From 7efd78ba06accd7705ac7650f7a6ab7019e80a17 Mon Sep 17 00:00:00 2001 From: Robert Smith Date: Thu, 27 Jun 2024 12:11:24 +1000 Subject: [PATCH 1/6] New dataset "dwi_deriv" for scanner-generated DWI derivatives --- dwi_deriv/README.md | 13 ++ dwi_deriv/dataset_description.json | 8 + dwi_deriv/sub-01/dwi/sub-01_ADC.json | 136 +++++++++++++++++ dwi_deriv/sub-01/dwi/sub-01_ADC.nii | 0 dwi_deriv/sub-01/dwi/sub-01_FA.json | 136 +++++++++++++++++ dwi_deriv/sub-01/dwi/sub-01_FA.nii | 0 dwi_deriv/sub-01/dwi/sub-01_colFA.json | 136 +++++++++++++++++ dwi_deriv/sub-01/dwi/sub-01_colFA.nii | 0 .../sub-01/dwi/sub-01_desc-tensor_T2w.json | 137 +++++++++++++++++ .../sub-01/dwi/sub-01_desc-tensor_T2w.nii | 0 dwi_deriv/sub-01/dwi/sub-01_dwi.bval | 1 + dwi_deriv/sub-01/dwi/sub-01_dwi.bvec | 3 + dwi_deriv/sub-01/dwi/sub-01_dwi.json | 138 ++++++++++++++++++ dwi_deriv/sub-01/dwi/sub-01_dwi.nii | 0 dwi_deriv/sub-01/dwi/sub-01_expADC.json | 137 +++++++++++++++++ dwi_deriv/sub-01/dwi/sub-01_expADC.nii | 0 dwi_deriv/sub-01/dwi/sub-01_trace.json | 137 +++++++++++++++++ dwi_deriv/sub-01/dwi/sub-01_trace.nii | 0 18 files changed, 982 insertions(+) create mode 100644 dwi_deriv/README.md create mode 100644 dwi_deriv/dataset_description.json create mode 100644 dwi_deriv/sub-01/dwi/sub-01_ADC.json create mode 100644 dwi_deriv/sub-01/dwi/sub-01_ADC.nii create mode 100644 dwi_deriv/sub-01/dwi/sub-01_FA.json create mode 100644 dwi_deriv/sub-01/dwi/sub-01_FA.nii create mode 100644 dwi_deriv/sub-01/dwi/sub-01_colFA.json create mode 100644 dwi_deriv/sub-01/dwi/sub-01_colFA.nii create mode 100644 dwi_deriv/sub-01/dwi/sub-01_desc-tensor_T2w.json create mode 100644 dwi_deriv/sub-01/dwi/sub-01_desc-tensor_T2w.nii create mode 100644 dwi_deriv/sub-01/dwi/sub-01_dwi.bval create mode 100644 dwi_deriv/sub-01/dwi/sub-01_dwi.bvec create mode 100644 dwi_deriv/sub-01/dwi/sub-01_dwi.json create mode 100644 dwi_deriv/sub-01/dwi/sub-01_dwi.nii create mode 100644 dwi_deriv/sub-01/dwi/sub-01_expADC.json create mode 100644 dwi_deriv/sub-01/dwi/sub-01_expADC.nii create mode 100644 dwi_deriv/sub-01/dwi/sub-01_trace.json create mode 100644 dwi_deriv/sub-01/dwi/sub-01_trace.nii 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..8eeba3e3f --- /dev/null +++ b/dwi_deriv/sub-01/dwi/sub-01_ADC.json @@ -0,0 +1,136 @@ +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "ImagingFrequency": 123.213411, + "Manufacturer": "Siemens", + "ManufacturersModelName": "MAGNETOM Vida", + "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..a6d8238b3 --- /dev/null +++ b/dwi_deriv/sub-01/dwi/sub-01_FA.json @@ -0,0 +1,136 @@ +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "ImagingFrequency": 123.213411, + "Manufacturer": "Siemens", + "ManufacturersModelName": "MAGNETOM Vida", + "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": "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_FA.nii b/dwi_deriv/sub-01/dwi/sub-01_FA.nii new file mode 100644 index 000000000..e69de29bb diff --git a/dwi_deriv/sub-01/dwi/sub-01_colFA.json b/dwi_deriv/sub-01/dwi/sub-01_colFA.json new file mode 100644 index 000000000..b161eed4b --- /dev/null +++ b/dwi_deriv/sub-01/dwi/sub-01_colFA.json @@ -0,0 +1,136 @@ +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "ImagingFrequency": 123.213411, + "Manufacturer": "Siemens", + "ManufacturersModelName": "MAGNETOM Vida", + "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 ], + "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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-0.90565 0 -0.264061 0.1578 0.110748 -0.857285 0.752338 -0.282976 -0.273323 0.995333 0 -0.170222 -0.519639 0.207385 0.488988 -0.600374 0.580648 -0.935583 0.887057 0 -0.592598 -0.512633 0.338979 0.666192 -0.860658 0.273614 0.231028 0.00661219 0 diff --git a/dwi_deriv/sub-01/dwi/sub-01_dwi.json b/dwi_deriv/sub-01/dwi/sub-01_dwi.json new file mode 100644 index 000000000..467dc9c6d --- /dev/null +++ b/dwi_deriv/sub-01/dwi/sub-01_dwi.json @@ -0,0 +1,138 @@ +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "ImagingFrequency": 123.213411, + "Manufacturer": "Siemens", + "ManufacturersModelName": "MAGNETOM Vida", + "BodyPartExamined": "BRAIN", + "PatientPosition": "HFS", + "SoftwareVersions": "syngo MR XA50", + "MRAcquisitionType": "2D", + "SeriesDescription": "DWI_2p5mm_AllDerivatives_Free", + "ProtocolName": "DWI_2p5mm_AllDerivatives_Free", + "ScanningSequence": "EP", + "SequenceVariant": "SK\\SP", + "ScanOptions": "FS", + "PulseSequenceName": "*epse2d1_96", + "ImageType": ["ORIGINAL", "PRIMARY", "DIFFUSION", "NONE"], + "ImageTypeText": ["ORIGINAL", "PRIMARY", "DIFFUSION", "NONE", "ND", "NORM"], + "NonlinearGradientCorrection": false, + "SeriesNumber": 136, + "AcquisitionTime": "16:28:5.352500", + "AcquisitionNumber": 1, + "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": "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, + "AcquisitionDuration": 195.33, + "TotalReadoutTime": 0.0275496, + "PixelBandwidth": 2003, + "DwellTime": 2.6e-06, + "PhaseEncodingDirection": "j-", + "SliceTiming": [ + 3.285, + 0, + 2.24, + 0.15, + 2.39, + 0.2975, + 2.5375, + 0.4475, + 2.6875, + 0.5975, + 2.8375, + 0.7475, + 2.9875, + 0.895, + 3.135, + 1.195, + 3.435, + 1.3425, + 3.5825, + 1.4925, + 3.7325, + 1.6425, + 3.8825, + 1.7925, + 4.0325, + 1.94, + 4.18, + 2.09, + 4.33, + 1.045, + 3.285, + 0, + 2.24, + 0.15, + 2.39, + 0.2975, + 2.5375, + 0.4475, + 2.6875, + 0.5975, + 2.8375, + 0.7475, + 2.9875, + 0.895, + 3.135, + 1.195, + 3.435, + 1.3425, + 3.5825, + 1.4925, + 3.7325, + 1.6425, + 3.8825, + 1.7925, + 4.0325, + 1.94, + 4.18, + 2.09, + 4.33, + 1.045 ], + "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_dwi.nii b/dwi_deriv/sub-01/dwi/sub-01_dwi.nii new file mode 100644 index 000000000..e69de29bb diff --git a/dwi_deriv/sub-01/dwi/sub-01_expADC.json b/dwi_deriv/sub-01/dwi/sub-01_expADC.json new file mode 100644 index 000000000..fcd9d76d8 --- /dev/null +++ b/dwi_deriv/sub-01/dwi/sub-01_expADC.json @@ -0,0 +1,137 @@ +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "ImagingFrequency": 123.213411, + "Manufacturer": "Siemens", + "ManufacturersModelName": "MAGNETOM Vida", + "BodyPartExamined": "BRAIN", + "PatientPosition": "HFS", + "SoftwareVersions": "syngo MR XA50", + "MRAcquisitionType": "2D", + "SeriesDescription": "DWI_2p5mm_AllDerivatives_Free_EXP", + "ProtocolName": "DWI_2p5mm_AllDerivatives_Free", + "ScanningSequence": "EP", + "SequenceVariant": "SK\\SP", + "ScanOptions": "FS", + "PulseSequenceName": "*epse2d1_96", + "ImageType": ["DERIVED", "PRIMARY", "DIFFUSION", "EXP"], + "ImageTypeText": ["DERIVED", "PRIMARY", "DIFFUSION", "EXP", "ND", "NORM"], + "NonlinearGradientCorrection": false, + "RawImage": false, + "SeriesNumber": 139, + "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": "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_expADC.nii b/dwi_deriv/sub-01/dwi/sub-01_expADC.nii new file mode 100644 index 000000000..e69de29bb diff --git a/dwi_deriv/sub-01/dwi/sub-01_trace.json b/dwi_deriv/sub-01/dwi/sub-01_trace.json new file mode 100644 index 000000000..76c453b2f --- /dev/null +++ b/dwi_deriv/sub-01/dwi/sub-01_trace.json @@ -0,0 +1,137 @@ +{ + "Modality": "MR", + "MagneticFieldStrength": 3, + "ImagingFrequency": 123.213411, + "Manufacturer": "Siemens", + "ManufacturersModelName": "MAGNETOM Vida", + "BodyPartExamined": "BRAIN", + "PatientPosition": "HFS", + "SoftwareVersions": "syngo MR XA50", + "MRAcquisitionType": "2D", + "SeriesDescription": "DWI_2p5mm_AllDerivatives_Free_TRACEW", + "ProtocolName": "DWI_2p5mm_AllDerivatives_Free", + "ScanningSequence": "EP", + "SequenceVariant": "SK\\SP", + "ScanOptions": "FS", + "PulseSequenceName": "*epse2d1_96", + "ImageType": ["DERIVED", "PRIMARY", "DIFFUSION", "TRACEW"], + "ImageTypeText": ["DERIVED", "PRIMARY", "DIFFUSION", "TRACEW", "ND", "NORM"], + "NonlinearGradientCorrection": false, + "RawImage": false, + "SeriesNumber": 138, + "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": "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_trace.nii b/dwi_deriv/sub-01/dwi/sub-01_trace.nii new file mode 100644 index 000000000..e69de29bb From a8d0e621ee9398a2f10b61fc7d0504a4f1b191ef Mon Sep 17 00:00:00 2001 From: Robert Smith Date: Mon, 12 Aug 2024 12:33:52 +1000 Subject: [PATCH 2/6] dwi_deriv: Rename tensor-model-derived b=0 estimate image --- .../sub-01/dwi/{sub-01_desc-tensor_T2w.json => sub-01_S0map.json} | 0 .../sub-01/dwi/{sub-01_desc-tensor_T2w.nii => sub-01_S0map.nii} | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename dwi_deriv/sub-01/dwi/{sub-01_desc-tensor_T2w.json => sub-01_S0map.json} (100%) rename dwi_deriv/sub-01/dwi/{sub-01_desc-tensor_T2w.nii => sub-01_S0map.nii} (100%) diff --git a/dwi_deriv/sub-01/dwi/sub-01_desc-tensor_T2w.json b/dwi_deriv/sub-01/dwi/sub-01_S0map.json similarity index 100% rename from dwi_deriv/sub-01/dwi/sub-01_desc-tensor_T2w.json rename to dwi_deriv/sub-01/dwi/sub-01_S0map.json diff --git a/dwi_deriv/sub-01/dwi/sub-01_desc-tensor_T2w.nii b/dwi_deriv/sub-01/dwi/sub-01_S0map.nii similarity index 100% rename from dwi_deriv/sub-01/dwi/sub-01_desc-tensor_T2w.nii rename to dwi_deriv/sub-01/dwi/sub-01_S0map.nii From 18e19878bc47498ed5f1e60ceeed751fce62e1b2 Mon Sep 17 00:00:00 2001 From: Robert Smith Date: Thu, 15 Aug 2024 10:45:16 +1000 Subject: [PATCH 3/6] "dwi_deriv": Add InstitutionName Prevents irerlevant validator warning. --- dwi_deriv/sub-01/dwi/sub-01_ADC.json | 1 + dwi_deriv/sub-01/dwi/sub-01_FA.json | 1 + dwi_deriv/sub-01/dwi/sub-01_S0map.json | 1 + dwi_deriv/sub-01/dwi/sub-01_colFA.json | 1 + dwi_deriv/sub-01/dwi/sub-01_dwi.json | 1 + dwi_deriv/sub-01/dwi/sub-01_expADC.json | 1 + dwi_deriv/sub-01/dwi/sub-01_trace.json | 1 + 7 files changed, 7 insertions(+) diff --git a/dwi_deriv/sub-01/dwi/sub-01_ADC.json b/dwi_deriv/sub-01/dwi/sub-01_ADC.json index 8eeba3e3f..83c9daf7a 100644 --- a/dwi_deriv/sub-01/dwi/sub-01_ADC.json +++ b/dwi_deriv/sub-01/dwi/sub-01_ADC.json @@ -4,6 +4,7 @@ "ImagingFrequency": 123.213411, "Manufacturer": "Siemens", "ManufacturersModelName": "MAGNETOM Vida", + "InstitutionName": "REDACTED", "BodyPartExamined": "BRAIN", "PatientPosition": "HFS", "SoftwareVersions": "syngo MR XA50", diff --git a/dwi_deriv/sub-01/dwi/sub-01_FA.json b/dwi_deriv/sub-01/dwi/sub-01_FA.json index a6d8238b3..1fef1f391 100644 --- a/dwi_deriv/sub-01/dwi/sub-01_FA.json +++ b/dwi_deriv/sub-01/dwi/sub-01_FA.json @@ -4,6 +4,7 @@ "ImagingFrequency": 123.213411, "Manufacturer": "Siemens", "ManufacturersModelName": "MAGNETOM Vida", + "InstitutionName": "REDACTED", "BodyPartExamined": "BRAIN", "PatientPosition": "HFS", "SoftwareVersions": "syngo MR XA50", diff --git a/dwi_deriv/sub-01/dwi/sub-01_S0map.json b/dwi_deriv/sub-01/dwi/sub-01_S0map.json index 410817b34..1dfa727c7 100644 --- a/dwi_deriv/sub-01/dwi/sub-01_S0map.json +++ b/dwi_deriv/sub-01/dwi/sub-01_S0map.json @@ -4,6 +4,7 @@ "ImagingFrequency": 123.213411, "Manufacturer": "Siemens", "ManufacturersModelName": "MAGNETOM Vida", + "InstitutionName": "REDACTED", "BodyPartExamined": "BRAIN", "PatientPosition": "HFS", "SoftwareVersions": "syngo MR XA50", diff --git a/dwi_deriv/sub-01/dwi/sub-01_colFA.json b/dwi_deriv/sub-01/dwi/sub-01_colFA.json index b161eed4b..f1f2ae7bb 100644 --- a/dwi_deriv/sub-01/dwi/sub-01_colFA.json +++ b/dwi_deriv/sub-01/dwi/sub-01_colFA.json @@ -4,6 +4,7 @@ "ImagingFrequency": 123.213411, "Manufacturer": "Siemens", "ManufacturersModelName": "MAGNETOM Vida", + "InstitutionName": "REDACTED", "BodyPartExamined": "BRAIN", "PatientPosition": "HFS", "SoftwareVersions": "syngo MR XA50", diff --git a/dwi_deriv/sub-01/dwi/sub-01_dwi.json b/dwi_deriv/sub-01/dwi/sub-01_dwi.json index 467dc9c6d..3243604c8 100644 --- a/dwi_deriv/sub-01/dwi/sub-01_dwi.json +++ b/dwi_deriv/sub-01/dwi/sub-01_dwi.json @@ -4,6 +4,7 @@ "ImagingFrequency": 123.213411, "Manufacturer": "Siemens", "ManufacturersModelName": "MAGNETOM Vida", + "InstitutionName": "REDACTED", "BodyPartExamined": "BRAIN", "PatientPosition": "HFS", "SoftwareVersions": "syngo MR XA50", diff --git a/dwi_deriv/sub-01/dwi/sub-01_expADC.json b/dwi_deriv/sub-01/dwi/sub-01_expADC.json index fcd9d76d8..6a301eebd 100644 --- a/dwi_deriv/sub-01/dwi/sub-01_expADC.json +++ b/dwi_deriv/sub-01/dwi/sub-01_expADC.json @@ -4,6 +4,7 @@ "ImagingFrequency": 123.213411, "Manufacturer": "Siemens", "ManufacturersModelName": "MAGNETOM Vida", + "InstitutionName": "REDACTED", "BodyPartExamined": "BRAIN", "PatientPosition": "HFS", "SoftwareVersions": "syngo MR XA50", diff --git a/dwi_deriv/sub-01/dwi/sub-01_trace.json b/dwi_deriv/sub-01/dwi/sub-01_trace.json index 76c453b2f..4cd193f50 100644 --- a/dwi_deriv/sub-01/dwi/sub-01_trace.json +++ b/dwi_deriv/sub-01/dwi/sub-01_trace.json @@ -4,6 +4,7 @@ "ImagingFrequency": 123.213411, "Manufacturer": "Siemens", "ManufacturersModelName": "MAGNETOM Vida", + "InstitutionName": "REDACTED", "BodyPartExamined": "BRAIN", "PatientPosition": "HFS", "SoftwareVersions": "syngo MR XA50", From 4c5541d263e772e43376a885761912df12d8699f Mon Sep 17 00:00:00 2001 From: Chris Markiewicz Date: Thu, 29 Aug 2024 14:42:01 -0400 Subject: [PATCH 4/6] TMP: Use schema from associated specification PR --- .github/workflows/validate_datasets.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/validate_datasets.yml b/.github/workflows/validate_datasets.yml index ba405411f..9749e1dca 100644 --- a/.github/workflows/validate_datasets.yml +++ b/.github/workflows/validate_datasets.yml @@ -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 From 698f7ba018bc7cba6d581f653fbc7b6d753d8947 Mon Sep 17 00:00:00 2001 From: Chris Markiewicz Date: Thu, 29 Aug 2024 14:43:09 -0400 Subject: [PATCH 5/6] Only validate dw_deriv with schema validator --- .github/workflows/validate_datasets.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/validate_datasets.yml b/.github/workflows/validate_datasets.yml index 9749e1dca..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 From 883bbe43c7683e1846cec6e2068bddf93be6dad2 Mon Sep 17 00:00:00 2001 From: Chris Markiewicz Date: Thu, 29 Aug 2024 14:48:00 -0400 Subject: [PATCH 6/6] Remove AcquisitionDuration for now --- dwi_deriv/sub-01/dwi/sub-01_dwi.json | 1 - 1 file changed, 1 deletion(-) diff --git a/dwi_deriv/sub-01/dwi/sub-01_dwi.json b/dwi_deriv/sub-01/dwi/sub-01_dwi.json index 3243604c8..5bd106cdf 100644 --- a/dwi_deriv/sub-01/dwi/sub-01_dwi.json +++ b/dwi_deriv/sub-01/dwi/sub-01_dwi.json @@ -60,7 +60,6 @@ "ParallelAcquisitionTechnique": "SMS", "EffectiveEchoSpacing": 0.000289996, "DerivedVendorReportedEchoSpacing": 0.000579993, - "AcquisitionDuration": 195.33, "TotalReadoutTime": 0.0275496, "PixelBandwidth": 2003, "DwellTime": 2.6e-06,