Glossary of schema objects
This section compiles the object definitions in the schema.
4DBti (enums)
Name: 4D BTI
Type: Enums
Description: ALS orientation and the origin between the ears.
ACCEL (enums)
Name: ACCEL
Type: Enums
Description:
Accelerometer channel, one channel for each spatial axis. Column component for the axis MUST be added to the *_channels.tsv file (x, y, or z).
Schema information:
tags:
- fnirs
- motion
ACCELChannelCount (metadata)
Name: Acceleration channel count
Type: Metadata
Description: Number of acceleration channels.
Schema information:
minimum: 0
type: integer
ACPC (enums)
Name: ACPC
Type: Enums
Description: The origin of the coordinate system is at the Anterior Commissure and the negative y-axis is passing through the Posterior Commissure. The positive z-axis is passing through a mid-hemispheric point in the superior direction. The anatomical landmarks are determined in the individual's anatomical scan and no scaling or deformations have been applied to the individual's anatomical scan. For more information, see the ACPC site on the FieldTrip toolbox wiki.
ADC (enums)
Name: ADC
Type: Enums
Description: Analog to Digital input.
Schema information:
tags:
- meg
- ieeg
- fnirs
ANGACCEL (enums)
Name: ANGACCEL
Type: Enums
Description:
Angular acceleration channel, one channel for each spatial axis. Column component for the axis MUST be added to the *_channels.tsv file (x, y, or z).
Schema information:
tags:
- motion
ANGACCELChannelCount (metadata)
Name: Angular acceleration channel count
Type: Metadata
Description: Number of angular acceleration channels.
Schema information:
minimum: 0
type: integer
AUDIO (enums)
Name: AUDIO
Type: Enums
Description: Audio signal.
Schema information:
tags:
- eeg
- meg
- ieeg
- fnirs
Absent (enums)
Name: Absent
Type: Enums
Description: No specific M0 information is present.
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 analyze 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
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
BARIUM (enums)
Name: BARIUM
Type: Enums
Description: A Contrast Bolus Ingredient: Barium
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
Brain (enums)
Name: Brain mask
Type: Enums
Description: A brain mask.
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
CARBON_DIOXIDE (enums)
Name: CARBON DIOXIDE
Type: Enums
Description: A Contrast Bolus Ingredient: Carbon Dioxide
CARS (suffixes)
Name: Coherent anti-Stokes Raman spectroscopy
Type: Suffix
Format: <entities>_CARS.<extension>
Description: Coherent anti-Stokes Raman spectroscopy imaging data
CASL (enums)
Name: Continuous arterial spin labeling
Type: Enums
Description: Continuous arterial spin labeling was employed.
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
CITATION (files)
Name: CITATION.cff
Type: Files And Directories
Description: A description of the citation information for the dataset, following the Citation File Format specification. This file permits more detailed and structured descriptions than dataset_description.json.
Schema information:
file_type: regular
COMBINED (enums)
Name: COMBINED
Type: Enums
Description: A spoiling type: COMBINED
CONF (suffixes)
Name: Confocal microscopy
Type: Suffix
Format: <entities>_CONF.<extension>
Description: Confocal microscopy imaging data
CTF (enums)
Name: CTF
Type: Enums
Description: ALS orientation and the origin between the ears.
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
CapTrak (enums)
Name: CapTrak
Type: Enums
Description: RAS orientation and the origin approximately between LPA and RPA
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
ChietiItab (enums)
Name: Chieti ITAB
Type: Enums
Description: RAS orientation and the origin between the ears.
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, UNKNOWN, NONE
Description:
Active ingredient of agent. Corresponds to DICOM Tag 0018, 1048 Contrast/Bolus Ingredient.
Schema information:
type: string
DAC (enums)
Name: DAC
Type: Enums
Description: Digital to Analog output.
Schema information:
tags:
- meg
- ieeg
- fnirs
DBS (enums)
Name: DBS
Type: Enums
Description: Electrode channel.
Schema information:
tags:
- meg
- ieeg
- fnirs
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
DatasetLinks (metadata)
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
Delimiter (metadata)
Name: Delimiter
Type: Metadata
Description: If rows in a column may be interpreted as a lists of values, the character that separates one value from the next.
Schema information:
type: string
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
ECG (enums)
Name: ECG
Type: Enums
Description: Electrocardiogram (heart).
Schema information:
tags:
- eeg
- meg
- ieeg
- fnirs
ECGChannelCount (metadata)
Name: ECG Channel Count
Type: Metadata
Description: Number of ECG channels.
Schema information:
minimum: 0
type: integer
ECOG (enums)
Name: ECOG
Type: Enums
Description: Electrode channel.
Schema information:
tags:
- meg
- ieeg
- fnirs
ECOGChannelCount (metadata)
Name: ECOG Channel Count
Type: Metadata
Description: Number of ECoG channels.
Schema information:
minimum: 0
type: integer
EEG (enums)
Name: EEG
Type: Enums
Description: Electroencephalogram channel.
Schema information:
tags:
- eeg
- meg
- ieeg
- fnirs
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
EEGLAB (enums)
Name: EEGLAB
Type: Enums
Description: ALS orientation and the origin exactly between LPA and RPA. For more information, see the EEGLAB wiki page.
EEGLAB-HJ (enums)
Name: EEGLAB-HJ
Type: Enums
Description: ALS orientation and the origin exactly between LHJ and RHJ. For more information, see the EEGLAB wiki page.
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
EMG (enums)
Name: EMG
Type: Enums
Description: Electromyogram (muscle).
Schema information:
tags:
- eeg
- meg
- ieeg
- fnirs
EMGChannelCount (metadata)
Name: EMG Channel Count
Type: Metadata
Description: Number of EMG channels.
Schema information:
minimum: 0
type: integer
EOG (enums)
Name: EOG
Type: Enums
Description: Generic electrooculogram (eye), different from HEOG and VEOG.
Schema information:
tags:
- eeg
- meg
- ieeg
- fnirs
EOGChannelCount (metadata)
Name: EOG Channel Count
Type: Metadata
Description: Number of EOG channels.
Schema information:
minimum: 0
type: integer
EYEGAZE (enums)
Name: EYEGAZE
Type: Enums
Description: Eye tracker gaze.
Schema information:
tags:
- eeg
- meg
- ieeg
- fnirs
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
ElektaNeuromag (enums)
Name: Elekta Neuromag
Type: Enums
Description: RAS orientation and the origin between the ears.
Epigenomic (enums)
Name: Epigenomic
Type: Enums
Description: Data link to participants' characterization of reversible modifications of DNA.
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
Estimate (enums)
Name: Estimate
Type: Enums
Description: A single whole-brain M0 value is provided in the metadata.
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
FERMI (enums)
Name: Fermi pulse
Type: Enums
Description: A Fermi-shaped pulse.
FITERR (enums)
Name: FITERR
Type: Enums
Description: Fit error signal from each head localization coil.
Schema information:
tags:
- meg
- fnirs
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
Face (enums)
Name: Face mask
Type: Enums
Description: A face mask.
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
GADOLINIUM (enums)
Name: GADOLINIUM
Type: Enums
Description: A Contrast Bolus Ingredient: Gadolinium
GAUSSHANN (enums)
Name: Gaussian-Hanning pulse.
Type: Enums
Description: A Gaussian pulse with a Hanning window.
GAUSSIAN (enums)
Name: Gaussian pulse
Type: Enums
Description: A Gaussian pulse.
GRADIENT (enums)
Name: GRADIENT
Type: Enums
Description: A spoiling type: GRADIENT
GSR (enums)
Name: GSR
Type: Enums
Description: Galvanic skin response.
Schema information:
tags:
- eeg
GYRO (enums)
Name: GYRO
Type: Enums
Description:
Gyrometer channel, one channel for each spatial axis. Column component for the axis MUST be added to the *_channels.tsv file (x, y, or z).
Schema information:
tags:
- fnirs
- motion
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
Genetic (enums)
Name: Genetic
Type: Enums
Description:
Data report on a single genetic location (typically directly in the participants.tsv file).
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".
For more information on these levels, see Multi-omics approaches to disease by Hasin et al. 2017.
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
required_fields:
- Dataset
type: object
Genomic (enums)
Name: Genomic
Type: Enums
Description: Data link to participants' genome (multiple genetic locations).
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
HARD (enums)
Name: Hard pulse
Type: Enums
Description: A very brief, strong, rectangular pulse.
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
HEOG (enums)
Name: HEOG
Type: Enums
Description: Horizontal EOG (eye).
Schema information:
tags:
- eeg
- meg
- ieeg
- fnirs
HLU (enums)
Name: HLU
Type: Enums
Description: Measured position of head and head coils.
Schema information:
tags:
- meg
- fnirs
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
HeadStabilization (metadata)
Name: Head stabilization
Type: Metadata
Description: Head restraint method used during the experiment to prevent rotation and/or translation of the head. Example: "chin-rest", "head-rest", "bite-bar", "chin-rest and head-rest", "none"
Schema information:
type: string
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
ICBM452AirSpace (enums)
Name: ICBM452AirSpace
Type: Enums
Description: Reference space defined by the "average of 452 T1-weighted MRIs of normal young adult brains" with "linear transforms of the subjects into the atlas space using a 12-parameter affine transformation".
ICBM452Warp5Space (enums)
Name: ICBM452Warp5Space
Type: Enums
Description: Reference space defined by the "average of 452 T1-weighted MRIs of normal young adult brains" "based on a 5th order polynomial transformation into the atlas space".
IODINE (enums)
Name: IODINE
Type: Enums
Description: A Contrast Bolus Ingredient: Iodine
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).
IXI549Space (enums)
Name: IXI549Space
Type: Enums
Description:
Reference space defined by the average of the "549 (...) subjects from the IXI dataset" linearly transformed to ICBM MNI 452.
Used by SPM12.
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
Included (enums)
Name: Included
Type: Enums
Description:
An m0scan volume is contained within the associated asl file.
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
JNTANG (enums)
Name: JNTANG
Type: Enums
Description:
Joint angle channel between two fixed axis belonging to two bodyparts. Angle SHOULD be defined between proximal and distal bodypart in deg.
Schema information:
tags:
- motion
JNTANGChannelCount (metadata)
Name: Joint angle channel count
Type: Metadata
Description: Number of joint angle channels.
Schema information:
minimum: 0
type: integer
KitYokogawa (enums)
Name: KIT/Yokogawa
Type: Enums
Description: ALS orientation and the origin between the ears.
LATENCY (enums)
Name: LATENCY
Type: Enums
Description:
Latency of samples in seconds from recording onset. MUST be in form of ss[.000000], where [.000000] is an optional subsecond resolution between 1 and 6 decimal points.
Schema information:
tags:
- motion
LATENCYChannelCount (metadata)
Name: Latency channel count
Type: Metadata
Description: Number of Latency channels.
Schema information:
minimum: 0
type: integer
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.*. 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
Lesion (enums)
Name: Lesion mask
Type: Enums
Description: A lesion mask.
Levels (metadata)
Name: Levels
Type: Metadata
Description: For categorical variables: An object of possible values (keys) and their descriptions (values).
Schema information:
additionalProperties:
anyOf:
- type: string
- properties:
Description:
type: string
TermURL:
format: uri
type: string
type: object
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
MAGN (enums)
Name: MAGN
Type: Enums
Description:
Magnetic field strength, one channel for each spatial axis. Column component for the axis MUST be added to the *_channels.tsv file (x, y or z).
Schema information:
tags:
- fnirs
- motion
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
MEGGRADAXIAL (enums)
Name: MEGGRADAXIAL
Type: Enums
Description: MEG axial gradiometer.
Schema information:
tags:
- meg
- fnirs
MEGGRADPLANAR (enums)
Name: MEGGRADPLANAR
Type: Enums
Description: MEG planargradiometer.
Schema information:
tags:
- meg
- fnirs
MEGMAG (enums)
Name: MEGMAG
Type: Enums
Description: MEG magnetometer.
Schema information:
tags:
- meg
- fnirs
MEGOTHER (enums)
Name: MEGOTHER
Type: Enums
Description: Any other type of MEG sensor.
Schema information:
tags:
- meg
- ieeg
- fnirs
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
MEGREFGRADAXIAL (enums)
Name: MEGREFGRADAXIAL
Type: Enums
Description: MEG reference axial gradiometer.
Schema information:
tags:
- meg
- fnirs
MEGREFGRADPLANAR (enums)
Name: MEGREFGRADPLANAR
Type: Enums
Description: MEG reference planar gradiometer.
Schema information:
tags:
- meg
- fnirs
MEGREFMAG (enums)
Name: MEGREFMAG
Type: Enums
Description: MEG reference magnetometer.
Schema information:
tags:
- meg
- fnirs
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.
MISC (enums)
Name: MISC
Type: Enums
Description: Miscellaneous channels.
Schema information:
tags:
- eeg
- meg
- ieeg
- fnirs
- motion
MISCChannelCount (metadata)
Name: Miscellaneous channel count
Type: Metadata
Description: Number of miscellaneous channels not covered otherwise.
Schema information:
minimum: 0
type: integer
MNI152Lin (enums)
Name: MNI152Lin
Type: Enums
Description:
Also known as ICBM (version with linear coregistration).
Used by SPM99 to SPM8.
MNI152NLin2009aAsym (enums)
Name: MNI152NLin2009aAsym
Type: Enums
Description:
Also known as ICBM (non-linear coregistration with 40 iterations, released in 2009). This is the first asymmetric version.
Used by the DARTEL toolbox in SPM12b.
MNI152NLin2009aSym (enums)
Name: MNI152NLin2009aSym
Type: Enums
Description:
Also known as ICBM (non-linear coregistration with 40 iterations, released in 2009). This is the first symmetric version.
Used by the DARTEL toolbox in SPM12b.
MNI152NLin2009bAsym (enums)
Name: MNI152NLin2009bAsym
Type: Enums
Description:
Also known as ICBM (non-linear coregistration with 40 iterations, released in 2009). This is the second asymmetric version.
Used by the DARTEL toolbox in SPM12b.
MNI152NLin2009bSym (enums)
Name: MNI152NLin2009bSym
Type: Enums
Description:
Also known as ICBM (non-linear coregistration with 40 iterations, released in 2009). This is the second symmetric version.
Used by the DARTEL toolbox in SPM12b.
MNI152NLin2009cAsym (enums)
Name: MNI152NLin2009cAsym
Type: Enums
Description:
Also known as ICBM (non-linear coregistration with 40 iterations, released in 2009). This is the third asymmetric version.
Used by the DARTEL toolbox in SPM12b.
MNI152NLin2009cSym (enums)
Name: MNI152NLin2009cSym
Type: Enums
Description:
Also known as ICBM (non-linear coregistration with 40 iterations, released in 2009). This is the third symmetric version.
Used by the DARTEL toolbox in SPM12b.
MNI152NLin6ASym (enums)
Name: MNI152NLin6ASym
Type: Enums
Description:
A variation of MNI152NLin6Sym built by A. Janke that is released as the MNI template of FSL. Volumetric templates included with HCP-Pipelines correspond to this template too.
Used by FSL and HPC-Pipelines.
MNI152NLin6Sym (enums)
Name: MNI152NLin6Sym
Type: Enums
Description:
Also known as symmetric ICBM 6th generation (non-linear coregistration).
Used by FSL.
MNI305 (enums)
Name: MNI205
Type: Enums
Description: Also known as avg305.
MNIColin27 (enums)
Name: MNIColin27
Type: Enums
Description:
Average of 27 T1 scans of a single subject.
Used by SPM96.
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
Metabolomic (enums)
Name: Metabolomic
Type: Enums
Description: Data link to participants' products of cellular metabolic functions.
MiscChannelCount (metadata)
Name: Misc Channel Count
Type: Metadata
Description: Number of miscellaneous analog channels for auxiliary signals.
Schema information:
minimum: 0
type: integer
MissingValues (metadata)
Name: MissingValues
Type: Metadata
Description: Describes how missing values are represented in the given recording system (for example a tracking system in motion), can take values such as, "NaN", "0".
Schema information:
type: string
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
MotionChannelCount (metadata)
Name: Motion Channel Count
Type: Metadata
Description:
Number of motion channels (for example, 275).
Schema information:
minimum: 0
type: integer
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
NIHPD (enums)
Name: NIHPD
Type: Enums
Description: Pediatric templates generated from the NIHPD sample. Available for different age groups (4.5-18.5 y.o., 4.5-8.5 y.o., 7-11 y.o., 7.5-13.5 y.o., 10-14 y.o., 13-18.5 y.o.). This template also comes in either -symmetric or -asymmetric flavor.
NIRSCWAMPLITUDE (enums)
Name: NIRSCWAMPLITUDE
Type: Enums
Description: Continuous wave amplitude measurements. Equivalent to dataType 001 in SNIRF.
Schema information:
tags:
- fnirs
NIRSCWFLUORESCENSEAMPLITUDE (enums)
Name: NIRSCWFLUORESCENSEAMPLITUDE
Type: Enums
Description: Continuous wave fluorescence amplitude measurements. Equivalent to dataType 051 in SNIRF.
Schema information:
tags:
- fnirs
NIRSCWHBO (enums)
Name: NIRSCWHBO
Type: Enums
Description: Continuous wave oxygenated hemoglobin (oxyhemoglobin) concentration measurements. Equivalent to dataTypeLabel HbO in SNIRF.
Schema information:
tags:
- fnirs
NIRSCWHBR (enums)
Name: NIRSCWHBR
Type: Enums
Description: Continuous wave deoxygenated hemoglobin (deoxyhemoglobin) concentration measurements. Equivalent to dataTypeLabel HbR in SNIRF.
Schema information:
tags:
- fnirs
NIRSCWMUA (enums)
Name: NIRSCWMUA
Type: Enums
Description: Continuous wave optical absorption measurements. Equivalent to dataTypeLabel mua in SNIRF.
Schema information:
tags:
- fnirs
NIRSCWOPTICALDENSITY (enums)
Name: NIRSCWOPTICALDENSITY
Type: Enums
Description: Continuous wave change in optical density measurements. Equivalent to dataTypeLabel dOD in SNIRF.
Schema information:
tags:
- fnirs
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
OASIS30AntsOASISAnts (enums)
Name: OASIS30AntsOASISAnts
Type: Enums
Description: OASIS30AntsOASISAnts
OASIS30Atropos (enums)
Name: OASIS30Atropos
Type: Enums
Description: OASIS30Atropos
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.
ORNT (enums)
Name: ORNT
Type: Enums
Description:
Orientation channel, one channel for each spatial axis or quaternion component. Column component for the axis or quaternion label MUST be added to the *_channels.tsv file (x, y, z, quat_x, quat_y, quat_z, or quat_w).
Schema information:
tags:
- fnirs
- motion
ORNTChannelCount (metadata)
Name: Orientation Channel Count
Type: Metadata
Description: Number of orientation channels.
Schema information:
minimum: 0
type: integer
OTHER (enums)
Name: OTHER
Type: Enums
Description: Any other type of channel.
Schema information:
tags:
- meg
- fnirs
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
Other (enums)
Name: Other
Type: Enums
Description: Other coordinate system.
OtherAcquisitionParameters (metadata)
Name: Other Acquisition Parameters
Type: Metadata
Description: Description of other relevant image acquisition parameters.
Schema information:
type: string
PASL (enums)
Name: Pulsed arterial spin labeling
Type: Enums
Description: Pulsed arterial spin labeling was employed.
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
PCASL (enums)
Name: Pseudo-continuous arterial spin labeling
Type: Enums
Description: Pseudo-continuous arterial spin labeling was employed.
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 (enums)
Name: PD
Type: Enums
Description: Photodiode.
Schema information:
tags:
- meg
- ieeg
- fnirs
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). A two-volume 4D image, where the volumes are, respectively, PDw and T2w images acquired simultaneously. If separated into 3D volumes, the PDw and T2w suffixes SHOULD be used instead, and an acquisition entity MAY be used to distinguish the images from others with the same suffix, for example, acq-PDT2_PDw.nii and acq-PDT2_T2w.nii.
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. This contrast is achieved at short echo times and long repetition times; for gradient echo, this weighting is also possible with a short TR (TR<<T1) and a small flip angle.
Schema information:
unit: arbitrary
PLI (suffixes)
Name: Polarized-light microscopy
Type: Suffix
Format: <entities>_PLI.<extension>
Description: Polarized-light microscopy imaging data
POS (enums)
Name: POS
Type: Enums
Description:
Position in space, one channel for each spatial axis. Column component for the axis MUST be added to the *_channels.tsv file (x, y or z).
Schema information:
tags:
- motion
POSChannelCount (metadata)
Name: Position Channel Count
Type: Metadata
Description: Number of position channels.
Schema information:
minimum: 0
type: integer
PPG (enums)
Name: PPG
Type: Enums
Description: Photoplethysmography.
Schema information:
tags:
- eeg
PUPIL (enums)
Name: PUPIL
Type: Enums
Description: Eye tracker pupil diameter.
Schema information:
tags:
- eeg
- meg
- ieeg
- fnirs
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, i-, j, j-, k, 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
Pixels (enums)
Name: Pixels
Type: Enums
Description: If electrodes are localized in 2D space (only x and y are specified and z is n/a), then the positions in this file must correspond to the locations expressed in pixels on the photo/drawing/rendering of the electrodes on the brain. In this case, coordinates must be (row,column) pairs, with (0,0) corresponding to the upper left pixel and (N,0) corresponding to the lower left pixel.
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
Proteomic (enums)
Name: Proteomic
Type: Enums
Description: Data link to participants peptides and proteins quantification.
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
REF (enums)
Name: REF
Type: Enums
Description: Reference channel.
Schema information:
tags:
- eeg
- ieeg
RESP (enums)
Name: RESP
Type: Enums
Description: Respiration.
Schema information:
tags:
- eeg
RF (enums)
Name: RF
Type: Enums
Description: A spoiling type: RF
ROI (enums)
Name: ROI mask
Type: Enums
Description: A region of interest mask.
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
ReferencesAndLinks (metadata)
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
RotationOrder (metadata)
Name: RotationOrder
Type: Metadata
Allowed values: XYZ, XZY, YXZ, YZX, ZXY, ZYX, n/a
Description: Specify the sequence in which the elemental 3D extrinsic rotations are applied around the three distinct axes.
Schema information:
type: string
RotationRule (metadata)
Name: Rotation Rule
Type: Metadata
Allowed values: left-hand, right-hand, n/a
Description: In case orientation channels are present, indicate whether rotations are applied clockwise around an axis when seen from the positive direction (left-hand rule) or counter-clockwise (right-hand rule). Must be one of: "left-hand", "right-hand".
Schema information:
type: string
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.
SEEG (enums)
Name: SEEG
Type: Enums
Description: Electrode channel.
Schema information:
tags:
- meg
- ieeg
- fnirs
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
SINC (enums)
Name: Sinc pulse
Type: Enums
Description: A sinc-shaped pulse.
SINCGAUSS (enums)
Name: Sinc-Gauss pulse
Type: Enums
Description: A sinc-shaped pulse with a Gaussian window.
SINCHANN (enums)
Name: Sinc-Hanning pulse
Type: Enums
Description: A sinc-shaped pulse with a Hanning window.
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
SYSCLOCK (enums)
Name: SYSCLOCK
Type: Enums
Description: System time showing elapsed time since trial started.
Schema information:
tags:
- eeg
- meg
- ieeg
- fnirs
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 catalog 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 catalog 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
SamplingFrequencyEffective (metadata)
Name: Effective Sampling Frequency
Type: Metadata
Description:
Effective sampling frequency (in Hz) of all the data in the recording, regardless of their type (for example, 2400) which can be determined if timestamps per sample are provided.
Schema information:
type: number
unit: Hz
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
ScanRAS (enums)
Name: ScanRAS
Type: Enums
Description:
The origin of the coordinate system is the center of the gradient coil for the corresponding T1w image of the subject, and the x-axis increases left to right, the y-axis increases posterior to anterior and the z-axis increases inferior to superior. For more information see the Nipy Documentation. It is strongly encouraged to align the subject's T1w to ACPC so that the ACPC coordinate system can be used. If the subject's T1w in the BIDS dataset is not aligned to ACPC, ScanRAS should be used.
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
ScreenDistance (metadata)
Name: Screen Distance
Type: Metadata
Description:
Distance between the participant's eye and the screen. If no screen was used, use n/a.
Schema information:
anyOf:
- type: number
unit: m
- enum:
- n/a
type: string
ScreenRefreshRate (metadata)
Name: Screen Refresh Rate
Type: Metadata
Description: Refresh rate of the screen (when used), in Hertz (equivalent to frames per second, "FPS").
Schema information:
type: number
unit: Hz
ScreenResolution (metadata)
Name: Screen Resolution
Type: Metadata
Description:
Screen resolution in pixel (for example [1920, 1200] for a screen of 1920-width by 1080-height pixels), if no screen use n/a.
Schema information:
anyOf:
- items:
maxItems: 2
minItems: 2
type: integer
type: array
- enum:
- n/a
type: string
ScreenSize (metadata)
Name: Screen Size
Type: Metadata
Description:
Screen size in m, excluding potential screen borders (for example [0.472, 0.295] for a screen of 47.2-width by 29.5-height cm), if no screen use n/a.
Schema information:
anyOf:
- items:
maxItems: 2
minItems: 2
type: number
unit: m
type: array
- enum:
- n/a
type: string
Separate (enums)
Name: Separate
Type: Enums
Description:
A separate m0scan file is present.
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, i-, j, j-, k, 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
SpatialAxes (metadata)
Name: Spatial axes
Type: Metadata
Description: Refers to the coordinate system in which the motion data are to be interpreted, if the recorded data can be mapped to a fixed reference frame. A sequence of characters F/B (forward-backward), L/R (left-right), and U/D (up-down). The position of a character in the sequence determines which of the X,Y,Z axes it maps to. For example, "FRD" for X-forward, Y-right, Z-down. For 1D or 2D cases, only specify the used axes and use the character "_" for unused axes ("F_R" when the Y axis is not used, for instance).
Schema information:
type: string
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: degree
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). This data MAY be specified with sub-second precision using the syntax s[.000000], where s reflects whole seconds, and .000000 reflects OPTIONAL fractional seconds.
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.
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
ScreenDistance:
anyOf:
- type: number
unit: m
- enum:
- n/a
type: string
description: 'Distance between the participant''s eye and the screen. If no screen
was used, use `n/a`.
'
display_name: Screen Distance
name: ScreenDistance
ScreenRefreshRate:
description: 'Refresh rate of the screen (when used), in Hertz (equivalent to
frames per second, "FPS").
'
display_name: Screen Refresh Rate
name: ScreenRefreshRate
type: number
unit: Hz
ScreenResolution:
anyOf:
- items:
maxItems: 2
minItems: 2
type: integer
type: array
- enum:
- n/a
type: string
description: 'Screen resolution in pixel
(for example `[1920, 1200]` for a screen of 1920-width by 1080-height pixels),
if no screen use `n/a`.
'
display_name: Screen Resolution
name: ScreenResolution
ScreenSize:
anyOf:
- items:
maxItems: 2
minItems: 2
type: number
unit: m
type: array
- enum:
- n/a
type: string
description: 'Screen size in m, excluding potential screen borders
(for example `[0.472, 0.295]` for a screen of 47.2-width by 29.5-height cm),
if no screen use `n/a`.
'
display_name: Screen Size
name: ScreenSize
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
- ScreenDistance
- ScreenRefreshRate
- ScreenResolution
- ScreenSize
- SoftwareName
- SoftwareRRID
- SoftwareVersion
- Code
- HeadStabilization
type: object
SubjectArtefactDescription (metadata)
Name: Subject Artifact Description
Type: Metadata
Description:
Freeform description of the observed subject artifact and its possible cause (for example, "Vagus Nerve Stimulator", "non-removable implant"). If this field is set to "n/a", it will be interpreted as absence of major source of artifacts except cardiac and blinks.
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
TEMP (enums)
Name: TEMP
Type: Enums
Description: Temperature.
Schema information:
tags:
- eeg
TRIG (enums)
Name: TRIG
Type: Enums
Description: Analog (TTL in Volt) or digital (binary TTL) trigger channel.
Schema information:
tags:
- eeg
- meg
- ieeg
- fnirs
Talairach (enums)
Name: Talairach
Type: Enums
Description: Piecewise linear scaling of the brain is implemented as described in TT88.
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 filename is derived from this "TaskName" field by removing all non-alphanumeric characters (that is, all except those matching [0-9a-zA-Z]). For example "TaskName" "faces n-back" or "head nodding" will correspond to task labels facesnback and headnodding, respectively.
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. For example: https://www.ncbi.nlm.nih.gov/mesh/68008297 for "male".
Schema information:
format: uri
type: string
ThreeD (enums)
Name: Three-dimensional
Type: Enums
Description: Three-dimensional MR acquisition.
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 labeling 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
TrackedPointsCount (metadata)
Name: Tracked Points Count
Type: Metadata
Description: Number of different tracked points tracked in a motion tracking system.
Schema information:
type: number
unit: m
TrackingSystemName (metadata)
Name: Tracking System Name
Type: Metadata
Description:
A human-readable name of the tracking system to complement "tracksys" label of the corresponding *_motion.tsv filename.
Schema information:
type: string
Transcriptomic (enums)
Name: Transcriptomic
Type: Enums
Description: Data link to participants RNA levels.
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
TwoD (enums)
Name: Two-dimensional
Type: Enums
Description: Two-dimensional MR acquisition.
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
UNCInfant (enums)
Name: UNCInfant
Type: Enums
Description: Infant Brain Atlases from Neonates to 1- and 2-year-olds.
UNCInfant0V21 (enums)
Name: UNCInfant0V21
Type: Enums
Description: Infant Brain Atlases from Neonates to 1- and 2-year-olds. See https://www.nitrc.org/projects/pediatricatlas. For new datasets, the recommended alternative is UNCInfant.
UNCInfant0V22 (enums)
Name: UNCInfant0V22
Type: Enums
Description: Infant Brain Atlases from Neonates to 1- and 2-year-olds. See https://www.nitrc.org/projects/pediatricatlas. For new datasets, the recommended alternative is UNCInfant.
UNCInfant0V23 (enums)
Name: UNCInfant0V23
Type: Enums
Description: Infant Brain Atlases from Neonates to 1- and 2-year-olds. See https://www.nitrc.org/projects/pediatricatlas. For new datasets, the recommended alternative is UNCInfant.
UNCInfant1V21 (enums)
Name: UNCInfant1V21
Type: Enums
Description: Infant Brain Atlases from Neonates to 1- and 2-year-olds. See https://www.nitrc.org/projects/pediatricatlas. For new datasets, the recommended alternative is UNCInfant.
UNCInfant1V22 (enums)
Name: UNCInfant1V22
Type: Enums
Description: Infant Brain Atlases from Neonates to 1- and 2-year-olds. See https://www.nitrc.org/projects/pediatricatlas. For new datasets, the recommended alternative is UNCInfant.
UNCInfant1V23 (enums)
Name: UNCInfant1V23
Type: Enums
Description: Infant Brain Atlases from Neonates to 1- and 2-year-olds. See https://www.nitrc.org/projects/pediatricatlas. For new datasets, the recommended alternative is UNCInfant.
UNCInfant2V21 (enums)
Name: UNCInfant2V21
Type: Enums
Description: Infant Brain Atlases from Neonates to 1- and 2-year-olds. See https://www.nitrc.org/projects/pediatricatlas. For new datasets, the recommended alternative is UNCInfant.
UNCInfant2V22 (enums)
Name: UNCInfant2V22
Type: Enums
Description: Infant Brain Atlases from Neonates to 1- and 2-year-olds. See https://www.nitrc.org/projects/pediatricatlas. For new datasets, the recommended alternative is UNCInfant.
UNCInfant2V23 (enums)
Name: UNCInfant2V23
Type: Enums
Description: Infant Brain Atlases from Neonates to 1- and 2-year-olds. See https://www.nitrc.org/projects/pediatricatlas. For new datasets, the recommended alternative is UNCInfant.
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
VEL (enums)
Name: VEL
Type: Enums
Description:
Velocity, one channel for each spatial axis. Column component for the axis MUST be added to the *_channels.tsv file (x, y or z).
Schema information:
tags:
- motion
VELChannelCount (metadata)
Name: Velocity Channel Count
Type: Metadata
Description: Number of linear velocity channels.
Schema information:
minimum: 0
type: integer
VEOG (enums)
Name: VEOG
Type: Enums
Description: Vertical EOG (eye).
Schema information:
tags:
- eeg
- meg
- ieeg
- fnirs
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
VisionCorrection (metadata)
Name: Vision correction
Type: Metadata
Description: Equipment used to correct participant vision during an experiment. Example: "spectacles", "lenses", "none".
Schema information:
type: string
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
XENON (enums)
Name: XENON
Type: Enums
Description: A Contrast Bolus Ingredient: Xenon
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).
It is recommended to tag participant ages that are 89 or higher as 89+, for privacy purposes.
Schema information:
type: number
unit: year
amniotic_fluid (enums)
Name: amniotic fluid
Type: Enums
Description: The origin of a sample: amniotic fluid
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. This screenshot is based on DICOM macro C.8.13.5.14.
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.
bad (enums)
Name: bad
Type: Enums
Description: A bad status (for example the status of a recording channel).
balanced (enums)
Name: balanced
Type: Enums
Description: PCASL Type: when balanced gradient pulses are used.
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:".
bile (enums)
Name: Bile
Type: Enums
Description: The origin of a sample: bile
blood (enums)
Name: blood
Type: Enums
Description: The origin of a sample: blood
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".
brain (enums)
Name: brain
Type: Enums
Description: The origin of a sample: brain
breast_milk (enums)
Name: breast milk
Type: Enums
Description: The origin of a sample: breast milk
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.
calibration (enums)
Name: calibration
Type: Enums
Description: The fine-calibration file, is produced by the MaxFilter software and the work of Neuromag/Elekta/MEGIN engineers during maintenance of the MEG acquisition system. It is specific to the site of recording and may change in the process of regular system maintenance. it is usually shared with a crosstalk file.
cardiac (columns)
Name: Cardiac measurement
Type: Column
Description: continuous pulse measurement
Schema information:
type: number
cbf (enums)
Name: cbf
Type: Enums
Description: An ASL volume type: cbf
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
cell_free_sample (enums)
Name: cell-free sample
Type: Enums
Description:
A biosample type (sample_type): cell-free sample
cell_line (enums)
Name: cell line
Type: Enums
Description:
A biosample type (sample_type): cell line
channel (columns)
Name: Channel
Type: Column
Description:
Channel(s) associated with an event. If multiple channels are specified, they MUST be separated by a delimiter specified in the "Delimiter" field describing the channel column. For example, channels separated with a comma (,) require the events.json file to contain "channel": {"Delimiter": ","}. In the absence of a delimiter, tools MUST interpret any character as being part of a channel name.
Schema information:
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 images of the same physical sample with different fields of view acquired in the same imaging experiment. This entity applies to collections of 2D images, 3D volumes or 4D volume series (for example, diffusion weighted images), and may be used to indicate different anatomical structures or regions of the same structure.
Schema information:
format: index
type: string
cloning_host (enums)
Name: cloning host
Type: Enums
Description:
A biosample type (sample_type): cloning host
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
component (columns)
Name: Component
Type: Column
Allowed values: x, y, z, quat_x, quat_y, quat_z, quat_w, n/a
Description:
Description of the spatial axis or label of quaternion component associated with the channel. For example, x,y,z for position channels, or quat_x, quat_y, quat_z, quat_w for quaternion orientation channels.
Schema information:
type: string
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.
continuous (enums)
Name: Continuous recording
Type: Enums
Description: Continuous recording.
control (enums)
Name: control
Type: Enums
Description: An ASL volume type: control
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.
crosstalk (enums)
Name: crosstalk
Type: Enums
Description: The crosstalk file, is produced by the MaxFilter software and the work of Neuromag/Elekta/MEGIN engineers during maintenance of the MEG acquisition system. It is specific to the site of recording and may change in the process of regular system maintenance. it is usually shared with a fine-calibration file.
csf (enums)
Name: CSF
Type: Enums
Description: Cerebrospinal fluid (for example, the origin of a sample or tissue)
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)
13. motion (motion)
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.
deltam (enums)
Name: deltam
Type: Enums
Description: An ASL volume type: deltam
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.
derivative (enums)
Name: derivative
Type: Enums
Description: A derived BIDS dataset.
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 (enums)
Name: detector
Type: Enums
Description: A photoelectric transducer, sometimes called a receiver.
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
discontinuous (enums)
Name: Discontinuous recording
Type: Enums
Description: Discontinuous recording.
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.
double_coil (enums)
Name: double-coil
Type: Enums
Description: CASL Type: when a double coil is used for labeling.
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.
epoched (enums)
Name: Epoched recording
Type: Enums
Description: Recording is limited to time windows around events of interest (for example, stimulus presentations or subject responses).
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.
ex_vivo (enums)
Name: ex vivo
Type: Enums
Description: The environment of a sample: ex vivo
extension (common_principles)
Name: File extension
Type: Common Principle
Description:
A portion of the filename 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.
fsLR (enums)
Name: fsLR
Type: Enums
Description:
The fsLR is a dual template providing both volumetric and surface coordinates references. The volumetric template corresponds to MNI152NLin6Asym. Surface templates are given at several sampling densities: 164k (used by HCP pipelines for 3T and 7T anatomical analysis), 59k (used by HCP pipelines for 7T MRI bold and DWI analysis), 32k (used by HCP pipelines for 3T MRI bold and DWI analysis), or 4k (used by HCP pipelines for MEG analysis) fsaverage_LR surface reconstructed from the T1w image.
Used by Freesurfer.
fsaverage (enums)
Name: fsaverage
Type: Enums
Description:
The fsaverage is a dual template providing both volumetric and surface coordinates references. The volumetric template corresponds to a FreeSurfer variant of MNI305 space. The fsaverage atlas also defines a surface reference system (formerly described as fsaverage[3|4|5|6|sym]).
Used by Freesurfer.
fsaverage3 (enums)
Name: fsaverage3
Type: Enums
Description: Images were sampled to the FreeSurfer surface reconstructed from the subject's T1w image, and registered to an fsaverage template. For new datasets, the recommended alternative is fsaverage.
fsaverage4 (enums)
Name: fsaverage4
Type: Enums
Description: Images were sampled to the FreeSurfer surface reconstructed from the subject's T1w image, and registered to an fsaverage template. For new datasets, the recommended alternative is fsaverage.
fsaverage5 (enums)
Name: fsaverage5
Type: Enums
Description: Images were sampled to the FreeSurfer surface reconstructed from the subject's T1w image, and registered to an fsaverage template. For new datasets, the recommended alternative is fsaverage.
fsaverage6 (enums)
Name: fsaverage6
Type: Enums
Description: Images were sampled to the FreeSurfer surface reconstructed from the subject's T1w image, and registered to an fsaverage template. For new datasets, the recommended alternative is fsaverage.
fsaverageSym (enums)
Name: fsaverageSym
Type: Enums
Description:
The fsaverage is a dual template providing both volumetric and surface coordinates references. The volumetric template corresponds to a FreeSurfer variant of MNI305 space. The fsaverageSym atlas also defines a symmetric surface reference system (formerly described as fsaveragesym).
Used by Freesurfer.
fsaveragesym (enums)
Name: fsaveragesym
Type: Enums
Description: Images were sampled to the FreeSurfer surface reconstructed from the subject's T1w image, and registered to an fsaverage template. For new datasets, the recommended alternative is fsaverageSym.
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
good (enums)
Name: good
Type: Enums
Description: A good status (for example the status of a recording channel).
gray_matter (enums)
Name: gray matter
Type: Enums
Description: The origin of a tissue: gray matter
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
i (enums)
Name: i
Type: Enums
Description: The encoding direction is along the first axis of the data in the NIFTI file, and the encoding value increases from the zero index to the maximum index.
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, ScanRAS, 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: pixels, m, mm, cm, 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
iMinus (enums)
Name: i-
Type: Enums
Description: The encoding direction is along the first axis of the data in the NIFTI file, and the encoding value decreases from the zero index to the maximum index.
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.
imaginary (enums)
Name: Imaginary
Type: Enums
Description: An imaginary-valued image, typically paird with an associated "real" image.
impedance (columns)
Name: Electrode impedance
Type: Column
Description:
Impedance of the electrode, units MUST be in kOhm.
Schema information:
type: number
unit: kOhm
in_vitro (enums)
Name: in vitro
Type: Enums
Description: The environment of a sample: in vitro
in_vitro_differentiated_cells (enums)
Name: in vitro differentiated cells
Type: Enums
Description:
A biosample type (sample_type): in vitro differentiated cells
in_vivo (enums)
Name: in vivo
Type: Enums
Description: The environment of a sample: in vivo
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]+
Description: Non-negative, optionally prefixed with leading zeros for better visual homogeneity and sorting.
individual (enums)
Name: individual
Type: Enums
Description:
Participant specific anatomical space (for example derived from T1w and/or T2w images). This coordinate system requires specifying an additional, participant-specific file to be fully defined. In context of surfaces this space has been referred to as fsnative.
In order for this space to be interpretable, SpatialReference metadata MUST be provided.
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
j (enums)
Name: j
Type: Enums
Description: The encoding direction is along the second axis of the data in the NIFTI file, and the encoding value increases from the zero index to the maximum index.
jMinus (enums)
Name: j-
Type: Enums
Description: The encoding direction is along the second axis of the data in the NIFTI file, and the encoding value decreases from the zero index to the maximum index.
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.
k (enums)
Name: k
Type: Enums
Description: The encoding direction is along the third axis of the data in the NIFTI file, and the encoding value increases from the zero index to the maximum index.
kMinus (enums)
Name: k-
Type: Enums
Description: The encoding direction is along the third axis of the data in the NIFTI file, and the encoding value decreases from the zero index to the maximum index.
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 (enums)
Name: label
Type: Enums
Description: An ASL volume type: label
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.
left_hand (enums)
Name: left-hand
Type: Enums
Description: A rotation rule: rotations are applied clockwise around an axis when seen from the positive direction
left_hemisphere (enums)
Name: Left Hemisphere
Type: Enums
Description: A left hemibrain image.
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 (enums)
Name: m0scan
Type: Enums
Description: An ASL volume type: m0scan
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.
macrovascular (enums)
Name: macrovascular
Type: Enums
Description: The origin of a tissue: macrovascular
magnitude (enums)
Name: Magnitude
Type: Enums
Description: A magnitude image, typically paired with an associated "phase" image.
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.
meninges (enums)
Name: meninges
Type: Enums
Description: The origin of a tissue: meninges
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.
microvascular (enums)
Name: microvascular
Type: Enums
Description: The origin of a tissue: microvascular
mixed (enums)
Name: mixed
Type: Enums
Description:
Mixed detector types were used for this NIRS recording, specify in optodes.tsv.
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
motion (datatypes)
Name: Motion
Type: Datatype
Description: Motion data from a tracking system
motion (modalities)
Name: Motion
Type: Modalities
Description: Data acquired with Motion-Capture systems.
motion (suffixes)
Name: Motion
Type: Suffix
Format: <entities>_motion.<extension>
Description: Data recorded from a tracking system store.
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 notch filters are applied at multiple frequencies, these frequencies MAY be specified as a list, for example, [60, 120, 180]. If no notch filter was applied, use n/a.
Schema information:
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.
off sense 1 (enums)
Name: Off
Type: Enums
Description: The image acquired in the absence of the magnetization transfer pulse.
on sense 1 (enums)
Name: On
Type: Enums
Description: The image acquired in the presence of the magnetization transfer pulse, also known as the off-resonance pulse.
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.
organoid (enums)
Name: organoid
Type: Enums
Description:
A biosample type (sample_type): organoid
orig (enums)
Name: orig
Type: Enums
Description: A (potentially unique) per-image space. Useful for describing the source of transforms from an input image to a target space.
other_biospecimen (enums)
Name: other biospecimen
Type: Enums
Description: The origin of a sample: other biospecimen
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, species and strain. 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 participants.tsv files are age, sex, handedness, strain, and strain_rrid.
The RECOMMENDED species column SHOULD be a binomial species name from the NCBI Taxonomy (for examples homo sapiens, mus musculus, rattus norvegicus). For backwards compatibility, if species is absent, the participant is assumed to be homo sapiens.
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 (enums)
Name: Phase
Type: Enums
Description:
A phase image, typically paird with an associated "magnitude" (part-mag) image. Images with this key/value pair 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.
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.
phenotype (files)
Name: Phenotype
Type: Files And Directories
Description:
A directory where to store participant level measurements (for example responses from multiple questionnaires) split into individual files separate from participants.tsv. See the relevant section for more information.
Schema information:
file_type: directory
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.
pixels (enums)
Name: pixels
Type: Enums
Description: A dimension specified in pixels.
placement sense 1 (columns)
Name: Placement
Type: Column
Description: Placement of the tracked point on the body (for example, participant, avatar centroid, torso, left arm). It can refer to an external vocabulary for describing body parts.
Schema information:
type: string
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.
primary_cell (enums)
Name: primary cell
Type: Enums
Description:
A biosample type (sample_type): primary cell
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
quat_w (enums)
Name: quat_w
Type: Enums
Description: The quaternion w dimension of the coordinate system.
quat_x (enums)
Name: quat_x
Type: Enums
Description: The quaternion x dimension of the coordinate system.
quat_y (enums)
Name: quat_y
Type: Enums
Description: The quaternion y dimension of the coordinate system.
quat_z (enums)
Name: quat_z
Type: Enums
Description: The quaternion z dimension of the coordinate system.
raw (enums)
Name: raw
Type: Enums
Description: A raw BIDS dataset.
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.
real (enums)
Name: Real
Type: Enums
Description: A real-valued image, typically paired with an associated "imaginary" (part-imag) image.
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
reference_frame (columns)
Name: Reference frame
Type: Column
Description:
Specification of a reference frame in which the motion data are to be interpreted. The description of the levels in *_channels.json SHOULD use RotationRule, RotationOrder, and SpatialAxis, and MAY use Description for the specification.
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
right_hand (enums)
Name: right-hand
Type: Enums
Description: A rotation rule: rotations are applied counter-clockwise around an axis when seen from the positive direction
right_hemisphere (enums)
Name: Right Hemisphere
Type: Enums
Description: A right hemibrain image.
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
saliva (enums)
Name: saliva
Type: Enums
Description: The origin of a sample: saliva
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 filename within the dataset. Each sample MUST be described by one and only one row.
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.
scanner (enums)
Name: scanner
Type: Enums
Description:
The intrinsic coordinate system of the original image (the first entry of RawSources) after reconstruction and conversion to NIfTI or equivalent for the case of surfaces and dual volume/surface files.
The scanner coordinate system is implicit and assumed by default if the derivative filename does not define any space-<label>. Please note that space-scanner SHOULD NOT be used, it is mentioned in this specification to make its existence explicit.
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).
segmentation (entities)
Name: Segmentation
Type: Entity
Description:
The seg-<label> key/value pair corresponds to a custom label the user MAY use to distinguish different segmentations.
This entity is only applicable to derivative data.
Schema information:
format: label
type: string
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
single_coil (enums)
Name: single-coil
Type: Enums
Description: CASL Type: when a single coil is used for labeling.
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 (enums)
Name: source
Type: Enums
Description: A light emitting device, sometimes called a transmitter.
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 filenames, 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 "SampleSecondaryAntibodies" 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.
study (enums)
Name: study
Type: Enums
Description:
Custom space defined using a group/study-specific template. This coordinate system requires specifying an additional file to be fully defined.
In order for this space to be interpretable, SpatialReference metadata MUST be provided.
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
technical_sample (enums)
Name: technical sample
Type: Enums
Description:
A biosample type (sample_type): technical sample
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".
tissue (enums)
Name: tissue
Type: Enums
Description:
A biosample type (sample_type): tissue
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
tracked_point sense 1 (columns)
Name: Tracked point channel
Type: Column
Description:
Label of the point that is being tracked, for example, label of a tracker or a marker (for example,"LeftFoot", "RightWrist").
Schema information:
type: string
tracksys (entities)
Name: Tracking system
Type: Entity
Description:
The tracksys-<label> entity can be used as a key-value pair to label _motion.tsv and _motion.json files. It can also be used to label _channel.tsv or _events.tsv files when they belong to a specific tracking system.
This entity corresponds to the "TrackingSystemName" metadata field in a *_motion.json file. tracksys-<label> entity is a concise string whereas "TrackingSystemName" may be longer and more human readable.
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: ACCEL, ADC, ANGACCEL, AUDIO, DAC, DBS, ECG, ECOG, EEG, EMG, EOG, EYEGAZE, FITERR, GSR, GYRO, HEOG, HLU, JNTANG, LATENCY, MAGN, MEGGRADAXIAL, MEGGRADPLANAR, MEGMAG, MEGOTHER, MEGREFGRADAXIAL, MEGREFGRADPLANAR, MEGREFMAG, MISC, NIRSCWAMPLITUDE, NIRSCWFLUORESCENSEAMPLITUDE, NIRSCWHBO, NIRSCWHBR, NIRSCWMUA, NIRSCWOPTICALDENSITY, ORNT, OTHER, PD, POS, PPG, PUPIL, REF, RESP, SEEG, SYSCLOCK, TEMP, TRIG, VEL, 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: Electrode type
Type: Column
Description: Type of the electrode (for example, cup, ring, clip-on, wire, needle).
Schema information:
type: string
type sense 3 (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
unbalanced (enums)
Name: unbalanced
Type: Enums
Description: PCASL Type: when unbalanced gradient pulses are used.
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
units sense 3 (columns)
Name: Units
Type: Column
Description:
Physical or virtual unit of the value represented in this channel, for example, '"rad"' or '"deg"' for angular quantities or '"m"' for position data. If motion data is recorded in a virtual space and deviate from standard SI units, the unit used MUST be specified in the sidecar *_motion.json file (for example "vm" for virtual meters). "rad" is used for Euler angles and "n/a" for quaternions. For guidelines about units see the Appendix and Common Principles pages.
Schema information:
format: unit
type: string
unknown (enums)
Name: unknown
Type: Enums
Description: An unknown unit.
uri (formats)
Name: Uniform resource indicator
Type: Format
Regular expression: (([^:/?#]+):)?(//([^/?#]*))?([^?#]*)(\?([^#]*))?(#(.*))?
Description: A uniform resource indicator.
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
white_matter (enums)
Name: white matter
Type: Enums
Description: The origin of a tissue: white matter
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
whole_organisms (enums)
Name: whole organisms
Type: Enums
Description:
A biosample type (sample_type): whole organisms
x (enums)
Name: x
Type: Enums
Description: The x dimension of the coordinate system.
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 (enums)
Name: y
Type: Enums
Description: The y dimension of the coordinate system.
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 (enums)
Name: z
Type: Enums
Description: The z dimension of the coordinate system.
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