ENH: Add example datasets corresponding to BEP020

.github/workflows/validate_datasets.yml

@@ -111,7 +111,7 @@ jobs:
       # Update this URL to the schema.json from PRs to the spec, when needed.
       # If this variable is unset, dev will generally track the latest development
       # release of https://jsr.io/@bids/schema
-      run: echo BIDS_SCHEMA=https://bids-specification.readthedocs.io/en/latest/schema.json >> $GITHUB_ENV
+      run: echo BIDS_SCHEMA=https://bids-specification--1128.org.readthedocs.build/en/1128/schema.json >> $GITHUB_ENV
 
     - name: Validate all BIDS datasets using bids-validator
       run: |

eyetracking1/CHANGES

@@ -0,0 +1,2 @@
+1.0.0 2025-01-14
+  - first adaptation from https://doi.org/10.18112/openneuro.ds004158.v2.0.4

eyetracking1/README

@@ -0,0 +1,8 @@
+Eye-tracking example for BEP020 from OpenNeuro's ds004158
+
+Curated-by: Oscar Esteban
+Sourcedata: https://doi.org/10.18112/openneuro.ds004158.v2.0.4
+
+Please refer to the source dataset to learn more about the original
+experiment, or to access the full dataset.
+

eyetracking1/dataset_description.json

@@ -0,0 +1,12 @@
+{
+    "Name": "rest_eye",
+    "BIDSVersion": "1.1.1",
+    "Authors": [
+        "Martin Szinte",
+        "Anna Montagnini",
+        "Guillaume Masson"
+    ],
+    "Note": "These data are part of a larger dataset and presented here only to provide an example to BIDS eyetracking modality",
+    "DatasetDOI": "doi:10.18112/openneuro.ds004158.v2.0.4",
+    "License": "CC0"
+}

eyetracking1/participants.json

@@ -0,0 +1,24 @@
+{
+	"participant_id": {
+		"LongName": "patient idnetification",
+		"Description": "anonymized, BIDS compatible identification"
+			  },
+	"sex": {
+		"Levels": { 
+			"M" : "Male",
+			"F" : "Female"
+			  }
+		},
+	"age": {
+		"Description" : "Age of the subject at time of scan with 3 digits"
+		},
+    "GUID": {
+        "Description" : "Unique participant ID as set in the INT"
+    },
+    "eTIV": {
+    	"LongName": "EstimatedTotalIntraCranialVol",
+        "Description" : "Estimated total intracranial volume as measured with 'mri_segstats' function of Freesurfer (mri_segstats --subject subjid --etiv-only)",
+        "Units": "mm3"
+    }
+
+}

eyetracking1/participants.tsv

@@ -0,0 +1,4 @@
+participant_id	sex	age	GUID	eTIV
+sub-01	M	35	19B10ABE8F9F	1775498
+sub-02	F	47	1108F8301DB6	1460403
+

eyetracking1/sub-01/ses-01/anat/sub-01_ses-01_T1w.json

@@ -0,0 +1,68 @@
+{
+	"Modality": "MR",
+	"MagneticFieldStrength": 3,
+	"ImagingFrequency": 123.232,
+	"Manufacturer": "Siemens",
+	"ManufacturersModelName": "Prisma",
+	"InstitutionalDepartmentName": "Department",
+	"DeviceSerialNumber": "66072",
+	"StationName": "AWP66072",
+	"BodyPartExamined": "HEAD",
+	"PatientPosition": "HFS",
+	"ProcedureStepDescription": "Projets_pRFseqTest",
+	"SoftwareVersions": "syngo_MR_E11",
+	"MRAcquisitionType": "3D",
+	"SeriesDescription": "T1w_MPRAGE_0p8iso_CS3_WIP925B",
+	"ProtocolName": "T1w_MPRAGE_0p8iso_CS3_WIP925B",
+	"ScanningSequence": "GR_IR",
+	"SequenceVariant": "SK_SP_MP",
+	"ScanOptions": "IR_WE",
+	"SequenceName": "WIP_cmp3d1_16ns",
+	"ImageType": ["ORIGINAL", "PRIMARY", "M", "NORM", "DIS3D", "DIS2D"],
+	"SeriesNumber": 37,
+	"AcquisitionTime": "15:35:19.527500",
+	"AcquisitionNumber": 1,
+	"SliceThickness": 0.8,
+	"SAR": 0.0585032,
+	"EchoTime": 0.00228,
+	"RepetitionTime": 2.3,
+	"InversionTime": 0.9,
+	"FlipAngle": 9,
+	"PartialFourier": 1,
+	"BaseResolution": 320,
+	"ShimSetting": [
+		-603,
+		-10786,
+		-599,
+		28,
+		40,
+		-264,
+		7,
+		-16	],
+	"TxRefAmp": 279.362,
+	"PhaseResolution": 1,
+	"ReceiveCoilName": "HeadNeck_64",
+	"ReceiveCoilActiveElements": "HC1-7;NC1,2",
+	"CoilString": "HC1-7;NC1_2",
+	"PulseSequenceDetails": "%CustomerSeq%_cstfl_wip925b",
+	"WipMemBlock": "WIP_Identifier: WIP#925B",
+	"RefLinesPE": 32,
+	"ConsistencyInfo": "N4_VE11C_LATEST_20160120",
+	"PercentPhaseFOV": 100,
+	"PercentSampling": 100,
+	"PhaseEncodingSteps": 320,
+	"AcquisitionMatrixPE": 320,
+	"ReconMatrixPE": 320,
+	"PixelBandwidth": 210,
+	"DwellTime": 7.4e-06,
+	"ImageOrientationPatientDICOM": [
+		-0.0132997,
+		0.996304,
+		0.0848652,
+		-0.0278278,
+		0.084471,
+		-0.996037	],
+	"InPlanePhaseEncodingDirectionDICOM": "ROW",
+	"ConversionSoftware": "dcm2niix",
+	"ConversionSoftwareVersion": "v1.0.20200427"
+}

eyetracking1/sub-01/ses-01/anat/sub-01_ses-01_T2w.json

@@ -0,0 +1,69 @@
+{
+	"Modality": "MR",
+	"MagneticFieldStrength": 3,
+	"ImagingFrequency": 123.232,
+	"Manufacturer": "Siemens",
+	"ManufacturersModelName": "Prisma",
+	"InstitutionalDepartmentName": "Department",
+	"DeviceSerialNumber": "66072",
+	"BodyPartExamined": "HEAD",
+	"PatientPosition": "HFS",
+	"ProcedureStepDescription": "Projets_pRFseqTest",
+	"SoftwareVersions": "syngo_MR_E11",
+	"MRAcquisitionType": "3D",
+	"SeriesDescription": "T2w_vNav_0p8mm_RR",
+	"ProtocolName": "T2w_vNav_0p8mm",
+	"ScanningSequence": "SE",
+	"SequenceVariant": "SK_SP",
+	"ScanOptions": "PFP",
+	"SequenceName": "spc_360ns",
+	"ImageType": ["ORIGINAL", "PRIMARY", "M", "ND", "NORM"],
+	"SeriesNumber": 60,
+	"AcquisitionTime": "15:43:8.445000",
+	"AcquisitionNumber": 1,
+	"ImageComments": "sub-test_19660101_20.06.23-14:32:14-DST-1.3.12.2.1107.5.2.43.66072_2",
+	"SliceThickness": 0.8,
+	"EchoTime": 0.564,
+	"RepetitionTime": 3.2,
+	"FlipAngle": 120,
+	"PartialFourier": 1,
+	"BaseResolution": 320,
+	"ShimSetting": [
+		-603,
+		-10786,
+		-599,
+		28,
+		40,
+		-264,
+		7,
+		-16	],
+	"TxRefAmp": 279.362,
+	"PhaseResolution": 1,
+	"ReceiveCoilName": "HeadNeck_64",
+	"ReceiveCoilActiveElements": "HC1-7;NC1,2",
+	"CoilString": "HC1-7;NC1_2",
+	"PulseSequenceDetails": "%CustomerSeq%_tse_vfl_mgh_epinav_ABCD",
+	"WipMemBlock": "Prisma_epi_moco_navigator_ABCD_tse_vfl.prot",
+	"RefLinesPE": 32,
+	"ConsistencyInfo": "N4_VE11C_LATEST_20160120",
+	"PercentPhaseFOV": 100,
+	"PercentSampling": 100,
+	"EchoTrainLength": 326,
+	"PhaseEncodingSteps": 287,
+	"AcquisitionMatrixPE": 320,
+	"ReconMatrixPE": 320,
+	"ParallelReductionFactorInPlane": 2,
+	"PixelBandwidth": 745,
+	"DwellTime": 2.1e-06,
+	"PhaseEncodingDirection": "i",
+	"ImageOrientationPatientDICOM": [
+		-0.0132997,
+		0.996304,
+		0.0848652,
+		-0.0278278,
+		0.084471,
+		-0.996037	],
+	"InPlanePhaseEncodingDirectionDICOM": "ROW",
+	"ConversionSoftware": "dcm2niix",
+	"ConversionSoftwareVersion": "v1.0.20200427"
+}

eyetracking1/sub-01/ses-01/fmap/sub-01_ses-01_dir-AP_epi.json

@@ -0,0 +1,138 @@
+{
+	"Modality": "MR",
+	"MagneticFieldStrength": 3,
+	"ImagingFrequency": 123.232,
+	"Manufacturer": "Siemens",
+	"ManufacturersModelName": "Prisma",
+	"InstitutionalDepartmentName": "Department",
+	"DeviceSerialNumber": "66072",
+	"StationName": "AWP66072",
+	"BodyPartExamined": "HEAD",
+	"PatientPosition": "HFS",
+	"ProcedureStepDescription": "Projets_pRFseqTest",
+	"SoftwareVersions": "syngo_MR_E11",
+	"MRAcquisitionType": "2D",
+	"SeriesDescription": "Fieldmap1_topup_AP",
+	"ProtocolName": "Fieldmap1_topup_AP",
+	"ScanningSequence": "EP",
+	"SequenceVariant": "SK",
+	"ScanOptions": "FS",
+	"SequenceName": "epse2d1_100",
+	"ImageType": ["ORIGINAL", "PRIMARY", "M", "ND", "NORM", "MOSAIC"],
+	"SeriesNumber": 12,
+	"AcquisitionTime": "15:13:52.060000",
+	"AcquisitionNumber": 1,
+	"ImageComments": "SENSE1",
+	"SliceThickness": 2,
+	"SpacingBetweenSlices": 2,
+	"SAR": 0.201168,
+	"EchoTime": 0.059,
+	"RepetitionTime": 7.06,
+	"FlipAngle": 90,
+	"PartialFourier": 1,
+	"BaseResolution": 100,
+	"ShimSetting": [
+		-598,
+		-10766,
+		-563,
+		478,
+		88,
+		146,
+		-126,
+		1	],
+	"TxRefAmp": 279.362,
+	"PhaseResolution": 1,
+	"ReceiveCoilName": "HeadNeck_64",
+	"ReceiveCoilActiveElements": "HC1-6",
+	"PulseSequenceDetails": "%CustomerSeq%_cmrr_mbep2d_se",
+	"WipMemBlock": "acac0380-3b63-4f50-b5e2-d6bf5c1e586c||Sequence: R016 ve11c/master r/e634e98; Dec 19 2017 11:22:56 by eja",
+	"ConsistencyInfo": "N4_VE11C_LATEST_20160120",
+	"PercentPhaseFOV": 100,
+	"PercentSampling": 100,
+	"EchoTrainLength": 100,
+	"PhaseEncodingSteps": 100,
+	"AcquisitionMatrixPE": 100,
+	"ReconMatrixPE": 100,
+	"BandwidthPerPixelPhaseEncode": 18.519,
+	"EffectiveEchoSpacing": 0.000539986,
+	"DerivedVendorReportedEchoSpacing": 0.000539986,
+	"TotalReadoutTime": 0.0534586,
+	"PixelBandwidth": 2175,
+	"DwellTime": 2.3e-06,
+	"PhaseEncodingDirection": "j-",
+	"SliceTiming": [
+		3.52,
+		0,
+		3.6375,
+		0.1175,
+		3.7525,
+		0.235,
+		3.87,
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+	"ImageOrientationPatientDICOM": [
+		0.999563,
+		0.0141216,
+		-0.0259813,
+		-0.018669,
+		0.982731,
+		-0.184097	],
+	"InPlanePhaseEncodingDirectionDICOM": "COL",
+	"ConversionSoftware": "dcm2niix",
+	"ConversionSoftwareVersion": "v1.0.20200427",
+	"IntendedFor": [
+		"ses-01/func/sub-01_ses-01_task-rest_run-01_bold.nii.gz",
+		"ses-01/func/sub-01_ses-01_task-rest_run-02_bold.nii.gz"
+	]
+}