Example pheno dataset with irregular sessions for BEP tests

pheno_nipoppy01/README.md

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+## Sample BIDS dataset with async visits and sessions
+
+This is sample BIDS dataset create for BIDS pheno BEP testing. This includes two subjects with imaging (`anat`) and phenotypical tabular data. The data collection for imaging and phenotypic assessments is NOT in sync. Therefore the session dates (for a given subject) do not coincide for MRI and muttiple phenotypic assessments (i.e. MoCA and UPDRS3). 

pheno_nipoppy01/dataset_description.json

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+{
+ "Name": "Sample BIDS dataset with async visits and sessions",
+ "BIDSVersion": "1.6.0",
+ "DatasetType": "raw",
+ "License": "CC0",
+ "Authors": [
+ "NB",
+ "RG"
+ ],
+ "Acknowledgements": "Special thanks to the BIDS team",
+ "HowToAcknowledge": "Please cite this paper: ",
+ "Funding": [
+ "",
+ ""
+ ],
+ "EthicsApprovals": [
+ ""
+ ],
+ "ReferencesAndLinks": [
+ ""
+ ],
+ "DatasetDOI": "doi:10.0.2.3/dfjj.10",
+ "HEDVersion": "8.0.0",
+ "GeneratedBy": [
+ {
+ "Name": "reproin",
+ "Version": "0.6.0",
+ "Container": {
+ "Type": "docker",
+ "Tag": "repronim/reproin:0.6.0"
+ }
+ }
+ ],
+ "SourceDatasets": [
+ {
+ "URL": "https://bids-standard.github.io/bids-examples/",
+ "Version": ""
+ }
+ ]
+}

pheno_nipoppy01/participants.json

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+{
+ "age": {
+ "Description": "age of the participant",
+ "Units": "years"
+ },
+ "sex": {
+ "Description": "sex of the participant as reported by the participant",
+ "Levels": {
+ "M": "male",
+ "F": "female"
+ }
+ },
+ "group": {
+ "Description": "experimental group the participant belonged to",
+ "Levels": {
+ "read": "participants who read an inspirational text before the experiment",
+ "write": "participants who wrote an inspirational text before the experiment"
+ }
+ }
+}

pheno_nipoppy01/participants.tsv

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+participant_id age sex group
+sub-01 50 female PD
+sub-02 60 male control

pheno_nipoppy01/phenotype/demographics.json

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+{
+ "AGE": {
+ "LongName": "AGE (question ID 208)",
+ "Description": "1. What is your current age?"
+ },
+ "SEX": {
+ "LongName": "SEX (question ID 117530)",
+ "Description": "2. What sex were you assigned at birth, on your original birth certificate?",
+ "Levels": {
+ "1": "Male",
+ "2": "Female",
+ "3": "Other"
+ }
+ },
+ "EDUCATION": {
+ "LongName": "EDUCATION (question ID 58226)",
+ "Description": "10. Education level:",
+ "Levels": {
+ "0": "High school graduate or above",
+ "1": "Some college or above",
+ "2": "Associates degree or above",
+ "3": "Bachelors degree or above",
+ "4": "Advanced/professional degree"
+ }
+ },
+ "LANGUAGE": {
+ "LongName": "LANGUAGE (question ID 49916)",
+ "Description": "14. What is your primary language?"
+ },
+ "INCOME": {
+ "LongName": "INCOME (question ID 15416)",
+ "Description": "12. Household income:",
+ "Levels": {
+ "1": "Less than $10,000",
+ "2": "$10,001 to $15,000",
+ "3": "$15,001 to $25,000",
+ "4": "$25,001 to $35,000",
+ "5": "$35,001 to $50,000",
+ "6": "$50,001 to $75,000",
+ "7": "$75,001 to $100,000",
+ "8": "$100,001 to $150,000",
+ "9": "$150,000 to $199,999",
+ "10": "$200,000 or more"
+ }
+ }
+}

pheno_nipoppy01/phenotype/demographics.tsv

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+participant_id AGE SEX EDUCATION INCOME LANGUAGE
+sub-01 50 female 4 8 English
+sub-02 60 male 3 7 French

pheno_nipoppy01/phenotype/moca.json

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+{
+ "participant_id": {
+ "Description": "ID of the subject."
+ },
+ "session_id": {
+ "Description": "ID of the subject visit for the type of assessment."
+ },
+ "MOCA_TOTAL": {
+ "LongName": "Montreal Cognitive Assessment total score value.",
+ "Description": " Total points earned on Montreal Cognitive Assessment (MOCA) "
+ }
+}

pheno_nipoppy01/phenotype/moca.tsv

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+participant_id session_id MOCA_TOTAL
+sub-01 ses-CogV01 25
+sub-02 ses-CogV01 28
+sub-01 ses-CogV02 24

pheno_nipoppy01/phenotype/updrs3.json

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+{
+ "participant_id": {
+ "Description": "ID of the subject."
+ },
+ "session_id": {
+ "Description": "ID of the subject visit for the type of assessment."
+ },
+ "UPDRS3_TOTAL": {
+ "LongName": "MDS-Unified Parkinson's Disease Rating Scale (Part 3).",
+ "Description": " Total points earned on UPDRS III measuring motor function."
+ }
+}

pheno_nipoppy01/phenotype/updrs3.tsv

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+participant_id session_id UPDRS3_TOTAL
+sub-01 ses-MotorV01 65
+sub-02 ses-MotorV01 56
+sub-01 ses-MotorV02 70

pheno_nipoppy01/sub-01/ses-A/anat/sub-01_ses-A_run-1_T1w.json

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+{
+ "AcquisitionMatrixPE": 256,
+ "AcquisitionNumber": 1,
+ "AcquisitionTime": "14:32:49.072500",
+ "BaseResolution": 256,
+ "BodyPartExamined": "BRAIN",
+ "DwellTime": 8.2e-06,
+ "EchoTime": 0.00298,
+ "FlipAngle": 9,
+ "ImageOrientationPatientDICOM": [0, 1, 0, 0, 0, -1],
+ "ImageOrientationText": "Sag",
+ "ImagingFrequency": 123.25,
+ "InPlanePhaseEncodingDirectionDICOM": "ROW",
+ "InstitutionAddress": "Bagel Steet",
+ "InstitutionName": "ParkCore",
+ "InstitutionalDepartmentName": "NiPoppy",
+ "InversionTime": 0.9,
+ "MRAcquisitionType": "3D",
+ "MagneticFieldStrength": 3,
+ "Manufacturer": "Siemens",
+ "ManufacturersModelName": "Prisma_fit",
+ "MatrixCoilMode": "GRAPPA",
+ "Modality": "MR",
+ "NonlinearGradientCorrection": false,
+ "ParallelReductionFactorInPlane": 2,
+ "PartialFourier": 1,
+ "PatientPosition": "HFS",
+ "PercentPhaseFOV": 100,
+ "PercentSampling": 100,
+ "PhaseEncodingSteps": 255,
+ "PhaseResolution": 1,
+ "PixelBandwidth": 240,
+ "ProcedureStepDescription": "",
+ "ProtocolName": "3DT1",
+ "PulseSequenceDetails": "",
+ "ReceiveCoilActiveElements": "HEA;HEP",
+ "ReceiveCoilName": "Head_32",
+ "ReconMatrixPE": 256,
+ "RefLinesPE": 24,
+ "RepetitionTime": 2.3,
+ "SAR": 0.0556662,
+ "ScanOptions": "IR",
+ "ScanningSequence": "GR\\IR",
+ "SequenceName": "*tfl3d1_16ns",
+ "SeriesDescription": "3DT1",
+ "SeriesNumber": 2,
+ "SliceThickness": 1}

pheno_nipoppy01/sub-01/sub-01_sessions.tsv

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+session_id acq_time assessment_type visit_label visit_order
+ses-A 2009-06-15T13:45:30 imaging MRI 1
+ses-CogV01 2009-06-15T13:45:30 phenotype Cog 1
+ses-CogV02 2010-06-15T13:45:30 phenotype Cog 2
+ses-MotorV01 2009-10-15T13:45:30 phenotype Motor 1
+ses-MotorV02 2010-11-15T13:45:30 phenotype Motor 2

pheno_nipoppy01/sub-02/ses-A/anat/sub-02_ses-A_run-1_T1w.json

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+{
+ "AcquisitionMatrixPE": 256,
+ "AcquisitionNumber": 1,
+ "AcquisitionTime": "14:32:49.072500",
+ "BaseResolution": 256,
+ "BodyPartExamined": "BRAIN",
+ "DwellTime": 8.2e-06,
+ "EchoTime": 0.00298,
+ "FlipAngle": 9,
+ "ImageOrientationPatientDICOM": [0, 1, 0, 0, 0, -1],
+ "ImageOrientationText": "Sag",
+ "ImagingFrequency": 123.25,
+ "InPlanePhaseEncodingDirectionDICOM": "ROW",
+ "InstitutionAddress": "Bagel Steet",
+ "InstitutionName": "ParkCore",
+ "InstitutionalDepartmentName": "NiPoppy",
+ "InversionTime": 0.9,
+ "MRAcquisitionType": "3D",
+ "MagneticFieldStrength": 3,
+ "Manufacturer": "Siemens",
+ "ManufacturersModelName": "Prisma_fit",
+ "MatrixCoilMode": "GRAPPA",
+ "Modality": "MR",
+ "NonlinearGradientCorrection": false,
+ "ParallelReductionFactorInPlane": 2,
+ "PartialFourier": 1,
+ "PatientPosition": "HFS",
+ "PercentPhaseFOV": 100,
+ "PercentSampling": 100,
+ "PhaseEncodingSteps": 255,
+ "PhaseResolution": 1,
+ "PixelBandwidth": 240,
+ "ProcedureStepDescription": "",
+ "ProtocolName": "3DT1",
+ "PulseSequenceDetails": "",
+ "ReceiveCoilActiveElements": "HEA;HEP",
+ "ReceiveCoilName": "Head_32",
+ "ReconMatrixPE": 256,
+ "RefLinesPE": 24,
+ "RepetitionTime": 2.3,
+ "SAR": 0.0556662,
+ "ScanOptions": "IR",
+ "ScanningSequence": "GR\\IR",
+ "SequenceName": "*tfl3d1_16ns",
+ "SeriesDescription": "3DT1",
+ "SeriesNumber": 2,
+ "SliceThickness": 1}

pheno_nipoppy01/sub-02/sub-02_sessions.tsv

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+session_id acq_time assessment_type visit_label visit_order
+ses-A 2009-08-30T13:45:30 imaging MRI 1
+ses-CogV01 2009-07-30T13:45:30 phenotype Cog 1
+ses-MotorV01 2009-09-30T13:45:30 phenotype Motor 1