Merge pull request #452 from Lestropie/dwi_scanner_derivatives

New dataset "dwi_deriv" for scanner-generated DWI derivatives
bids-standard · Oct 24, 2024 · 7de1e8c · 7de1e8c
2 parents 1d7cf31 + 883bbe4
commit 7de1e8c
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Showing 19 changed files with 990 additions and 2 deletions.
diff --git 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
@@ -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 <[email protected]>.
+
+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
@@ -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
@@ -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
diff --git a/dwi_deriv/sub-01/dwi/sub-01_FA.json 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": "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