dcm2niix is designed to convert complicated DICOM images in to simple NIfTI images. However, the NIfTI images are unable to store much metadata that might be useful for analyses. Therefore, dcm2niix can create Brain Imaging Data Structure (BIDS) files that retain useful information. These are simple human-readable text files in the JSON format. The tables below provide details regarding the JSON fields generated by dcm2niix. Some of these are defined by the BIDS standard, while others are unique to dcm2niix.
Note that dcm2niix cannot provide information that is not in the DICOM header. Common reasons for absent fields are:
- Irrelevance to the scan type, e.g. MagneticFieldStrength for CT
- It was removed from the DICOM during anonymization, possibly by accident or overzealousness
- Difficulty interpreting the storage format used by the manufacturer
- The manufacturer simply neglected to write it
The units listed in this document can be extracted into JSON format using
./extract_units.py, as long as they are in tables where the first two columns
are Field and Unit. It can also optionally extract only the units that are used
in a given BIDS sidecar - e.g. if you have a BIDS sidecar file named
my_series.json from dcm2niix, you can use extract_units.py to get
my_series_units.json.
Help on using extract_units.py is available from running extract_units.py -h.
The Defined By column uses:
- B : The BIDS standard
- D : dcm2niix (often, but not always, these come directly from the DICOM header without transformation)
The Unit column uses:
- b : boolean
- deg : degrees
- f : fraction
- kg : Kilogram
- list : list of text strings
- MBq : megabecquerel
- MHz : megahertz
- mA : milliampere
- mm : millimeter
- s : second
- T : tesla
- V : volt
These fields are present regardless of modality (e.g. MR, CT, PET).
These fields should be the same for all images acquired on a specific scanner.
| Field | Unit | Comments | Defined By |
|---|---|---|---|
| Manufacturer | DICOM tag 0008,0070 | B | |
| DeviceSerialNumber | DICOM tag 0018,1000 | B | |
| StationName | DICOM tag 0008,1010 | B | |
| SoftwareVersions | DICOM tag 0018,1020 | B | |
| Modality | DICOM tag 0008,1060 | D | |
| ManufacturersModelName | DICOM tag 0008,1090 | B | |
| InstitutionName | DICOM tag 0008,0080 | B | |
| InstitutionalDepartmentName | DICOM tag 0008,1040 | B | |
| InstitutionAddress | DICOM tag 0008,0081 | B | |
| DeviceSerialNumber | DICOM tag 0018,1000 | B | |
| StationName | DICOM tag 0008,1010 | B | |
| ConversionSoftware | e.g. dcm2niix |
D | |
| ConversionSoftwareVersion | e.g. v1.0.20210317 |
D |
These fields are present regardless of modality (e.g. MR, CT, PET).
| Field | Unit | Comments | Defined By |
|---|---|---|---|
| BodyPartExamined | DICOM tag 0018,0015 | D | |
| PatientPosition | DICOM tag 0020,0032 | D | |
| ProcedureStepDescription | DICOM tag 0040,0254 | D | |
| SoftwareVersions | DICOM tag 0020,1020 | B | |
| SeriesDescription | DICOM tag 0008,103E | D | |
| ProtocolName | DICOM tag 0018,1030 | D | |
| ScanningSequence | DICOM tag 0018,0020 | B | |
| SequenceVariant | DICOM tag 0018,0021 | B | |
| ScanOptions | DICOM tag 0018,0022 | B | |
| SequenceName | DICOM tag 0018,0024 | B | |
| ImageType | list | DICOM tag 0008,0008 | D |
| AcquisitionTime | DICOM tag 0008,0032 | D | |
| AcquisitionNumber | DICOM tag 0020,0012 | D | |
| ImageComments | DICOM tag 0020,4000 | D |
These fields contain personally identifiable information. By default dcm2niix will create anonymized files without these fields. The option -ba n will retain private information.
| Field | Unit | Comments | Defined By |
|---|---|---|---|
| SeriesInstanceUID | DICOM tag 0020,000E | D | |
| StudyInstanceUID | DICOM tag 0020,000D | D | |
| ReferringPhysicianName | DICOM tag 0008,0090 | D | |
| StudyID | DICOM tag 0020,0010 | D | |
| PatientName | DICOM tag 0010,0010 | D | |
| PatientID | DICOM tag 0010,0020 | D | |
| AccessionNumber | DICOM tag 0008,0050 | D | |
| PatientBirthDate | DICOM tag 0010,0030 | D | |
| PatientWeight | kg | DICOM tag 0010,1030 | D |
| AcquisitionDateTime | DICOM tag 0008,002A | D |
These fields are specific to modality (e.g. MR, CT, PET).
Fields specific to CT scans.
| Field | Unit | Comments | Defined By |
|---|---|---|---|
| ExposureTime | s | DICOM tag 0018,1150 | D |
| XRayTubeCurrent | mA | DICOM tag 0018,1151 | D |
| XRayExposure | mAs | DICOM tag 0018,1152 | D |
Fields specific to MRI scans.
| Field | Unit | Comments | Defined By |
|---|---|---|---|
| AcquisitionMatrixPE | DICOM tag 0018,9231 (aka PhaseEncodingLines) | D | |
| DerivedVendorReportedEchoSpacing | s | D | |
| EchoNumber | Only multi-echo series | D | |
| EchoTime | s | DICOM tag 0018,0081 | B |
| EchoTrainLength | DICOM tag 0018,0091 | D | |
| EffectiveEchoSpacing | s | D | |
| EstimatedEffectiveEchoSpacing | s | D | |
| EstimatedTotalReadoutTime | s | D | |
| FlipAngle | deg | DICOM tag 0018,1314 | B |
| VariableFlipAngleFlag | b | DICOM tag 0018,1315 | D |
| ImageOrientationPatientDICOM | DICOM tag 0020,0037 | D | |
| ImagingFrequency | MHz | DICOM tag 0018,0084 or 0018,9098 | D |
| InPlanePhaseEncodingDirectionDICOM | DICOM tag 0018,1312 | D | |
| InversionTime | s | DICOM tag 0018,0082 | B |
| MagneticFieldStrength | T | DICOM tag 0018,0087 | B |
| MRAcquisitionType | DICOM tag 0018,0023 | B | |
| MTState | 0018,9020 | B | |
| MultibandAccelerationFactor | aka SMS, HyperBand |
B | |
| NumberOfAverages | DICOM tag 0018,0083 | D | |
| ParallelAcquisitionTechnique | DICOM tag 0018, 9078, aka SENSE, GRAPPA |
B | |
| ParallelReductionFactorInPlane | DICOM tag 0018,9069 | B | |
| ParallelReductionFactorOutOfPlane | DICOM tag 0018,9155 | B | |
| PartialFourierDirection | DICOM tag 0018,9036 | B | |
| PercentPhaseFOV | DICOM tag 0018,0094 | D | |
| PercentSampling | DICOM tag 0018,0093 | D | |
| PhaseEncodingAxis | When polarity unknown | B | |
| PhaseEncodingDirection | When polarity known | B | |
| FrequencyEncodingSteps | DICOM tag 0018,9058 | D | |
| PhaseEncodingSteps | DICOM tag 0018,0089 or 0018,9231 aka PhaseEncodingStepsInPlane | D | |
| PhaseEncodingStepsOutOfPlane | DICOM tag 0018,9232 | D | |
| PixelBandwidth | Hz | DICOM tag 0018,0095 | D |
| ReceiveCoilName | DICOM tag 0018,1250 | B | |
| RepetitionTime | s | DICOM tag 0018,0080 | B |
| RepetitionTimeExcitation | s | DICOM tag 0018, 0080 for some manufacturers | B |
| RepetitionTimeInversion | s | D | |
| SAR | DICOM tag 0018,1316 or 0018,9181 defined by 0018,9179 | D | |
| SliceThickness | mm | nb | D |
| SliceTiming | s | B | |
| SpacingBetweenSlices | mm | nb | D |
| SpoilingState | 0018,9016 or 0018,0021 | B | |
| SpoilingType | 0018,9016 | B | |
| TotalReadoutTime | s | FSL definition | B |
| Units | Hz,rad (field maps) |
B |
PET fields extracted from DICOM tags. See BIDS BEP009 Positron Emission Tomography. Be aware that many of the fields required by BEP009 are not stored in DICOM or ECAT files. Since dcm2niix is limited to the information provided by the input files, it will generate JSON fields that reflect the meta data stored in the source images.
The term ECAT in the comments suggests that values are defined by the ECAT7 format. Therefore, these fields will not be populated for DICOM data.
| Field | Unit | Comments | Defined By |
|---|---|---|---|
| Radiopharmaceutical | DICOM tag 0018,0031 or ECAT | D | |
| RadionuclidePositronFraction | f | DICOM tag 0018,1076 | D |
| RadionuclideTotalDose | MBq | DICOM tag 0018,1074 | D |
| RadionuclideHalfLife | s | DICOM tag 0018,1075 | D |
| DoseCalibrationFactor | DICOM tag 0054,1322 | D | |
| IsotopeHalfLife | ECAT | D | |
| Dosage | ECAT | D | |
| ConvolutionKernel | DICOM tag 0018,1210 | D | |
| Units | DICOM tag 0054,1001 | D | |
| DecayCorrection | DICOM tag 0054,1102 | D | |
| AttenuationCorrectionMethod | DICOM tag 0054,1101 | D | |
| ReconstructionMethod | DICOM tag 0054,1103 | D | |
| DecayFactor | DICOM tag 0054,1321 | D | |
| FrameTimesStart | s | DICOM tags 0008,0022 | D |
| FrameDuration | s | DICOM tag 0018,1242 | D |
These fields are specific to manufacturer (e.g. GE, Philips, Siemens). For further manufacturer details see:
Data unique to GE. Determining these fields from a DICOM image requires decoding the compressed Protocol Data Block (0025,101B).
| Field | Unit | Comments | Defined By |
|---|---|---|---|
| PulseSequenceName | epi or epiRT |
D | |
| InternalPulseSequenceName | EPI or EPI2 |
D | |
| PhaseEncodingPolarityGE | Unflipped or Flipped |
D | |
| PostLabelingDelay | s | DICOM tag 0018,0082 (TI) | B |
| NumberOfPointsPerArm | DICOM tag 0027,1060 | D | |
| NumberOfArms | DICOM tag 0027,1061 | D | |
| NumberOfExcitations | DICOM tag 0027,1062 | D | |
| ShimSetting[0] | DICOM tag 0043,1002 | D | |
| ShimSetting[1] | DICOM tag 0043,1003 | D | |
| ShimSetting[2] | DICOM tag 0043,1004 | D | |
| ParallelReductionFactorInPlane | DICOM tag 0043,1083 | B | |
| PrescanReuseString | DICOM tag 0043,1095 | D | |
| MultibandAccelerationFactor | DICOM tag 0043,1083 | B | |
| ASLContrastTechnique | DICOM tag 0043,10A3 | D | |
| ASLLabelingTechnique | DICOM tag 0043,10A4 | D | |
| LabelingDuration | s | DICOM tag 0043,10A5 | B |
| SliceTiming | s | see notes | B |
| CompressedSensingFactor | DICOM tag 0043,10b7 | D | |
| DeepLearningFactor | DICOM tag 0043,10ca | D |
Data unique to Philips, including custom intensity scaling
| Field | Unit | Comments | Defined By |
|---|---|---|---|
| TriggerDelayTime | s | DICOM tag 0020,9153 or 0018,1060 | D |
| PhilipsRWVSlope | DICOM tag 0040,9225 | D | |
| PhilipsRWVIntercept | DICOM tag 0040,9224 | D | |
| PhilipsRescaleSlope | DICOM tag 0028,1053 | D | |
| PhilipsRescaleIntercept | DICOM tag 0028,1052 | D | |
| PhilipsScaleSlope | DICOM tag 2005,100E | D | |
| UsePhilipsFloatNotDisplayScaling | dcm2niix option -p y or -p n |
D | |
| PartialFourierEnabled | DICOM tag 0018,9081, YES |
D | |
| PhaseEncodingStepsNoPartialFourier | DICOM tag 0018,9231 | D | |
| WaterFatShift | DICOM tag 2001,1022 | D |
See BIDS BEP005 Arterial Spin Labeling. All these values are specific to Siemens V*-series (e.g. VB, VE) MRI systems (e.g. Verio, Trio, Prisma) from the CSA header. Note that many of the fields listed by BIDS do not have DICOM equivalents.
| Field | Unit | Comments | Defined By |
|---|---|---|---|
| ArterialSpinLabelingType | PASL or PCASL |
B | |
| LabelOffset | 2D pCASL ep2d_pcasl | D | |
| PostLabelDelay | s | 2D pCASL ep2d_pcasl, FAIREST (ep2d_fairest) |
D |
| PostInversionDelay | s | 2D FAIREST (ep2d_fairest) |
D |
| NumRFBlocks | 2D pCASL ep2d_pcasl | D | |
| RFGap | 2,3D pCASL ep2d_pcasl, tgse_pcasl | D | |
| MeanGzx10 | 2,3D pCASL ep2d_pcasl, tgse_pcasl | D | |
| PhiAdjust | 2D pCASL ep2d_pcasl | D | |
| InversionTime | s | 2D,3D PASL product (ep2d_pasl, tgse_pasl), VEPCASL (to_ep2d_VEPCASL) |
D |
| BolusDuration | s | 2D,3D PASL product (ep2d_pasl, tgse_pasl), VEPCASL (to_ep2d_VEPCASL) |
D |
| MeanGzx10 | 3D pCASL tgse_pcasl | D | |
| TagRFFlipAngle | deg | 2,3D VEPCASL (to_ep2d_VEPCASL, jw_tgse_VEPCASL) |
D |
| TagRFDuration | s | 2,3D VEPCASL (to_ep2d_VEPCASL, jw_tgse_VEPCASL) |
D |
| TagRFSeparation | 2,3D VEPCASL (to_ep2d_VEPCASL, jw_tgse_VEPCASL) |
D | |
| MeanTagGradient | 2D VEPCASL (to_ep2d_VEPCASL) |
D | |
| TagGradientAmplitude | 2D VEPCASL (to_ep2d_VEPCASL) |
D | |
| TagDuration | s | 2D VEPCASL (to_ep2d_VEPCASL) |
D |
| MaximumT1Opt | 2,3D VEPCASL (to_ep2d_VEPCASL, jw_tgse_VEPCASL) |
D | |
| InitialPostLabelDelay | s | 2D VEPCASL (to_ep2d_VEPCASL) |
D |
| sWipMemBlockAdFree* | multiple values | 2D VEPCASL (to_ep2d_VEPCASL) |
D |
| TagPlaneDThickness | 2D VEPCASL (to_ep2d_VEPCASL) |
D | |
| TagPlaneUlShape | 2D VEPCASL (to_ep2d_VEPCASL) |
D | |
| TagPlaneSPositionDTra | 2D VEPCASL (to_ep2d_VEPCASL) |
D | |
| TagPlaneSNormalDTra | 2D VEPCASL (to_ep2d_VEPCASL) |
D | |
| Tag* (if not explicitly listed) | One value for each | Post-label delays, 3D VEPCASL (jw_tgse_VEPCASL) |
D |
Fields specific to Siemens V*-series (e.g. VB, VE) MRI systems (e.g. Verio, Trio, Skyra, Prisma) from the CSA header.
| Field | Unit | Comments | Defined By |
|---|---|---|---|
| EchoTime1 | s | For Fieldmaps created with two echo times | B |
| EchoTime2 | s | For Fieldmaps created with two echo times | B |
| PartialFourier | f | Partial fourier fraction, e.g. image with 6/8 pF will report 0.75. Different tags depending on manufacturer |
B |
| Interpolation2D | If present, slices interpolated within plane | D | |
| Interpolation3D | If present, image interpolated in all spatial dimensions | D | |
| BaseResolution | integer | # of acquisition lines? | D |
| ShimSetting | DAC for 1st order terms, mA for 2nd order terms | The 1st 3 values are the 1st order shims from sGRADSPEC.lOffset{X,Y,Z}. The next 5 are 2nd order shims from sGRADSPEC.alShimCurrent[0-4]. Converting to the first order terms to uT/m may be possible using the "gradient sensitivities". Converting the second order terms to uT/m^2 requires information not stored in the DICOM header, but they are fixed for a given shim hardware configuration. | D |
| DiffusionScheme | Monopolar or Bipolar |
D | |
| DelayTime | s | Pause between EPI volumes, where TR is longer than required by TA (sparse imaging) |
D |
| TxRefAmp | V | D | |
| ParallelReductionFactorInPlane | DICOM tag 0021,1009 | B | |
| ParallelReductionFactorOutOfPlane | CSA sPat.lAccelFact3D |
B | |
| PhaseResolution | f | D | |
| PhaseOversampling | D | ||
| MultibandAccelerationFactor | DICOM tag 0021,1009 | B | |
| VendorReportedEchoSpacing | B | ||
| ReceiveCoilActiveElements | Given as groups of channels, instead of individual ones, e.g. "HC1-7" for HeadNeck_64. | B | |
| CoilString | May or may not match ReceiveCoilName |
D | |
| PulseSequenceDetails | pulse sequence label, e.g. "%SiemensSeq%\\tgse_pasl" | B | |
| FmriExternalInfo | D | ||
| WipMemBlock | D | ||
| AveragesDouble | CSA dAveragesDouble, fractions possible, independent of DICOM NumberOfAverages (0018,0083) |
D | |
| ProtocolName | Check SeriesDescription - they might be switched around | D | |
| RefLinesPE | # of reference lines in the phase encoding direction for acceleration (GRAPPA) | D | |
| ConsistencyInfo | The more complete software version, e.g. VE11C or VE11E instead of just VE11. | D | |
| CoilCombinationMethod | Detects Sum of Squares and Adaptive Combine |
B | |
| MatrixCoilMode | Detects SENSE and GRAPPA |
B | |
| DwellTime | DICOM tag 0019,1018 | B | |
| BandwidthPerPixelPhaseEncode | Hz | DICOM tag 0019,1028 | D |
| ImageOrientationText | DICOM tag 0051,100E | D | |
| NonlinearGradientCorrection | b | DICOM tag 0008,0008 | B |
Fields specific to Siemens XA-series MRI systems (Sola, Vida).
| Field | Unit | Comments | Defined By |
|---|---|---|---|
| ReceiveCoilActiveElements | DICOM tag 0021,114F | B | |
| BandwidthPerPixelPhaseEncode | Hz | DICOM tag 0021,1153 | D |
| ScanningSequence | DICOM tag 0021,105a | D | |
| PostLabelDelay | s | DICOM tag 0018,9258 | D |
| NonlinearGradientCorrection | b | 0008,0008 or 0021,1175 | B |
| PhaseEncodingDirection | polarity from 0021,111c | B | |
| SpoilingState | 0021,105B | B |
Siemens also includes some sequence information in the private MRPhoenixProtocol (0021,1019) tag. You can view this with gdcmdump, e.g. gdcmdump --mrprotocol img.dcm. Fields that dcm2niix inspects include sPat.lAccelFact3D , sPat.lAccelFactPE, sPat.lRefLinesPE and sPat.ucPATMode. The behavior of dcm2niix will be more well documented as our understanding of this tag improves.
Fields specific to United Imaging Healthcare systems (e.g. uMR 770).
| Field | Unit | Comments | Defined By |
|---|---|---|---|
| BandwidthPerPixelPhaseEncode | Hz | DICOM tag 0019,1028 | B |
| ParallelReductionFactorInPlane | DICOM tag 0065,100D | B |