diff --git a/.github/workflows/validate_datasets.yml b/.github/workflows/validate_datasets.yml index ba405411f..7642b0087 100644 --- a/.github/workflows/validate_datasets.yml +++ b/.github/workflows/validate_datasets.yml @@ -99,7 +99,7 @@ jobs: shell: bash - name: Skip MRS validation for legacy validator - run: for DS in mrs_*; do touch $DS/.SKIP_VALIDATION; done + run: for DS in mrs_* dwi_deriv; do touch $DS/.SKIP_VALIDATION; done if: "matrix.bids-validator != 'master-deno'" shell: bash @@ -111,4 +111,4 @@ jobs: env: # When proposing new features, schema changes may be necessary. # Update this URL to the schema.json from PRs to the spec, when needed. - BIDS_SCHEMA: https://bids-specification.readthedocs.io/en/latest/schema.json + BIDS_SCHEMA: https://bids-specification--1864.org.readthedocs.build/en/1864/schema.json diff --git a/dwi_deriv/README.md b/dwi_deriv/README.md new file mode 100644 index 000000000..70887caca --- /dev/null +++ b/dwi_deriv/README.md @@ -0,0 +1,13 @@ +# Scanner-generated Diffusion MRI derivatives + +This single-subject dataset exemplifies the storage of diffusion MRI derivates +that may be generated on the Siemens XA platform. + +Author: Robert E. Smith . + +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/. + +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. diff --git a/dwi_deriv/dataset_description.json b/dwi_deriv/dataset_description.json new file mode 100644 index 000000000..49bf8d1e2 --- /dev/null +++ b/dwi_deriv/dataset_description.json @@ -0,0 +1,8 @@ +{ + "Name": "Scanner-denerated Diffusion MRI derivatives", + "DatasetType": "raw", + "BIDSVersion": "1.10.0", + "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/.", + "Authors": ["Robert E. Smith"], + "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." +} diff --git a/dwi_deriv/sub-01/dwi/sub-01_ADC.json b/dwi_deriv/sub-01/dwi/sub-01_ADC.json new file mode 100644 index 000000000..83c9daf7a --- /dev/null +++ b/dwi_deriv/sub-01/dwi/sub-01_ADC.json @@ -0,0 +1,137 @@ +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "ImagingFrequency": 123.213411, + "Manufacturer": "Siemens", + "ManufacturersModelName": "MAGNETOM Vida", + "InstitutionName": "REDACTED", + "BodyPartExamined": "BRAIN", + "PatientPosition": "HFS", + "SoftwareVersions": "syngo MR XA50", + "MRAcquisitionType": "2D", + "SeriesDescription": "DWI_2p5mm_AllDerivatives_Free_ADC", + "ProtocolName": "DWI_2p5mm_AllDerivatives_Free", + "ScanningSequence": "EP", + "SequenceVariant": "SK\\SP", + "ScanOptions": "FS", + "PulseSequenceName": "*epse2d1_96", + "ImageType": ["DERIVED", "PRIMARY", "DIFFUSION", "ADC"], + "ImageTypeText": ["DERIVED", "PRIMARY", "DIFFUSION", "ADC", "ND", "NORM"], + "NonlinearGradientCorrection": false, + "RawImage": false, + "SeriesNumber": 137, + "AcquisitionTime": "16:28:5.352500", + "SliceThickness": 2.5, + "SpacingBetweenSlices": 2.5, + "EchoTime": 0.085, + "RepetitionTime": 4.5, + "MTState": false, + "FlipAngle": 90, + "PartialFourier": 1, + "BaseResolution": 96, + "ShimSetting": [ + 2161, + -4596, + -2252, + 507, + 29, + -351, + -55, + -7 ], + "TxRefAmp": 333.194, + "PhaseResolution": 1, + "ReceiveCoilName": "HeadNeck_64_CS", + "ReceiveCoilActiveElements": "HC1-7", + "CoilString": "HeadNeck_64_CS", + "PulseSequenceDetails": "%SiemensSeq%\\ep2d_diff", + "RefLinesPE": 24, + "CoilCombinationMethod": "Adaptive Combine", + "MultibandAccelerationFactor": 2, + "PercentPhaseFOV": 100, + "PercentSampling": 100, + "EchoTrainLength": 47, + "PhaseEncodingSteps": 96, + "FrequencyEncodingSteps": 96, + "AcquisitionMatrixPE": 96, + "ReconMatrixPE": 96, + "BandwidthPerPixelPhaseEncode": 35.92, + "ParallelReductionFactorInPlane": 2, + "ParallelAcquisitionTechnique": "SMS", + "EffectiveEchoSpacing": 0.000289996, + "DerivedVendorReportedEchoSpacing": 0.000579993, + "TotalReadoutTime": 0.0275496, + "PixelBandwidth": 2003, + "DwellTime": 2.6e-06, + "PhaseEncodingDirection": "j-", + "SliceTiming": [ + 3.4525, + 0, + 3.5675, + 0.115, + 3.6825, + 0.23, + 3.7975, + 0.345, + 3.9125, + 0.46, + 4.0275, + 0.575, + 4.1425, + 0.69, + 4.26, + 0.805, + 4.375, + 0.92, + 4.49, + 1.035, + 4.605, + 1.15, + 4.72, + 1.265, + 4.835, + 1.3825, + 4.95, + 1.4975, + 5.065, + 1.6125, + 5.18, + 1.7275, + 5.295, + 1.8425, + 5.41, + 1.9575, + 5.525, + 2.0725, + 5.64, + 2.1875, + 5.755, + 2.3025, + 5.87, + 2.4175, + 5.985, + 2.5325, + 6.1, + 2.6475, + 6.215, + 2.7625, + 6.33, + 2.8775, + 6.445, + 2.9925, + 6.56, + 3.1075, + 6.675, + 3.2225, + 6.79, + 3.3375 ], + "ImageOrientationPatientDICOM": [ + 0.999631, + -0.000740811, + -0.0271479, + -6.72663e-09, + 0.999628, + -0.0272781 ], + "InPlanePhaseEncodingDirectionDICOM": "COL", + "ConversionSoftware": "dcm2niix", + "ConversionSoftwareVersion": "v1.0.20230411" +} diff --git a/dwi_deriv/sub-01/dwi/sub-01_ADC.nii b/dwi_deriv/sub-01/dwi/sub-01_ADC.nii new file mode 100644 index 000000000..e69de29bb diff --git a/dwi_deriv/sub-01/dwi/sub-01_FA.json b/dwi_deriv/sub-01/dwi/sub-01_FA.json new file mode 100644 index 000000000..1fef1f391 --- /dev/null +++ b/dwi_deriv/sub-01/dwi/sub-01_FA.json @@ -0,0 +1,137 @@ +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "ImagingFrequency": 123.213411, + "Manufacturer": "Siemens", + "ManufacturersModelName": "MAGNETOM Vida", + "InstitutionName": "REDACTED", + "BodyPartExamined": "BRAIN", + "PatientPosition": "HFS", + "SoftwareVersions": "syngo MR XA50", + "MRAcquisitionType": "2D", + "SeriesDescription": "DWI_2p5mm_AllDerivatives_Free_FA", + "ProtocolName": "DWI_2p5mm_AllDerivatives_Free", + "ScanningSequence": "EP", + "SequenceVariant": "SK\\SP", + "ScanOptions": "FS", + "PulseSequenceName": "*epse2d1_96", + "ImageType": ["DERIVED", "PRIMARY", "DIFFUSION", "FA"], + "ImageTypeText": ["DERIVED", "PRIMARY", "DIFFUSION", "FA", "ND", "NORM"], + "NonlinearGradientCorrection": false, + "RawImage": false, + "SeriesNumber": 140, + "AcquisitionTime": "16:28:5.352500", + "SliceThickness": 2.5, + "SpacingBetweenSlices": 2.5, + "EchoTime": 0.085, + "RepetitionTime": 4.5, + "MTState": false, + "FlipAngle": 90, + "PartialFourier": 1, + "BaseResolution": 96, + "ShimSetting": [ + 2161, + -4596, + -2252, + 507, + 29, + -351, + -55, + -7 ], + "TxRefAmp": 333.194, + "PhaseResolution": 1, + "ReceiveCoilName": "HeadNeck_64_CS", + "ReceiveCoilActiveElements": "HC1-7", + "CoilString": "HeadNeck_64_CS", + "PulseSequenceDetails": "%SiemensSeq%\\ep2d_diff", + "RefLinesPE": 24, + "CoilCombinationMethod": 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"SoftwareVersions": "syngo MR XA50", + "MRAcquisitionType": "2D", + "SeriesDescription": "DWI_2p5mm_AllDerivatives_Free_TENSOR_B0", + "ProtocolName": "DWI_2p5mm_AllDerivatives_Free", + "ScanningSequence": "EP", + "SequenceVariant": "SK\\SP", + "ScanOptions": "FS", + "PulseSequenceName": "*epse2d1_96", + "ImageType": ["DERIVED", "PRIMARY", "DIFFUSION", "TENSOR", "B0"], + "ImageTypeText": ["DERIVED", "PRIMARY", "DIFFUSION", "TENSOR", "B0", "ND", "NORM"], + "NonlinearGradientCorrection": false, + "RawImage": false, + "SeriesNumber": 143, + "AcquisitionTime": "16:28:5.352500", + "SliceThickness": 2.5, + "SpacingBetweenSlices": 2.5, + "EchoTime": 0.085, + "RepetitionTime": 4.5, + "MTState": false, + "FlipAngle": 90, + "PartialFourier": 1, + "BaseResolution": 96, + "ShimSetting": [ + 2161, + -4596, + -2252, + 507, + 29, + -351, + -55, + -7 ], + "DiffusionScheme": "Bipolar", + "TxRefAmp": 333.194, + "PhaseResolution": 1, + "ReceiveCoilName": "HeadNeck_64_CS", + "ReceiveCoilActiveElements": 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"Manufacturer": "Siemens", + "ManufacturersModelName": "MAGNETOM Vida", + "InstitutionName": "REDACTED", + "BodyPartExamined": "BRAIN", + "PatientPosition": "HFS", + "SoftwareVersions": "syngo MR XA50", + "MRAcquisitionType": "2D", + "SeriesDescription": "DWI_2p5mm_AllDerivatives_Free_ColFA", + "ProtocolName": "DWI_2p5mm_AllDerivatives_Free", + "ScanningSequence": "EP", + "SequenceVariant": "SK\\SP", + "ScanOptions": "FS", + "PulseSequenceName": "*epse2d1_96", + "ImageType": ["DERIVED", "PRIMARY", "DIFFUSION", "FA"], + "ImageTypeText": ["DERIVED", "PRIMARY", "DIFFUSION", "FA", "ND", "NORM"], + "NonlinearGradientCorrection": false, + "RawImage": false, + "SeriesNumber": 141, + "AcquisitionTime": "16:28:5.352500", + "SliceThickness": 2.5, + "SpacingBetweenSlices": 2.5, + "EchoTime": 0.085, + "RepetitionTime": 4.5, + "MTState": false, + "FlipAngle": 90, + "PartialFourier": 1, + "BaseResolution": 96, + "ShimSetting": [ + 2161, + -4596, + -2252, + 507, + 29, + -351, + -55, + -7 ], + 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@@ +0 0 1000 1000 1000 1000 1000 1000 1000 1000 0 1000 1000 1000 1000 1000 1000 1000 1000 0 1000 1000 1000 1000 1000 1000 1000 1000 0 1000 1000 1000 1000 1000 1000 1000 1000 0 diff --git a/dwi_deriv/sub-01/dwi/sub-01_dwi.bvec b/dwi_deriv/sub-01/dwi/sub-01_dwi.bvec new file mode 100644 index 000000000..4acdaa1d8 --- /dev/null +++ b/dwi_deriv/sub-01/dwi/sub-01_dwi.bvec @@ -0,0 +1,3 @@ +0 0 0.32988 -0.907002 0.584132 0.146425 0.244222 -0.701127 0.599621 -0.271802 0 0.914122 -0.260378 -0.724944 0.294809 0.654106 -0.843842 -0.154855 -0.0913855 0 0.874698 -0.404728 0.895947 -0.862693 0.195563 -0.110428 -0.3167 -0.165616 0 -0.648333 0.527544 -0.595287 0.630408 0.506149 0.563545 0.115895 -0.998449 0 +0 0 0.932264 0.0230801 -0.451247 -0.538667 0.708692 -0.293644 -0.791827 -0.325458 0 0.307658 0.952524 -0.679846 0.422078 0.0783106 0.455911 -0.949376 -0.0309862 0 -0.453794 0.752443 0.392773 0.12904 -0.775439 -0.806631 0.156161 0.430931 0 -0.478008 0.677425 0.72851 -0.398464 -0.0555027 0.779457 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