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Merge pull request #452 from Lestropie/dwi_scanner_derivatives
New dataset "dwi_deriv" for scanner-generated DWI derivatives
2 parents 1d7cf31 + 883bbe4 commit 7de1e8c

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‎.github/workflows/validate_datasets.yml

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shell: bash
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- name: Skip MRS validation for legacy validator
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run: for DS in mrs_*; do touch $DS/.SKIP_VALIDATION; done
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run: for DS in mrs_* dwi_deriv; do touch $DS/.SKIP_VALIDATION; done
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if: "matrix.bids-validator != 'master-deno'"
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shell: bash
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env:
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# When proposing new features, schema changes may be necessary.
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# Update this URL to the schema.json from PRs to the spec, when needed.
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BIDS_SCHEMA: https://bids-specification.readthedocs.io/en/latest/schema.json
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BIDS_SCHEMA: https://bids-specification--1864.org.readthedocs.build/en/1864/schema.json

‎dwi_deriv/README.md

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# Scanner-generated Diffusion MRI derivatives
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This single-subject dataset exemplifies the storage of diffusion MRI derivates
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that may be generated on the Siemens XA platform.
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Author: Robert E. Smith <[email protected]>.
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This dataset is made available under the Public Domain Dedication and License v1.0,
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whose full text can be found at http://www.opendatacommons.org/licenses/pddl/1.0/.
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The author acknowledges the facilities and scientific and technical assistance of the National Imaging Facility,
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a National Collaborative Research Infrastructure Strategy (NCRIS) capability,
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at the Melbourne Brain Centre (Austin), Florey Institute, Heidelberg, Victoria, Australia.

‎dwi_deriv/dataset_description.json

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{
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"Name": "Scanner-denerated Diffusion MRI derivatives",
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"DatasetType": "raw",
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"BIDSVersion": "1.10.0",
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"License": "This dataset is made available under the Public Domain Dedication and License v1.0, whose full text can be found at http://www.opendatacommons.org/licenses/pddl/1.0/.",
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"Authors": ["Robert E. Smith"],
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"Acknowledgements": "The author acknowledges the facilities and scientific and technical assistance of the National Imaging Facility, a National Collaborative Research Infrastructure Strategy (NCRIS) capability, at the Melbourne Brain Centre (Austin), Florey Institute, Heidelberg, Victoria, Australia."
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}

‎dwi_deriv/sub-01/dwi/sub-01_ADC.json

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{
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"Modality": "MR",
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"MagneticFieldStrength": 3,
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"ImagingFrequency": 123.213411,
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"Manufacturer": "Siemens",
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"ManufacturersModelName": "MAGNETOM Vida",
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"InstitutionName": "REDACTED",
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"BodyPartExamined": "BRAIN",
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"PatientPosition": "HFS",
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"SoftwareVersions": "syngo MR XA50",
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"MRAcquisitionType": "2D",
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"SeriesDescription": "DWI_2p5mm_AllDerivatives_Free_ADC",
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"ProtocolName": "DWI_2p5mm_AllDerivatives_Free",
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"ScanningSequence": "EP",
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"SequenceVariant": "SK\\SP",
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"ScanOptions": "FS",
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"PulseSequenceName": "*epse2d1_96",
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"ImageType": ["DERIVED", "PRIMARY", "DIFFUSION", "ADC"],
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"ImageTypeText": ["DERIVED", "PRIMARY", "DIFFUSION", "ADC", "ND", "NORM"],
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"NonlinearGradientCorrection": false,
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"RawImage": false,
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"SeriesNumber": 137,
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"AcquisitionTime": "16:28:5.352500",
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"SliceThickness": 2.5,
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"SpacingBetweenSlices": 2.5,
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"EchoTime": 0.085,
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"RepetitionTime": 4.5,
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"MTState": false,
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"FlipAngle": 90,
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"PartialFourier": 1,
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"BaseResolution": 96,
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"TxRefAmp": 333.194,
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"PhaseResolution": 1,
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"ReceiveCoilName": "HeadNeck_64_CS",
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"ReceiveCoilActiveElements": "HC1-7",
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"CoilString": "HeadNeck_64_CS",
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"PulseSequenceDetails": "%SiemensSeq%\\ep2d_diff",
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"RefLinesPE": 24,
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"CoilCombinationMethod": "Adaptive Combine",
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"MultibandAccelerationFactor": 2,
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"PercentPhaseFOV": 100,
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"PercentSampling": 100,
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"EchoTrainLength": 47,
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"PhaseEncodingSteps": 96,
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"AcquisitionMatrixPE": 96,
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"ReconMatrixPE": 96,
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"BandwidthPerPixelPhaseEncode": 35.92,
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"ParallelReductionFactorInPlane": 2,
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"ParallelAcquisitionTechnique": "SMS",
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"EffectiveEchoSpacing": 0.000289996,
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"DerivedVendorReportedEchoSpacing": 0.000579993,
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"TotalReadoutTime": 0.0275496,
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"PixelBandwidth": 2003,
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"DwellTime": 2.6e-06,
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"PhaseEncodingDirection": "j-",
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"ImageOrientationPatientDICOM": [
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"InPlanePhaseEncodingDirectionDICOM": "COL",
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"ConversionSoftware": "dcm2niix",
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"ConversionSoftwareVersion": "v1.0.20230411"
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}

‎dwi_deriv/sub-01/dwi/sub-01_ADC.nii

Whitespace-only changes.

‎dwi_deriv/sub-01/dwi/sub-01_FA.json

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{
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"Modality": "MR",
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"MagneticFieldStrength": 3,
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"ImagingFrequency": 123.213411,
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"Manufacturer": "Siemens",
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"ManufacturersModelName": "MAGNETOM Vida",
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"InstitutionName": "REDACTED",
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"BodyPartExamined": "BRAIN",
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"PatientPosition": "HFS",
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"SoftwareVersions": "syngo MR XA50",
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"MRAcquisitionType": "2D",
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"SeriesDescription": "DWI_2p5mm_AllDerivatives_Free_FA",
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"ProtocolName": "DWI_2p5mm_AllDerivatives_Free",
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"ScanningSequence": "EP",
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"SequenceVariant": "SK\\SP",
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"ScanOptions": "FS",
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"PulseSequenceName": "*epse2d1_96",
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"ImageType": ["DERIVED", "PRIMARY", "DIFFUSION", "FA"],
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"ImageTypeText": ["DERIVED", "PRIMARY", "DIFFUSION", "FA", "ND", "NORM"],
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"NonlinearGradientCorrection": false,
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"RawImage": false,
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"SeriesNumber": 140,
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"AcquisitionTime": "16:28:5.352500",
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"SliceThickness": 2.5,
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"SpacingBetweenSlices": 2.5,
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"EchoTime": 0.085,
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"RepetitionTime": 4.5,
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"ReceiveCoilActiveElements": "HC1-7",
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"CoilString": "HeadNeck_64_CS",
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"PulseSequenceDetails": "%SiemensSeq%\\ep2d_diff",
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"RefLinesPE": 24,
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"CoilCombinationMethod": "Adaptive Combine",
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"MultibandAccelerationFactor": 2,
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"PercentPhaseFOV": 100,
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"PercentSampling": 100,
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"EchoTrainLength": 47,
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"PhaseEncodingSteps": 96,
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"FrequencyEncodingSteps": 96,
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"AcquisitionMatrixPE": 96,
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"ReconMatrixPE": 96,
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"BandwidthPerPixelPhaseEncode": 35.92,
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"ParallelReductionFactorInPlane": 2,
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"ParallelAcquisitionTechnique": "SMS",
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"EffectiveEchoSpacing": 0.000289996,
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"DerivedVendorReportedEchoSpacing": 0.000579993,
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"TotalReadoutTime": 0.0275496,
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"PixelBandwidth": 2003,
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"DwellTime": 2.6e-06,
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"ConversionSoftwareVersion": "v1.0.20230411"
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}

‎dwi_deriv/sub-01/dwi/sub-01_FA.nii

Whitespace-only changes.

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