Magnetic Resonance Imaging data

Common metadata fields

MR Data described in sections 8.3.x 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

Field name Definition
Manufacturer RECOMMENDED. Manufacturer of the equipment that produced the composite instances. Corresponds to DICOM Tag 0008, 0070 Manufacturer
ManufacturersModelName RECOMMENDED. Manufacturer's model name of the equipment that produced the composite instances. Corresponds to DICOM Tag 0008, 1090 Manufacturers Model Name
DeviceSerialNumber RECOMMENDED. 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. Institution defined name of the machine that produced the composite instances. Corresponds to DICOM Tag 0008, 1010 Station Name
SoftwareVersions RECOMMENDED. Manufacturer’s designation of software version of the equipment that produced the composite instances. Corresponds to DICOM Tag 0018, 1020 Software Versions
HardcopyDeviceSoftwareVersion (Deprecated) 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. Nominal field strength of MR magnet in Tesla. Corresponds to DICOM Tag 0018,0087 Magnetic Field Strength
ReceiveCoilName RECOMMENDED. 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. 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. As an example, 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 (e.g., 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
GradientSetType RECOMMENDED. It should be possible to infer the gradient coil from the scanner model. If not, e.g. 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. 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. (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 (e.g. GRAPPA, SENSE) imaging
CoilCombinationMethod RECOMMENDED. 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

Sequence Specifics

Field name Definition
PulseSequenceType RECOMMENDED. A general description of the pulse sequence used for the scan (i.e. MPRAGE, Gradient Echo EPI, Spin Echo EPI, Multiband gradient echo EPI).
ScanningSequence RECOMMENDED. Description of the type of data acquired. Corresponds to DICOM Tag 0018, 0020 Scanning Sequence.
SequenceVariant RECOMMENDED. Variant of the ScanningSequence. Corresponds to DICOM Tag 0018, 0021 Sequence Variant.
ScanOptions RECOMMENDED. Parameters of ScanningSequence. Corresponds to DICOM Tag 0018, 0022 Scan Options.
SequenceName RECOMMENDED. Manufacturer’s designation of the sequence name. Corresponds to DICOM Tag 0018, 0024 Sequence Name.
PulseSequenceDetails RECOMMENDED. Information beyond pulse sequence type that identifies the specific pulse sequence used (i.e. "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 stating if the image saved has been corrected for gradient nonlinearities by the scanner sequence.

In-Plane Spatial Encoding

Field name Definition
NumberShots RECOMMENDED. 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. The parallel imaging (e.g, 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. The type of parallel imaging used (e.g. GRAPPA, SENSE). Corresponds to DICOM Tag 0018, 9078 Parallel Acquisition Technique.
PartialFourier RECOMMENDED. The fraction of partial Fourier information collected. Corresponds to DICOM Tag 0018, 9081 Partial Fourier.
PartialFourierDirection RECOMMENDED. The direction where only partial Fourier information was collected. Corresponds to DICOM Tag 0018, 9036 Partial Fourier Direction.
PhaseEncodingDirection RECOMMENDED. 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. 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. 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 "FSL definition", i.e, the time between the center of the first "effective" echo and the center of the last "effective" echo.

Timing Parameters

Field name Definition
EchoTime RECOMMENDED. The echo time (TE) for the acquisition, specified in seconds. This parameter is REQUIRED if corresponding fieldmap data is present or the data comes from a multi echo sequence. Corresponds to DICOM Tag 0018, 0081 Echo Time (please note that the DICOM term is in milliseconds not seconds).
InversionTime RECOMMENDED. 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. 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 (in JSON format) 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 (i.e., the final entry in the SliceTiming list is the time of acquisition of slice 0). This parameter is REQUIRED for sparse sequences that do not have the DelayTime field set. In addition without this parameter slice time correction will not be possible.
SliceEncodingDirection RECOMMENDED. 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. 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

Field name Definition
FlipAngle RECOMMENDED. Flip angle for the acquisition, specified in degrees. Corresponds to: DICOM Tag 0018, 1314 Flip Angle.
MultibandAccelerationFactor RECOMMENDED. The multiband factor, for multiband acquisitions.
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

Field name Definition
MultibandAccelerationFactor RECOMMENDED. The multiband factor, for multiband acquisitions.

Anatomical landmarks

Useful for multimodal co-registration with MEG, (S)EEG, TMS, etc.

Field name Definition
AnatomicalLandmarkCoordinates RECOMMENDED. 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, (e.g. {"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]}).

Institution information

Field name Definition
InstitutionName RECOMMENDED. The name of the institution in charge of the equipment that produced the composite instances. Corresponds to DICOM Tag 0008, 0080 InstitutionName.
InstitutionAddress RECOMMENDED. The address of the institution in charge of the equipment that produced the composite instances. Corresponds to DICOM Tag 0008, 0081 InstitutionAddress.
InstitutionalDepartmentName RECOMMENDED. 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.

Anatomy imaging data

Template:

sub-<label>/[ses-<label>/]
    anat/
        sub-<label>[_ses-<label>][_acq-<label>][_ce-<label>][_rec-<label>][_run-<index>]_<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

The run entity

If several scans of the same modality are acquired they MUST be indexed with a key-value pair: _run-1, _run-2, _run-3 etc. (only 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 acq entity

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 (e.g. RARE and FLASH for T1w) this field can also be used to make that distinction. At what level of detail to make the distinction (e.g. just between RARE and FLASH, or between RARE, FLASH, and FLASHsubsampled) remains at the discretion of the researcher.

The ce entity

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.

The rec entity

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

If the structural images included in the dataset were defaced (to protect identity of participants) one CAN 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 label for eg: T1w, inplaneT1, referenced by a defacemask image. E.g., sub-01_mod-T1w_defacemask.nii.gz.

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:

Field name Definition
ContrastBolusIngredient OPTIONAL. Active ingredient of agent. Values MUST be one of: IODINE, GADOLINIUM, CARBON DIOXIDE, BARIUM, XENON Corresponds to DICOM Tag 0018,1048.

Task (including resting state) imaging data

Currently supported image contrasts include:

Name contrast_label 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 Phase information associated with magnitude information stored in BOLD contrast

Template:

sub-<label>/[ses-<label>/]
    func/
        sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_ce-<label>][_dir-<label>][_rec-<label>][_run-<index>][_echo-<index>]_<contrast_label>.nii[.gz]
        sub-<label>[_ses-<label>]_task-<label>[_acq-<label>][_ce-<label>][_dir-<label>][_rec-<label>][_run-<index>][_echo-<index>]_sbref.nii[.gz]

Imaging data acquired during functional imaging (i.e. imaging which supports rapid temporal repetition). This includes but is not limited to task based fMRI as well as resting state fMRI (i.e. rest is treated as another 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 (e.g. 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). Those labels MUST be consistent across subjects and sessions.

If more than one run of the same task has been acquired a key/value pair: _run-1, _run-2, _run-3 etc. MUST be used. 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. Each file shares the same name with the exception of the _echo-<index> key/value. 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 a form of an integer) of the echo not the echo time value which needs to be stored in the field EchoTime of the separate JSON file.

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

Required fields

Field name Definition
RepetitionTime REQUIRED. The time in seconds between the beginning of an acquisition of one volume and the beginning of acquisition of the volume following it (TR). Please note that this definition includes time between scans (when no data has been acquired) in case of sparse acquisition schemes. This value needs to 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 and is derived from DICOM Tag 0018, 0080 and converted to seconds.
VolumeTiming REQUIRED. The time at which each volume was acquired during the acquisition. It is described using a list of times (in JSON format) 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. Name of the task. No two tasks should have the same name. Task label (task-) included in the file name is derived from this field by removing all non alphanumeric ([a-zA-Z0-9]) characters. For example task name faces n-back will corresponds 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 (e.g., 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
Field name Definition
NumberOfVolumesDiscardedByScanner RECOMMENDED. 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. 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. 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. Duration (in seconds) of volume acquisition. Corresponds to DICOM Tag 0018,9073 Acquisition Duration. This field is REQUIRED for sequences that are described with the VolumeTiming field and that not have the SliceTiming field set to allowed for accurate calculation of "acquisition time". This field is mutually exclusive with RepetitionTime.
DelayAfterTrigger RECOMMENDED. 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 those options can 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 ] --> has to be filled - [ ] --> has to be left empty - empty cell --> can be specified but not required

fMRI task information
Field name Definition
Instructions RECOMMENDED. 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. Longer description of the task.
CogAtlasID RECOMMENDED. URL of the corresponding Cognitive Atlas Task term.
CogPOID RECOMMENDED. URL 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

Template:

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

Diffusion-weighted imaging data acquired for that participant. The OPTIONAL acq-<label> key/value pair corresponds to a custom label the user may use to distinguish different set of parameters. For example this should be used when a study includes two diffusion images - one single band and one multiband. In such case two files could have the following names: sub-01_acq-singleband_dwi.nii.gz and sub-01_acq-multiband_dwi.nii.gz, however the user is free to choose any other label than singleband and multiband as long as they are consistent across subjects and sessions. For multiband acquisitions, one can also save the single-band reference image as type sbref (e.g. dwi/sub-control01_sbref.nii[.gz]) The bvec and bval files are in the FSL format: The bvec files contain 3 rows with n space-delimited floating-point numbers (corresponding to the n volumes in the relevant NIfTI file). The first row contains the x elements, the second row contains the y elements and 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 volumes. Inherent to the FSL format for bvec specification is the fact that the coordinate system of the bvecs is with respect to the participant (i.e., defined by the axes of the corresponding dwi.nii file) and not the magnet’s coordinate system, which means that any rotations applied to dwi.nii also need to be applied to the corresponding bvec file.

bvec example:

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 bval file contains the b-values (in s/mm2) corresponding to the volumes in the relevant NIfTI file), with 0 designating non-diffusion-weighted volumes, space-delimited.

bval example:

0 0 2000 2000 1000 1000

.bval and .bvec files can be saved on any level of the directory structure and thus define those values for all sessions and/or subjects in one place (see Inheritance principle).

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. Please note that in all cases fieldmap data can be linked to a specific scan(s) it was acquired for by filling the IntendedFor field in the corresponding JSON file. For example:

{
   "IntendedFor": "func/sub-01_task-motor_bold.nii.gz"
}

The IntendedFor field may contain one or more filenames with paths relative to the subject subfolder. The path needs to use forward slashes instead of backward slashes. Here’s an example with multiple target scans:

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

The IntendedFor field is OPTIONAL and in case the fieldmaps do not correspond to any particular scans it does not have to be filled.

Multiple fieldmaps can be stored. In such case the _run-1, _run-2 should be used. The OPTIONAL acq-<label> key/value pair corresponds to a custom label the user may use to distinguish different set of parameters.

Case 1: Phase difference image 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]

OPTIONAL

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

This is a common output for build in fieldmap sequence on Siemens scanners. In this particular case the sidecar JSON file has to define the Echo Times of the two phase images used to create the difference image. EchoTime1 corresponds to the shorter echo time and EchoTime2 to the longer echo time. Similarly _magnitude1 image corresponds to the shorter echo time and the OPTIONAL _magnitude2 image to the longer echo time. For example:

{
   "EchoTime1": 0.00600,
   "EchoTime2": 0.00746,
   "IntendedFor": "func/sub-01_task-motor_bold.nii.gz"
}

Case 2: Two phase images and two magnitude images

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]

Similar to the case above, but instead of a precomputed phase difference map two separate phase images are presented. The two sidecar JSON file need to specify corresponding EchoTime values. For example:

{
   "EchoTime": 0.00746,
   "IntendedFor": "func/sub-01_task-motor_bold.nii.gz"
}

Case 3: A real fieldmap image

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

In some cases (for example GE) the scanner software will output a precomputed fieldmap denoting the B0 inhomogeneities along with a magnitude image used for coregistration. In this case the sidecar JSON file needs to include the units of the fieldmap. The possible options are: Hz, rad/s, or Tesla. For example:

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

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

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 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. Examples of tools using this kind of images are FSL TOPUP, AFNI 3dqwarp and SPM. In such a case, the phase encoding direction is specified in the corresponding JSON file as one of: i, j, k, i-, j-, k-. For these differentially phase encoded sequences, one also needs to specify the Total Readout Time defined as the time (in seconds) from the center of the first echo to the center of the last echo (aka "FSL definition" - see here and here how to calculate it). For example

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

label value of _dir- can be set to arbitrary alphanumeric label ([a-zA-Z0-9]+ for example LR or AP) that can help users to distinguish between different files, but should not be used to infer any scanning parameters (such as phase encoding directions) of the corresponding sequence. Please rely only on the JSON file to obtain scanning parameters. _epi files can be a 3D or 4D - in the latter case all timepoints share the same scanning parameters. To indicate which run is intended to be used with which functional or diffusion scan the IntendedFor field in the JSON file should be used.