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

In-Plane Spatial Encoding

Key name Requirement level Data type Description
NumberShots RECOMMENDED number The number of RF excitations need to reconstruct a slice or volume. Please mind that this is not the same as Echo Train Length which denotes the number of lines of k-space collected after an excitation.
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).

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 number 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).
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 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 number Flip angle for the acquisition, specified in degrees. Corresponds to: DICOM Tag 0018, 1314 Flip Angle.
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>]_<modality_label>.nii[.gz]
        sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>][_mod-<label>]_defacemask.nii[.gz]

Anatomical (structural) data acquired for that participant. Currently supported modalities include:

Name modality_label Description
T1 weighted T1w
T2 weighted T2w
T1 Rho map T1rho Quantitative T1rho brain imaging
https://www.ncbi.nlm.nih.gov/pubmed/24474423
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4346383/
T1 map T1map quantitative T1 map
T2 map T2map quantitative T2 map
T2* T2star High resolution T2* image
FLAIR FLAIR
FLASH FLASH
Proton density PD
Proton density map PDmap
Combined PD/T2 PDT2
Inplane T1 inplaneT1 T1-weighted anatomical image matched to functional acquisition
Inplane T2 inplaneT2 T2-weighted anatomical image matched to functional acquisition
Angiography angio

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 of the same modality are acquired they MUST be indexed with the run-<index> key-value pair: _run-1, _run-2, _run-3, and so on (only nonnegative integers are allowed as run labels). When there is only one scan of a given type the run key MAY be omitted. Please note that diffusion imaging data is stored elsewhere (see below).

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).

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>][_dir-<label>][_rec-<label>][_run-<index>][_echo-<index>][_part-<label>]_bold.nii[.gz]
        sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_ce-<label>][_dir-<label>][_rec-<label>][_run-<index>][_echo-<index>][_part-<label>]_cbv.nii[.gz]
        sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_ce-<label>][_dir-<label>][_rec-<label>][_run-<index>][_echo-<index>][_part-<label>]_sbref.nii[.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.nii[.gz]
       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>]_sbref.nii[.gz]
       sub-<label>[_ses-<label>][_acq-<label>][_dir-<label>][_run-<index>][_part-<label>]_sbref.json

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
}

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>]_phasediff.nii[.gz]
        sub-<label>[_ses-<label>][_acq-<label>][_run-<index>]_phasediff.json
        sub-<label>[_ses-<label>][_acq-<label>][_run-<index>]_magnitude1.nii[.gz]
        sub-<label>[_ses-<label>][_acq-<label>][_run-<index>]_magnitude2.nii[.gz]  # OPTIONAL

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>]_phase1.nii[.gz]
        sub-<label>[_ses-<label>][_acq-<label>][_run-<index>]_phase1.json
        sub-<label>[_ses-<label>][_acq-<label>][_run-<index>]_phase2.nii[.gz]
        sub-<label>[_ses-<label>][_acq-<label>][_run-<index>]_phase2.json
        sub-<label>[_ses-<label>][_acq-<label>][_run-<index>]_magnitude1.nii[.gz]
        sub-<label>[_ses-<label>][_acq-<label>][_run-<index>]_magnitude2.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>]_magnitude.nii[.gz]
       sub-<label>[_ses-<label>][_acq-<label>][_run-<index>]_fieldmap.nii[.gz]
       sub-<label>[_ses-<label>][_acq-<label>][_run-<index>]_fieldmap.json

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

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"
    ]
}