From a985fa60512df8b40f64135166e1d37e0efbe7be Mon Sep 17 00:00:00 2001 From: Chris Markiewicz Date: Fri, 15 Nov 2024 10:58:27 -0500 Subject: [PATCH 1/2] chore(links): Fix http -> https 301 redirects --- src/schema/objects/metadata.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/schema/objects/metadata.yaml b/src/schema/objects/metadata.yaml index f97f629589..fc359fd351 100644 --- a/src/schema/objects/metadata.yaml +++ b/src/schema/objects/metadata.yaml @@ -2899,10 +2899,10 @@ RepetitionTime: 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](http://dicomlookup.com/dicomtags/(0020,0110)): + [DICOM Tag 0020, 0110](https://dicomlookup.com/dicomtags/(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](http://dicomlookup.com/dicomtags/(0018,0080)): + [DICOM Tag 0018, 0080](https://dicomlookup.com/dicomtags/(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". @@ -2919,7 +2919,7 @@ RepetitionTimeExcitation: display_name: Repetition Time Excitation description: | The interval, in seconds, between two successive excitations. - [DICOM Tag 0018, 0080](http://dicomlookup.com/dicomtags/(0018,0080)) + [DICOM Tag 0018, 0080](https://dicomlookup.com/dicomtags/(0018,0080)) best refers to this parameter. This field may be used together with the `"RepetitionTimePreparation"` for certain use cases, such as From 9ec45792c1180bdfe60afdcd39d3e05fb3213a4b Mon Sep 17 00:00:00 2001 From: Chris Markiewicz Date: Fri, 15 Nov 2024 11:12:12 -0500 Subject: [PATCH 2/2] enh: Link all DICOM tags following standard pattern --- .../magnetic-resonance-imaging-data.md | 4 +- src/schema/objects/metadata.yaml | 95 ++++++++++--------- src/schema/rules/checks/asl.yaml | 4 +- src/schema/rules/sidecars/mri.yaml | 40 +++++--- src/schema/rules/sidecars/mrs.yaml | 3 +- src/schema/rules/sidecars/pet.yaml | 78 ++++++++++----- 6 files changed, 138 insertions(+), 86 deletions(-) diff --git a/src/modality-specific-files/magnetic-resonance-imaging-data.md b/src/modality-specific-files/magnetic-resonance-imaging-data.md index 2b2078fe04..692fb00a0f 100644 --- a/src/modality-specific-files/magnetic-resonance-imaging-data.md +++ b/src/modality-specific-files/magnetic-resonance-imaging-data.md @@ -78,7 +78,7 @@ A guide for using macros can be found at 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 +"BandwidthPerPixelPhaseEncode" in [DICOM Tag 0019, 1028](https://dicomlookup.com/dicomtags/(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 @@ -944,7 +944,7 @@ accompanied by two ancillary files: `*_asl.json` and `*_aslcontext.tsv`. The `*_aslcontext.tsv` table consists of a single column of labels identifying the `volume_type` of each volume in the corresponding `*_asl.nii[.gz]` file. -Volume types are defined in the following table, based on DICOM Tag 0018, 9257 `ASL Context`. +Volume types are defined in the following table, based on [DICOM Tag 0018, 9257](https://dicomlookup.com/dicomtags/(0018,9257)) `ASL Context`. Note that the volume_types `control` and `label` within BIDS only serve to specify the magnetization state of the blood and thus the ASL subtraction order. See the [ASL Appendix](../appendices/arterial-spin-labeling.md#which-image-is-control-and-which-is-label) diff --git a/src/schema/objects/metadata.yaml b/src/schema/objects/metadata.yaml index fc359fd351..5ed86c5dc6 100644 --- a/src/schema/objects/metadata.yaml +++ b/src/schema/objects/metadata.yaml @@ -21,7 +21,7 @@ AcquisitionDuration: display_name: Acquisition Duration description: | Duration (in seconds) of volume acquisition. - Corresponds to DICOM Tag 0018, 9073 `Acquisition Duration`. + Corresponds to [DICOM Tag 0018, 9073](https://dicomlookup.com/dicomtags/(0018,9073)) `Acquisition Duration`. This field is mutually exclusive with `"RepetitionTime"`. type: number exclusiveMinimum: 0 @@ -349,7 +349,7 @@ BolusCutOffDelayTime: cut-off saturation pulses. For Q2TIPS, only the values for the first and last bolus cut-off saturation pulses are provided. - Based on DICOM Tag 0018, 925F `ASL Bolus Cut-off Delay Time`. + Based on [DICOM Tag 0018, 925F](https://dicomlookup.com/dicomtags/(0018,925F)) `ASL Bolus Cut-off Delay Time`. anyOf: - type: number minimum: 0 @@ -364,14 +364,14 @@ BolusCutOffFlag: display_name: Bolus Cut Off Flag description: | Boolean indicating if a bolus cut-off technique is used. - Corresponds to DICOM Tag 0018, 925C `ASL Bolus Cut-off Flag`. + Corresponds to [DICOM Tag 0018, 925C](https://dicomlookup.com/dicomtags/(0018,925C)) `ASL Bolus Cut-off Flag`. type: boolean BolusCutOffTechnique: name: BolusCutOffTechnique display_name: Bolus Cut Off Technique description: | Name of the technique used, for example `"Q2TIPS"`, `"QUIPSS"`, `"QUIPSSII"`. - Corresponds to DICOM Tag 0018, 925E `ASL Bolus Cut-off Technique`. + Corresponds to [DICOM Tag 0018, 925E](https://dicomlookup.com/dicomtags/(0018,925E)) `ASL Bolus Cut-off Technique`. type: string BrainLocation: name: BrainLocation @@ -429,7 +429,7 @@ ChemicalShiftReference: display_name: Chemical Shift Reference description: | The chemical shift at the transmitter frequency, specified in ppm (for example, `2.68`). - Corresponds to DICOM Tag 0018, 9053 `Chemical Shift Reference`. + Corresponds to [DICOM Tag 0018, 9053](https://dicomlookup.com/dicomtags/(0018,9053)) `Chemical Shift Reference`. type: number unit: ppm ChunkTransformationMatrix: @@ -531,7 +531,7 @@ ContrastBolusIngredient: display_name: Contrast Bolus Ingredient description: | Active ingredient of agent. - Corresponds to DICOM Tag 0018, 1048 `Contrast/Bolus Ingredient`. + Corresponds to [DICOM Tag 0018, 1048](https://dicomlookup.com/dicomtags/(0018,1048)) `Contrast/Bolus Ingredient`. type: string enum: - $ref: objects.enums.IODINE.value @@ -596,7 +596,7 @@ DeidentificationMethod: display_name: Deidentification Method description: | A description of the mechanism or method used to remove the Patient's identity. - Corresponds to DICOM Tag 0012, 0063 `De-identification Method`. + Corresponds to [DICOM Tag 0012, 0063](https://dicomlookup.com/dicomtags/(0012,0063)) `De-identification Method`. type: array items: type: string @@ -605,7 +605,8 @@ DeidentificationMethodCodeSequence: display_name: Deidentification Method Code Sequence description: | A sequence of code objects describing the mechanism or method use to remove the Patient's identity. - Corresponds to DICOM Tag 0012, 0064 `De-identification Method Code Sequence`. + Corresponds to [DICOM Tag 0012, 0064](https://dicomlookup.com/dicomtags/(0012,0064)) + `De-identification Method Code Sequence`. type: array items: type: object @@ -621,25 +622,26 @@ DeidentificationMethodCodeSequence: description: | An identifier that is unambiguous within the Coding Scheme denoted by Coding Scheme Designator and Coding Scheme Version. - Corresponds to DICOM Tag 0008, 0100 `Code Value`. + Corresponds to [DICOM Tag 0008, 0100](https://dicomlookup.com/dicomtags/(0008,0100)) `Code Value`. CodeMeaning: name: CodeMeaning type: string description: | Text that has meaning to a human and conveys the meaning of the term - Corresponds to DICOM Tag 0008, 0104 `Code Meaning`. + Corresponds to [DICOM Tag 0008, 0104](https://dicomlookup.com/dicomtags/(0008,0104)) `Code Meaning`. CodingSchemeDesignator: name: CodingSchemeDesignator type: string description: | The identifier of the coding scheme in which the coded entry is defined. - Corresponds to DICOM Tag 0008, 0102 `Coding Scheme Designator`. + Corresponds to [DICOM Tag 0008, 0102](https://dicomlookup.com/dicomtags/(0008,0102)) + `Coding Scheme Designator`. CodingSchemeVersion: name: CodingSchemeVersion type: string description: | An identifier of the version of the coding scheme if necessary to resolve ambiguity. - Corresponds to DICOM Tag 0008, 0103 `Coding Scheme Version`. + Corresponds to [DICOM Tag 0008, 0103](https://dicomlookup.com/dicomtags/(0008,0103)) `Coding Scheme Version`. DelayAfterTrigger: name: DelayAfterTrigger display_name: Delay After Trigger @@ -808,7 +810,7 @@ DoseCalibrationFactor: display_name: Dose Calibration Factor description: | Multiplication factor used to transform raw data (in counts/sec) to meaningful unit (Bq/ml). - Corresponds to DICOM Tag 0054, 1322 `Dose Calibration Factor`. + Corresponds to [DICOM Tag 0054, 1322](https://dicomlookup.com/dicomtags/(0054,1322)) `Dose Calibration Factor`. type: number DwellTime: name: DwellTime @@ -935,7 +937,7 @@ EchoTime: display_name: Echo Time description: | The echo time (TE) for the acquisition, specified in seconds. - Corresponds to DICOM Tag 0018, 0081 `Echo Time` + Corresponds to [DICOM Tag 0018, 0081](https://dicomlookup.com/dicomtags/(0018,0081)) `Echo Time` (please note that the DICOM term is in milliseconds not seconds). The data type number may apply to files from any MRI modality concerned with a single value for this field, or to the files in a @@ -1181,7 +1183,7 @@ FlipAngle: display_name: Flip Angle description: | Flip angle (FA) for the acquisition, specified in degrees. - Corresponds to: DICOM Tag 0018, 1314 `Flip Angle`. + Corresponds to: [DICOM Tag 0018, 1314](https://dicomlookup.com/dicomtags/(0018,1314)) `Flip Angle`. The data type number may apply to files from any MRI modality concerned with a single value for this field, or to the files in a [file collection](SPEC_ROOT/appendices/file-collections.md) @@ -1203,8 +1205,8 @@ FrameDuration: display_name: Frame Duration description: | Time duration of each frame in default unit seconds. - This corresponds to DICOM Tag 0018, 1242 `Actual Frame Duration` converted - to seconds. + This corresponds to [DICOM Tag 0018, 1242](https://dicomlookup.com/dicomtags/(0018,1242)) + `Actual Frame Duration` converted to seconds. type: array items: type: number @@ -1383,7 +1385,8 @@ HardcopyDeviceSoftwareVersion: description: | Manufacturer's designation of the software of the device that created this Hardcopy Image (the printer). - Corresponds to DICOM Tag 0018, 101A `Hardcopy Device Software Version`. + Corresponds to [DICOM Tag 0018, 101A](https://dicomlookup.com/dicomtags/(0018,101A)) + `Hardcopy Device Software Version`. type: string HardwareFilters: name: HardwareFilters @@ -1605,7 +1608,7 @@ InjectedRadioactivity: Total amount of radioactivity injected into the patient (for example, `400`). For bolus-infusion experiments, this value should be the sum of all injected radioactivity originating from both bolus and infusion. - Corresponds to DICOM Tag 0018, 1074 `Radionuclide Total Dose`. + Corresponds to [DICOM Tag 0018, 1074](https://dicomlookup.com/dicomtags/(0018,1074)) `Radionuclide Total Dose`. type: number InjectedRadioactivityUnits: name: InjectedRadioactivityUnits @@ -1635,8 +1638,8 @@ InjectionStart: description: | Time of start of injection with respect to `"TimeZero"` in the default unit seconds. - This corresponds to DICOM Tag 0018, 1072 `Contrast/Bolus Start Time` - converted to seconds relative to `"TimeZero"`. + This corresponds to [DICOM Tag 0018, 1072](https://dicomlookup.com/dicomtags/(0018,1072)) + `Contrast/Bolus Start Time` converted to seconds relative to `"TimeZero"`. type: number unit: s InstitutionAddress: @@ -1713,7 +1716,7 @@ InversionTime: 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` + Corresponds to [DICOM Tag 0018, 0082](https://dicomlookup.com/dicomtags/(0018,0082)) `Inversion Time` (please note that the DICOM term is in milliseconds not seconds). type: number unit: s @@ -1752,7 +1755,7 @@ LabelingDuration: In case an array of numbers is provided, its length should be equal to the number of volumes specified in `*_aslcontext.tsv`. - Corresponds to DICOM Tag 0018, 9258 `ASL Pulse Train Duration`. + Corresponds to [DICOM Tag 0018, 9258](https://dicomlookup.com/dicomtags/(0018,9258)) `ASL Pulse Train Duration`. anyOf: - type: number minimum: 0 @@ -1789,7 +1792,7 @@ LabelingOrientation: Orientation of the labeling plane (`(P)CASL`) or slab (`PASL`). The direction cosines of a normal vector perpendicular to the ASL labeling slab or plane with respect to the patient. - Corresponds to DICOM Tag 0018, 9255 `ASL Slab Orientation`. + Corresponds to [DICOM Tag 0018, 9255](https://dicomlookup.com/dicomtags/(0018,9255)) `ASL Slab Orientation`. type: array items: type: number @@ -1851,7 +1854,7 @@ LabelingSlabThickness: description: | Thickness of the labeling slab in millimeters. For non-selective FAIR a zero is entered. - Corresponds to DICOM Tag 0018, 9254 `ASL Slab Thickness`. + Corresponds to [DICOM Tag 0018, 9254](https://dicomlookup.com/dicomtags/(0018,9254)) `ASL Slab Thickness`. type: number exclusiveMinimum: 0 unit: mm @@ -2003,7 +2006,7 @@ MRAcquisitionType: display_name: MR Acquisition Type description: | Type of sequence readout. - Corresponds to DICOM Tag 0018, 0023 `MR Acquisition Type`. + Corresponds to [DICOM Tag 0018, 0023](https://dicomlookup.com/dicomtags/(0018,0023)) `MR Acquisition Type`. type: string enum: - $ref: objects.enums.OneD.value @@ -2014,7 +2017,7 @@ MRTransmitCoilSequence: display_name: MR Transmit Coil Sequence description: | This is a relevant field if a non-standard transmit coil is used. - Corresponds to DICOM Tag 0018, 9049 `MR Transmit Coil Sequence`. + Corresponds to [DICOM Tag 0018, 9049](https://dicomlookup.com/dicomtags/(0018,9049)) `MR Transmit Coil Sequence`. type: string MTNumberOfPulses: name: MTNumberOfPulses @@ -2066,14 +2069,14 @@ MTState: display_name: MT State description: | Boolean stating whether the magnetization transfer pulse is applied. - Corresponds to DICOM Tag 0018, 9020 `Magnetization Transfer`. + Corresponds to [DICOM Tag 0018, 9020](https://dicomlookup.com/dicomtags/(0018,9020)) `Magnetization Transfer`. type: boolean MagneticFieldStrength: name: MagneticFieldStrength display_name: Magnetic Field Strength description: | Nominal field strength of MR magnet in Tesla. - Corresponds to DICOM Tag 0018, 0087 `Magnetic Field Strength`. + Corresponds to [DICOM Tag 0018, 0087](https://dicomlookup.com/dicomtags/(0018,0087)) `Magnetic Field Strength`. type: number Magnification: name: Magnification @@ -2209,7 +2212,8 @@ MolarActivity: display_name: Molar Activity description: | Molar activity of compound injected. - Corresponds to DICOM Tag 0018, 1077 `Radiopharmaceutical Specific Activity`. + Corresponds to [DICOM Tag 0018, 1077](https://dicomlookup.com/dicomtags/(0018,1077)) + `Radiopharmaceutical Specific Activity`. type: number MolarActivityMeasTime: name: MolarActivityMeasTime @@ -2473,7 +2477,8 @@ ParallelAcquisitionTechnique: display_name: Parallel Acquisition Technique description: | The type of parallel imaging used (for example `"GRAPPA"`, `"SENSE"`). - Corresponds to DICOM Tag 0018, 9078 `Parallel Acquisition Technique`. + Corresponds to [DICOM Tag 0018, 9078](https://dicomlookup.com/dicomtags/(0018,9078)) + `Parallel Acquisition Technique`. type: string ParallelReductionFactorInPlane: name: ParallelReductionFactorInPlane @@ -2482,7 +2487,8 @@ ParallelReductionFactorInPlane: The parallel imaging (for instance, GRAPPA) factor in plane. 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`. + Corresponds to [DICOM Tag 0018, 9069](https://dicomlookup.com/dicomtags/(0018,9069)) + `Parallel Reduction Factor In-plane`. type: number ParallelReductionFactorOutOfPlane: name: ParallelReductionFactorOutOfPlane @@ -2494,21 +2500,22 @@ ParallelReductionFactorOutOfPlane: Will typically be 1 for 2D sequences, as each slice in a 2D acquisition is usually fully encoded. `ParallelReductionFactorOutOfPlane` should not be confused with `MultibandAccelerationFactor`, as they imply different methods of accelerating the acquisition. - Corresponds to DICOM Tag 0018, 9155 `Parallel Reduction Factor out-of-plane`. + Corresponds to [DICOM Tag 0018, 9155](https://dicomlookup.com/dicomtags/(0018,9155)) + `Parallel Reduction Factor out-of-plane`. type: number PartialFourier: name: PartialFourier display_name: Partial Fourier description: | The fraction of partial Fourier information collected. - Corresponds to DICOM Tag 0018, 9081 `Partial Fourier`. + Corresponds to [DICOM Tag 0018, 9081](https://dicomlookup.com/dicomtags/(0018,9081)) `Partial Fourier`. type: number PartialFourierDirection: name: PartialFourierDirection display_name: Partial Fourier Direction description: | The direction where only partial Fourier information was collected. - Corresponds to DICOM Tag 0018, 9036 `Partial Fourier Direction`. + Corresponds to [DICOM Tag 0018, 9036](https://dicomlookup.com/dicomtags/(0018,9036)) `Partial Fourier Direction`. type: string PharmaceuticalDoseAmount: name: PharmaceuticalDoseAmount @@ -2772,7 +2779,7 @@ ReceiveCoilName: display_name: Receive Coil Name description: | Information describing the receiver coil. - Corresponds to DICOM Tag 0018, 1250 `Receive Coil Name`, + Corresponds to [DICOM Tag 0018, 1250](https://dicomlookup.com/dicomtags/(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. @@ -2976,7 +2983,7 @@ ResonantNucleus: The isotope of interest of an MR experiment (for example, `"1H"`, `"13C"`, `"31P"`). For multi-nuclei experiments such as 1H-[13C] MR, an array can be used: `["1H", "13C"]`. - Corresponds to DICOM Tag 0018, 9100 `Resonant Nucleus`. + Corresponds to [DICOM Tag 0018, 9100](https://dicomlookup.com/dicomtags/(0018,9100)) `Resonant Nucleus`. type: array items: type: string @@ -3165,7 +3172,7 @@ ScanOptions: display_name: Scan Options description: | Parameters of ScanningSequence. - Corresponds to DICOM Tag 0018, 0022 `Scan Options`. + Corresponds to [DICOM Tag 0018, 0022](https://dicomlookup.com/dicomtags/(0018,0022)) `Scan Options`. anyOf: - type: string - type: array @@ -3183,7 +3190,7 @@ ScanningSequence: display_name: Scanning Sequence description: | Description of the type of data acquired. - Corresponds to DICOM Tag 0018, 0020 `Scanning Sequence`. + Corresponds to [DICOM Tag 0018, 0020](https://dicomlookup.com/dicomtags/(0018,0020)) `Scanning Sequence`. anyOf: - type: string - type: array @@ -3265,14 +3272,14 @@ SequenceName: display_name: Sequence Name description: | Manufacturer's designation of the sequence name. - Corresponds to DICOM Tag 0018, 0024 `Sequence Name`. + Corresponds to [DICOM Tag 0018, 0024](https://dicomlookup.com/dicomtags/(0018,0024)) `Sequence Name`. type: string SequenceVariant: name: SequenceVariant display_name: Sequence Variant description: | Variant of the ScanningSequence. - Corresponds to DICOM Tag 0018, 0021 `Sequence Variant`. + Corresponds to [DICOM Tag 0018, 0021](https://dicomlookup.com/dicomtags/(0018,0021)) `Sequence Variant`. anyOf: - type: string - type: array @@ -3525,7 +3532,7 @@ SpectralWidth: display_name: Spectral Width description: | The spectral bandwidth of the MR signal that is sampled, specified in Hz. - Corresponds to DICOM Tag 0018, 9052 `Spectral Width`. + Corresponds to [DICOM Tag 0018, 9052](https://dicomlookup.com/dicomtags/(0018,9052)) `Spectral Width`. type: number unit: Hz SpectrometerFrequency: @@ -3842,7 +3849,7 @@ VascularCrushing: display_name: Vascular Crushing description: | Boolean indicating if Vascular Crushing is used. - Corresponds to DICOM Tag 0018, 9259 `ASL Crusher Flag`. + Corresponds to [DICOM Tag 0018, 9259](https://dicomlookup.com/dicomtags/(0018,9259)) `ASL Crusher Flag`. type: boolean VascularCrushingVENC: name: VascularCrushingVENC @@ -3852,7 +3859,7 @@ VascularCrushingVENC: Specify either one number for the total time-series, or provide an array of numbers, for example when using QUASAR, using the value zero to identify volumes for which `VascularCrushing` was turned off. - Corresponds to DICOM Tag 0018, 925A `ASL Crusher Flow Limit`. + Corresponds to [DICOM Tag 0018, 925A](https://dicomlookup.com/dicomtags/(0018,925A)) `ASL Crusher Flow Limit`. anyOf: - type: number unit: cm/s diff --git a/src/schema/rules/checks/asl.yaml b/src/schema/rules/checks/asl.yaml index 2ae11ebeb0..393935d9b9 100644 --- a/src/schema/rules/checks/asl.yaml +++ b/src/schema/rules/checks/asl.yaml @@ -47,7 +47,7 @@ ASLFlipAngleNiftiLength: message: | The number of values for 'FlipAngle' for this file does not match the 4th dimension of the NIfTI header. 'FlipAngle' is the flip angle (FA) for the acquisition, specified in degrees. - Corresponds to: DICOM Tag 0018, 1314 `Flip Angle`. + Corresponds to: [DICOM Tag 0018, 1314](https://dicomlookup.com/dicomtags/(0018,1314)) `Flip Angle`. The data type number may apply to files from any MRI modality concerned with a single value for this field, or to the files in a file collection where the value of this field is iterated using the flip entity. The data type array provides a value for each volume in a 4D dataset and should only be used when the @@ -70,7 +70,7 @@ ASLFlipAngleASLContextLength: The number of values for 'FlipAngle' for this file does not match the number of volumes in the associated 'aslcontext.tsv'. 'FlipAngle' is the flip angle (FA) for the acquisition, specified in degrees. - Corresponds to: DICOM Tag 0018, 1314 `Flip Angle`. + Corresponds to: [DICOM Tag 0018, 1314](https://dicomlookup.com/dicomtags/(0018,1314)) `Flip Angle`. The data type number may apply to files from any MRI modality concerned with a single value for this field, or to the files in a file collection where the value of this field is iterated using the flip entity. The data type array provides a value for each volume in a 4D dataset and should only be used when the volume diff --git a/src/schema/rules/sidecars/mri.yaml b/src/schema/rules/sidecars/mri.yaml index ba1d43fda2..577f819c88 100644 --- a/src/schema/rules/sidecars/mri.yaml +++ b/src/schema/rules/sidecars/mri.yaml @@ -13,19 +13,24 @@ MRIHardware: fields: Manufacturer: level: recommended - description_addendum: Corresponds to DICOM Tag 0008, 0070 `Manufacturer`. + description_addendum: | + Corresponds to [DICOM Tag 0008, 0070](https://dicomlookup.com/dicomtags/(0008,0070)) `Manufacturer`. ManufacturersModelName: level: recommended - description_addendum: Corresponds to DICOM Tag 0008, 1090 `Manufacturers Model Name`. + description_addendum: | + Corresponds to [DICOM Tag 0008, 1090](https://dicomlookup.com/dicomtags/(0008,1090)) `Manufacturers Model Name`. DeviceSerialNumber: level: recommended - description_addendum: Corresponds to DICOM Tag 0018, 1000 `DeviceSerialNumber`. + description_addendum: | + Corresponds to [DICOM Tag 0018, 1000](https://dicomlookup.com/dicomtags/(0018,1000)) `DeviceSerialNumber`. StationName: level: recommended - description_addendum: Corresponds to DICOM Tag 0008, 1010 `Station Name`. + description_addendum: | + Corresponds to [DICOM Tag 0008, 1010](https://dicomlookup.com/dicomtags/(0008,1010)) `Station Name`. SoftwareVersions: level: recommended - description_addendum: Corresponds to DICOM Tag 0018, 1020 `Software Versions`. + description_addendum: | + Corresponds to [DICOM Tag 0018, 1020](https://dicomlookup.com/dicomtags/(0018,1020)) `Software Versions`. HardcopyDeviceSoftwareVersion: deprecated MagneticFieldStrength: level: recommended @@ -62,7 +67,8 @@ MRISample: fields: BodyPart: level: optional - description_addendum: Corresponds to DICOM Tag 0018, 0015 `Body Part Examined`. + description_addendum: | + Corresponds to [DICOM Tag 0018, 0015](https://dicomlookup.com/dicomtags/(0018,0015)) `Body Part Examined`. BodyPartDetails: optional BodyPartDetailsOntology: optional @@ -87,7 +93,8 @@ MRISequenceSpecifics: echo EPI"`. ScanningSequence: level: recommended - description_addendum: Corresponds to DICOM Tag 0018, 0020 `Scanning Sequence`. + description_addendum: | + Corresponds to [DICOM Tag 0018, 0020](https://dicomlookup.com/dicomtags/(0018,0020)) `Scanning Sequence`. SequenceVariant: recommended ScanOptions: recommended SequenceName: recommended @@ -325,7 +332,7 @@ MRIFlipAngleLookLockerTrue: You should define 'FlipAngle' for this file, in case of a LookLocker acquisition. 'FlipAngle' is the flip angle (FA) for the acquisition, specified in degrees. - Corresponds to: DICOM Tag 0018, 1314 `Flip Angle`. The data + Corresponds to: [DICOM Tag 0018, 1314](https://dicomlookup.com/dicomtags/(0018,1314)) `Flip Angle`. The data type number may apply to files from any MRI modality concerned with a single value for this field, or to the files in a file collection where the value of this field is iterated using the @@ -371,13 +378,17 @@ MRIInstitutionInformation: fields: InstitutionName: level: recommended - description_addendum: Corresponds to DICOM Tag 0008, 0080 `InstitutionName`. + description_addendum: | + Corresponds to [DICOM Tag 0008, 0080](https://dicomlookup.com/dicomtags/(0008,0080)) `InstitutionName`. InstitutionAddress: level: recommended - description_addendum: Corresponds to DICOM Tag 0008, 0081 `InstitutionAddress`. + description_addendum: | + Corresponds to [DICOM Tag 0008, 0081](https://dicomlookup.com/dicomtags/(0008,0081)) `InstitutionAddress`. InstitutionalDepartmentName: level: recommended - description_addendum: Corresponds to DICOM Tag 0008, 1040 `Institutional Department Name`. + description_addendum: | + Corresponds to [DICOM Tag 0008, 1040](https://dicomlookup.com/dicomtags/(0008,1040)) + `Institutional Department Name`. DeidentificationMethod: selectors: @@ -386,7 +397,10 @@ DeidentificationMethod: fields: DeidentificationMethod: level: optional - description_addendum: Corresponds to DICOM Tag 0012, 0063 `De-identification Method`. + description_addendum: | + Corresponds to [DICOM Tag 0012, 0063](https://dicomlookup.com/dicomtags/(0012,0063)) `De-identification Method`. DeidentificationMethodCodeSequence: level: optional - description_addendum: Corresponds to DICOM Tag 0012, 0064 `De-identification Method Code Sequence`. + description_addendum: | + Corresponds to [DICOM Tag 0012, 0064](https://dicomlookup.com/dicomtags/(0012,0064)) + `De-identification Method Code Sequence`. diff --git a/src/schema/rules/sidecars/mrs.yaml b/src/schema/rules/sidecars/mrs.yaml index 67d8d5e13b..5c38f0fdea 100644 --- a/src/schema/rules/sidecars/mrs.yaml +++ b/src/schema/rules/sidecars/mrs.yaml @@ -39,7 +39,8 @@ MRSSample: BodyPart: level: optional level_addendum: required if `voi` entity is present - description_addendum: Corresponds to DICOM Tag 0018, 0015 `Body Part Examined`. + description_addendum: | + Corresponds to [DICOM Tag 0018, 0015](https://dicomlookup.com/dicomtags/(0018,0015)) `Body Part Examined`. BodyPartDetails: level: optional level_addendum: required if `voi` entity is present diff --git a/src/schema/rules/sidecars/pet.yaml b/src/schema/rules/sidecars/pet.yaml index 2b2264a59b..1cdc2a2489 100644 --- a/src/schema/rules/sidecars/pet.yaml +++ b/src/schema/rules/sidecars/pet.yaml @@ -7,18 +7,21 @@ PETHardware: fields: Manufacturer: level: required - description_addendum: Corresponds to DICOM Tag 0008, 0070 `Manufacturer`. + description_addendum: | + Corresponds to [DICOM Tag 0008, 0070](https://dicomlookup.com/dicomtags/(0008,0070)) `Manufacturer`. ManufacturersModelName: level: required - description_addendum: Corresponds to DICOM Tag 0008, 1090 `Manufacturers Model Name`. + description_addendum: | + Corresponds to [DICOM Tag 0008, 1090](https://dicomlookup.com/dicomtags/(0008,1090)) `Manufacturers Model Name`. Units: level: required description_addendum: | SI unit for radioactivity (Becquerel) should be used (for example, "Bq/mL"). - Corresponds to DICOM Tag 0054, 1001 `Units`. + Corresponds to [DICOM Tag 0054, 1001](https://dicomlookup.com/dicomtags/(0054,1001)) `Units`. BodyPart: level: recommended - description_addendum: Corresponds to DICOM Tag 0018, 0015 `Body Part Examined`. + description_addendum: | + Corresponds to [DICOM Tag 0018, 0015](https://dicomlookup.com/dicomtags/(0018,0015)) `Body Part Examined`. PETInstitutionInformation: selectors: @@ -27,13 +30,17 @@ PETInstitutionInformation: fields: InstitutionName: level: recommended - description_addendum: Corresponds to DICOM Tag 0008, 0080 `InstitutionName`. + description_addendum: | + Corresponds to [DICOM Tag 0008, 0080](https://dicomlookup.com/dicomtags/(0008,0080)) `InstitutionName`. InstitutionAddress: level: recommended - description_addendum: Corresponds to DICOM Tag 0008, 0081 `InstitutionAddress`. + description_addendum: | + Corresponds to [DICOM Tag 0008, 0081](https://dicomlookup.com/dicomtags/(0008,0081)) `InstitutionAddress`. InstitutionalDepartmentName: level: recommended - description_addendum: Corresponds to DICOM Tag 0008, 1040 `Institutional Department Name`. + description_addendum: | + Corresponds to [DICOM Tag 0008, 1040](https://dicomlookup.com/dicomtags/(0008,1040)) + `Institutional Department Name`. PETSample: selectors: @@ -42,7 +49,8 @@ PETSample: fields: BodyPart: level: optional - description_addendum: Corresponds to DICOM Tag 0018, 0015 `Body Part Examined`. + description_addendum: | + Corresponds to [DICOM Tag 0018, 0015](https://dicomlookup.com/dicomtags/(0018,0015)) `Body Part Examined`. BodyPartDetails: optional BodyPartDetailsOntology: optional @@ -114,10 +122,12 @@ PETPharmaceuticals: fields: PharmaceuticalName: level: recommended - description_addendum: Corresponds to DICOM Tag 0008, 0034 `Intervention Drug Name`. + description_addendum: | + Corresponds to [DICOM Tag 0008, 0034](https://dicomlookup.com/dicomtags/(0008,0034)) `Intervention Drug Name`. PharmaceuticalDoseAmount: level: recommended - description_addendum: Corresponds to DICOM Tag 0008, 0028 `Intervention Drug Dose`. + description_addendum: | + Corresponds to [DICOM Tag 0008, 0028](https://dicomlookup.com/dicomtags/(0008,0028)) `Intervention Drug Dose`. PharmaceuticalDoseUnits: recommended PharmaceuticalDoseRegimen: recommended PharmaceuticalDoseTime: @@ -136,17 +146,20 @@ PETTime: ScanStart: required InjectionStart: level: required - description_addendum: Corresponds to DICOM Tag 0018, 1072 `Radiopharmaceutical Start Time`. + description_addendum: | + Corresponds to [DICOM Tag 0018, 1072](https://dicomlookup.com/dicomtags/(0018,1072)) + `Radiopharmaceutical Start Time`. FrameTimesStart: required FrameDuration: required InjectionEnd: level: recommended description_addendum: | - Corresponds to DICOM Tag 0018, 1073 `Radiopharmaceutical Stop Time` - converted to seconds relative to TimeZero. + Corresponds to [DICOM Tag 0018, 1073](https://dicomlookup.com/dicomtags/(0018,1073)) + `Radiopharmaceutical Stop Time` converted to seconds relative to TimeZero. ScanDate: level: deprecated - description_addendum: Corresponds to DICOM Tag 0008, 0022 `Acquisition Date`. + description_addendum: | + Corresponds to [DICOM Tag 0008, 0022](https://dicomlookup.com/dicomtags/(0008,0022)) `Acquisition Date`. PETReconstruction: selectors: @@ -158,40 +171,57 @@ PETReconstruction: ImageDecayCorrectionTime: required ReconMethodName: level: required - description_addendum: This partly matches the DICOM Tag 0054, 1103 `Reconstruction Method`. + description_addendum: | + This partly matches the [DICOM Tag 0054, 1103](https://dicomlookup.com/dicomtags/(0054,1103)) + `Reconstruction Method`. ReconMethodParameterLabels: level: required - description_addendum: This partly matches the DICOM Tag 0054, 1103 `Reconstruction Method`. + description_addendum: | + This partly matches the [DICOM Tag 0054, 1103](https://dicomlookup.com/dicomtags/(0054,1103)) + `Reconstruction Method`. ReconMethodParameterUnits: level: recommended level_addendum: required if `ReconMethodParameterLabels` does not contain `"none"` - description_addendum: This partly matches the DICOM Tag 0054, 1103 `Reconstruction Method`. + description_addendum: | + This partly matches the [DICOM Tag 0054, 1103](https://dicomlookup.com/dicomtags/(0054,1103)) + `Reconstruction Method`. ReconMethodParameterValues: level: recommended level_addendum: required if `ReconMethodParameterLabels` does not contain `"none"` - description_addendum: This partly matches the DICOM Tag 0054, 1103 `Reconstruction Method`. + description_addendum: | + This partly matches the [DICOM Tag 0054, 1103](https://dicomlookup.com/dicomtags/(0054,1103)) + `Reconstruction Method`. ReconFilterType: level: required - description_addendum: This partly matches the DICOM Tag 0018, 1210 `Convolution Kernel`. + description_addendum: | + This partly matches the [DICOM Tag 0018, 1210](https://dicomlookup.com/dicomtags/(0018,1210)) + `Convolution Kernel`. ReconFilterSize: level: recommended level_addendum: required if `ReconFilterType` is not `"none"` - description_addendum: This partly matches the DICOM Tag 0018, 1210 `Convolution Kernel`. + description_addendum: | + This partly matches the [DICOM Tag 0018, 1210](https://dicomlookup.com/dicomtags/(0018,1210)) + `Convolution Kernel`. AttenuationCorrection: level: required - description_addendum: This corresponds to DICOM Tag 0054, 1101 `Attenuation Correction Method`. + description_addendum: | + This corresponds to [DICOM Tag 0054, 1101](https://dicomlookup.com/dicomtags/(0054,1101)) + `Attenuation Correction Method`. ReconMethodImplementationVersion: recommended AttenuationCorrectionMethodReference: recommended ScaleFactor: recommended ScatterFraction: level: recommended - description_addendum: Corresponds to DICOM Tag 0054, 1323 `Scatter Fraction Factor`. + description_addendum: | + Corresponds to [DICOM Tag 0054, 1323](https://dicomlookup.com/dicomtags/(0054,1323)) `Scatter Fraction Factor`. DecayCorrectionFactor: level: recommended - description_addendum: Corresponds to DICOM Tag 0054, 1321 `Decay Factor`. + description_addendum: | + Corresponds to [DICOM Tag 0054, 1321](https://dicomlookup.com/dicomtags/(0054,1321)) `Decay Factor`. DoseCalibrationFactor: level: recommended - description_addendum: Corresponds to DICOM Tag 0054, 1322 `Dose Calibration Factor`. + description_addendum: | + Corresponds to [DICOM Tag 0054, 1322](https://dicomlookup.com/dicomtags/(0054,1322)) `Dose Calibration Factor`. PromptRate: recommended SinglesRate: recommended RandomRate: recommended