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Magnetic Resonance Imaging

Common metadata fields

MR Data described in the following sections share the following RECOMMENDED metadata fields (stored in sidecar JSON files). MRI acquisition parameters are divided into several categories based on "A checklist for fMRI acquisition methods reporting in the literature" by Ben Inglis:

Scanner Hardware

Key name Requirement level Data type Description
Manufacturer RECOMMENDED string Manufacturer of the equipment that produced the composite instances. Corresponds to DICOM Tag 0008, 0070 Manufacturer
ManufacturersModelName RECOMMENDED string Manufacturer's model name of the equipment that produced the composite instances. Corresponds to DICOM Tag 0008, 1090 Manufacturers Model Name
DeviceSerialNumber RECOMMENDED string The serial number of the equipment that produced the composite instances. Corresponds to DICOM Tag 0018, 1000 DeviceSerialNumber. A pseudonym can also be used to prevent the equipment from being identifiable, so long as each pseudonym is unique within the dataset
StationName RECOMMENDED string Institution defined name of the machine that produced the composite instances. Corresponds to DICOM Tag 0008, 1010 Station Name
SoftwareVersions RECOMMENDED string Manufacturer's designation of software version of the equipment that produced the composite instances. Corresponds to DICOM Tag 0018, 1020 Software Versions
HardcopyDeviceSoftwareVersion DEPRECATED string 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
MagneticFieldStrength RECOMMENDED, but REQUIRED for Arterial Spin Labeling number Nominal field strength of MR magnet in Tesla. Corresponds to DICOM Tag 0018,0087 Magnetic Field Strength
ReceiveCoilName RECOMMENDED string 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
ReceiveCoilActiveElements RECOMMENDED string Information describing the active/selected elements of the receiver coil. This doesn't correspond to a tag in the DICOM ontology. The vendor-defined terminology for active coil elements can go in this field. See an example below the table.
GradientSetType RECOMMENDED string 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
MRTransmitCoilSequence RECOMMENDED string This is a relevant field if a non-standard transmit coil is used. Corresponds to DICOM Tag 0018, 9049 MR Transmit Coil Sequence
MatrixCoilMode RECOMMENDED string (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
CoilCombinationMethod RECOMMENDED string 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

Example for ReceiveCoilActiveElements:

For Siemens, coil channels are typically not activated/selected individually, but rather in pre-defined selectable "groups" of individual channels, and the list of the "groups" of elements that are active/selected in any given scan populates the Coil String entry in Siemens' private DICOM fields (for example, HEA;HEP for the Siemens standard 32 ch coil when both the anterior and posterior groups are activated). This is a flexible field that can be used as most appropriate for a given vendor and coil to define the "active" coil elements. Since individual scans can sometimes not have the intended coil elements selected, it is preferable for this field to be populated directly from the DICOM for each individual scan, so that it can be used as a mechanism for checking that a given scan was collected with the intended coil elements selected

Sequence Specifics

Key name Requirement level Data type Description
PulseSequenceType RECOMMENDED string A general description of the pulse sequence used for the scan (for example, "MPRAGE", "Gradient Echo EPI", "Spin Echo EPI", "Multiband gradient echo EPI").
ScanningSequence RECOMMENDED string or array of strings Description of the type of data acquired. Corresponds to DICOM Tag 0018, 0020 Scanning Sequence.
SequenceVariant RECOMMENDED string or array of strings Variant of the ScanningSequence. Corresponds to DICOM Tag 0018, 0021 Sequence Variant.
ScanOptions RECOMMENDED string or array of strings Parameters of ScanningSequence. Corresponds to DICOM Tag 0018, 0022 Scan Options.
SequenceName RECOMMENDED string Manufacturer's designation of the sequence name. Corresponds to DICOM Tag 0018, 0024 Sequence Name.
PulseSequenceDetails RECOMMENDED string 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").
NonlinearGradientCorrection RECOMMENDED, but REQUIRED if PET data are present boolean Boolean stating if the image saved has been corrected for gradient nonlinearities by the scanner sequence.
MRAcquisitionType RECOMMENDED, but REQUIRED for Arterial Spin Labeling string Possible values: "2D" or "3D". Type of sequence readout. Corresponds to DICOM Tag 0018,0023 MR Acquisition Type.
MTState RECOMMENDED boolean Boolean stating whether the magnetization transfer pulse is applied. Corresponds to DICOM tag (0018, 9020) Magnetization Transfer.
MTOffsetFrequency RECOMMENDED if the MTstate is True. number The frequency offset of the magnetization transfer pulse with respect to the central H1 Larmor frequency in Hertz (Hz).
MTPulseBandwidth RECOMMENDED if the MTstate is True. number The excitation bandwidth of the magnetization transfer pulse in Hertz (Hz).
MTNumberOfPulses RECOMMENDED if the MTstate is True. number The number of magnetization transfer RF pulses applied before the readout.
MTPulseShape RECOMMENDED if the MTstate is True. string Shape of the magnetization transfer RF pulse waveform. Accepted values: "HARD", "GAUSSIAN", "GAUSSHANN" (gaussian pulse with Hanning window), "SINC", "SINCHANN" (sinc pulse with Hanning window), "SINCGAUSS" (sinc pulse with Gaussian window), "FERMI".
MTPulseDuration RECOMMENDED if the MTstate is True. number Duration of the magnetization transfer RF pulse in seconds.
SpoilingState RECOMMENDED boolean Boolean stating whether the pulse sequence uses any type of spoiling strategy to suppress residual transverse magnetization.
SpoilingType RECOMMENDED if the SpoilingState is True. string Specifies which spoiling method(s) are used by a spoiled sequence. Accepted values: "RF", "GRADIENT" or "COMBINED".
SpoilingRFPhaseIncrement RECOMMENDED if the SpoilingType is "RF" or "COMBINED". number 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.
SpoilingGradientMoment RECOMMENDED if the SpoilingType is "GRADIENT" or "COMBINED". number Zeroth moment of the spoiler gradient lobe in millitesla times second per meter (mT.s/m).
SpoilingGradientDuration RECOMMENDED if the SpoilingType is "GRADIENT" or "COMBINED". number 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.

In-Plane Spatial Encoding

Key name Requirement level Data type Description
NumberShots RECOMMENDED number or array of numbers 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.
ParallelReductionFactorInPlane RECOMMENDED number 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.
ParallelAcquisitionTechnique RECOMMENDED string The type of parallel imaging used (for example GRAPPA, SENSE). Corresponds to DICOM Tag 0018, 9078 Parallel Acquisition Technique.
PartialFourier RECOMMENDED number The fraction of partial Fourier information collected. Corresponds to DICOM Tag 0018, 9081 Partial Fourier.
PartialFourierDirection RECOMMENDED string The direction where only partial Fourier information was collected. Corresponds to DICOM Tag 0018, 9036 Partial Fourier Direction.
PhaseEncodingDirection RECOMMENDED string Possible values: "i", "j", "k", "i-", "j-", "k-". 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. This parameter is REQUIRED if corresponding fieldmap data is present or when using multiple runs with different phase encoding directions (which can be later used for field inhomogeneity correction).
EffectiveEchoSpacing RECOMMENDED number 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 DwellTime parameter below 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.2 This parameter is REQUIRED if corresponding fieldmap data is present.
TotalReadoutTime RECOMMENDED number 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).3 . This parameter is REQUIRED if corresponding "field/distortion" maps acquired with opposing phase encoding directions are present (see 8.9.4).
MixingTime RECOMMENDED number 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.

2Conveniently, for Siemens data, this value is easily obtained as 1 / (BWPPPE * ReconMatrixPE), where BWPPPE is the "BandwidthPerPixelPhaseEncode" in DICOM tag (0019,1028) and ReconMatrixPE is the size of the actual reconstructed data in the phase direction (which is NOT reflected in a single DICOM tag for all possible aforementioned scan manipulations). See here and here

3We use the time between the center of the first "effective" echo and the center of the last "effective" echo, sometimes called the "FSL definition".

Timing Parameters

Key name Requirement level Data type Description
EchoTime RECOMMENDED, but REQUIRED if corresponding fieldmap data is present, or the data comes from a multi echo sequence or Arterial Spin Labeling number or array of numbers 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.
InversionTime RECOMMENDED number 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).
SliceTiming RECOMMENDED, but REQUIRED for sparse sequences that do not have the DelayTime field set, and Arterial Spin Labeling with MRAcquisitionType set on 2D. array of numbers 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.
SliceEncodingDirection RECOMMENDED string Possible values: "i", "j", "k", "i-", "j-", "k-" (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.
DwellTime RECOMMENDED number 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).

RF & Contrast

Key name Requirement level Data type Description
FlipAngle RECOMMENDED, but REQUIRED if LookLocker is set true number or array of numbers 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.
NegativeContrast OPTIONAL boolean 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.

Slice Acceleration

Key name Requirement level Data type Description
MultibandAccelerationFactor RECOMMENDED number The multiband factor, for multiband acquisitions.

Anatomical landmarks

Useful for multimodal co-registration with MEG, (S)EEG, TMS, and so on.

Key name Requirement level Data type Description
AnatomicalLandmarkCoordinates RECOMMENDED object of arrays 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.

Institution information

Key name Requirement level Data type Description
InstitutionName RECOMMENDED string The name of the institution in charge of the equipment that produced the composite instances. Corresponds to DICOM Tag 0008, 0080 InstitutionName.
InstitutionAddress RECOMMENDED string The address of the institution in charge of the equipment that produced the composite instances. Corresponds to DICOM Tag 0008, 0081 InstitutionAddress.
InstitutionalDepartmentName RECOMMENDED string The department in the institution in charge of the equipment that produced the composite instances. Corresponds to DICOM Tag 0008, 1040 Institutional Department Name.

When adding additional metadata please use the CamelCase version of DICOM ontology terms whenever possible. See also recommendations on JSON files.

Anatomy imaging data

Template:

sub-<label>/
    [ses-<label>/]
        anat/
            sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>][_part-<label>]_<suffix>.json
            sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>][_part-<label>]_<suffix>.nii[.gz]
            sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>]_<suffix>.json
            sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>]_<suffix>.nii[.gz]
            sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>][_mod-<label>]_defacemask.json
            sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>][_mod-<label>]_defacemask.nii[.gz]
            sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>]_echo-<index>[_part-<label>]_MEGRE.json
            sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>]_echo-<index>[_part-<label>]_MEGRE.nii[.gz]
            sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>]_echo-<index>[_part-<label>]_MESE.json
            sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>]_echo-<index>[_part-<label>]_MESE.nii[.gz]
            sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>]_flip-<index>[_part-<label>]_VFA.json
            sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>]_flip-<index>[_part-<label>]_VFA.nii[.gz]
            sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>]_inv-<index>[_part-<label>]_IRT1.json
            sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>]_inv-<index>[_part-<label>]_IRT1.nii[.gz]
            sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>][_echo-<index>][_flip-<index>]_inv-<index>[_part-<label>]_MP2RAGE.json
            sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>][_echo-<index>][_flip-<index>]_inv-<index>[_part-<label>]_MP2RAGE.nii[.gz]
            sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>][_echo-<index>]_flip-<index>_mt-<label>[_part-<label>]_MPM.json
            sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>][_echo-<index>]_flip-<index>_mt-<label>[_part-<label>]_MPM.nii[.gz]
            sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>][_echo-<index>]_flip-<index>_mt-<label>[_part-<label>]_MTS.json
            sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>][_echo-<index>]_flip-<index>_mt-<label>[_part-<label>]_MTS.nii[.gz]
            sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>]_mt-<label>[_part-<label>]_MTR.json
            sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>]_mt-<label>[_part-<label>]_MTR.nii[.gz]

Anatomical (structural) data acquired for that participant. Currently supported non-parametric structural MR images include:

Name suffix Description
T1 weighted images T1w 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).
T2 weighted images T2w 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.
Proton density (PD) weighted images PDw 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.
T2star weighted images T2starw 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.
Fluid attenuated inversion recovery images FLAIR 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.
Inplane T1 inplaneT1 In arbitrary units (arbitrary). T1 weighted structural image matched to a functional (task) image.
Inplane T2 inplaneT2 In arbitrary units (arbitrary). T2 weighted structural image matched to a functional (task) image.
PD and T2 weighted images PDT2 In arbitrary units (arbitrary). PDw and T2w images acquired using a dual echo FSE sequence through view sharing process (Johnson et al. 1994).
Homogeneous (flat) T1-weighted MP2RAGE image UNIT1 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 from T1w. Plase see MP2RAGE specific notes in the qMRI appendix for further information.

If the structural images included in the dataset were defaced (to protect identity of participants) one MAY provide the binary mask that was used to remove facial features in the form of _defacemask files. In such cases, the OPTIONAL mod-<label> key/value pair corresponds to modality suffix, such as T1w or inplaneT1, referenced by the defacemask image. For example, sub-01_mod-T1w_defacemask.nii.gz.

If several scans 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.

The OPTIONAL 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 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.

Similarly the OPTIONAL 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 be also be added in the JSON file, with the same label.

Some meta information about the acquisition MAY be provided in an additional JSON file. See Common metadata fields for a list of terms and their definitions. There are also some OPTIONAL JSON fields specific to anatomical scans:

Key name Requirement level Data type Description
ContrastBolusIngredient OPTIONAL string Active ingredient of agent. Values MUST be one of: "IODINE", "GADOLINIUM", "CARBON DIOXIDE", "BARIUM", "XENON" Corresponds to DICOM Tag 0018,1048.
RepetitionTimeExcitation OPTIONAL number The interval, in seconds, between two successive excitations. The DICOM tag that best refers to this parameter is (0018, 0080). 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.
RepetitionTimePreparation OPTIONAL number or array of numbers 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.

The part-<label> key/value pair is used to indicate which component of the complex representation of the MRI signal is represented in voxel data. This entity is associated with the DICOM tag 0008,9208. Allowed label values for this entity are phase, mag, real and imag, which are typically used in part-mag/part-phase or part-real/part-imag pairs of files. For example:

sub-01_part-mag_T1w.nii.gz
sub-01_part-mag_T1w.json
sub-01_part-phase_T1w.nii.gz
sub-01_part-phase_T1w.json

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. For example:

sub-01_part-phase_T1w.json

{
   "Units": "rad"
}

When there is only a magnitude image of a given type, the part key MAY be omitted.

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

Structural MR images whose intensity is represented in a non-arbitrary scale constitute parametric maps. Currently supported parametric maps include:

Name suffix Description
Longitudinal relaxation time map T1map 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.
Longitudinal relaxation rate map R1map In seconds-1 (1/s). R1 maps (R1 = 1/T1) are REQUIRED to use this suffix regardless of the method used to generate them.
True transverse relaxation time map T2map In seconds (s). T2 maps are REQUIRED to use this suffix regardless of the method used to generate them.
True transverse relaxation rate map R2map In seconds-1 (1/s). R2 maps (R2 = 1/T2) are REQUIRED to use this suffix regardless of the method used to generate them.
Observed transverse relaxation time map T2starmap In seconds (s). T2-star maps are REQUIRED to use this suffix regardless of the method used to generate them.
Observed transverse relaxation rate map R2starmap 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.
Proton density map PDmap In arbitrary units (arbitrary). PD maps are REQUIRED to use this suffix regardless of the method used to generate them.
Magnetization transfer ratio map MTRmap 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%.
Magnetization transfer saturation map MTsat In arbitrary units (arbitrary). MTsat maps are REQUIRED to use this suffix regardless of the method used to generate them.
T1 in rotating frame (T1 rho) map T1rho In seconds (s). T1-rho maps are REQUIRED to use this suffix regardless of the method used to generate them.
Myelin water fraction map MWFmap 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%.
Macromolecular tissue volume (MTV) map MTVmap In arbitrary units (arbitrary). MTV maps are REQUIRED to use this suffix regardless of the method used to generate them.
Combined PD/T2 map PDT2map In arbitrary units (arbitrary). Combined PD/T2 maps are REQUIRED to use this suffix regardless of the method used to generate them.
Quantitative susceptibility map (QSM) Chimap 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.
RF transmit field map TB1map 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 .
RF receive sensitivity map RB1map 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.
Observed signal amplitude (S0) map S0map 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.
Equilibrium magnetization (M0) map M0map 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).

Parametric images listed in the table above are typically generated by processing a file collection. Please visit the file collections appendix to see the list of suffixes available for quantitative MRI (qMRI) applications associated with these maps. For any other details on the organization of parametric maps, their recommended metadata fields, and the application specific entity or metadata requirement levels of file collections that can generate them, visit the qMRI appendix.

Deprecated suffixes

Some suffixes that were available in versions of the specification prior to 1.5.0 have been deprecated. These suffixes are ambiguous and have been superseded by more precise conventions. Therefore, they are not recommended for use in new datasets. They are, however, still valid suffixes, to maintain backwards compatibility.

The following suffixes are valid, but SHOULD NOT be used for new BIDS compatible datasets (created after version 1.5.0.):

Name suffix Reason to deprecate
T2* T2star Ambiguous, may refer to a parametric image or to a conventional image. Change: Replaced by T2starw or T2starmap.
FLASH FLASH 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.
Proton density PD Ambiguous, may refer to a parametric image or to a conventional image. Change: Replaced by PDw or PDmap.

Task (including resting state) imaging data

Currently supported image contrasts include:

Name suffix Description
BOLD bold Blood-Oxygen-Level Dependent contrast (specialized T2* weighting)
CBV cbv Cerebral Blood Volume contrast (specialized T2* weighting or difference between T1 weighted images)
Phase phase 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.

Template:

sub-<label>/
    [ses-<label>/]
        func/
            sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_ce-<label>][_rec-<label>][_dir-<label>][_run-<index>][_echo-<index>][_part-<label>]_bold.json
            sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_ce-<label>][_rec-<label>][_dir-<label>][_run-<index>][_echo-<index>][_part-<label>]_bold.nii[.gz]
            sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_ce-<label>][_rec-<label>][_dir-<label>][_run-<index>][_echo-<index>][_part-<label>]_cbv.json
            sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_ce-<label>][_rec-<label>][_dir-<label>][_run-<index>][_echo-<index>][_part-<label>]_cbv.nii[.gz]
            sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_ce-<label>][_rec-<label>][_dir-<label>][_run-<index>][_echo-<index>][_part-<label>]_sbref.json
            sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_ce-<label>][_rec-<label>][_dir-<label>][_run-<index>][_echo-<index>][_part-<label>]_sbref.nii[.gz]
            sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_ce-<label>][_rec-<label>][_dir-<label>][_run-<index>][_echo-<index>]_phase.json
            sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_ce-<label>][_rec-<label>][_dir-<label>][_run-<index>][_echo-<index>]_phase.nii[.gz]
            sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_ce-<label>][_rec-<label>][_dir-<label>][_run-<index>]_events.json
            sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_ce-<label>][_rec-<label>][_dir-<label>][_run-<index>]_events.tsv
            sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_ce-<label>][_rec-<label>][_dir-<label>][_run-<index>][_recording-<label>]_physio.json
            sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_ce-<label>][_rec-<label>][_dir-<label>][_run-<index>][_recording-<label>]_physio.tsv.gz
            sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_ce-<label>][_rec-<label>][_dir-<label>][_run-<index>][_recording-<label>]_stim.json
            sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_ce-<label>][_rec-<label>][_dir-<label>][_run-<index>][_recording-<label>]_stim.tsv.gz

Functional imaging consists of techniques that support rapid temporal repetition. This includes but is not limited to task based fMRI as well as resting state fMRI, which is treated like any other task. For task based fMRI a corresponding task events file (see below) MUST be provided (please note that this file is not necessary for resting state scans). For multiband acquisitions, one MAY also save the single-band reference image as type sbref (for example, sub-control01_task-nback_sbref.nii.gz).

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

If more than one run of the same task has been acquired the run-<index> key/value pair MUST be used: _run-1, _run-2, _run-3, and so on. If only one run was acquired the run-<index> can be omitted. In the context of functional imaging a run is defined as the same task, but in some cases it can mean different set of stimuli (for example randomized order) and participant responses.

The OPTIONAL acq-<label> key/value pair corresponds to a custom label one may use to distinguish different set of parameters used for acquiring the same task. For example this should be used when a study includes two resting state images - one single band and one multiband. In such case two files could have the following names: sub-01_task-rest_acq-singleband_bold.nii.gz and sub-01_task-rest_acq-multiband_bold.nii.gz, however the user is MAY choose any other label than singleband and multiband as long as they are consistent across subjects and sessions and consist only of the legal label characters.

Similarly the OPTIONAL 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 be also be added in the JSON file, with the same label.

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

Similarly the OPTIONAL dir-<label> and rec-<label> key/values can be used to distinguish different phase-encoding directions and reconstruction algorithms (for example ones using motion correction). See fmap Case 4 for more information on dir field specification.

Multi-echo data MUST be split into one file per echo using the echo-<index> key-value pair. For example:

sub-01/
   func/
      sub-01_task-cuedSGT_run-1_echo-1_bold.nii.gz
      sub-01_task-cuedSGT_run-1_echo-1_bold.json
      sub-01_task-cuedSGT_run-1_echo-2_bold.nii.gz
      sub-01_task-cuedSGT_run-1_echo-2_bold.json
      sub-01_task-cuedSGT_run-1_echo-3_bold.nii.gz
      sub-01_task-cuedSGT_run-1_echo-3_bold.json

Please note that the <index> denotes the number/index (in the form of a nonnegative integer) of the echo not the echo time value which needs to be stored in the field EchoTime of the separate JSON file.

Complex-valued data MUST be split into one file for each data type. For BOLD data, there are separate suffixes for magnitude (_bold) and phase (_phase) data, but the _phase suffix is deprecated. Newly generated datasets SHOULD NOT use the _phase suffix, and the suffix will be removed from the specification in the next major release. For backwards compatibility, _phase is considered equivalent to _part-phase_bold. When the _phase suffix is not used, each file shares the same name with the exception of the part-<mag|phase> or part-<real|imag> key/value. For example:

sub-01/
   func/
      sub-01_task-cuedSGT_part-mag_bold.nii.gz
      sub-01_task-cuedSGT_part-mag_bold.json
      sub-01_task-cuedSGT_part-phase_bold.nii.gz
      sub-01_task-cuedSGT_part-phase_bold.json
      sub-01_task-cuedSGT_part-mag_sbref.nii.gz
      sub-01_task-cuedSGT_part-mag_sbref.json
      sub-01_task-cuedSGT_part-phase_sbref.nii.gz
      sub-01_task-cuedSGT_part-phase_sbref.json

Some meta information about the acquisition MUST be provided in an additional JSON file.

Required fields

Key name Requirement level Data type Description
RepetitionTime REQUIRED number 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.
VolumeTiming REQUIRED array of numbers 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.
TaskName REQUIRED string 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. A RECOMMENDED convention is to name resting state task using labels beginning with rest.

For the fields described above and in the following section, the term "Volume" refers to a reconstruction of the object being imaged (for example, brain or part of a brain). In case of multiple channels in a coil, the term "Volume" refers to a combined image rather than an image from each coil.

Timing Parameters

Key name Requirement level Data type Description
NumberOfVolumesDiscardedByScanner RECOMMENDED integer 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 doesn't discard dummy scans would have this set to 0. Please note that the onsets recorded in the _event.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.
NumberOfVolumesDiscardedByUser RECOMMENDED integer 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 _event.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.
DelayTime RECOMMENDED number 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.
AcquisitionDuration RECOMMENDED, but REQUIRED for sequences that are described with the VolumeTiming field and that do not have the SliceTiming field set to allow for accurate calculation of "acquisition time" number Duration (in seconds) of volume acquisition. Corresponds to DICOM Tag 0018,9073 Acquisition Duration. This field is mutually exclusive with RepetitionTime.
DelayAfterTrigger RECOMMENDED number 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.

The following table recapitulates the different ways that specific fields have to be populated for functional sequences. Note that all these options can be used for non sparse sequences but that only options B, D and E are valid for sparse sequences.

RepetitionTime SliceTiming AcquisitionDuration DelayTime VolumeTiming
option A [ X ] [ ] [ ]
option B [ ] [ X ] [ ] [ X ]
option C [ ] [ X ] [ ] [ X ]
option D [ X ] [ X ] [ ] [ ]
option E [ X ] [ ] [ X ] [ ]

Legend

  • [ X ] --> MUST be defined
  • [ ] --> MUST NOT be defined
  • empty cell --> MAY be specified

fMRI task information

Key name Requirement level Data type Description
Instructions RECOMMENDED string Text of the instructions given to participants before the scan. This is especially important in context of resting state fMRI and distinguishing between eyes open and eyes closed paradigms.
TaskDescription RECOMMENDED string Longer description of the task.
CogAtlasID RECOMMENDED string URI of the corresponding Cognitive Atlas Task term.
CogPOID RECOMMENDED string URI of the corresponding CogPO term.

See Common metadata fields for a list of additional terms and their definitions.

Example:

sub-control01/
    func/
        sub-control01_task-nback_bold.json
{
   "TaskName": "N Back",
   "RepetitionTime": 0.8,
   "EchoTime": 0.03,
   "FlipAngle": 78,
   "SliceTiming": [0.0, 0.2, 0.4, 0.6, 0.0, 0.2, 0.4, 0.6, 0.0, 0.2, 0.4, 0.6, 0.0, 0.2, 0.4, 0.6],
   "MultibandAccelerationFactor": 4,
   "ParallelReductionFactorInPlane": 2,
   "PhaseEncodingDirection": "j",
   "InstitutionName": "Stanford University",
   "InstitutionAddress": "450 Serra Mall, Stanford, CA 94305-2004, USA",
   "DeviceSerialNumber": "11035"
}

If this information is the same for all participants, sessions and runs it can be provided in task-<label>_bold.json (in the root directory of the dataset). However, if the information differs between subjects/runs it can be specified in the sub-<label>/func/sub-<label>_task-<label>[_acq-<label>][_run-<index>]_bold.json file. If both files are specified fields from the file corresponding to a particular participant, task and run takes precedence.

Diffusion imaging data

Diffusion-weighted imaging data acquired for a participant. Currently supported image types include:

Name suffix Description
DWI dwi Diffusion-weighted imaging contrast (specialized T2* weighting).
Single-Band Reference sbref Single-band reference for one or more multi-band dwi images.

Template:

sub-<label>/
    [ses-<label>/]
        dwi/
            sub-<label>[_ses-<label>][_acq-<label>][_dir-<label>][_run-<index>][_part-<label>]_dwi.bval
            sub-<label>[_ses-<label>][_acq-<label>][_dir-<label>][_run-<index>][_part-<label>]_dwi.bvec
            sub-<label>[_ses-<label>][_acq-<label>][_dir-<label>][_run-<index>][_part-<label>]_dwi.json
            sub-<label>[_ses-<label>][_acq-<label>][_dir-<label>][_run-<index>][_part-<label>]_dwi.nii[.gz]
            sub-<label>[_ses-<label>][_acq-<label>][_dir-<label>][_run-<index>][_part-<label>]_sbref.json
            sub-<label>[_ses-<label>][_acq-<label>][_dir-<label>][_run-<index>][_part-<label>]_sbref.nii[.gz]

If more than one run of the same acquisition and direction has been acquired, the run-<index> key/value pair MUST be used: _run-1, _run-2, _run-3 (and so forth.) When there is only one scan of a given acquisition and direction, the run key MAY be omitted. The run-<index> key/value pair is RECOMMENDED to encode the splits of multipart DWI scans (see below.)

The OPTIONAL acq-<label> key/value pair corresponds to a custom label the user may use to distinguish different sets of parameters.

The OPTIONAL dir-<label> key/value pair corresponds to a custom label the user may use to distinguish different sets of phase-encoding directions.

Combining multi- and single-band acquisitions. The single-band reference image MAY be stored with suffix sbref (for example, dwi/sub-control01_sbref.nii[.gz]) as long as the image has no corresponding gradient information ([*_]dwi.bval and [*_]dwi.bvec sidecar files) to be stored.

Otherwise, if some gradient information is associated to the single-band diffusion image and a multi-band diffusion image also exists, the acq-<label> key/value pair MUST be used to distinguish both images. In such a case, two files could have the following names: sub-01_acq-singleband_dwi.nii.gz and sub-01_acq-multiband_dwi.nii.gz. The user is free to choose any other label than singleband and multiband, as long as they are consistent across subjects and sessions.

REQUIRED gradient orientation information

The REQUIRED gradient orientation information corresponding to a DWI acquisition MUST be stored using [*_]dwi.bval and [*_]dwi.bvec pairs of files. The [*_]dwi.bval and [*_]dwi.bvec files MAY be saved on any level of the directory structure and thus define those values for all sessions and/or subjects in one place (see the inheritance principle).

As an exception to the common principles that parameters are constant across runs, the gradient table information (stored within the [*_]dwi.bval and [*_]dwi.bvec files) MAY change across DWI runs.

Gradient orientation file formats. The [*_]dwi.bval and [*_]dwi.bvec files MUST follow the FSL format: The [*_]dwi.bvec 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 [*_]dwi.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 implication for this choice is that any rotations applied to the DWI data also need to be applied to the b vectors in the [*_]dwi.bvec file.

Example of [*_]dwi.bvec file, with N=6, with two b=0 volumes in the beginning:

0 0 0.021828 -0.015425 -0.70918 -0.2465
0 0 0.80242 0.22098 -0.00063106 0.1043
0 0 -0.59636 0.97516 -0.70503 -0.96351

The [*_]dwi.bval file contains the b-values (in s/mm2) corresponding to the volumes in the relevant NIfTI file), with 0 designating b=0 volumes, space-delimited.

Example of [*_]dwi.bval file, corresponding to the previous [*_]dwi.bvec example:

0 0 2000 2000 1000 1000

Multipart (split) DWI schemes

Some MR schemes cannot be acquired directly by some scanner devices, requiring to generate several DWI runs that were originally meant to belong in a single one. For instance, some GE scanners cannot collect more than ≈160 volumes in a single run under fast-changing gradients, so acquiring HCP-style diffusion images will require splitting the DWI scheme in several runs. Because researchers will generally optimize the data splits, these will likely not be able to be directly concatenated. BIDS permits defining arbitrary groupings of these multipart scans with the following metadata:

Key name Requirement level Data type Description
MultipartID REQUIRED string A unique (per participant) label tagging DWI runs that are part of a multipart scan.

JSON example:

{
  "MultipartID": "dwi_1"
}

For instance, if there are two phase-encoding directions (AP, PA), and two runs each, and the intent of the researcher is that all of them are part of a unique multipart scan, then they will tag all four runs with the same MultipartID (shown at the right-hand side of the file listing):

sub-<label>/[ses-<label>/]         # MultipartID
  dwi/
    sub-1_dir-AP_run-1_dwi.nii.gz  # dwi_1
    sub-1_dir-AP_run-2_dwi.nii.gz  # dwi_1
    sub-1_dir-PA_run-1_dwi.nii.gz  # dwi_1
    sub-1_dir-PA_run-2_dwi.nii.gz  # dwi_1

If, conversely, the researcher wanted to store two multipart scans, one possibility is to combine matching phase-encoding directions:

sub-<label>/[ses-<label>/]         # MultipartID
  dwi/
    sub-1_dir-AP_run-1_dwi.nii.gz  # dwi_1
    sub-1_dir-AP_run-2_dwi.nii.gz  # dwi_1
    sub-1_dir-PA_run-1_dwi.nii.gz  # dwi_2
    sub-1_dir-PA_run-2_dwi.nii.gz  # dwi_2

Alternatively, the researcher's intent could be combining opposed phase-encoding runs instead:

sub-<label>/[ses-<label>/]         # MultipartID
  dwi/
    sub-1_dir-AP_run-1_dwi.nii.gz  # dwi_1
    sub-1_dir-AP_run-2_dwi.nii.gz  # dwi_2
    sub-1_dir-PA_run-1_dwi.nii.gz  # dwi_1
    sub-1_dir-PA_run-2_dwi.nii.gz  # dwi_2

The MultipartID metadata MAY be used with the acq-<label> key/value pair, for example:

sub-<label>/[ses-<label>/]             # MultipartID
  dwi/
    sub-1_acq-shell1_run-1_dwi.nii.gz  # dwi_1
    sub-1_acq-shell1_run-2_dwi.nii.gz  # dwi_2
    sub-1_acq-shell2_run-1_dwi.nii.gz  # dwi_1
    sub-1_acq-shell2_run-2_dwi.nii.gz  # dwi_2

The PhaseEncodingDirection and TotalReadoutTime metadata fields are RECOMMENDED to enable the correction of geometrical distortions with fieldmap information. See Common metadata fields for a list of additional terms that can be included in the corresponding JSON file.

JSON example:

{
  "PhaseEncodingDirection": "j-",
  "TotalReadoutTime": 0.095
}

Arterial Spin Labeling perfusion data

Template:

sub-<label>/
    [ses-<label>/]
        perf/
            sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_dir-<label>][_run-<index>]_asl.json
            sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_dir-<label>][_run-<index>]_asl.nii[.gz]
            sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_dir-<label>][_run-<index>]_m0scan.json
            sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_dir-<label>][_run-<index>]_m0scan.nii[.gz]
            sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_dir-<label>][_run-<index>]_aslcontext.json
            sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_dir-<label>][_run-<index>]_aslcontext.tsv
            sub-<label>[_ses-<label>][_acq-<label>][_rec-<label>][_run-<index>]_asllabeling.jpg

The complete ASL time series should be stored as a 4D NIfTI file in the original acquisition order, accompanied by two ancillary files: *_asl.json and *_aslcontext.tsv.

*_aslcontext.tsv

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. Volume types are defined in the following table, based on DICOM Tag (0018,9257) ASL Context. Note that the volume_types control and label within BIDS only serve to specify the magnetization state of the blood and thus the ASL subtraction order. See Appendix XII - ASL for more information on control and label.

volume_type Definition
control The control image is acquired in the exact same way as the label image, except that the magnetization of the blood flowing into the imaging region has not been inverted.
label The label image is acquired in the exact same way as the control image, except that the blood magnetization flowing into the imaging region has been inverted.
m0scan The M0 image is a calibration image, used to estimate the equilibrium magnetization of blood.
deltam The deltaM image is a perfusion-weighted image, obtained by the subtraction of control - label.
cbf The cerebral blood flow (CBF) image is produced by dividing the deltaM by the M0, quantified into mL/100g/min (See also doi:10.1002/mrm.25197).

If the control and label images are not available, their derivative deltam should be stored within the *_asl.nii[.gz] and specified in the *_aslcontext.tsv instead. If the deltam is not available, cbf should be stored within the *_asl.nii[.gz] and specified in the *_aslcontext.tsv. When cbf is stored within the *_asl.nii[.gz], its units need to be specified in the *_asl.json as well. Note that the raw images, including the m0scan, may also be used for quality control. See Appendix XII - ASL for examples of the three possible cases, in order of decreasing preference.

Scaling

The *_asl.nii.gz and *_m0scan.nii.gz should contain appropriately scaled data, and no additional scaling factors are allowed other than the scale slope in the respective NIfTI headers.

M0

The m0scan can either be stored inside the 4D ASL time-series NIfTI file or as a separate NIfTI file, depending on whether it was acquired within the ASL time-series or as a separate scan. These and other M0 options are specified in the REQUIRED M0Type field of the *_asl.json file. It can also be stored under fmap/sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>]_dir-<label>[_run-<index>]_m0scan.nii[.gz], when the pepolar approach is used.

*_asl.json file

Depending on the method used for ASL acquisition ((P)CASL or PASL) different metadata fields are applicable. Additionally, some common metadata fields are REQUIRED for the *_asl.json: MagneticFieldStrength, MRAcquisitionType, EchoTime, SliceTiming in case MRAcquisitionType is defined as 2D, RepetitionTimePreparation, and FlipAngle in case LookLocker is true. See Appendix XII - ASL for more information on the most common ASL sequences.

Common metadata fields applicable to both (P)CASL and PASL

Key name Requirement level Data type Description
ArterialSpinLabelingType REQUIRED string "CASL", "PCASL", "PASL".
PostLabelingDelay REQUIRED number or array of numbers 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.
BackgroundSuppression REQUIRED boolean Boolean indicating if background suppression is used.
M0Type REQUIRED string Describes the presence of M0 information, as either: "Separate" when a separate *_m0scan.nii[.gz] is present, "Included" when an m0scan volume is contained within the current *_asl.nii[.gz], "Estimate" when a single whole-brain M0 value is provided, or "Absent" when no specific M0 information is present.
TotalAcquiredPairs REQUIRED number The total number of acquired control-label pairs. A single pair consists of a single control and a single label image.
VascularCrushing RECOMMENDED boolean Boolean indicating if Vascular Crushing is used. Corresponds to DICOM Tag 0018,9259 ASL Crusher Flag.
AcquisitionVoxelSize RECOMMENDED array of numbers 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.
M0Estimate OPTIONAL, but REQUIRED when M0Type is defined as Estimate number 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).
BackgroundSuppressionNumberPulses OPTIONAL, RECOMMENDED if BackgroundSuppression is true number The number of background suppression pulses used. Note that this excludes any effect of background suppression pulses applied before the labeling.
BackgroundSuppressionPulseTime OPTIONAL, RECOMMENDED if BackgroundSuppression is true array of numbers 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.
VascularCrushingVENC OPTIONAL, RECOMMENDED if VascularCrushing is true number or array of numbers 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.
LabelingOrientation RECOMMENDED array of numbers 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.
LabelingDistance RECOMMENDED number 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.
LabelingLocationDescription RECOMMENDED string 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.
LookLocker OPTIONAL boolean Boolean indicating if a Look-Locker readout is used.
LabelingEfficiency OPTIONAL number Labeling efficiency, specified as a number between zero and one, only if obtained externally (for example phase-contrast based).

(P)CASL-specific metadata fields

These fields can only be used when ArterialSpinLabelingType is "CASL" or "PCASL". See Appendix XII - ASL for more information on the (P)CASL sequence and the Labeling Pulse fields.

Key name Requirement level Data type Description
LabelingDuration REQUIRED number or array of numbers 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.
PCASLType RECOMMENDED if ArterialSpinLabelingType is "PCASL" string Type the gradient pulses used in the "control" condition: "balanced" or "unbalanced".
CASLType RECOMMENDED if ArterialSpinLabelingType is "CASL" string Describes if a separate coil is used for labeling: "single-coil" or "double-coil".
LabelingPulseAverageGradient RECOMMENDED number The average labeling gradient, in milliteslas per meter.
LabelingPulseMaximumGradient RECOMMENDED number The maximum amplitude of the gradient switched on during the application of the labeling RF pulse(s), in milliteslas per meter.
LabelingPulseAverageB1 RECOMMENDED number The average B1-field strength of the RF labeling pulses, in microteslas. As an alternative, LabelingPulseFlipAngle can be provided.
LabelingPulseDuration RECOMMENDED number Duration of the individual labeling pulses, in milliseconds.
LabelingPulseFlipAngle RECOMMENDED number The flip angle of a single labeling pulse, in degrees, which can be given as an alternative to LabelingPulseAverageB1.
LabelingPulseInterval RECOMMENDED number Delay between the peaks of the individual labeling pulses, in milliseconds.

PASL-specific metadata fields

These fields can only be used when ArterialSpinLabelingType is PASL. See Appendix XII - ASL for more information on the PASL sequence and the BolusCutOff fields.

Key name Requirement level Data type Description
BolusCutOffFlag REQUIRED boolean Boolean indicating if a bolus cut-off technique is used. Corresponds to DICOM Tag 0018,925C ASL Bolus Cut-off Flag.
PASLType RECOMMENDED string Type of the labeling pulse of the PASL labeling, for example "FAIR", "EPISTAR", or "PICORE".
LabelingSlabThickness RECOMMENDED number Thickness of the labeling slab in millimeters. For non-selective FAIR a zero is entered. Corresponds to DICOM Tag 0018,9254 ASL Slab Thickness.
BolusCutOffDelayTime OPTIONAL, REQUIRED if BolusCutOffFlag is true number or array of numbers 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.
BolusCutOffTechnique OPTIONAL, REQUIRED if BolusCutOffFlag is true string Name of the technique used, for example "Q2TIPS", "QUIPSS", "QUIPSSII". Corresponds to DICOM Tag 0018,925E ASL Bolus Cut-off Technique.

m0scan metadata fields

Some common metadata fields are REQUIRED for the *_m0scan.json: EchoTime, RepetitionTimePreparation, and FlipAngle in case LookLocker is true.

Key name Requirement level Data type Description
IntendedFor REQUIRED string or array of strings One or more filenames with paths relative to the subject subfolder, with forward slashes, referring to ASL time series for which the *_m0scan.nii[.gz] is intended.
AcquisitionVoxelSize RECOMMENDED array of numbers 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.

The following table recapitulates the ASL field dependencies. If Source field (column 1) contains the Value specified in column 2, then the Requirements in column 4 are imposed on the Dependent fields in column 3. See Appendix XII for this information in the form of flowcharts.

Source field Value Dependent field Requirements
MRAcquisitionType 2D / 3D SliceTiming [X] / []
LookLocker true FlipAngle [X]
ArterialSpinLabelingType PCASL LabelingDuration [X]
ArterialSpinLabelingType PASL BolusCutOffFlag [X]
BolusCutOffFlag true / false BolusCutOffDelayTime [X] / []
BolusCutOffFlag true / false BolusCutOffTechnique [X] / []
M0Type Separate */perf/ contains *_m0scan.nii[.gz] and *_m0scan.json
M0Type Included *_aslcontext.tsv contains m0scan
M0Type Estimate M0Estimate [X]
*_aslcontext.tsv cbf Units [X]

Legend

  • [ X ] --> MUST be defined
  • [ ] --> MUST NOT be defined

Fieldmap data

Data acquired to correct for B0 inhomogeneities can come in different forms. The current version of this standard considers four different scenarios:

  1. Phase-difference map
  2. Two phase maps
  3. Direct field mapping
  4. "PEpolar" fieldmaps

These four different types of field mapping strategies can be encoded using the following image types:

Name suffix Description
Magnitude magnitude[1,2] 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.
Phase phase{1,2} Phase map generated by GRE or similar schemes, each associated with the first (phase1) or second (phase2) echoes in the sequence.
Phase-difference phasediff 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.
Fieldmap fieldmap Some MR schemes such as spiral-echo (SE) sequences are able to directly provide maps of the B0 field inhomogeneity.
EPI epi 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.

Two OPTIONAL entities, following more general rules of the specification, are allowed across all the four scenarios:

  • The OPTIONAL run-<index> key/value pair corresponds to a one-based index to distinguish multiple fieldmaps with the same parameters.

  • The OPTIONAL acq-<label> key/value pair corresponds to a custom label the user may use to distinguish different set of parameters.

Types of fieldmaps

Case 1: Phase-difference map and at least one magnitude image

Template:

sub-<label>/
    [ses-<label>/]
        fmap/
            sub-<label>[_ses-<label>][_acq-<label>][_run-<index>]_magnitude1.json
            sub-<label>[_ses-<label>][_acq-<label>][_run-<index>]_magnitude1.nii[.gz]
            sub-<label>[_ses-<label>][_acq-<label>][_run-<index>]_magnitude2.json
            sub-<label>[_ses-<label>][_acq-<label>][_run-<index>]_magnitude2.nii[.gz]
            sub-<label>[_ses-<label>][_acq-<label>][_run-<index>]_phasediff.json
            sub-<label>[_ses-<label>][_acq-<label>][_run-<index>]_phasediff.nii[.gz]

where the REQUIRED _phasediff image corresponds to the phase-drift map between echo times, the REQUIRED _magnitude1 image corresponds to the shorter echo time, and the OPTIONAL _magnitude2 image to the longer echo time.

Required fields:

Key name Requirement level Data type Description
EchoTime1 REQUIRED number The time (in seconds) when the first (shorter) echo occurs.
EchoTime2 REQUIRED number The time (in seconds) when the second (longer) echo occurs.

In this particular case, the sidecar JSON file sub-<label>[_ses-<label>][_acq-<label>][_run-<index>]_phasediff.json MUST define the time of two echos used to map the phase and finally calculate the phase-difference map. For example:

{
   "EchoTime1": 0.00600,
   "EchoTime2": 0.00746
}

Case 2: Two phase maps and two magnitude images

Similar to case 1, but instead of a precomputed phase-difference map, two separate phase images and two magnitude images corresponding to first and second echos are available.

Template:

sub-<label>/
    [ses-<label>/]
        fmap/
            sub-<label>[_ses-<label>][_acq-<label>][_run-<index>]_magnitude1.json
            sub-<label>[_ses-<label>][_acq-<label>][_run-<index>]_magnitude1.nii[.gz]
            sub-<label>[_ses-<label>][_acq-<label>][_run-<index>]_magnitude2.json
            sub-<label>[_ses-<label>][_acq-<label>][_run-<index>]_magnitude2.nii[.gz]
            sub-<label>[_ses-<label>][_acq-<label>][_run-<index>]_phase1.json
            sub-<label>[_ses-<label>][_acq-<label>][_run-<index>]_phase1.nii[.gz]
            sub-<label>[_ses-<label>][_acq-<label>][_run-<index>]_phase2.json
            sub-<label>[_ses-<label>][_acq-<label>][_run-<index>]_phase2.nii[.gz]

Required fields:

Key name Requirement level Data type Description
EchoTime REQUIRED number The time (in seconds) when the echo corresponding to this phase map was acquired.

Each phase map has a corresponding sidecar JSON file to specify its corresponding EchoTime. For example, sub-<label>[_ses-<label>][_acq-<label>][_run-<index>]_phase2.json may read:

{
   "EchoTime": 0.00746
}

Case 3: Direct field mapping

In some cases (for example GE), the scanner software will directly reconstruct a B0 field map along with a magnitude image used for anatomical reference.

Template:

sub-<label>/
    [ses-<label>/]
        fmap/
            sub-<label>[_ses-<label>][_acq-<label>][_run-<index>]_fieldmap.json
            sub-<label>[_ses-<label>][_acq-<label>][_run-<index>]_fieldmap.nii[.gz]
            sub-<label>[_ses-<label>][_acq-<label>][_run-<index>]_magnitude.json
            sub-<label>[_ses-<label>][_acq-<label>][_run-<index>]_magnitude.nii[.gz]

Required fields:

Key name Requirement level Data type Description
Units REQUIRED string Units of the fieldmap: Hertz ("Hz"), Radians per second ("rad/s"), or Tesla ("T").

For example:

{
   "Units": "rad/s",
   "IntendedFor": "func/sub-01_task-motor_bold.nii.gz"
}

See Using IntendedFor metadata for details on the IntendedFor field.

Case 4: Multiple phase encoded directions ("pepolar")

The phase-encoding polarity (PEpolar) technique combines two or more Spin Echo EPI scans with different phase encoding directions to estimate the distortion map corresponding to the nonuniformities of the B0 field. These *_epi.nii[.gz] - or *_m0scan.nii[.gz] for arterial spin labeling perfusion data - files can be 3D or 4D -- in the latter case, all timepoints share the same scanning parameters. Examples of software tools using these kinds of images are FSL TOPUP, AFNI 3dqwarp, and SPM.

Template:

sub-<label>/
    [ses-<label>/]
        fmap/
            sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>]_dir-<label>[_run-<index>]_epi.json
            sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>]_dir-<label>[_run-<index>]_epi.nii[.gz]

The dir-<label> entity is REQUIRED for these files. This key-value pair MUST be used in addition to the REQUIRED PhaseEncodingDirection metadata field (see File name structure).

Required fields:

Key name Requirement level Data type Description
PhaseEncodingDirection REQUIRED string See in-plane spatial encoding table of fields.
TotalReadoutTime REQUIRED number See in-plane spatial encoding table of fields.

For example:

{
   "PhaseEncodingDirection": "j-",
   "TotalReadoutTime": 0.095,
   "IntendedFor": "func/sub-01_task-motor_bold.nii.gz"
}

See Using IntendedFor metadata for details on the IntendedFor field.

As for other EPI sequences, these field mapping sequences may have any of the in-plane spatial encoding metadata keys. However, please note that PhaseEncodingDirection and TotalReadoutTime keys are REQUIRED for these field mapping sequences.

Expressing the MR protocol intent for fieldmaps

Fieldmaps are typically acquired with the purpose of correcting one or more EPI scans under func/ or dwi/ for distortions derived from B0 nonuniformity. This linking between fieldmaps and their targetted data MAY be encoded with the IntendedFor metadata.

Using IntendedFor metadata

Fieldmap data MAY be linked to the specific scan(s) it was acquired for by filling the IntendedFor field in the corresponding JSON file.

Key name Requirement level Data type Description
IntendedFor RECOMMENDED string or array of string Contains one or more filenames with paths relative to the participant subfolder. The path needs to use forward slashes instead of backward slashes. This field is OPTIONAL, and in case the fieldmaps do not correspond to any particular scans, it does not have to be filled.

For example:

{
   "IntendedFor": [
        "ses-pre/func/sub-01_ses-pre_task-motor_run-1_bold.nii.gz",
        "ses-pre/func/sub-01_ses-pre_task-motor_run-2_bold.nii.gz"
    ]
}