordinate Processing Reference

Type: Metadata

Description: A reference to a paper that defines in more detail the method used to localize the electrodes and to post-process the electrode positions.

Schema information:

type: string

iEEGCoordinateSystem (metadata)

Name: iEEG Coordinate System

Type: Metadata

Allowed values: Pixels, ACPC, Other, ICBM452AirSpace, ICBM452Warp5Space, IXI549Space, fsaverage, fsaverageSym, fsLR, MNIColin27, MNI152Lin, MNI152NLin2009aSym, MNI152NLin2009bSym, MNI152NLin2009cSym, MNI152NLin2009aAsym, MNI152NLin2009bAsym, MNI152NLin2009cAsym, MNI152NLin6Sym, MNI152NLin6ASym, MNI305, NIHPD, OASIS30AntsOASISAnts, OASIS30Atropos, Talairach, UNCInfant, fsaverage3, fsaverage4, fsaverage5, fsaverage6, fsaveragesym, UNCInfant0V21, UNCInfant1V21, UNCInfant2V21, UNCInfant0V22, UNCInfant1V22, UNCInfant2V22, UNCInfant0V23, UNCInfant1V23, UNCInfant2V23

Description: 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.

Schema information:

type: string

iEEGCoordinateSystemDescription (metadata)

Name: iEEG Coordinate System Description

Type: Metadata

Description: 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.

Schema information:

type: string

iEEGCoordinateUnits (metadata)

Name: iEEG Coordinate Units

Type: Metadata

Allowed values: m, mm, cm, pixels, n/a

Description: Units of the *_electrodes.tsv. MUST be "pixels" if iEEGCoordinateSystem is Pixels.

Schema information:

type: string

iEEGElectrodeGroups (metadata)

Name: iEEG Electrode Groups

Type: Metadata

Description: 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".

Schema information:

type: string

iEEGGround (metadata)

Name: iEEG Ground

Type: Metadata

Description: Description of the location of the ground electrode ("placed on right mastoid (M2)").

Schema information:

type: string

iEEGPlacementScheme (metadata)

Name: iEEG Placement Scheme

Type: Metadata

Description: 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").

Schema information:

type: string

iEEGReference (metadata)

Name: iEEG Reference

Type: Metadata

Description: 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.

Schema information:

type: string

ieeg (datatypes)

Name: Intracranial electroencephalography

Type: Datatype

Description: Intracranial electroencephalography (iEEG) or electrocorticography (ECoG) data

ieeg (modalities)

Name: Intracranial Electroencephalography

Type: Modalities

Description: Data acquired with iEEG.

ieeg (suffixes)

Name: Intracranial Electroencephalography

Type: Suffix

Format: <entities>_ieeg.<extension>

Description: Intracranial electroencephalography recording data.

impedance (columns)

Name: Electrode impedance

Type: Column

Description: Impedance of the electrode, units MUST be in kOhm.

Schema information:

type: number
unit: kOhm

index (columns)

Name: Label index

Type: Column

Description: The label integer index.

Schema information:

type: integer

index (common_principles)

Name: index

Type: Common Principle

Description: A nonnegative integer, possibly prefixed with arbitrary number of 0s for consistent indentation, for example, it is 01 in run-01 following run-<index> specification.

index (formats)

Name: Index

Type: Format

Regular expression: [0-9]*[1-9]+[0-9]*

Description: Non-negative, non-zero integers, optionally prefixed with leading zeros for sortability. An index may not be all zeros.

inplaneT1 (suffixes)

Name: Inplane T1

Type: Suffix

Format: <entities>_inplaneT1.<extension>

Description: In arbitrary units (arbitrary). T1 weighted structural image matched to a functional (task) image.

Schema information:

unit: arbitrary

inplaneT2 (suffixes)

Name: Inplane T2

Type: Suffix

Format: <entities>_inplaneT2.<extension>

Description: In arbitrary units (arbitrary). T2 weighted structural image matched to a functional (task) image.

Schema information:

unit: arbitrary

integer (formats)

Name: Integer

Type: Format

Regular expression: [+-]?\d+

Description: An integer which may be positive or negative.

inversion (entities)

Name: Inversion Time

Type: Entity

Description: If files belonging to an entity-linked file collection are acquired at different inversion times, the inv-<index> entity MUST be used to distinguish individual files.
This entity represents the "InversionTime metadata field. Therefore, if the inv-<index> entity is present in a filename, "InversionTime" MUST be defined in the associated metadata. Please note that the <index> denotes the number/index (in the form of a nonnegative integer), not the "InversionTime" value of the separate JSON file.

Schema information:

format: index
type: string

jpg (extensions)

Name: Joint Photographic Experts Group Format

Type: Extension

Format: <entities>_<suffix>.jpg

Description: A JPEG image file.

json (extensions)

Name: JavaScript Object Notation

Type: Extension

Format: <entities>_<suffix>.json

Description: A JSON file.
In the BIDS specification, JSON files are primarily used as "sidecar" files, in which metadata describing "data" files are encoded. These sidecar files follow the inheritance principle.
There are also a few special cases of JSON files being first-order data files, such as genetic_info.json.

kdf (extensions)

Name: KRISS KDF

Type: Extension

Format: <entities>_<suffix>.kdf

Description: A KRISS (file with extension .kdf) file.
Each experimental run on the KRISS system produces a file with extension .kdf. Additional files that may be available in the same directory include the digitized positions of the head points (\_digitizer.txt), the position of the center of the MEG coils (.chn), and the event markers (.trg).

label (common_principles)

Name: label

Type: Common Principle

Description: An alphanumeric value, possibly prefixed with arbitrary number of 0s for consistent indentation, for example, it is rest in task-rest following task-<label> specification. Note that labels MUST not collide when casing is ignored (see Case collision intolerance).

label (entities)

Name: Label

Type: Entity

Description: Tissue-type label, following a prescribed vocabulary. Applies to binary masks and probabilistic/partial volume segmentations that describe a single tissue type.
This entity is only applicable to derivative data.

Schema information:

format: label
type: string

label (formats)

Name: Label

Type: Format

Regular expression: [0-9a-zA-Z]+

Description: Freeform labels without special characters.

labelgii (extensions)

Name: GIFTI label/annotation file

Type: Extension

Format: <entities>_<suffix>.label.gii

Description: A GIFTI label/annotation file.
This extension may only be used in derivative datasets.

low_cutoff (columns)

Name: Low cutoff

Type: Column

Description: Frequencies used for the high-pass filter applied to the channel in Hz. If no high-pass filter applied, use n/a.

Schema information:

anyOf:
- type: number
  unit: Hz
- enum:
  - n/a
  type: string

m0scan (suffixes)

Name: M0 image

Type: Suffix

Format: <entities>_m0scan.<extension>

Description: The M0 image is a calibration image, used to estimate the equilibrium magnetization of blood.

magnitude (suffixes)

Name: Magnitude

Type: Suffix

Format: <entities>_magnitude.<extension>

Description: Field-mapping MR schemes such as gradient-recalled echo (GRE) generate a Magnitude image to be used for anatomical reference. Requires the existence of Phase, Phase-difference or Fieldmap maps.

magnitude1 (suffixes)

Name: Magnitude

Type: Suffix

Format: <entities>_magnitude1.<extension>

Description: Magnitude map generated by GRE or similar schemes, associated with the first echo in the sequence.

magnitude2 (suffixes)

Name: Magnitude

Type: Suffix

Format: <entities>_magnitude2.<extension>

Description: Magnitude map generated by GRE or similar schemes, associated with the second echo in the sequence.

manufacturer (columns)

Name: Manufacturer

Type: Column

Description: The manufacturer for each electrode. Can be used if electrodes were manufactured by more than one company.

Schema information:

type: string

mapping (columns)

Name: Label mapping

Type: Column

Description: Corresponding integer label in the standard BIDS label lookup.

Schema information:

type: integer

markers (suffixes)

Name: MEG Sensor Coil Positions

Type: Suffix

Format: <entities>_markers.<extension>

Description: Another manufacturer-specific detail pertains to the KIT/Yokogawa/Ricoh system, which saves the MEG sensor coil positions in a separate file with two possible filename extensions (.sqd, .mrk). For these files, the markers suffix MUST be used. For example: sub-01_task-nback_markers.sqd

mask (suffixes)

Name: Binary Mask

Type: Suffix

Format: <entities>_mask.<extension>

Description: A binary mask that functions as a discrete "label" for a single structure.
This suffix may only be used in derivative datasets.

material (columns)

Name: Electrode material

Type: Column

Description: Material of the electrode (for example, Tin, Ag/AgCl, Gold).

Schema information:

type: string

md (extensions)

Name: Markdown

Type: Extension

Format: <entities>_<suffix>.md

Description: A Markdown file.

mefd (extensions)

Name: Multiscale Electrophysiology File Format Version 3.0

Type: Extension

Format: <entities>_<suffix>.mefd/

Description: A directory in the MEF3 format.
Each recording consists of a .mefd directory.

meg (datatypes)

Name: Magnetoencephalography

Type: Datatype

Description: Magnetoencephalography

meg (modalities)

Name: Magnetoencephalography

Type: Modalities

Description: Data acquired with an MEG scanner.

meg (suffixes)

Name: Magnetoencephalography

Type: Suffix

Format: <entities>_meg.<extension>

Description: Unprocessed MEG data stored in the native file format of the MEG instrument with which the data was collected.

metabolite_parent_fraction (columns)

Name: Metabolite parent fraction

Type: Column

Description: Parent fraction of the radiotracer (0-1).

Schema information:

maximum: 1
minimum: 0
type: number

metabolite_polar_fraction (columns)

Name: Metabolite polar fraction

Type: Column

Description: Polar metabolite fraction of the radiotracer (0-1).

Schema information:

maximum: 1
minimum: 0
type: number

mhd (extensions)

Name: ITAB Binary Header

Type: Extension

Format: <entities>_<suffix>.mhd

Description: Produced by ITAB-ARGOS153 systems. This file a binary header file, and is generated along with a raw data file with the .raw extension.

micr (datatypes)

Name: Microscopy

Type: Datatype

Description: Microscopy

micr (modalities)

Name: Microscopy

Type: Modalities

Description: Data acquired with a microscope.

modality (common_principles)

Name: Modality

Type: Common Principle

Description: The category of brain data recorded by a file. For MRI data, different pulse sequences are considered distinct modalities, such as T1w, bold or dwi. For passive recording techniques, such as EEG, MEG or iEEG, the technique is sufficiently uniform to define the modalities eeg, meg and ieeg. When applicable, the modality is indicated in the suffix. The modality may overlap with, but should not be confused with the data type.

modality (entities)

Name: Corresponding Modality

Type: Entity

Description: The mod-<label> entity corresponds to modality label for defacing masks, for example, T1w, inplaneT1, referenced by a defacemask image. For example, sub-01_mod-T1w_defacemask.nii.gz.

Schema information:

format: label
type: string

mri (modalities)

Name: Magnetic Resonance Imaging

Type: Modalities

Description: Data acquired with an MRI scanner.

mrk (extensions)

Name: MRK

Type: Extension

Format: <entities>_<suffix>.mrk

Description: A file containing MEG sensor coil positions.
Used by KIT, Yokogawa, and Ricoh MEG systems. Successor to the .sqd extension for marker files.

mtransfer (entities)

Name: Magnetization Transfer

Type: Entity

Allowed values: on, off

Description: If files belonging to an entity-linked file collection are acquired at different magnetization transfer (MT) states, the _mt-<label> entity MUST be used to distinguish individual files.
This entity represents the "MTState" metadata field. Therefore, if the mt-<label> entity is present in a filename, "MTState" MUST be defined in the associated metadata. Allowed label values for this entity are on and off, for images acquired in presence and absence of an MT pulse, respectively.

Schema information:

format: label
type: string

name sense 1 (columns)

Name: Channel name

Type: Column

Description: Label of the channel.

Schema information:

type: string

name sense 2 (columns)

Name: Electrode name

Type: Column

Description: Name of the electrode contact point.

Schema information:

type: string

name sense 3 (columns)

Name: Optode name

Type: Column

Description: Name of the optode, must be unique.

Schema information:

type: string

name sense 4 (columns)

Name: Label name

Type: Column

Description: The unique label name.

Schema information:

type: string

nii (extensions)

Name: NIfTI

Type: Extension

Format: <entities>_<suffix>.nii

Description: A Neuroimaging Informatics Technology Initiative (NIfTI) data file.

niigz (extensions)

Name: Compressed NIfTI

Type: Extension

Format: <entities>_<suffix>.nii.gz

Description: A compressed Neuroimaging Informatics Technology Initiative (NIfTI) data file.

nirs (datatypes)

Name: Near-Infrared Spectroscopy

Type: Datatype

Description: Near-Infrared Spectroscopy data organized around the SNIRF format

nirs (modalities)

Name: Near-Infrared Spectroscopy

Type: Modalities

Description: Data acquired with NIRS.

nirs (suffixes)

Name: Near Infrared Spectroscopy

Type: Suffix

Format: <entities>_nirs.<extension>

Description: Data associated with a Shared Near Infrared Spectroscopy Format file.

notch (columns)

Name: Notch frequencies

Type: Column

Description: Frequencies used for the notch filter applied to the channel, in Hz. If no notch filter applied, use n/a.

Schema information:

anyOf:
- type: number
  unit: Hz
- enum:
  - n/a
  type: string

number (formats)

Name: Number

Type: Format

Regular expression: [+-]?([0-9]+([.][0-9]*)?|[.][0-9]+)([eE][+-]?[0-9]+)?

Description: A number which may be an integer or float, positive or negative.

nwb (extensions)

Name: Neurodata Without Borders Format

Type: Extension

Format: <entities>_<suffix>.nwb

Description: A Neurodata Without Borders file.
Each recording consists of a single .nwb file.

onset (columns)

Name: Event onset

Type: Column

Description: Onset (in seconds) of the event, measured from the beginning of the acquisition of the first data point stored in the corresponding task data file. Negative onsets are allowed, to account for events that occur prior to the first stored data point. For example, in case there is an in-scanner training phase that begins before the scanning sequence has started events from this sequence should have negative onset time counting down to the beginning of the acquisition of the first volume.
If any data points have been discarded before forming the data file (for example, "dummy volumes" in BOLD fMRI), a time of 0 corresponds to the first stored data point and not the first acquired data point.

Schema information:

type: number
unit: s

optodes (suffixes)

Name: Optodes

Type: Suffix

Format: <entities>_optodes.<extension>

Description: Either a light emitting device, sometimes called a transmitter, or a photoelectric transducer, sometimes called a receiver.

orientation_component (columns)

Name: Orientation Component

Type: Column

Allowed values: x, y, z

Description: Description of the orientation of the channel.

Schema information:

type: string

part (entities)

Name: Part

Type: Entity

Allowed values: mag, phase, real, imag

Description: This entity is used to indicate which component of the complex representation of the MRI signal is represented in voxel data. The part-<label> entity is associated with the DICOM Tag 0008, 9208. Allowed label values for this entity are phase, mag, real and imag, which are typically used in part-mag/part-phase or part-real/part-imag pairs of files.
Phase images MAY be in radians or in arbitrary units. The sidecar JSON file MUST include the units of the phase image. The possible options are "rad" or "arbitrary".
When there is only a magnitude image of a given type, the part entity MAY be omitted.

Schema information:

format: label
type: string

participant_id (columns)

Name: Participant ID

Type: Column

Description: A participant identifier of the form sub-<label>, matching a participant entity found in the dataset.

Schema information:

type: string

participant_relative (formats)

Name: Path relative to the participant directory

Type: Format

Regular expression: (?!/)(?!sub-)[0-9a-zA-Z/\_\-\.]+

Description: A path to a file, relative to the participant's directory in the dataset.
The validation for this format is minimal. It simply ensures that the value is a string with any characters that may appear in a valid path, without starting with "/" (an absolute path) or "sub/" (a relative path starting with the participant directory, rather than relative to that directory).

participants (files)

Name: Participant Information

Type: Files And Directories

Description: The purpose of this RECOMMENDED file is to describe properties of participants such as age, sex, handedness. If this file exists, it MUST contain the column participant_id, which MUST consist of sub-<label> values identifying one row for each participant, followed by a list of optional columns describing participants. Each participant MUST be described by one and only one row.
Commonly used optional columns in participant.tsv files are age, sex, and handedness. We RECOMMEND to make use of these columns, and in case that you do use them, we RECOMMEND to use the following values for them:
- age: numeric value in years (float or integer value)
- sex: string value indicating phenotypical sex, one of "male", "female", "other"
- for "male", use one of these values: male, m, M, MALE, Male
- for "female", use one of these values: female, f, F, FEMALE, Female
- for "other", use one of these values: other, o, O, OTHER, Other
- handedness: string value indicating one of "left", "right", "ambidextrous"
- for "left", use one of these values: left, l, L, LEFT, Left
- for "right", use one of these values: right, r, R, RIGHT, Right
- for "ambidextrous", use one of these values: ambidextrous, a, A, AMBIDEXTROUS, Ambidextrous
Throughout BIDS you can indicate missing values with n/a (for "not available").

Schema information:

file_type: regular

pathology (columns)

Name: Pathology

Type: Column

Description: String value describing the pathology of the sample or type of control. When different from healthy, pathology SHOULD be specified. The pathology may be specified in either samples.tsv or sessions.tsv, depending on whether the pathology changes over time.

Schema information:

type: string

perf (datatypes)

Name: Perfusion imaging

Type: Datatype

Description: Blood perfusion imaging data, including arterial spin labeling (ASL)

pet (datatypes)

Name: Positron Emission Tomography

Type: Datatype

Description: Positron emission tomography data

pet (modalities)

Name: Positron Emission Tomography

Type: Modalities

Description: Data acquired with PET.

pet (suffixes)

Name: Positron Emission Tomography

Type: Suffix

Format: <entities>_pet.<extension>

Description: PET imaging data SHOULD be stored in 4D (or 3D, if only one volume was acquired) NIfTI files with the _pet suffix. Volumes MUST be stored in chronological order (the order they were acquired in).

phase (suffixes)

Name: Phase image

Type: Suffix

Format: <entities>_phase.<extension>

Description: DEPRECATED. Phase information associated with magnitude information stored in BOLD contrast. This suffix should be replaced by the part-phase in conjunction with the bold suffix.

Schema information:

anyOf:
- unit: arbitrary
- unit: rad

phase1 (suffixes)

Name: Phase

Type: Suffix

Format: <entities>_phase1.<extension>

Description: Phase map generated by GRE or similar schemes, associated with the first echo in the sequence.

phase2 (suffixes)

Name: Phase

Type: Suffix

Format: <entities>_phase2.<extension>

Description: Phase map generated by GRE or similar schemes, associated with the second echo in the sequence.

phasediff (suffixes)

Name: Phase-difference

Type: Suffix

Format: <entities>_phasediff.<extension>

Description: Some scanners subtract the phase1 from the phase2 map and generate a unique phasediff file. For instance, this is a common output for the built-in fieldmap sequence of Siemens scanners.

photo (suffixes)

Name: Photo File

Type: Suffix

Format: <entities>_photo.<extension>

Description: Photos of the anatomical landmarks, head localization coils or tissue sample.

physio (suffixes)

Name: Physiological recording

Type: Suffix

Format: <entities>_physio.<extension>

Description: Physiological recordings such as cardiac and respiratory signals.

plasma_radioactivity (columns)

Name: Plasma radioactivity

Type: Column

Description: Radioactivity in plasma, in unit of plasma radioactivity (for example, kBq/mL).

Schema information:

type: number

png (extensions)

Name: Portable Network Graphics

Type: Extension

Format: <entities>_<suffix>.png

Description: A Portable Network Graphics file.

pos (extensions)

Name: Head Point Position

Type: Extension

Format: <entities>_<suffix>.pos

Description: File containing digitized positions of the head points.
This may be produced by a 4D neuroimaging/BTi MEG system or a CTF MEG system.

probseg (suffixes)

Name: Probabilistic Segmentation

Type: Suffix

Format: <entities>_probseg.<extension>

Description: A probabilistic segmentation.
This suffix may only be used in derivative datasets.

processing (entities)

Name: Processed (on device)

Type: Entity

Description: 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 Neuromag/Elekta/MEGIN's MaxFilter (for example, sss, tsss, trans, quat or mc), which some installations impose to be run on raw data because of active shielding software corrections before the MEG data can actually be exploited.

Schema information:

format: label
type: string

raw (extensions)

Name: RAW

Type: Extension

Format: <entities>_<suffix>.raw

Description: When produced by a KIT / Yokogawa / Ricoh MEG system, this file contains trial-based evoked fields.
When produced by an ITAB-ARGOS153 system, this file contains raw data and is generated along with an associated binary header file with the .mhd extension.

reconstruction (entities)

Name: Reconstruction

Type: Entity

Description: The rec-<label> entity can be used to distinguish different reconstruction algorithms (for example, MoCo for the ones using motion correction).

Schema information:

format: label
type: string

recording (entities)

Name: Recording

Type: Entity

Description: The recording-<label> entity can be used to distinguish continuous recording files.
This entity is commonly applied when continuous recordings have different sampling frequencies or start times. For example, physiological recordings with different sampling frequencies may be distinguished using labels like recording-100Hz and recording-500Hz.

Schema information:

format: label
type: string

reference sense 1 (columns)

Name: Electrode reference

Type: Column

Description: Name of the reference electrode(s). This column is not needed when it is common to all channels. In that case the reference electrode(s) can be specified in *_eeg.json as EEGReference).

Schema information:

type: string

reference sense 2 (columns)

Name: Electrode reference

Type: Column

Description: 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.

Schema information:

anyOf:
- type: string
- enum:
  - n/a
  type: string

resolution (entities)

Name: Resolution

Type: Entity

Description: Resolution of regularly sampled N-dimensional data.
This entity represents the "Resolution" metadata field. Therefore, if the res-<label> entity is present in a filename, "Resolution" MUST also be added in the JSON file, to provide interpretation.
This entity is only applicable to derivative data.

Schema information:

format: label
type: string

respiratory (columns)

Name: Respiratory measurement

Type: Column

Description: continuous breathing measurement

Schema information:

type: number

response_time (columns)

Name: Response time

Type: Column

Description: Response time measured in seconds. A negative response time can be used to represent preemptive responses and n/a denotes a missed response.

Schema information:

anyOf:
- type: number
  unit: s
- enum:
  - n/a
  type: string

rrid (formats)

Name: Research resource identifier

Type: Format

Regular expression: RRID:.+_.+

Description: A research resource identifier.

rst (extensions)

Name: reStructuredText

Type: Extension

Format: <entities>_<suffix>.rst

Description: A reStructuredText file.

run (common_principles)

Name: Run

Type: Common Principle

Description: An uninterrupted repetition of data acquisition that has the same acquisition parameters and task (however events can change from run to run due to different subject response or randomized nature of the stimuli). Run is a synonym of a data acquisition. Note that "uninterrupted" may look different by modality due to the nature of the recording. For example, in MRI or MEG, if a subject leaves the scanner, the acquisition must be restarted. For some types of PET acquisitions, a subject may leave and re-enter the scanner without interrupting the scan.

run (entities)

Name: Run

Type: Entity

Description: The run-<index> entity is used to distinguish separate data acquisitions with the same acquisition parameters and (other) entities.
If several data acquisitions (for example, MRI scans or EEG recordings) with the same acquisition parameters are acquired in the same session, they MUST be indexed with the run-<index> entity: _run-1, _run-2, _run-3, and so on (only nonnegative integers are allowed as run indices).
If different entities apply, such as a different session indicated by [ses-<label>][./appendices/entities.md#ses), or different acquisition parameters indicated by acq-<label>, then run is not needed to distinguish the scans and MAY be omitted.

Schema information:

format: index
type: string

sample (columns)

Name: Sample index

Type: Column

Description: Onset of the event according to the sampling scheme of the recorded modality (that is, referring to the raw data file that the events.tsv file accompanies). When there are several sampling schemes present in the raw data file (as can be the case for example for .edf files), this column is ambiguous and SHOULD NOT be used.

Schema information:

type: integer

sample (common_principles)

Name: Sample

Type: Common Principle

Description: A sample pertaining to a subject such as tissue, primary cell or cell-free sample. Sample labels MUST be unique within a subject and it is RECOMMENDED that they be unique throughout the dataset.

sample (entities)

Name: Sample

Type: Entity

Description: A sample pertaining to a subject such as tissue, primary cell or cell-free sample. The sample-<label> entity is used to distinguish between different samples from the same subject. The label MUST be unique per subject and is RECOMMENDED to be unique throughout the dataset.

Schema information:

format: label
type: string

sample_id (columns)

Name: Sample ID

Type: Column

Description: A sample identifier of the form sample-<label>, matching a sample entity found in the dataset.

Schema information:

type: string

sample_type (columns)

Name: Sample type

Type: Column

Allowed values: cell line, in vitro differentiated cells, primary cell, cell-free sample, cloning host, tissue, whole organisms, organoid, technical sample

Description: Biosample type defined by ENCODE Biosample Type.

Schema information:

type: string

samples (files)

Name: Sample Information

Type: Files And Directories

Description: The purpose of this file is to describe properties of samples, indicated by the sample entity. This file is REQUIRED if sample-<label> is present in any file name within the dataset. If this file exists, it MUST contain the three following columns:
- sample_id: MUST consist of sample-<label> values identifying one row for each sample
- participant_id: MUST consist of sub-<label>
- sample_type: MUST consist of sample type values, either cell line, in vitro differentiated cells, primary cell, cell-free sample, cloning host, tissue, whole organisms, organoid or technical sample from ENCODE Biosample Type
Other optional columns MAY be used to describe the samples. Each sample MUST be described by one and only one row.
Commonly used optional columns in samples.tsv files are pathology and derived_from. We RECOMMEND to make use of these columns, and in case that you do use them, we RECOMMEND to use the following values for them:
- pathology: string value describing the pathology of the sample or type of control. When different from healthy, pathology SHOULD be specified in samples.tsv. The pathology MAY instead be specified in Sessions files in case it changes over time.
- derived_from: sample-<label> key/value pair from which a sample is derived from, for example a slice of tissue (sample-02) derived from a block of tissue (sample-01)

Schema information:

file_type: regular

sampling_frequency (columns)

Name: Channel sampling frequency

Type: Column

Description: Sampling rate of the channel in Hz.

Schema information:

type: number
unit: Hz

sbref (suffixes)

Name: Single-band reference image

Type: Suffix

Format: <entities>_sbref.<extension>

Description: Single-band reference for one or more multi-band dwi images.

scans (suffixes)

Name: Scans file

Type: Suffix

Format: <entities>_scans.<extension>

Description: The purpose of this file is to describe timing and other properties of each imaging acquisition sequence (each run file) within one session. Each neural recording file SHOULD be described by exactly one row. Some recordings consist of multiple parts, that span several files, for example through echo-, part-, or split- entities. Such recordings MUST be documented with one row per file. Relative paths to files should be used under a compulsory filename header. If acquisition time is included it should be listed under the acq_time header. Acquisition time refers to when the first data point in each run was acquired. Furthermore, if this header is provided, the acquisition times of all files that belong to a recording MUST be identical. Datetime should be expressed as described in Units. Additional fields can include external behavioral measures relevant to the scan. For example vigilance questionnaire score administered after a resting state scan. All such included additional fields SHOULD be documented in an accompanying _scans.json file that describes these fields in detail (see Tabular files).

session (common_principles)

Name: Session

Type: Common Principle

Description: A logical grouping of neuroimaging and behavioral data consistent across subjects. Session can (but doesn't have to) be synonymous to a visit in a longitudinal study. In general, subjects will stay in the scanner during one session. However, for example, if a subject has to leave the scanner room and then be re-positioned on the scanner bed, the set of MRI acquisitions will still be considered as a session and match sessions acquired in other subjects. Similarly, in situations where different data types are obtained over several visits (for example fMRI on one day followed by DWI the day after) those can be grouped in one session. Defining multiple sessions is appropriate when several identical or similar data acquisitions are planned and performed on all -or most- subjects, often in the case of some intervention between sessions (for example, training). In the PET context, a session may also indicate a group of related scans, taken in one or more visits.

session (entities)

Name: Session

Type: Entity

Description: A logical grouping of neuroimaging and behavioral data consistent across subjects. Session can (but doesn't have to) be synonymous to a visit in a longitudinal study. In general, subjects will stay in the scanner during one session. However, for example, if a subject has to leave the scanner room and then be re-positioned on the scanner bed, the set of MRI acquisitions will still be considered as a session and match sessions acquired in other subjects. Similarly, in situations where different data types are obtained over several visits (for example fMRI on one day followed by DWI the day after) those can be grouped in one session.
Defining multiple sessions is appropriate when several identical or similar data acquisitions are planned and performed on all -or most- subjects, often in the case of some intervention between sessions (for example, training).

Schema information:

format: label
type: string

session_id (columns)

Name: Session ID

Type: Column

Description: A session identifier of the form ses-<label>, matching a session found in the dataset.

Schema information:

type: string

sessions (suffixes)

Name: Sessions file

Type: Suffix

Format: <entities>_sessions.<extension>

Description: In case of multiple sessions there is an option of adding additional sessions.tsv files describing variables changing between sessions. In such case one file per participant SHOULD be added. These files MUST include a session_id column and describe each session by one and only one row. Column names in sessions.tsv files MUST be different from group level participant key column names in the participants.tsv file.

set (extensions)

Name: EEGLAB SET

Type: Extension

Format: <entities>_<suffix>.set

Description: An EEGLAB file.
The format used by the MATLAB toolbox EEGLAB. Each recording consists of a .set file with an optional .fdt file.

sex (columns)

Name: Sex

Type: Column

Allowed values: male, m, M, MALE, Male, female, f, F, FEMALE, Female, other, o, O, OTHER, Other, n/a

Description: String value indicating phenotypical sex, one of "male", "female", "other".
For "male", use one of these values: male, m, M, MALE, Male.
For "female", use one of these values: female, f, F, FEMALE, Female.
For "other", use one of these values: other, o, O, OTHER, Other.

Schema information:

type: string

short_channel (columns)

Name: Short Channel

Type: Column

Description: Is the channel designated as short. The total number of channels listed as short channels SHOULD be stored in ShortChannelCount in *_nirs.json.

Schema information:

type: boolean

size (columns)

Name: Electrode size

Type: Column

Description: Surface area of the electrode, units MUST be in mm^2.

Schema information:

type: number
unit: mm^2

snirf (extensions)

Name: Shared Near Infrared Spectroscopy Format

Type: Extension

Format: <entities>_<suffix>.snirf

Description: HDF5 file organized according to the SNIRF specification

software_filters (columns)

Name: Software filters

Type: Column

Description: List of temporal and/or spatial software filters applied (for example, 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.

Schema information:

anyOf:
- type: string
- enum:
  - n/a
  type: string

source sense 1 (columns)

Name: Source name

Type: Column

Description: Name of the source as specified in the *_optodes.tsv file. n/a for channels that do not contain fNIRS signals (for example, acceleration).

Schema information:

anyOf:
- type: string
- enum:
  - n/a
  type: string

source sense 2 (columns)

Name: Source type

Type: Column

Description: The type of source. Only to be used if the field SourceType in *_nirs.json is set to mixed.

Schema information:

anyOf:
- type: string

sourcedata (files)

Name: Source data

Type: Files And Directories

Description: A directory where to store data before harmonization, reconstruction, and/or file format conversion (for example, E-Prime event logs or DICOM files). See the relevant section for more information.

Schema information:

file_type: directory

space (entities)

Name: Space

Type: Entity

Description: The space-<label> entity can be used to indicate the way in which electrode positions are interpreted (for EEG/MEG/iEEG data) or the spatial reference to which a file has been aligned (for MRI data). The <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 EEG/MEG/iEEG data, this entity can be applied to raw data, but for other data types, it is restricted to derivative data.

Schema information:

format: label
type: string

species (columns)

Name: Species

Type: Column

Description: The species column SHOULD be a binomial species name from the NCBI Taxonomy (for example, homo sapiens, mus musculus, rattus norvegicus). For backwards compatibility, if species is absent, the participant is assumed to be homo sapiens.

Schema information:

type: string

split (entities)

Name: Split

Type: Entity

Description: In the case of long data recordings that exceed a file size of 2Gb, .fif files are conventionally split into multiple parts. Each of these files has an internal pointer to the next file. This is important when renaming these split recordings to the BIDS convention.
Instead of a simple renaming, files should be read in and saved under their new names with dedicated tools like MNE-Python, which will ensure that not only the file names, but also the internal file pointers, will be updated.
It is RECOMMENDED that .fif files with multiple parts use the split-<index> entity to indicate each part. If there are multiple parts of a recording and the optional scans.tsv is provided, all files MUST be listed separately in scans.tsv and the entries for the acq_time column in scans.tsv MUST all be identical, as described in Scans file.

Schema information:

format: index
type: string

sqd (extensions)

Name: SQD

Type: Extension

Format: <entities>_<suffix>.sqd

Description: A file containing either raw MEG data or MEG sensor coil positions. While this extension is still valid, it has been succeeded by .con for raw MEG data and .mrk for marker information.
Used by KIT, Yokogawa, and Ricoh MEG systems.

stain (entities)

Name: Stain

Type: Entity

Description: The stain-<label> key/pair values can be used to distinguish image files from the same sample using different stains or antibodies for contrast enhancement.
This entity represents the "SampleStaining" metadata field. Therefore, if the stain-<label> entity is present in a filename, "SampleStaining" SHOULD be defined in the associated metadata, although the label may be different.
Descriptions of antibodies SHOULD also be indicated in the "SamplePrimaryAntibodies" and/or "SampleSecondaryAntobodies" metadata fields, as appropriate.

Schema information:

format: label
type: string

status (columns)

Name: Channel status

Type: Column

Allowed values: good, bad, n/a

Description: 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].

Schema information:

type: string

status_description (columns)

Name: Channel status description

Type: Column

Description: 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.

Schema information:

type: string

stim (suffixes)

Name: Continuous recording

Type: Suffix

Format: <entities>_stim.<extension>

Description: Continuous measures, such as parameters of a film or audio stimulus.

stim_file (columns)

Name: Stimulus file

Type: Column

Description: Represents the location of the stimulus file (such as an image, video, or audio file) presented at the given onset time. There are no restrictions on the file formats of the stimuli files, but they should be stored in the /stimuli directory (under the root directory of the dataset; with optional subdirectories). The values under the stim_file column correspond to a path relative to /stimuli. For example images/cat03.jpg will be translated to /stimuli/images/cat03.jpg.

Schema information:

format: stimuli_relative
type: string

stimuli (files)

Name: Stimulus files

Type: Files And Directories

Description: A directory to store any stimulus files used during an experiment. See the relevant section for more information.

Schema information:

file_type: directory

stimuli_relative (formats)

Name: Path relative to the stimuli directory

Type: Format

Regular expression: (?!/)(?!stimuli/)[0-9a-zA-Z/\_\-\.]+

Description: A path to a stimulus file, relative to a /stimuli directory somewhere.
The validation for this format is minimal. It simply ensures that the value is a string with any characters that may appear in a valid path, without starting with "/" (an absolute path) or "stimuli/" (a relative path starting with the stimuli directory, rather than relative to that directory).

strain (columns)

Name: Strain

Type: Column

Description: For species different from homo sapiens, string value indicating the strain of the species, for example: C57BL/6J.

Schema information:

type: string

strain_rrid (columns)

Name: Strain RRID

Type: Column

Description: For species different from homo sapiens, research resource identifier (RRID) of the strain of the species, for example: RRID:IMSR_JAX:000664.

Schema information:

format: rrid
type: string

string (formats)

Name: String

Type: Format

Regular expression: .*

Description: The basic string type (not a specific format). This should allow any free-form string.

subject (common_principles)

Name: Subject

Type: Common Principle

Description: A person or animal participating in the study. Used interchangeably with term Participant.

subject (entities)

Name: Subject

Type: Entity

Description: A person or animal participating in the study.

Schema information:

format: label
type: string

suffix (common_principles)

Name: suffix

Type: Common Principle

Description: An alphanumeric string that forms part of a filename, located after all entities and following a final _, right before the file extension; for example, it is eeg in sub-05_task-matchingpennies_eeg.vhdr.

task (common_principles)

Name: Task

Type: Common Principle

Description: A set of structured activities performed by the participant. Tasks are usually accompanied by stimuli and responses, and can greatly vary in complexity. For the purpose of this specification we consider the so-called "resting state" a task. In the context of brain scanning, a task is always tied to one data acquisition. Therefore, even if during one acquisition the subject performed multiple conceptually different behaviors (with different sets of instructions) they will be considered one (combined) task.

task (entities)

Name: Task

Type: Entity

Description: A set of structured activities performed by the participant. Tasks are usually accompanied by stimuli and responses, and can greatly vary in complexity.
In the context of brain scanning, a task is always tied to one data acquisition. Therefore, even if during one acquisition the subject performed multiple conceptually different behaviors (with different sets of instructions) they will be considered one (combined) task.
While tasks may be repeated across multiple acquisitions, a given task may have different sets of stimuli (for example, randomized order) and participant responses across subjects, sessions, and runs.
The task-<label> MUST be consistent across subjects and sessions.
Files with the task-<label> entity SHOULD have an associated events file, as well as certain metadata fields in the associated JSON file.
For the purpose of this specification we consider the so-called "resting state" a task, although events files are not expected for resting state data. Additionally, a common convention in the specification is to include the word "rest" in the task label for resting state files (for example, task-rest).

Schema information:

format: label
type: string

template_x (columns)

Name: X template position

Type: Column

Description: Assumed or ideal position along the x axis.

Schema information:

anyOf:
- type: number
- enum:
  - n/a
  type: string

template_y (columns)

Name: Y template position

Type: Column

Description: Assumed or ideal position along the y axis.

Schema information:

anyOf:
- type: number
- enum:
  - n/a
  type: string

template_z (columns)

Name: Z template position

Type: Column

Description: Assumed or ideal position along the z axis.

Schema information:

anyOf:
- type: number
- enum:
  - n/a
  type: string

tif (extensions)

Name: Tag Image File Format

Type: Extension

Format: <entities>_<suffix>.tif

Description: A Tag Image File Format file.

time (columns)

Name: Time

Type: Column

Description: Time, in seconds, relative to TimeZero defined by the *_pet.json. For example, 5.

Schema information:

type: number
unit: s

time (formats)

Name: Time

Type: Format

Regular expression: (?:2[0-3]|[01]?[0-9]):[0-5][0-9]:[0-5][0-9]

Description: A time in the form "hh:mm:ss".

tracer (entities)

Name: Tracer

Type: Entity

Description: The trc-<label> entity can be used to distinguish sequences using different tracers.
This entity represents the "TracerName" metadata field. Therefore, if the trc-<label> entity is present in a filename, "TracerName" MUST be defined in the associated metadata. Please note that the <label> does not need to match the actual value of the field.

Schema information:

format: label
type: string

trg (extensions)

Name: KRISS TRG

Type: Extension

Format: <entities>_<suffix>.trg

Description: A file generated by KRISS MEG systems containing the event markers.
Each experimental run on the KRISS system produces a file with extension .kdf. Additional files that may be available in the same directory include the digitized positions of the head points (\_digitizer.txt), the position of the center of the MEG coils (.chn), and the event markers (.trg).

trial_type (columns)

Name: Trial type

Type: Column

Description: Primary categorisation of each trial to identify them as instances of the experimental conditions. For example: for a response inhibition task, it could take on values go and no-go to refer to response initiation and response inhibition experimental conditions.

Schema information:

type: string

trigger (columns)

Name: Trigger

Type: Column

Description: continuous measurement of the scanner trigger signal

Schema information:

type: number

tsv (extensions)

Name: Tab-Delimited

Type: Extension

Format: <entities>_<suffix>.tsv

Description: A tab-delimited file.

tsvgz (extensions)

Name: Compressed Tab-Delimited

Type: Extension

Format: <entities>_<suffix>.tsv.gz

Description: A gzipped tab-delimited file. This file extension is only used for very large tabular data, such as physiological recordings. For smaller data, the unzipped .tsv extension is preferred.

txt (extensions)

Name: Text

Type: Extension

Format: <entities>_<suffix>.txt

Description: A free-form text file.
Tab-delimited files should have the .tsv extension rather than a .txt extension.

type sense 1 (columns)

Name: Channel type

Type: Column

Allowed values: AUDIO, EEG, EOG, ECG, EMG, EYEGAZE, GSR, HEOG, MISC, PPG, PUPIL, REF, RESP, SYSCLOCK, TEMP, TRIG, VEOG

Description: Type of channel; MUST use the channel types listed below. Note that the type MUST be in upper-case.

Schema information:

type: string

type sense 2 (columns)

Name: Channel type

Type: Column

Allowed values: MEGMAG, MEGGRADAXIAL, MEGGRADPLANAR, MEGREFMAG, MEGREFGRADAXIAL, MEGREFGRADPLANAR, MEGOTHER, EEG, ECOG, SEEG, DBS, VEOG, HEOG, EOG, ECG, EMG, TRIG, AUDIO, PD, EYEGAZE, PUPIL, MISC, SYSCLOCK, ADC, DAC, HLU, FITERR, OTHER

Description: Type of channel; MUST use the channel types listed below. Note that the type MUST be in upper-case.

Schema information:

type: string

type sense 3 (columns)

Name: Channel type

Type: Column

Allowed values: EEG, ECOG, SEEG, DBS, VEOG, HEOG, EOG, ECG, EMG, TRIG, AUDIO, PD, EYEGAZE, PUPIL, MISC, SYSCLOCK, ADC, DAC, REF, OTHER

Description: Type of channel; MUST use the channel types listed below. Note that the type MUST be in upper-case.

Schema information:

type: string

type sense 4 (columns)

Name: Channel type

Type: Column

Allowed values: NIRSCWAMPLITUDE, NIRSCWFLUORESCENSEAMPLITUDE, NIRSCWOPTICALDENSITY, NIRSCWHBO, NIRSCWHBR, NIRSCWMUA, MEGMAG, MEGGRADAXIAL, MEGGRADPLANAR, MEGREFMAG, MEGREFGRADAXIAL, MEGREFGRADPLANAR, MEGOTHER, EEG, ECOG, SEEG, DBS, VEOG, HEOG, EOG, ECG, EMG, TRIG, AUDIO, PD, EYEGAZE, PUPIL, MISC, SYSCLOCK, ADC, DAC, HLU, FITERR, ACCEL, GYRO, MAGN, MISC, OTHER

Description: Type of channel; MUST use the channel types listed below. Note that the type MUST be in upper-case.

Schema information:

type: string

type sense 5 (columns)

Name: Electrode type

Type: Column

Description: Type of the electrode (for example, cup, ring, clip-on, wire, needle).

Schema information:

type: string

type sense 6 (columns)

Name: Type

Type: Column

Allowed values: source, detector, n/a

Description: The type of the optode.

Schema information:

type: string

uCT (suffixes)

Name: Micro-CT

Type: Suffix

Format: <entities>_uCT.<extension>

Description: Micro-CT imaging data

unit (formats)

Name: A standardized unit

Type: Format

Regular expression: .*

Description: A unit. SI units in CMIXF formatting are RECOMMENDED (see Units).
Currently this matches any string.
TODO: Somehow reference the actual unit options in the Units appendix.

units sense 1 (columns)

Name: Units

Type: Column

Description: Physical unit of the value represented in this channel, for example, V for Volt, or fT/cm for femto Tesla per centimeter (see Units).

Schema information:

format: unit
type: string

units sense 2 (columns)

Name: Units

Type: Column

Description: Physical unit of the value represented in this channel, specified according to the SI unit symbol and possibly prefix symbol, or as a derived SI unit (for example, V, or unitless for changes in optical densities). For guidelines about units see the Appendix and Common Principles pages.

Schema information:

format: unit
type: string

uri (formats)

Name: Uniform resource indicator

Type: Format

Regular expression: (([^:/?#]+):)?(//([^/?#]*))?([^?#]*)(\?([^#]*))?(#(.*))?

Description: A uniform resource indicator.

value (columns)

Name: Marker value

Type: Column

Description: Marker value associated with the event (for example, the value of a TTL trigger that was recorded at the onset of the event).

Schema information:

anyOf:
- type: number
- type: string

vhdr (extensions)

Name: BrainVision Text Header

Type: Extension

Format: <entities>_<suffix>.vhdr

Description: A text header file in the BrainVision Core Data Format. These files come in three-file sets, including a .vhdr, a .vmrk, and a .eeg file.

vmrk (extensions)

Name: BrainVision Marker

Type: Extension

Format: <entities>_<suffix>.vmrk

Description: A text marker file in the BrainVision Core Data Format. These files come in three-file sets, including a .vhdr, a .vmrk, and a .eeg file.

volume_type (columns)

Name: ASL volume type

Type: Column

Allowed values: control, label, m0scan, deltam, cbf

Description: The *_aslcontext.tsv table consists of a single column of labels identifying the volume_type of each volume in the corresponding *_asl.nii[.gz] file.

Schema information:

type: string

wavelength_actual (columns)

Name: Wavelength actual

Type: Column

Description: Measured wavelength of light in nm. n/a for channels that do not contain raw NIRS signals (acceleration). This field is equivalent to measurementList.wavelengthActual in the SNIRF specification.

Schema information:

type: number

wavelength_emission_actual (columns)

Name: Wavelength emission actual

Type: Column

Description: Measured emission wavelength of light in nm. n/a for channels that do not contain raw NIRS signals (acceleration). This field is equivalent to measurementList.wavelengthEmissionActual in the SNIRF specification.

Schema information:

type: number

wavelength_nominal (columns)

Name: Wavelength nominal

Type: Column

Description: Specified wavelength of light in nm. n/a for channels that do not contain raw NIRS signals (for example, acceleration). This field is equivalent to /nirs(i)/probe/wavelengths in the SNIRF specification.

Schema information:

anyOf:
- type: number
- enum:
  - n/a
  type: string

whole_blood_radioactivity (columns)

Name: Whole blood radioactivity

Type: Column

Description: Radioactivity in whole blood samples, in unit of radioactivity measurements in whole blood samples (for example, kBq/mL).

Schema information:

type: number

x sense 1 (columns)

Name: X position

Type: Column

Description: Recorded position along the x-axis.

Schema information:

type: number

x sense 2 (columns)

Name: X position

Type: Column

Description: Recorded position along the x-axis. "n/a" if not available.

Schema information:

anyOf:
- type: number
- enum:
  - n/a
  type: string

y sense 1 (columns)

Name: Y position

Type: Column

Description: Recorded position along the y-axis.

Schema information:

type: number

y sense 2 (columns)

Name: Y position

Type: Column

Description: Recorded position along the y-axis. "n/a" if not available.

Schema information:

anyOf:
- type: number
- enum:
  - n/a
  type: string

z sense 1 (columns)

Name: Z position

Type: Column

Description: Recorded position along the z-axis.

Schema information:

anyOf:
- type: number
- enum:
  - n/a
  type: string

z sense 2 (columns)

Name: Z position

Type: Column

Description: Recorded position along the z-axis. "n/a" if not available.

Schema information:

anyOf:
- type: number
- enum:
  - n/a
  type: string