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Appendix XIV: Glossary of schema objects

This section compiles the object definitions in the schema.

.* (extensions)

name: Any Extension

description:

Any extension is allowed.

schema information:

{}

.ave (extensions)

name: AVE

description:

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

schema information:

{}

.bdf (extensions)

name: Biosemi Data Format

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.

schema information:

{}

.bval (extensions)

name: FSL-Format Gradient Amplitudes

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.

schema information:

{}

.bvec (extensions)

name: FSL-Format Gradient Directions

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.

schema information:

{}

.chn (extensions)

name: KRISS 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 folder 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).

schema information:

{}

.con (extensions)

name: KIT/Yokogawa/Ricoh Continuous Data

description:

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

schema information:

{}

.dat (extensions)

name: MEG Fine-Calibration Format

description:

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

schema information:

{}

.ds/ (extensions)

name: CTF MEG Dataset Folder

description:

A folder for MEG data, typically containing a .meg4 file for the data and a .res4 file for the resources.

schema information:

{}

.edf (extensions)

name: European Data Format

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.

schema information:

{}

.eeg (extensions)

name: BrainVision Binary Data

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.

schema information:

{}

.fdt (extensions)

name: EEGLAB 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.

schema information:

{}

.fif (extensions)

name: Functional Imaging File Format

description:

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

schema information:

{}

.jpg (extensions)

name: Joint Photographic Experts Group Format

description:

A JPEG image file.

schema information:

{}

.json (extensions)

name: JavaScript Object Notation

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.

schema information:

{}

.kdf (extensions)

name: KRISS 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 folder 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).

schema information:

{}

.md (extensions)

name: Markdown

description:

A Markdown file.

schema information:

{}

.mefd/ (extensions)

name: Multiscale Electrophysiology File Format Version 3.0

description:

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

schema information:

{}

.mhd (extensions)

name: ITAB Binary Header

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.

schema information:

{}

.mrk (extensions)

name: 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.

schema information:

{}

.nii (extensions)

name: NIfTI

description:

A Neuroimaging Informatics Technology Initiative (NIfTI) data file.

schema information:

{}

.nii.gz (extensions)

name: Compressed NIfTI

description:

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

schema information:

{}

.nwb (extensions)

name: Neurodata Without Borders Format

description:

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

schema information:

{}

.ome.btf (extensions)

name: Open Microscopy Environment BigTIFF

description:

A BigTIFF image file, for very large images.

schema information:

{}

.ome.tif (extensions)

name: Open Microscopy Environment Tag Image File Format

description:

An OME-TIFF image file.

schema information:

{}

.png (extensions)

name: Portable Network Graphics

description:

A Portable Network Graphics file.

schema information:

{}

.pos (extensions)

name: Head Point Position

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.

schema information:

{}

.raw (extensions)

name: 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.

schema information:

{}

.rst (extensions)

name: reStructuredText

description:

A reStructuredText file.

schema information:

{}

.set (extensions)

name: EEGLAB 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.

schema information:

{}

.sqd (extensions)

name: 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.

schema information:

{}

.tif (extensions)

name: Tag Image File Format

description:

A Tag Image File Format file.

schema information:

{}

.trg (extensions)

name: KRISS 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 folder 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).

schema information:

{}

.tsv (extensions)

name: Tab-Delimited

description:

A tab-delimited file.

schema information:

{}

.tsv.gz (extensions)

name: Compressed Tab-Delimited

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.

schema information:

{}

.txt (extensions)

name: Text

description:

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

schema information:

{}

.vhdr (extensions)

name: BrainVision Text Header

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.

schema information:

{}

.vmrk (extensions)

name: BrainVision Marker

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.

schema information:

{}

/ (extensions)

name: Folder

description:

A folder with no extension. Corresponds to BTi/4D data.

schema information:

{}

2PE (suffixes)

name: 2-photon excitation microscopy

description:

2-photon excitation microscopy imaging data

schema information:

{}

Acknowledgements (metadata)

name: Acknowledgements

description:

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

schema information:

{'type': 'string'}

AcquisitionDuration (metadata)

name: AcquisitionDuration

description:

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

schema information:

{'type': 'number', 'exclusiveMinimum': 0, 'unit': 's'}

AcquisitionMode (metadata)

name: AcquisitionMode

description:

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

schema information:

{'type': 'string'}

AcquisitionVoxelSize (metadata)

name: AcquisitionVoxelSize

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:

{'type': 'array', 'minItems': 3, 'maxItems': 3, 'items': {'type': 'number', 'exclusiveMinimum': 0, 'unit': 'mm'}}

Anaesthesia (metadata)

name: Anaesthesia

description:

Details of anaesthesia used, if any.

schema information:

{'type': 'string'}

AnalyticalApproach (metadata)

name: AnalyticalApproach

description:

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

schema information:

{'anyOf': [{'type': 'string'}, {'type': 'array', 'items': {'type': 'string'}}]}

AnatomicalLandmarkCoordinateSystem (metadata)

name: AnatomicalLandmarkCoordinateSystem

description:

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

schema information:

{'type': 'string', 'enum': ['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']}

AnatomicalLandmarkCoordinateSystemDescription (metadata)

name: AnatomicalLandmarkCoordinateSystemDescription

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: AnatomicalLandmarkCoordinateUnits

description:

Units of the coordinates of "AnatomicalLandmarkCoordinateSystem".

schema information:

{'type': 'string', 'enum': ['m', 'mm', 'cm', 'n/a']}

AnatomicalLandmarkCoordinates sense 1 (metadata)

name: AnatomicalLandmarkCoordinates

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:

{'type': 'object', 'additionalProperties': {'type': 'array', 'items': {'type': 'number'}, 'minItems': 3, 'maxItems': 3}}

AnatomicalLandmarkCoordinates sense 2 (metadata)

name: AnatomicalLandmarkCoordinates

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:

{'type': 'object', 'additionalProperties': {'type': 'array', 'items': {'type': 'number'}, 'minItems': 3, 'maxItems': 3}}

ArterialSpinLabelingType (metadata)

name: ArterialSpinLabelingType

description:

The arterial spin labeling type.

schema information:

{'type': 'string', 'enum': ['CASL', 'PCASL', 'PASL']}

AssociatedEmptyRoom (metadata)

name: AssociatedEmptyRoom

description:

A path pointing to an empty-room file associated with the subject's MEG recording. The path is relative to the BIDS dataset root. The path needs to use forward slashes instead of backward slashes (for example, "sub-emptyroom/ses-rest/meg/sub-emptyroom_ses-rest_task-noise_run-01_meg.ds"). Supplying a list of several paths to empty-room files is possible.

schema information:

{'anyOf': [{'type': 'array', 'items': {'type': 'string', 'format': 'dataset_relative'}}, {'type': 'string', 'format': 'dataset_relative'}]}

Atlas (metadata)

name: Atlas

description:

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

schema information:

{'type': 'string'}

AttenuationCorrection (metadata)

name: AttenuationCorrection

description:

Short description of the attenuation correction method used.

schema information:

{'type': 'string'}

AttenuationCorrectionMethodReference (metadata)

name: AttenuationCorrectionMethodReference

description:

Reference paper for the attenuation correction method used.

schema information:

{'type': 'string'}

Authors (metadata)

name: Authors

description:

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

schema information:

{'type': 'array', 'items': {'type': 'string'}}

B0FieldIdentifier (metadata)

name: B0FieldIdentifier

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'}, {'type': 'array', 'items': {'type': 'string'}}]}

B0FieldSource (metadata)

name: B0FieldSource

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'}, {'type': 'array', 'items': {'type': 'string'}}]}

BF (suffixes)

name: Bright-field microscopy

description:

Bright-field microscopy imaging data

schema information:

{}

BIDSVersion (metadata)

name: BIDSVersion

description:

The version of the BIDS standard that was used.

schema information:

{'type': 'string'}

BackgroundSuppression (metadata)

name: BackgroundSuppression

description:

Boolean indicating if background suppression is used.

schema information:

{'type': 'boolean'}

BackgroundSuppressionNumberPulses (metadata)

name: BackgroundSuppressionNumberPulses

description:

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

schema information:

{'type': 'number', 'minimum': 0}

BackgroundSuppressionPulseTime (metadata)

name: BackgroundSuppressionPulseTime

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:

{'type': 'array', 'items': {'type': 'number', 'minimum': 0, 'unit': 's'}}

BasedOn (metadata)

name: BasedOn

description:

List of files in a file collection to generate the map. Fieldmaps are also listed, if involved in the processing.

schema information:

{'anyOf': [{'type': 'string', 'format': 'participant_relative'}, {'type': 'array', 'items': {'type': 'string', 'format': 'participant_relative'}}]}

BloodDensity (metadata)

name: BloodDensity

description:

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

schema information:

{'type': 'number', 'unit': 'g/mL'}

BodyPart (metadata)

name: BodyPart

description:

Body part of the organ / body region scanned.

schema information:

{'type': 'string'}

BodyPartDetails (metadata)

name: BodyPartDetails

description:

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

schema information:

{'type': 'string'}

BodyPartDetailsOntology (metadata)

name: BodyPartDetailsOntology

description:

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

schema information:

{'type': 'string', 'format': 'uri'}

BolusCutOffDelayTime (metadata)

name: BolusCutOffDelayTime

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': [{'type': 'number', 'minimum': 0, 'unit': 's'}, {'type': 'array', 'items': {'type': 'number', 'unit': 's', 'minimum': 0}}]}

BolusCutOffFlag (metadata)

name: BolusCutOffFlag

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: BolusCutOffTechnique

description:

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

schema information:

{'type': 'string'}

BrainLocation (metadata)

name: BrainLocation

description:

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

schema information:

{'type': 'string'}

CARS (suffixes)

name: Coherent anti-Stokes Raman spectroscopy

description:

Coherent anti-Stokes Raman spectroscopy imaging data

schema information:

{}

CASLType (metadata)

name: CASLType

description:

Describes if a separate coil is used for labeling.

schema information:

{'type': 'string', 'enum': ['single-coil', 'double-coil']}

CHANGES (top_level_files)

name: CHANGES

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:

{}

CONF (suffixes)

name: Confocal microscopy

description:

Confocal microscopy imaging data

schema information:

{}

CapManufacturer (metadata)

name: CapManufacturer

description:

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

schema information:

{'type': 'string'}

CapManufacturersModelName (metadata)

name: CapManufacturersModelName

description:

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

schema information:

{'type': 'string'}

CellType (metadata)

name: CellType

description:

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

schema information:

{'type': 'string'}

Chimap (suffixes)

name: Quantitative susceptibility map (QSM)

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: ChunkTransformationMatrix

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': [{'type': 'array', 'minItems': 3, 'maxItems': 3, 'items': {'type': 'array', 'minItems': 3, 'maxItems': 3, 'items': {'type': 'number'}}}, {'type': 'array', 'minItems': 4, 'maxItems': 4, 'items': {'type': 'array', 'minItems': 4, 'maxItems': 4, 'items': {'type': 'number'}}}]}

ChunkTransformationMatrixAxis (metadata)

name: ChunkTransformationMatrixAxis

description:

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

schema information:

{'type': 'array', 'items': {'type': 'string', 'minItems': 2, 'maxItems': 3}}

Code (metadata)

name: Code

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:

{'type': 'string', 'format': 'uri'}

CogAtlasID (metadata)

name: CogAtlasID

description:

URI of the corresponding Cognitive Atlas Task term.

schema information:

{'type': 'string', 'format': 'uri'}

CogPOID (metadata)

name: CogPOID

description:

URI of the corresponding CogPO term.

schema information:

{'type': 'string', 'format': 'uri'}

CoilCombinationMethod (metadata)

name: CoilCombinationMethod

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

description:

Names of columns in file.

schema information:

{'type': 'array', 'items': {'type': 'string'}}

ContinuousHeadLocalization (metadata)

name: ContinuousHeadLocalization

description:

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

schema information:

{'type': 'boolean'}

ContrastBolusIngredient (metadata)

name: ContrastBolusIngredient

description:

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

schema information:

{'type': 'string', 'enum': ['IODINE', 'GADOLINIUM', 'CARBON DIOXIDE', 'BARIUM', 'XENON']}

DCOffsetCorrection (metadata)

name: DCOffsetCorrection

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

description:

Dark-field microscopy imaging data

schema information:

{}

DIC (suffixes)

name: Differential interference contrast microscopy

description:

Differential interference contrast microscopy imaging data

schema information:

{}

DatasetDOI (metadata)

name: DatasetDOI

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:

{'type': 'string', 'format': 'uri'}

DatasetType (metadata)

name: DatasetType

description:

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

schema information:

{'type': 'string', 'enum': ['raw', 'derivative']}

DecayCorrectionFactor (metadata)

name: DecayCorrectionFactor

description:

Decay correction factor for each frame.

schema information:

{'type': 'array', 'items': {'type': 'number'}}

DelayAfterTrigger (metadata)

name: DelayAfterTrigger

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: DelayTime

description:

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

schema information:

{'type': 'number', 'unit': 's'}

Density (metadata)

name: Density

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'}, {'type': 'object', 'additionalProperties': {'type': 'string'}}]}

Derivative (metadata)

name: Derivative

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

description:

Free-form natural language description.

schema information:

{'type': 'string'}

DeviceSerialNumber (metadata)

name: DeviceSerialNumber

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: DewarPosition

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: DigitizedHeadPoints

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: DigitizedHeadPoints

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 Elekta/Neuromag the head points will be stored in the fif file.

schema information:

{'type': 'string', 'format': 'file_relative'}

DigitizedHeadPointsCoordinateSystem (metadata)

name: DigitizedHeadPointsCoordinateSystem

description:

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

schema information:

{'type': 'string', 'enum': ['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']}

DigitizedHeadPointsCoordinateSystemDescription (metadata)

name: DigitizedHeadPointsCoordinateSystemDescription

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: DigitizedHeadPointsCoordinateUnits

description:

Units of the coordinates of "DigitizedHeadPointsCoordinateSystem".

schema information:

{'type': 'string', 'enum': ['m', 'mm', 'cm', 'n/a']}

DigitizedLandmarks (metadata)

name: DigitizedLandmarks

description:

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

schema information:

{'type': 'boolean'}

DispersionConstant (metadata)

name: DispersionConstant

description:

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

schema information:

{'type': 'number', 'unit': 's'}

DispersionCorrected (metadata)

name: DispersionCorrected

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: DoseCalibrationFactor

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: DwellTime

description:

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

schema information:

{'type': 'number', 'unit': 's'}

ECGChannelCount (metadata)

name: ECGChannelCount

description:

Number of ECG channels.

schema information:

{'type': 'integer', 'minimum': 0}

ECOGChannelCount (metadata)

name: ECOGChannelCount

description:

Number of ECoG channels.

schema information:

{'type': 'integer', 'minimum': 0}

EEGChannelCount (metadata)

name: EEGChannelCount

description:

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

schema information:

{'type': 'integer', 'minimum': 0}

EEGCoordinateSystem (metadata)

name: EEGCoordinateSystem

description:

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

schema information:

{'type': 'string', 'enum': ['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']}

EEGCoordinateSystemDescription (metadata)

name: EEGCoordinateSystemDescription

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: EEGCoordinateUnits

description:

Units of the coordinates of EEGCoordinateSystem.

schema information:

{'type': 'string', 'enum': ['m', 'mm', 'cm', 'n/a']}

EEGGround (metadata)

name: EEGGround

description:

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

schema information:

{'type': 'string'}

EEGPlacementScheme (metadata)

name: EEGPlacementScheme

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: EEGReference

description:

General description of the reference scheme used and (when applicable) of location of the reference electrode in the raw recordings (for example, "left mastoid", "Cz", "CMS"). If different channels have a different reference, this field should have a general description and the channel specific reference should be defined in the channels.tsv file.

schema information:

{'type': 'string'}

EMGChannelCount (metadata)

name: EMGChannelCount

description:

Number of EMG channels.

schema information:

{'type': 'integer', 'minimum': 0}

EOGChannelCount (metadata)

name: EOGChannelCount

description:

Number of EOG channels.

schema information:

{'type': 'integer', 'minimum': 0}

EchoTime sense 1 (metadata)

name: EchoTime

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': [{'type': 'number', 'unit': 's', 'exclusiveMinimum': 0}, {'type': 'array', 'items': {'type': 'number', 'unit': 's', 'exclusiveMinimum': 0}}]}

EchoTime sense 2 (metadata)

name: EchoTime

description:

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

schema information:

{'type': 'number', 'unit': 's', 'exclusiveMinimum': 0}

EchoTime1 (metadata)

name: EchoTime1

description:

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

schema information:

{'type': 'number', 'unit': 's', 'exclusiveMinimum': 0}

EchoTime2 (metadata)

name: EchoTime2

description:

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

schema information:

{'type': 'number', 'unit': 's', 'exclusiveMinimum': 0}

EffectiveEchoSpacing (metadata)

name: EffectiveEchoSpacing

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:

{'type': 'number', 'exclusiveMinimum': 0, 'unit': 's'}

ElectricalStimulation (metadata)

name: ElectricalStimulation

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: ElectricalStimulationParameters

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: ElectrodeManufacturer

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: ElectrodeManufacturersModelName

description:

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

schema information:

{'type': 'string'}

EpochLength (metadata)

name: EpochLength

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:

{'type': 'number', 'minimum': 0}

EstimationAlgorithm (metadata)

name: EstimationAlgorithm

description:

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

schema information:

{'type': 'string'}

EstimationReference (metadata)

name: EstimationReference

description:

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

schema information:

{'type': 'string'}

EthicsApprovals (metadata)

name: EthicsApprovals

description:

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

schema information:

{'type': 'array', 'items': {'type': 'string'}}

FLAIR (suffixes)

name: Fluid attenuated inversion recovery image

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

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.

schema information:

{}

FLUO (suffixes)

name: Fluorescence microscopy

description:

Fluorescence microscopy imaging data

schema information:

{}

FiducialsCoordinateSystem (metadata)

name: FiducialsCoordinateSystem

description:

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

schema information:

{'type': 'string', 'enum': ['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']}

FiducialsCoordinateSystemDescription (metadata)

name: FiducialsCoordinateSystemDescription

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: FiducialsCoordinateUnits

description:

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

schema information:

{'type': 'string', 'enum': ['m', 'mm', 'cm', 'n/a']}

FiducialsCoordinates (metadata)

name: FiducialsCoordinates

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:

{'type': 'object', 'additionalProperties': {'type': 'array', 'items': {'type': 'number'}, 'minItems': 3, 'maxItems': 3}}

FiducialsDescription (metadata)

name: FiducialsDescription

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: FlipAngle

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': [{'type': 'number', 'unit': 'degree', 'exclusiveMinimum': 0, 'maximum': 360}, {'type': 'array', 'items': {'type': 'number', 'unit': 'degree', 'exclusiveMinimum': 0, 'maximum': 360}}]}

FrameDuration (metadata)

name: FrameDuration

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:

{'type': 'array', 'items': {'type': 'number'}, 'unit': 's'}

FrameTimesStart (metadata)

name: FrameTimesStart

description:

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

schema information:

{'type': 'array', 'items': {'type': 'number'}, 'unit': 's'}

Funding (metadata)

name: Funding

description:

List of sources of funding (grant numbers).

schema information:

{'type': 'array', 'items': {'type': 'string'}}

GeneratedBy (metadata)

name: GeneratedBy

description:

Used to specify provenance of the dataset.

schema information:

{'type': 'array', 'minItems': 1, 'items': {'type': 'object', 'properties': {'Name': {'type': 'string'}, 'Version': {'type': 'string'}, 'Description': {'type': 'string'}, 'CodeURL': {'type': 'string', 'format': 'uri'}, 'Container': {'type': 'object', 'properties': {'Type': {'type': 'string'}, 'Tag': {'type': 'string'}, 'URI': {'type': 'string', 'format': 'uri'}}}}}}

GeneticLevel (metadata)

name: GeneticLevel

description:

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

schema information:

{'anyOf': [{'type': 'string', 'enum': ['Genetic', 'Genomic', 'Epigenomic', 'Transcriptomic', 'Metabolomic', 'Proteomic']}, {'type': 'array', 'items': {'type': 'string', 'enum': ['Genetic', 'Genomic', 'Epigenomic', 'Transcriptomic', 'Metabolomic', 'Proteomic']}}]}

Genetics (metadata)

name: Genetics

description:

An object containing information about the genetics descriptor.

schema information:

{'type': 'object', 'properties': {'Database': {'name': 'Database', 'description': '[URI](SPEC_ROOT/02-common-principles.md#uniform-resource-indicator)\nof database where the dataset is hosted.\n', 'type': 'string', 'format': 'uri'}, 'Dataset': {'name': 'Dataset', 'description': '[URI](SPEC_ROOT/02-common-principles.md#uniform-resource-indicator)\nwhere data can be retrieved.\n', 'type': 'string', 'format': 'uri'}, 'Descriptors': {'name': 'Descriptors', 'description': 'List of relevant descriptors (for example, journal articles) for dataset\nusing a valid\n[URI](SPEC_ROOT/02-common-principles.md#uniform-resource-indicator)\nwhen possible.\n', 'anyOf': [{'type': 'string'}, {'type': 'array', 'items': {'type': 'string'}}]}}}

GradientSetType (metadata)

name: GradientSetType

description:

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

schema information:

{'type': 'string'}

HED (columns)

name: HED

description:

Hierarchical Event Descriptor (HED) Tag. See Appendix III for details.

schema information:

{'type': 'string'}

HED (metadata)

name: HED

description:

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

schema information:

{'anyOf': [{'type': 'string'}, {'type': 'object', 'additionalProperties': {'type': 'string'}}]}

HEDVersion (metadata)

name: HEDVersion

description:

If HED tags are used: The version of the HED schema used to validate HED tags for study.

schema information:

{'type': 'string'}

Haematocrit (metadata)

name: Haematocrit

description:

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

schema information:

{'type': 'number'}

HardcopyDeviceSoftwareVersion (metadata)

name: HardcopyDeviceSoftwareVersion

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: HardwareFilters

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': [{'type': 'object', 'additionalProperties': {'type': 'object'}}, {'type': 'string', 'enum': ['n/a']}]}

HeadCircumference (metadata)

name: HeadCircumference

description:

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

schema information:

{'type': 'number', 'exclusiveMinimum': 0, 'unit': 'cm'}

HeadCoilCoordinateSystem (metadata)

name: HeadCoilCoordinateSystem

description:

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

schema information:

{'type': 'string', 'enum': ['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']}

HeadCoilCoordinateSystemDescription (metadata)

name: HeadCoilCoordinateSystemDescription

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: HeadCoilCoordinateUnits

description:

Units of the coordinates of HeadCoilCoordinateSystem.

schema information:

{'type': 'string', 'enum': ['m', 'mm', 'cm', 'n/a']}

HeadCoilCoordinates (metadata)

name: HeadCoilCoordinates

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 Elekta, 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:

{'type': 'object', 'additionalProperties': {'type': 'array', 'items': {'type': 'number'}, 'minItems': 3, 'maxItems': 3}}

HeadCoilFrequency (metadata)

name: HeadCoilFrequency

description:

List of frequencies (in Hz) used by the head localisation coils ('HLC' in CTF systems, 'HPI' in Elekta, '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'}, {'type': 'array', 'items': {'type': 'number', 'unit': 'Hz'}}]}

HowToAcknowledge (metadata)

name: HowToAcknowledge

description:

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

schema information:

{'type': 'string'}

IRT1 (suffixes)

name: Inversion recovery T1 mapping

description:

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

schema information:

{}

ImageAcquisitionProtocol (metadata)

name: ImageAcquisitionProtocol

description:

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

schema information:

{'type': 'string'}

ImageDecayCorrected (metadata)

name: ImageDecayCorrected

description:

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

schema information:

{'type': 'boolean'}

ImageDecayCorrectionTime (metadata)

name: ImageDecayCorrectionTime

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

description:

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

schema information:

{'type': 'string'}

InfusionRadioactivity (metadata)

name: InfusionRadioactivity

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: InfusionSpeed

description:

If given, infusion speed.

schema information:

{'type': 'number'}

InfusionSpeedUnits (metadata)

name: InfusionSpeedUnits

description:

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

schema information:

{'type': 'string', 'format': 'unit'}

InfusionStart (metadata)

name: InfusionStart

description:

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

schema information:

{'type': 'number', 'unit': 's'}

InjectedMass (metadata)

name: InjectedMass

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'}, {'type': 'string', 'enum': ['n/a']}]}

InjectedMassPerWeight (metadata)

name: InjectedMassPerWeight

description:

Injected mass per kilogram bodyweight.

schema information:

{'type': 'number'}

InjectedMassPerWeightUnits (metadata)

name: InjectedMassPerWeightUnits

description:

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

schema information:

{'type': 'string', 'format': 'unit'}

InjectedMassUnits (metadata)

name: InjectedMassUnits

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': [{'type': 'string', 'format': 'unit'}, {'type': 'string', 'enum': ['n/a']}]}

InjectedRadioactivity (metadata)

name: InjectedRadioactivity

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: InjectedRadioactivityUnits

description:

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

schema information:

{'type': 'string', 'format': 'unit'}

InjectedVolume (metadata)

name: InjectedVolume

description:

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

schema information:

{'type': 'number', 'unit': 'mL'}

InjectionEnd (metadata)

name: InjectionEnd

description:

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

schema information:

{'type': 'number', 'unit': 's'}

InjectionStart (metadata)

name: InjectionStart

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: InstitutionAddress

description:

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

schema information:

{'type': 'string'}

InstitutionName (metadata)

name: InstitutionName

description:

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

schema information:

{'type': 'string'}

InstitutionalDepartmentName (metadata)

name: InstitutionalDepartmentName

description:

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

schema information:

{'type': 'string'}

Instructions (metadata)

name: Instructions

description:

Text of the instructions given to participants before the recording.

schema information:

{'type': 'string'}

IntendedFor sense 1 (metadata)

name: IntendedFor

description:

The paths to files for which the associated file is intended to be used. Contains one or more filenames with paths relative to the participant subdirectory. Paths need to use forward slashes instead of backward slashes, regardless of operating system.

schema information:

{'anyOf': [{'type': 'string', 'format': 'participant_relative'}, {'type': 'array', 'items': {'type': 'string', 'format': 'participant_relative'}}]}

IntendedFor sense 2 (metadata)

name: IntendedFor

description:

The paths to files for which the associated file is intended to be used. Contains one or more filenames with paths relative to the dataset root. Paths need to use forward slashes instead of backward slashes, regardless of operating system.

schema information:

{'anyOf': [{'type': 'string', 'format': 'dataset_relative'}, {'type': 'array', 'items': {'type': 'string', 'format': 'dataset_relative'}}]}

InversionTime (metadata)

name: InversionTime

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:

{'type': 'number', 'unit': 's', 'exclusiveMinimum': 0}

LICENSE (top_level_files)

name: LICENSE

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:

{}

LabelingDistance (metadata)

name: LabelingDistance

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: LabelingDuration

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': [{'type': 'number', 'minimum': 0, 'unit': 's'}, {'type': 'array', 'items': {'type': 'number', 'unit': 's', 'minimum': 0}}]}

LabelingEfficiency (metadata)

name: LabelingEfficiency

description:

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

schema information:

{'type': 'number', 'exclusiveMinimum': 0}

LabelingLocationDescription (metadata)

name: LabelingLocationDescription

description:

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

schema information:

{'type': 'string'}

LabelingOrientation (metadata)

name: LabelingOrientation

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:

{'type': 'array', 'items': {'type': 'number'}}

LabelingPulseAverageB1 (metadata)

name: LabelingPulseAverageB1

description:

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

schema information:

{'type': 'number', 'exclusiveMinimum': 0, 'unit': 'uT'}

LabelingPulseAverageGradient (metadata)

name: LabelingPulseAverageGradient

description:

The average labeling gradient, in milliteslas per meter.

schema information:

{'type': 'number', 'exclusiveMinimum': 0, 'unit': 'mT/m'}

LabelingPulseDuration (metadata)

name: LabelingPulseDuration

description:

Duration of the individual labeling pulses, in milliseconds.

schema information:

{'type': 'number', 'exclusiveMinimum': 0, 'unit': 'ms'}

LabelingPulseFlipAngle (metadata)

name: LabelingPulseFlipAngle

description:

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

schema information:

{'type': 'number', 'exclusiveMinimum': 0, 'maximum': 360, 'unit': 'degree'}

LabelingPulseInterval (metadata)

name: LabelingPulseInterval

description:

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

schema information:

{'type': 'number', 'exclusiveMinimum': 0, 'unit': 'ms'}

LabelingPulseMaximumGradient (metadata)

name: LabelingPulseMaximumGradient

description:

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

schema information:

{'type': 'number', 'exclusiveMinimum': 0, 'unit': 'mT/m'}

LabelingSlabThickness (metadata)

name: LabelingSlabThickness

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:

{'type': 'number', 'exclusiveMinimum': 0, 'unit': 'mm'}

Levels (metadata)

name: Levels

description:

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

schema information:

{'type': 'object', 'additionalProperties': {'type': 'string'}}

License (metadata)

name: License

description:

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

schema information:

{'type': 'string'}

LongName (metadata)

name: LongName

description:

Long (unabbreviated) name of the column.

schema information:

{'type': 'string'}

LookLocker (metadata)

name: LookLocker

description:

Boolean indicating if a Look-Locker readout is used.

schema information:

{'type': 'boolean'}

M0Estimate (metadata)

name: M0Estimate

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:

{'type': 'number', 'exclusiveMinimum': 0}

M0Type (metadata)

name: M0Type

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', 'enum': ['Separate', 'Included', 'Estimate', 'Absent']}

M0map (suffixes)

name: Equilibrium magnetization (M0) map

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'}

MEGChannelCount (metadata)

name: MEGChannelCount

description:

Number of MEG channels (for example, 275).

schema information:

{'type': 'integer', 'minimum': 0}

MEGCoordinateSystem (metadata)

name: MEGCoordinateSystem

description:

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

schema information:

{'type': 'string', 'enum': ['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']}

MEGCoordinateSystemDescription (metadata)

name: MEGCoordinateSystemDescription

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: MEGCoordinateUnits

description:

Units of the coordinates of "MEGCoordinateSystem".

schema information:

{'type': 'string', 'enum': ['m', 'mm', 'cm', 'n/a']}

MEGRE (suffixes)

name: Multi-echo Gradient Recalled Echo

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.

schema information:

{}

MEGREFChannelCount (metadata)

name: MEGREFChannelCount

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:

{'type': 'integer', 'minimum': 0}

MESE (suffixes)

name: Multi-echo Spin Echo

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.

schema information:

{}

MP2RAGE (suffixes)

name: Magnetization Prepared Two Gradient Echoes

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).

schema information:

{}

MPE (suffixes)

name: Multi-photon excitation microscopy

description:

Multi-photon excitation microscopy imaging data

schema information:

{}

MPM (suffixes)

name: Multi-parametric Mapping

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.

schema information:

{}

MRAcquisitionType (metadata)

name: MRAcquisitionType

description:

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

schema information:

{'type': 'string', 'enum': ['2D', '3D']}

MRTransmitCoilSequence (metadata)

name: MRTransmitCoilSequence

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: MTNumberOfPulses

description:

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

schema information:

{'type': 'number'}

MTOffsetFrequency (metadata)

name: MTOffsetFrequency

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: MTPulseBandwidth

description:

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

schema information:

{'type': 'number', 'unit': 'Hz'}

MTPulseDuration (metadata)

name: MTPulseDuration

description:

Duration of the magnetization transfer RF pulse in seconds.

schema information:

{'type': 'number', 'unit': 's'}

MTPulseShape (metadata)

name: MTPulseShape

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', 'enum': ['HARD', 'GAUSSIAN', 'GAUSSHANN', 'SINC', 'SINCHANN', 'SINCGAUSS', 'FERMI']}

MTR (suffixes)

name: Magnetization Transfer Ratio

description:

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

schema information:

{}

MTRmap (suffixes)

name: Magnetization transfer ratio image

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:

{'unit': 'arbitrary', 'minValue': 0, 'maxValue': 100}

MTS (suffixes)

name: Magnetization transfer saturation

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).

schema information:

{}

MTState (metadata)

name: MTState

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

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

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

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:

{'unit': 'arbitrary', 'minValue': 0, 'maxValue': 100}

MagneticFieldStrength (metadata)

name: MagneticFieldStrength

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

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:

{'type': 'number', 'exclusiveMinimum': 0}

Manual (metadata)

name: Manual

description:

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

schema information:

{'type': 'boolean'}

Manufacturer (metadata)

name: Manufacturer

description:

Manufacturer of the equipment that produced the measurements.

schema information:

{'type': 'string'}

ManufacturersModelName (metadata)

name: ManufacturersModelName

description:

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

schema information:

{'type': 'string'}

MatrixCoilMode (metadata)

name: MatrixCoilMode

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: MaxMovement

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: MeasurementToolMetadata

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:

{'type': 'object', 'properties': {'TermURL': {'type': 'string', 'format': 'uri'}, 'Description': {'type': 'string'}}}

MetaboliteAvail (metadata)

name: MetaboliteAvail

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: MetaboliteMethod

description:

Method used to measure metabolites.

schema information:

{'type': 'string'}

MetaboliteRecoveryCorrectionApplied (metadata)

name: MetaboliteRecoveryCorrectionApplied

description:

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

schema information:

{'type': 'boolean'}

MiscChannelCount (metadata)

name: MiscChannelCount

description:

Number of miscellaneous analog channels for auxiliary signals.

schema information:

{'type': 'integer', 'minimum': 0}

MixingTime (metadata)

name: MixingTime

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: ModeOfAdministration

description:

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

schema information:

{'type': 'string'}

MolarActivity (metadata)

name: MolarActivity

description:

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

schema information:

{'type': 'number'}

MolarActivityMeasTime (metadata)

name: MolarActivityMeasTime

description:

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

schema information:

{'type': 'string', 'format': 'time'}

MolarActivityUnits (metadata)

name: MolarActivityUnits

description:

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

schema information:

{'type': 'string', 'format': 'unit'}

MultibandAccelerationFactor (metadata)

name: MultibandAccelerationFactor

description:

The multiband factor, for multiband acquisitions.

schema information:

{'type': 'number'}

MultipartID (metadata)

name: MultipartID

description:

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

schema information:

{'type': 'string'}

NLO (suffixes)

name: Nonlinear optical microscopy

description:

Nonlinear optical microscopy imaging data

schema information:

{}

Name (metadata)

name: Name

description:

Name of the dataset.

schema information:

{'type': 'string'}

NegativeContrast (metadata)

name: NegativeContrast

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

description:

A file with no extension.

schema information:

{}

NonlinearGradientCorrection (metadata)

name: NonlinearGradientCorrection

description:

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

schema information:

{'type': 'boolean'}

NumberOfVolumesDiscardedByScanner (metadata)

name: NumberOfVolumesDiscardedByScanner

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:

{'type': 'integer', 'minimum': 0}

NumberOfVolumesDiscardedByUser (metadata)

name: NumberOfVolumesDiscardedByUser

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:

{'type': 'integer', 'minimum': 0}

NumberShots (metadata)

name: NumberShots

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'}, {'type': 'array', 'items': {'type': 'number'}}]}

NumericalAperture (metadata)

name: NumericalAperture

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:

{'type': 'number', 'exclusiveMinimum': 0}

OCT (suffixes)

name: Optical coherence tomography

description:

Optical coherence tomography imaging data

schema information:

{}

OperatingSystem (metadata)

name: OperatingSystem

description:

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

schema information:

{'type': 'string'}

OtherAcquisitionParameters (metadata)

name: OtherAcquisitionParameters

description:

Description of other relevant image acquisition parameters.

schema information:

{'type': 'string'}

PASLType (metadata)

name: PASLType

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

description:

Phase-contrast microscopy imaging data

schema information:

{}

PCASLType (metadata)

name: PCASLType

description:

The type of gradient pulses used in the control condition.

schema information:

{'type': 'string', 'enum': ['balanced', 'unbalanced']}

PD (suffixes)

name: Proton density image

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

description:

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

schema information:

{'unit': 'arbitrary'}

PDT2map (suffixes)

name: Combined PD/T2 image

description:

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

schema information:

{'unit': 'arbitrary'}

PDmap (suffixes)

name: Proton density image

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

description:

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

schema information:

{'unit': 'arbitrary'}

PLI (suffixes)

name: Polarized-light microscopy

description:

Polarized-light microscopy imaging data

schema information:

{}

ParallelAcquisitionTechnique (metadata)

name: ParallelAcquisitionTechnique

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: ParallelReductionFactorInPlane

description:

The parallel imaging (for instance, GRAPPA) factor. 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'}

PartialFourier (metadata)

name: PartialFourier

description:

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

schema information:

{'type': 'number'}

PartialFourierDirection (metadata)

name: PartialFourierDirection

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: PharmaceuticalDoseAmount

description:

Dose amount of pharmaceutical coadministered with tracer.

schema information:

{'anyOf': [{'type': 'number'}, {'type': 'array', 'items': {'type': 'number'}}]}

PharmaceuticalDoseRegimen (metadata)

name: PharmaceuticalDoseRegimen

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: PharmaceuticalDoseTime

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'}, {'type': 'array', 'items': {'type': 'number', 'unit': 's'}}]}

PharmaceuticalDoseUnits (metadata)

name: PharmaceuticalDoseUnits

description:

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

schema information:

{'type': 'string', 'format': 'unit'}

PharmaceuticalName (metadata)

name: PharmaceuticalName

description:

Name of pharmaceutical coadministered with tracer.

schema information:

{'type': 'string'}

PhaseEncodingDirection (metadata)

name: PhaseEncodingDirection

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', 'enum': ['i', 'j', 'k', 'i-', 'j-', 'k-']}

PixelSize (metadata)

name: PixelSize

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:

{'type': 'array', 'minItems': 2, 'maxItems': 3, 'items': {'type': 'number', 'minimum': 0}}

PixelSizeUnits (metadata)

name: PixelSizeUnits

description:

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

schema information:

{'type': 'string', 'enum': ['mm', 'um', 'nm']}

PlasmaAvail (metadata)

name: PlasmaAvail

description:

Boolean that specifies if plasma measurements are available.

schema information:

{'type': 'boolean'}

PlasmaFreeFraction (metadata)

name: PlasmaFreeFraction

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:

{'type': 'number', 'minimum': 0, 'maximum': 100}

PlasmaFreeFractionMethod (metadata)

name: PlasmaFreeFractionMethod

description:

Method used to estimate free fraction.

schema information:

{'type': 'string'}

PostLabelingDelay (metadata)

name: PostLabelingDelay

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': [{'type': 'number', 'exclusiveMinimum': 0, 'unit': 's'}, {'type': 'array', 'items': {'type': 'number', 'exclusiveMinimum': 0, 'unit': 's'}}]}

PowerLineFrequency (metadata)

name: PowerLineFrequency

description:

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

schema information:

{'anyOf': [{'type': 'number', 'exclusiveMinimum': 0, 'unit': 'Hz'}, {'type': 'string', 'enum': ['n/a']}]}

PromptRate (metadata)

name: PromptRate

description:

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

schema information:

{'type': 'array', 'items': {'type': 'number'}}

PulseSequenceDetails (metadata)

name: PulseSequenceDetails

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: PulseSequenceType

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

description:

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

schema information:

{'type': 'number', 'minimum': 0, 'maximum': 100}

R1map (suffixes)

name: Longitudinal relaxation rate image

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

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

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

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).

schema information:

{}

RB1map (suffixes)

name: RF receive sensitivity map

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 (top_level_files)

name: README

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:

{}

RandomRate (metadata)

name: RandomRate

description:

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

schema information:

{'type': 'array', 'items': {'type': 'number'}}

RawSources (metadata)

name: RawSources

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.

schema information:

{'type': 'array', 'items': {'type': 'string', 'format': 'dataset_relative'}}

ReceiveCoilActiveElements (metadata)

name: ReceiveCoilActiveElements

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: ReceiveCoilName

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: ReconFilterSize

description:

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

schema information:

{'anyOf': [{'type': 'number', 'unit': 'mm'}, {'type': 'array', 'items': {'type': 'number', 'unit': 'mm'}}]}

ReconFilterType (metadata)

name: ReconFilterType

description:

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

schema information:

{'anyOf': [{'type': 'string'}, {'type': 'array', 'items': {'type': 'string'}}]}

ReconMethodImplementationVersion (metadata)

name: ReconMethodImplementationVersion

description:

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

schema information:

{'type': 'string'}

ReconMethodName (metadata)

name: ReconMethodName

description:

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

schema information:

{'type': 'string'}

ReconMethodParameterLabels (metadata)

name: ReconMethodParameterLabels

description:

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

schema information:

{'type': 'array', 'items': {'type': 'string'}}

ReconMethodParameterUnits (metadata)

name: ReconMethodParameterUnits

description:

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

schema information:

{'type': 'array', 'items': {'type': 'string', 'format': 'unit'}}

ReconMethodParameterValues (metadata)

name: ReconMethodParameterValues

description:

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

schema information:

{'type': 'array', 'items': {'type': 'number'}}

RecordingDuration (metadata)

name: RecordingDuration

description:

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

schema information:

{'type': 'number', 'unit': 's'}

RecordingType (metadata)

name: RecordingType

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', 'enum': ['continuous', 'epoched', 'discontinuous']}

name: ReferencesAndLinks

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: RepetitionTime

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:

{'type': 'number', 'exclusiveMinimum': 0, 'unit': 's'}

RepetitionTimeExcitation (metadata)

name: RepetitionTimeExcitation

description:

The interval, in seconds, between two successive excitations. [DICOM Tag 0018, 0080](http://dicomlookup.com/lookup.asp?sw=Tnumber&q=(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:

{'type': 'number', 'minimum': 0, 'unit': 's'}

RepetitionTimePreparation (metadata)

name: RepetitionTimePreparation

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': [{'type': 'number', 'minimum': 0, 'unit': 's'}, {'type': 'array', 'items': {'type': 'number', 'minimum': 0, 'unit': 's'}}]}

Resolution (metadata)

name: Resolution

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'}, {'type': 'object', 'additionalProperties': {'type': 'string'}}]}

S0map (suffixes)

name: Observed signal amplitude (S0) image

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.

schema information:

{}

SEEGChannelCount (metadata)

name: SEEGChannelCount

description:

Number of SEEG channels.

schema information:

{'type': 'integer', 'minimum': 0}

SEM (suffixes)

name: Scanning electron microscopy

description:

Scanning electron microscopy imaging data

schema information:

{}

SPIM (suffixes)

name: Selective plane illumination microscopy

description:

Selective plane illumination microscopy imaging data

schema information:

{}

SR (suffixes)

name: Super-resolution microscopy

description:

Super-resolution microscopy imaging data

schema information:

{}

SampleEmbedding (metadata)

name: SampleEmbedding

description:

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

schema information:

{'type': 'string'}

SampleEnvironment (metadata)

name: SampleEnvironment

description:

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

schema information:

{'type': 'string', 'enum': ['in vivo', 'ex vivo', 'in vitro']}

SampleExtractionInstitution (metadata)

name: SampleExtractionInstitution

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: SampleExtractionProtocol

description:

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

schema information:

{'type': 'string'}

SampleFixation (metadata)

name: SampleFixation

description:

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

schema information:

{'type': 'string'}

SampleOrigin (metadata)

name: SampleOrigin

description:

Describes from which tissue the genetic information was extracted.

schema information:

{'type': 'string', 'enum': ['blood', 'saliva', 'brain', 'csf', 'breast milk', 'bile', 'amniotic fluid', 'other biospecimen']}

SamplePrimaryAntibody (metadata)

name: SamplePrimaryAntibody

description:

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

schema information:

{'anyOf': [{'type': 'string'}, {'type': 'array', 'items': {'type': 'string'}}]}

SampleSecondaryAntibody (metadata)

name: SampleSecondaryAntibody

description:

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

schema information:

{'anyOf': [{'type': 'string'}, {'type': 'array', 'items': {'type': 'string'}}]}

SampleStaining (metadata)

name: SampleStaining

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'}, {'type': 'array', 'items': {'type': 'string'}}]}

SamplingFrequency (metadata)

name: SamplingFrequency

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'}

ScaleFactor (metadata)

name: ScaleFactor

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:

{'type': 'array', 'items': {'type': 'number'}}

ScanDate (metadata)

name: ScanDate

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:

{'type': 'string', 'format': 'date'}

ScanOptions (metadata)

name: ScanOptions

description:

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

schema information:

{'anyOf': [{'type': 'string'}, {'type': 'array', 'items': {'type': 'string'}}]}

ScanStart (metadata)

name: ScanStart

description:

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

schema information:

{'type': 'number', 'unit': 's'}

ScanningSequence (metadata)

name: ScanningSequence

description:

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

schema information:

{'anyOf': [{'type': 'string'}, {'type': 'array', 'items': {'type': 'string'}}]}

ScatterFraction (metadata)

name: ScatterFraction

description:

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

schema information:

{'type': 'array', 'items': {'type': 'number', 'minimum': 0, 'maximum': 100}}

SequenceName (metadata)

name: SequenceName

description:

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

schema information:

{'type': 'string'}

SequenceVariant (metadata)

name: SequenceVariant

description:

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

schema information:

{'anyOf': [{'type': 'string'}, {'type': 'array', 'items': {'type': 'string'}}]}

SinglesRate (metadata)

name: SinglesRate

description:

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

schema information:

{'type': 'array', 'items': {'type': 'number'}}

SkullStripped (metadata)

name: SkullStripped

description:

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

schema information:

{'type': 'boolean'}

SliceEncodingDirection (metadata)

name: SliceEncodingDirection

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', 'enum': ['i', 'j', 'k', 'i-', 'j-', 'k-']}

SliceThickness (metadata)

name: SliceThickness

description:

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

schema information:

{'type': 'number', 'unit': 'um', 'exclusiveMinimum': 0}

SliceTiming (metadata)

name: SliceTiming

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:

{'type': 'array', 'items': {'type': 'number', 'minimum': 0, 'unit': 's'}}

SoftwareFilters (metadata)

name: SoftwareFilters

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': [{'type': 'object', 'additionalProperties': {'type': 'object'}}, {'type': 'string', 'enum': ['n/a']}]}

SoftwareName (metadata)

name: SoftwareName

description:

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

schema information:

{'type': 'string'}

SoftwareRRID (metadata)

name: SoftwareRRID

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:

{'type': 'string', 'format': 'rrid'}

SoftwareVersion (metadata)

name: SoftwareVersion

description:

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

schema information:

{'type': 'string'}

SoftwareVersions (metadata)

name: SoftwareVersions

description:

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

schema information:

{'type': 'string'}

SourceDatasets (metadata)

name: SourceDatasets

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:

{'type': 'array', 'items': {'type': 'object', 'properties': {'URL': {'type': 'string', 'format': 'uri'}, 'DOI': {'type': 'string'}, 'Version': {'type': 'string'}}}}

Sources (metadata)

name: Sources

description:

A list of files with the paths specified relative to dataset root; 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.

schema information:

{'type': 'array', 'items': {'type': 'string', 'format': 'dataset_relative'}}

SpatialReference (metadata)

name: SpatialReference

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': [{'type': 'string', 'enum': ['orig']}, {'type': 'string', 'format': 'uri'}, {'type': 'string', 'format': 'dataset_relative'}, {'type': 'object', 'additionalProperties': {'anyOf': [{'type': 'string', 'enum': ['orig']}, {'type': 'string', 'format': 'uri'}, {'type': 'string', 'format': 'dataset_relative'}]}}]}

SpecificRadioactivity (metadata)

name: SpecificRadioactivity

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'}, {'type': 'string', 'enum': ['n/a']}]}

SpecificRadioactivityMeasTime (metadata)

name: SpecificRadioactivityMeasTime

description:

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

schema information:

{'type': 'string', 'format': 'time'}

SpecificRadioactivityUnits (metadata)

name: SpecificRadioactivityUnits

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': [{'type': 'string', 'format': 'unit'}, {'type': 'string', 'enum': ['n/a']}]}

SpoilingGradientDuration (metadata)

name: SpoilingGradientDuration

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: SpoilingGradientMoment

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: SpoilingRFPhaseIncrement

description:

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

schema information:

{'type': 'number', 'unit': 'degrees'}

SpoilingState (metadata)

name: SpoilingState

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: SpoilingType

description:

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

schema information:

{'type': 'string', 'enum': ['RF', 'GRADIENT', 'COMBINED']}

StartTime (metadata)

name: StartTime

description:

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

schema information:

{'type': 'number', 'unit': 's'}

StationName (metadata)

name: StationName

description:

Institution defined name of the machine that produced the measurements.

schema information:

{'type': 'string'}

StimulusPresentation (metadata)

name: StimulusPresentation

description:

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

schema information:

{'type': 'object', 'properties': {'OperatingSystem': {'name': 'OperatingSystem', 'description': 'Operating system used to run the stimuli presentation software\n(for formatting recommendations, see examples below this table).\n', 'type': 'string'}, 'SoftwareName': {'name': 'SoftwareName', 'description': 'Name of the software that was used to present the stimuli.\n', 'type': 'string'}, 'SoftwareRRID': {'name': 'SoftwareRRID', 'description': "[Research Resource Identifier](https://scicrunch.org/resources) of the\nsoftware that was used to present the stimuli.\nExamples: The RRID for Psychtoolbox is 'SCR_002881',\nand that of PsychoPy is 'SCR_006571'.\n", 'type': 'string', 'format': 'rrid'}, 'SoftwareVersion': {'name': 'SoftwareVersion', 'description': 'Version of the software that was used to present the stimuli.\n', 'type': 'string'}, 'Code': {'name': 'Code', 'description': '[URI](SPEC_ROOT/02-common-principles.md#uniform-resource-indicator)\nof the code used to present the stimuli.\nPersistent identifiers such as DOIs are preferred.\nIf multiple versions of code may be hosted at the same location,\nrevision-specific URIs are recommended.\n', 'type': 'string', 'format': 'uri'}}}

SubjectArtefactDescription (metadata)

name: SubjectArtefactDescription

description:

Freeform description of the observed subject artefact and its possible cause (for example, "Vagus Nerve Stimulator", "non-removable implant"). If this field is set to "n/a", it will be interpreted as absence of major source of artifacts except cardiac and blinks.

schema information:

{'type': 'string'}

T1map (suffixes)

name: Longitudinal relaxation time image

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

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

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

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

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

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

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

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

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.

schema information:

{}

TB1DAM (suffixes)

name: TB1DAM

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.

schema information:

{}

TB1EPI (suffixes)

name: TB1EPI

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.

schema information:

{}

TB1RFM (suffixes)

name: TB1RFM

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.

schema information:

{}

TB1SRGE (suffixes)

name: TB1SRGE

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).

schema information:

{}

TB1TFL (suffixes)

name: TB1TFL

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.

schema information:

{}

TB1map (suffixes)

name: RF transmit field image

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

description:

Transmission electron microscopy imaging data

schema information:

{}

TaskDescription (metadata)

name: TaskDescription

description:

Longer description of the task.

schema information:

{'type': 'string'}

TaskName (metadata)

name: TaskName

description:

Name of the task. No two tasks should have the same name. The task label included in the file name is derived from this "TaskName" field by removing all non-alphanumeric ([a-zA-Z0-9]) characters. For example "TaskName" "faces n-back" will correspond to task label facesnback.

schema information:

{'type': 'string'}

TermURL (metadata)

name: TermURL

description:

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

schema information:

{'type': 'string'}

TimeZero (metadata)

name: TimeZero

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:

{'type': 'string', 'format': 'time'}

TissueDeformationScaling (metadata)

name: TissueDeformationScaling

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:

{'type': 'number', 'exclusiveMinimum': 0}

TissueOrigin (metadata)

name: TissueOrigin

description:

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

schema information:

{'type': 'string', 'enum': ['gray matter', 'white matter', 'csf', 'meninges', 'macrovascular', 'microvascular']}

TotalAcquiredPairs (metadata)

name: TotalAcquiredPairs

description:

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

schema information:

{'type': 'number', 'exclusiveMinimum': 0}

TotalReadoutTime (metadata)

name: TotalReadoutTime

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: TracerMolecularWeight

description:

Accurate molecular weight of the tracer used.

schema information:

{'type': 'number'}

TracerMolecularWeightUnits (metadata)

name: TracerMolecularWeightUnits

description:

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

schema information:

{'type': 'string', 'format': 'unit'}

TracerName (metadata)

name: TracerName

description:

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

schema information:

{'type': 'string'}

TracerRadLex (metadata)

name: TracerRadLex

description:

ID of the tracer compound from the RadLex Ontology.

schema information:

{'type': 'string'}

TracerRadionuclide (metadata)

name: TracerRadionuclide

description:

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

schema information:

{'type': 'string'}

TracerSNOMED (metadata)

name: TracerSNOMED

description:

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

schema information:

{'type': 'string'}

TriggerChannelCount (metadata)

name: TriggerChannelCount

description:

Number of channels for digital (TTL bit level) triggers.

schema information:

{'type': 'integer', 'minimum': 0}

TubingLength (metadata)

name: TubingLength

description:

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

schema information:

{'type': 'number', 'unit': 'm'}

TubingType (metadata)

name: TubingType

description:

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

schema information:

{'type': 'string'}

Type (metadata)

name: Type

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', 'enum': ['Brain', 'Lesion', 'Face', 'ROI']}

UNIT1 (suffixes)

name: Homogeneous (flat) T1-weighted MP2RAGE image

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.

schema information:

{}

Units (metadata)

name: Units

description:

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

schema information:

{'type': 'string', 'format': 'unit'}

VFA (suffixes)

name: Variable flip angle

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).

schema information:

{}

VascularCrushing (metadata)

name: VascularCrushing

description:

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

schema information:

{'type': 'boolean'}

VascularCrushingVENC (metadata)

name: VascularCrushingVENC

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'}, {'type': 'array', 'items': {'type': 'number', 'unit': 'cm/s'}}]}

VolumeTiming (metadata)

name: VolumeTiming

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:

{'type': 'array', 'minItems': 1, 'items': {'type': 'number', 'unit': 's'}}

WholeBloodAvail (metadata)

name: WholeBloodAvail

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: WithdrawalRate

description:

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

schema information:

{'type': 'number', 'unit': 'mL/s'}

abbreviation (columns)

name: abbreviation

description:

The unique label abbreviation

schema information:

{'type': 'string'}

acq_time sense 1 (columns)

name: acq_time

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:

{'type': 'string', 'format': 'datetime'}

acq_time sense 2 (columns)

name: acq_time

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:

{'type': 'string', 'format': 'datetime'}

acquisition (entities)

name: Acquisition

description:

The acq-<label> key/value pair 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. At what level of detail to make the distinction (for example, just between RARE and FLASH, or between RARE, FLASH, and FLASHsubsampled) remains at the discretion of the researcher.

schema information:

{'entity': 'acq', 'type': 'string', 'format': 'label'}

age (columns)

name: age

description:

Numeric value in years (float or integer value).

schema information:

{'type': 'number', 'unit': 'year'}

anat (datatypes)

name: Anatomical Magnetic Resonance Imaging

description:

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

schema information:

{}

angio (suffixes)

name: Angiogram

description:

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

schema information:

{}

asl (suffixes)

name: Arterial Spin Labeling

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.

schema information:

{}

aslcontext (suffixes)

name: Arterial Spin Labeling Context

description:

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

schema information:

{}

asllabeling (suffixes)

name: ASL Labeling Screenshot

description:

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

schema information:

{}

atlas (entities)

name: Atlas

description:

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

schema information:

{'entity': 'atlas', 'type': 'string', 'format': 'label'}

beh (datatypes)

name: Behavioral Data

description:

Behavioral data.

schema information:

{}

beh (modalities)

name: Behavioral experiments

description:

Behavioral data acquired without accompanying neuroimaging data.

schema information:

{}

beh (suffixes)

name: Behavioral recording

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.

schema information:

{}

bids_uri (formats)

name: BIDS uniform resource indicator

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:".

schema information:

{'pattern': 'bids:[0-9a-zA-Z/#:\\?\\_\\-\\.]+'}

blood (suffixes)

name: Blood recording data

description:

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

schema information:

{}

bold (suffixes)

name: Blood-Oxygen-Level Dependent image

description:

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

schema information:

{}

boolean (formats)

name: Boolean

description:

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

schema information:

{'pattern': '(true|false)'}

cardiac (columns)

name: cardiac

description:

continuous pulse measurement

schema information:

{'type': 'number'}

cbv (suffixes)

name: Cerebral blood volume image

description:

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

schema information:

{}

ceagent (entities)

name: Contrast Enhancing Agent

description:

The ce-<label> key/value can be used to distinguish sequences using different contrast enhanced images. The label is the name of the contrast agent. The key "ContrastBolusIngredient" MAY also be added in the JSON file, with the same label.

schema information:

{'entity': 'ce', 'type': 'string', 'format': 'label'}

channels (suffixes)

name: Channels File

description:

Channel information.

schema information:

{}

chunk (entities)

name: Chunk

description:

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

schema information:

{'entity': 'chunk', 'type': 'string', 'format': 'index'}

code (associated_data)

name: Code

description:

A directory in which to store any code used to generate the derivatives from the source data.

schema information:

{}

color (columns)

name: color

description:

Hexadecimal. Label color for visualization.

schema information:

{'type': 'string', 'unit': 'hexadecimal'}

coordsystem (suffixes)

name: Coordinate System File

description:

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

schema information:

{}

dataset_description (top_level_files)

name: Dataset Description

description:

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

schema information:

{}

dataset_relative (formats)

name: Path relative to the BIDS dataset directory

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).

schema information:

{'pattern': '(?!/)[0-9a-zA-Z/\\_\\-\\.]+'}

date (formats)

name: Date

description:

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

schema information:

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

datetime (formats)

name: Datetime

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.

schema information:

{'pattern': '[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})?'}

defacemask (suffixes)

name: Defacing Mask

description:

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

schema information:

{}

density (entities)

name: Density

description:

Density of non-parametric surfaces. MUST have a corresponding Density metadata field to provide interpretation.
This entity is only applicable to derivative data.

schema information:

{'entity': 'den', 'type': 'string', 'format': 'label'}

derivatives (associated_data)

name: Derivative data

description:

Derivative data

schema information:

{}

derived_from (columns)

name: derived_from

description:

sample-<label> key/value pair 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', 'pattern': '^sample-[0-9a-zA-Z]+$'}

description (columns)

name: description

description:

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

schema information:

{'type': 'string'}

description (entities)

name: Description

description:

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

schema information:

{'entity': 'desc', 'type': 'string', 'format': 'label'}

dimension (columns)

name: dimension

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

description:

The dir-<label> key/value can be set to an arbitrary alphanumeric label (for example, dir-LR or dir-AP) to distinguish different phase-encoding directions.

schema information:

{'entity': 'dir', 'type': 'string', 'format': 'label'}

duration (columns)

name: duration

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': [{'type': 'number', 'unit': 's', 'minimum': 0}, {'type': 'string', 'enum': ['n/a']}]}

dwi (datatypes)

name: Diffusion-Weighted Imaging

description:

Diffusion-weighted imaging (DWI).

schema information:

{}

dwi (suffixes)

name: Diffusion-weighted image

description:

Diffusion-weighted imaging contrast (specialized T2 weighting).

schema information:

{}

echo (entities)

name: Echo

description:

If files belonging to an entity-linked file collection are acquired at different echo times, the _echo-<index> key/value pair MUST be used to distinguish individual files. This entity represents the "EchoTime" metadata field. Please note that the <index> denotes the number/index (in the form of a nonnegative integer), not the "EchoTime" value which needs to be stored in the field "EchoTime" of the separate JSON file.

schema information:

{'entity': 'echo', 'type': 'string', 'format': 'index'}

eeg (datatypes)

name: Electroencephalography

description:

Electroencephalography

schema information:

{}

eeg (modalities)

name: Electroencephalography

description:

Data acquired with EEG.

schema information:

{}

eeg (suffixes)

name: Electroencephalography

description:

Electroencephalography recording data.

schema information:

{}

electrodes (suffixes)

name: Electrodes

description:

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

schema information:

{}

epi (suffixes)

name: EPI

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.

schema information:

{}

events (suffixes)

name: Events

description:

Event timing information from a behavioral task.

schema information:

{}

fieldmap (suffixes)

name: Fieldmap

description:

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

schema information:

{}

file_relative (formats)

name: Path relative to the parent file

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).

schema information:

{'pattern': '(?!/)[0-9a-zA-Z/\\_\\-\\.]+'}

filename (columns)

name: filename

description:

Relative paths to files.

schema information:

{'type': 'string', 'format': 'participant_relative'}

flip (entities)

name: Flip Angle

description:

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

schema information:

{'entity': 'flip', 'type': 'string', 'format': 'index'}

fmap (datatypes)

name: Field maps

description:

MRI scans for estimating B0 inhomogeneity-induced distortions.

schema information:

{}

func (datatypes)

name: Task-Based Magnetic Resonance Imaging

description:

Task (including resting state) imaging data

schema information:

{}

genetic_info (top_level_files)

name: Genetic Information

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:

{}

group (columns)

name: group

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: handedness

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', 'enum': ['left', 'l', 'L', 'LEFT', 'Left', 'right', 'r', 'R', 'RIGHT', 'Right', 'ambidextrous', 'a', 'A', 'AMBIDEXTROUS', 'Ambidextrous', 'n/a']}

headshape (suffixes)

name: Headshape File

description:

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

schema information:

{}

hemisphere (columns)

name: hemisphere

description:

The hemisphere in which the electrode is placed.

schema information:

{'type': 'string', 'enum': ['L', 'R']}

hemisphere (entities)

name: Hemisphere

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:

{'entity': 'hemi', 'type': 'string', 'format': 'label', 'enum': ['L', 'R']}

high_cutoff (columns)

name: high_cutoff

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': [{'type': 'number', 'unit': 'Hz', 'minimum': 0}, {'type': 'string', 'enum': ['n/a']}]}

hplc_recovery_fractions (columns)

name: hplc_recovery_fractions

description:

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

schema information:

{'type': 'number', 'unit': 'arbitrary'}

iEEGCoordinateProcessingDescription (metadata)

name: iEEGCoordinateProcessingDescription

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: iEEGCoordinateProcessingReference

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: iEEGCoordinateSystem

description:

Defines the coordinate system for the iEEG sensors. See Appendix VIII 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', 'enum': ['Pixels', 'ACPC', 'Other', 'ICBM452AirSpace', 'ICBM452Warp5Space', 'IXI549Space', 'fsaverage', 'fsaverageSym', 'fsLR', 'MNIColin27', 'MNI152Lin', 'MNI152NLin2009aSym', 'MNI152NLin2009bSym', 'MNI152NLin2009cSym', 'MNI152NLin2009aAsym', 'MNI152NLin2009bAsym', 'MNI152NLin2009cAsym', 'MNI152NLin6Sym', 'MNI152NLin6ASym', 'MNI305', 'NIHPD', 'OASIS30AntsOASISAnts', 'OASIS30Atropos', 'Talairach', 'UNCInfant', 'fsaverage3', 'fsaverage4', 'fsaverage5', 'fsaverage6', 'fsaveragesym', 'UNCInfant0V21', 'UNCInfant1V21', 'UNCInfant2V21', 'UNCInfant0V22', 'UNCInfant1V22', 'UNCInfant2V22', 'UNCInfant0V23', 'UNCInfant1V23', 'UNCInfant2V23']}

iEEGCoordinateSystemDescription (metadata)

name: iEEGCoordinateSystemDescription

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: iEEGCoordinateUnits

description:

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

schema information:

{'type': 'string', 'enum': ['m', 'mm', 'cm', 'pixels', 'n/a']}

iEEGElectrodeGroups (metadata)

name: iEEGElectrodeGroups

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: iEEGGround

description:

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

schema information:

{'type': 'string'}

iEEGPlacementScheme (metadata)

name: iEEGPlacementScheme

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: iEEGReference

description:

General description of the reference scheme used and (when applicable) of location of the reference electrode in the raw recordings (for example, "left mastoid", "bipolar", "T01" for electrode with name T01, "intracranial electrode on top of a grid, not included with data", "upside down electrode"). If different channels have a different reference, this field should have a general description and the channel specific reference should be defined in the channels.tsv file.

schema information:

{'type': 'string'}

ieeg (datatypes)

name: Intracranial electroencephalography

description:

Intracranial electroencephalography (iEEG) or electrocorticography (ECoG) data

schema information:

{}

ieeg (modalities)

name: Intracranial Electroencephalography

description:

Data acquired with iEEG.

schema information:

{}

ieeg (suffixes)

name: Intracranial Electroencephalography

description:

Intracranial electroencephalography recording data.

schema information:

{}

impedance (columns)

name: impedance

description:

Impedance of the electrode, units MUST be in kOhm.

schema information:

{'type': 'number', 'unit': 'kOhm'}

index (columns)

name: index

description:

The label integer index.

schema information:

{'type': 'integer'}

index (formats)

name: Index

description:

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

schema information:

{'pattern': '[0-9]*[1-9]+[0-9]*'}

inplaneT1 (suffixes)

name: Inplane T1

description:

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

schema information:

{'unit': 'arbitrary'}

inplaneT2 (suffixes)

name: Inplane T2

description:

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

schema information:

{'unit': 'arbitrary'}

integer (formats)

name: Integer

description:

An integer which may be positive or negative.

schema information:

{'pattern': '[+-]?\\d+'}

inversion (entities)

name: Inversion Time

description:

If files belonging to an entity-linked file collection are acquired at different inversion times, the _inv-<index> key/value pair MUST be used to distinguish individual files. This entity represents the "InversionTime metadata field. Please note that the <index> denotes the number/index (in the form of a nonnegative integer), not the "InversionTime" value which needs to be stored in the field "InversionTime" of the separate JSON file.

schema information:

{'entity': 'inv', 'type': 'string', 'format': 'index'}

label (entities)

name: Label

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:

{'entity': 'label', 'type': 'string', 'format': 'label'}

label (formats)

name: Label

description:

Freeform labels without special characters.

schema information:

{'pattern': '[0-9a-zA-Z]+'}

low_cutoff (columns)

name: low_cutoff

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'}, {'type': 'string', 'enum': ['n/a']}]}

m0scan (suffixes)

name: M0 image

description:

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

schema information:

{}

magnitude (suffixes)

name: Magnitude

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.

schema information:

{}

magnitude1 (suffixes)

name: Magnitude

description:

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

schema information:

{}

magnitude2 (suffixes)

name: Magnitude

description:

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

schema information:

{}

manufacturer (columns)

name: manufacturer

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: mapping

description:

Corresponding integer label in the standard BIDS label lookup.

schema information:

{'type': 'integer'}

markers (suffixes)

name: MEG Sensor Coil Positions

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

schema information:

{}

material (columns)

name: material

description:

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

schema information:

{'type': 'string'}

meg (datatypes)

name: Magnetoencephalography

description:

Magnetoencephalography

schema information:

{}

meg (modalities)

name: Magnetoencephalography

description:

Data acquired with an MEG scanner.

schema information:

{}

meg (suffixes)

name: Magnetoencephalography

description:

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

schema information:

{}

metabolite_parent_fraction (columns)

name: metabolite_parent_fraction

description:

Parent fraction of the radiotracer (0-1).

schema information:

{'type': 'number', 'minimum': 0, 'maximum': 1}

metabolite_polar_fraction (columns)

name: metabolite_polar_fraction

description:

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

schema information:

{'type': 'number', 'minimum': 0, 'maximum': 1}

micr (datatypes)

name: Microscopy

description:

Microscopy

schema information:

{}

micr (modalities)

name: Microscopy

description:

Data acquired with a microscope.

schema information:

{}

modality (entities)

name: Corresponding Modality

description:

The mod-<label> key/value pair 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:

{'entity': 'mod', 'type': 'string', 'format': 'label'}

mri (modalities)

name: Magnetic Resonance Imaging

description:

Data acquired with an MRI scanner.

schema information:

{}

mtransfer (entities)

name: Magnetization Transfer

description:

If files belonging to an entity-linked file collection are acquired at different magnetization transfer (MT) states, the _mt-<label> key/value pair MUST be used to distinguish individual files. This entity represents the "MTState" metadata field. Allowed label values for this entity are on and off, for images acquired in presence and absence of an MT pulse, respectively.

schema information:

{'entity': 'mt', 'type': 'string', 'enum': ['on', 'off']}

name sense 1 (columns)

name: name

description:

Label of the channel.

schema information:

{'type': 'string'}

name sense 2 (columns)

name: name

description:

Name of the electrode contact point.

schema information:

{'type': 'string'}

name sense 3 (columns)

name: name

description:

The unique label name.

schema information:

{'type': 'string'}

notch (columns)

name: notch

description:

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

schema information:

{'anyOf': [{'type': 'number', 'unit': 'Hz'}, {'type': 'string', 'enum': ['n/a']}]}

number (formats)

name: Number

description:

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

schema information:

{'pattern': '[+-]?([0-9]+([.][0-9]*)?|[.][0-9]+)([eE][+-]?[0-9]+)?'}

onset (columns)

name: onset

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'}

part (entities)

name: Part

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> key/value pair 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 key MAY be omitted.

schema information:

{'entity': 'part', 'type': 'string', 'enum': ['mag', 'phase', 'real', 'imag']}

participant_id (columns)

name: participant_id

description:

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

schema information:

{'type': 'string', 'pattern': '^sub-[0-9a-zA-Z]+$'}

participant_relative (formats)

name: Path relative to the participant directory

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).

schema information:

{'pattern': '(?!/)(?!sub-)[0-9a-zA-Z/\\_\\-\\.]+'}

participants (top_level_files)

name: Participant Information

description:

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

schema information:

{}

pathology (columns)

name: pathology

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

description:

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

schema information:

{}

pet (datatypes)

name: Positron Emission Tomography

description:

Positron emission tomography data

schema information:

{}

pet (modalities)

name: Positron Emission Tomography

description:

Data acquired with PET.

schema information:

{}

pet (suffixes)

name: Positron Emission Tomography

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).

schema information:

{}

phase (suffixes)

name: Phase image

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

description:

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

schema information:

{}

phase2 (suffixes)

name: Phase

description:

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

schema information:

{}

phasediff (suffixes)

name: Phase-difference

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.

schema information:

{}

photo (suffixes)

name: Photo File

description:

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

schema information:

{}

physio (suffixes)

name: Physiological recording

description:

Physiological recordings such as cardiac and respiratory signals.

schema information:

{}

plasma_radioactivity (columns)

name: plasma_radioactivity

description:

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

schema information:

{'type': 'number'}

processing (entities)

name: Processed (on device)

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 Elekta'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:

{'entity': 'proc', 'type': 'string', 'format': 'label'}

reconstruction (entities)

name: Reconstruction

description:

The rec-<label> key/value can be used to distinguish different reconstruction algorithms (for example MoCo for the ones using motion correction).

schema information:

{'entity': 'rec', 'type': 'string', 'format': 'label'}

recording (entities)

name: Recording

description:

More than one continuous recording file can be included (with different sampling frequencies). In such case use different labels. For example: _recording-contrast, _recording-saturation.

schema information:

{'entity': 'recording', 'type': 'string', 'format': 'label'}

reference sense 1 (columns)

name: reference

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: reference

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'}, {'type': 'string', 'enum': ['n/a']}]}

resolution (entities)

name: Resolution

description:

Resolution of regularly sampled N-dimensional data. MUST have a corresponding "Resolution" metadata field to provide interpretation.
This entity is only applicable to derivative data.

schema information:

{'entity': 'res', 'type': 'string', 'format': 'label'}

respiratory (columns)

name: respiratory

description:

continuous breathing measurement

schema information:

{'type': 'number'}

response_time (columns)

name: response_time

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'}, {'type': 'string', 'enum': ['n/a']}]}

rrid (formats)

name: Research resource identifier

description:

A research resource identifier.

schema information:

{'pattern': 'RRID:.+_.+'}

run (entities)

name: Run

description:

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 labels).
If different entities apply, such as a different session indicated by ses-<label>, or different acquisition parameters indicated by acq-<label>, then run is not needed to distinguish the scans and MAY be omitted.

schema information:

{'entity': 'run', 'type': 'string', 'format': 'index'}

sample (columns)

name: sample

description:

Onset of the event according to the sampling scheme of the recorded modality (that is, referring to the raw data file that the events.tsv file accompanies).

schema information:

{'type': 'integer'}

sample (entities)

name: Sample

description:

A sample pertaining to a subject such as tissue, primary cell or cell-free sample. The sample-<label> key/value pair 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:

{'entity': 'sample', 'type': 'string', 'format': 'label'}

sample_id (columns)

name: sample_id

description:

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

schema information:

{'type': 'string', 'pattern': '^sample-[0-9a-zA-Z]+$'}

sample_type (columns)

name: sample_type

description:

Biosample type defined by ENCODE Biosample Type.

schema information:

{'type': 'string', 'enum': ['cell line', 'in vitro differentiated cells', 'primary cell', 'cell-free sample', 'cloning host', 'tissue', 'whole organisms', 'organoid', 'technical sample']}

samples (top_level_files)

name: Sample Information

description:

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

schema information:

{}

sampling_frequency (columns)

name: sampling_frequency

description:

Sampling rate of the channel in Hz.

schema information:

{'type': 'number', 'unit': 'Hz'}

sbref (suffixes)

name: Single-band reference image

description:

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

schema information:

{}

scans (suffixes)

name: Scans file

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).

schema information:

{}

session (entities)

name: Session

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:

{'entity': 'ses', 'type': 'string', 'format': 'label'}

session_id (columns)

name: session_id

description:

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

schema information:

{'type': 'string', 'pattern': '^ses-[0-9a-zA-Z]+$'}

sessions (suffixes)

name: Sessions file

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.

schema information:

{}

sex (columns)

name: sex

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', 'enum': ['male', 'm', 'M', 'MALE', 'Male', 'female', 'f', 'F', 'FEMALE', 'Female', 'other', 'o', 'O', 'OTHER', 'Other', 'n/a']}

size (columns)

name: size

description:

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

schema information:

{'type': 'number', 'unit': 'mm2'}

software_filters (columns)

name: software_filters

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'}, {'type': 'string', 'enum': ['n/a']}]}

sourcedata (associated_data)

name: Source data

description:

Data before harmonization, reconstruction, and/or file format conversion (for example, E-Prime event logs or DICOM files).

schema information:

{}

space (entities)

name: Space

description:

The space 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 space <label> MUST be taken from one of the modality specific lists in Appendix VIII. 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:

{'entity': 'space', 'type': 'string', 'format': 'label'}

species (columns)

name: species

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

description:

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

schema information:

{'entity': 'split', 'type': 'string', 'format': 'index'}

stain (entities)

name: Stain

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. Stains SHOULD be indicated in the "SampleStaining" key in the sidecar JSON file, although the label may be different. Description of antibodies SHOULD also be indicated in "SamplePrimaryAntibodies" and/or "SampleSecondaryAntobodies" as appropriate.

schema information:

{'entity': 'stain', 'type': 'string', 'format': 'label'}

status (columns)

name: status

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', 'enum': ['good', 'bad', 'n/a']}

status_description (columns)

name: status_description

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 [status].

schema information:

{'type': 'string'}

stim (suffixes)

name: Continuous recording

description:

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

schema information:

{}

stim_file (columns)

name: stim_file

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:

{'type': 'string', 'format': 'stimuli_relative'}

stimuli (associated_data)

name: Stimulus files

description:

The stimulus files can be added in a /stimuli directory (under the root directory of the dataset; with optional subdirectories) AND using a stim_file column in *_events.tsv mentioning which stimulus file was used for a given event.
There are no restrictions on the file formats of the stimuli files, but they should be stored in the /stimuli directory.

schema information:

{}

stimuli_relative (formats)

name: Path relative to the stimuli directory

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).

schema information:

{'pattern': '(?!/)(?!stimuli/)[0-9a-zA-Z/\\_\\-\\.]+'}

strain (columns)

name: strain

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

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:

{'type': 'string', 'format': 'rrid'}

string (formats)

name: String

description:

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

schema information:

{'pattern': '.*'}

subject (entities)

name: Subject

description:

A person or animal participating in the study.

schema information:

{'entity': 'sub', 'type': 'string', 'format': 'label'}

task (entities)

name: Task

description:

Each task has a unique label that MUST only consist of letters and/or numbers (other characters, including spaces and underscores, are not allowed). Those labels MUST be consistent across subjects and sessions.

schema information:

{'entity': 'task', 'type': 'string', 'format': 'label'}

time (columns)

name: time

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

description:

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

schema information:

{'pattern': '(?:2[0-3]|[01]?[0-9]):[0-5][0-9]:[0-5][0-9]'}

tracer (entities)

name: Tracer

description:

The trc-<label> key/value can be used to distinguish sequences using different tracers. The key "TracerName" MUST also be included in the associated JSON file, although the label may be different.

schema information:

{'entity': 'trc', 'type': 'string', 'format': 'label'}

trial_type (columns)

name: trial_type

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

description:

continuous measurement of the scanner trigger signal

schema information:

{'type': 'number'}

type sense 1 (columns)

name: type

description:

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

schema information:

{'type': 'string', 'enum': ['AUDIO', 'EEG', 'EOG', 'ECG', 'EMG', 'EYEGAZE', 'GSR', 'HEOG', 'MISC', 'PPG', 'PUPIL', 'REF', 'RESP', 'SYSCLOCK', 'TEMP', 'TRIG', 'VEOG']}

type sense 2 (columns)

name: type

description:

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

schema information:

{'type': 'string', 'enum': ['MEGMAG', 'MEGGRADAXIAL', 'MEGGRADPLANAR', 'MEGREFMAG', 'MEGREFGRADAXIAL', 'MEGREFGRADPLANAR', 'MEGOTHER', 'EEG', 'ECOG', 'SEEG', 'DBS', 'VEOG', 'HEOG', 'EOG', 'ECG', 'EMG', 'TRIG', 'AUDIO', 'PD', 'EYEGAZE', 'PUPIL', 'MISC', 'SYSCLOCK', 'ADC', 'DAC', 'HLU', 'FITERR', 'OTHER']}

type sense 3 (columns)

name: type

description:

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

schema information:

{'type': 'string', 'enum': ['EEG', 'ECOG', 'SEEG', 'DBS', 'VEOG', 'HEOG', 'EOG', 'ECG', 'EMG', 'TRIG', 'AUDIO', 'PD', 'EYEGAZE', 'PUPIL', 'MISC', 'SYSCLOCK', 'ADC', 'DAC', 'REF', 'OTHER']}

type sense 4 (columns)

name: type

description:

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

schema information:

{'type': 'string'}

uCT (suffixes)

name: Micro-CT

description:

Micro-CT imaging data

schema information:

{}

unit (formats)

name: A standardized unit

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.

schema information:

{'pattern': '.*'}

units (columns)

name: units

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:

{'type': 'string', 'format': 'unit'}

uri (formats)

name: Uniform resource indicator

description:

A uniform resource indicator.

schema information:

{'pattern': '(([^:/?#]+):)?(//([^/?#]*))?([^?#]*)(\\?([^#]*))?(#(.*))?'}

value (columns)

name: value

description:

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

schema information:

{'anyOf': [{'type': 'number'}, {'type': 'string'}]}

volume_type (columns)

name: volume_type

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', 'enum': ['control', 'label', 'm0scan', 'deltam', 'cbf']}

whole_blood_radioactivity (columns)

name: whole_blood_radioactivity

description:

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

schema information:

{'type': 'number'}

x (columns)

name: x

description:

Recorded position along the x-axis.

schema information:

{'type': 'number'}

y (columns)

name: y

description:

Recorded position along the y-axis.

schema information:

{'type': 'number'}

z (columns)

name: z

description:

Recorded position along the z-axis.

schema information:

{'anyOf': [{'type': 'number'}, {'type': 'string', 'enum': ['n/a']}]}