[BEP036] Tabular phenotype example datasets #465
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| # Pheno001 example dataset: One session with imaging and phenotypic data | ||
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| This dataset contains imaging and phenotypic data from a single session. Phenotype and imaging data were collected at the same session. The file tree is as follows: | ||
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| ```bash | ||
| pheno001 | ||
| |-- README.md | ||
| |-- participants.json | ||
| |-- participants.tsv | ||
| |-- phenotype | ||
| | |-- tool-ACE_phenotype.json | ||
| | `-- tool-ACE_phenotype.tsv | ||
| |-- sub-01 | ||
| | `-- anat | ||
| | |-- sub-01_T1w.json | ||
| | `-- sub-01_T1w.nii.gz | ||
| `-- sub-02 | ||
| `-- anat | ||
| |-- sub-02_T1w.json | ||
| `-- sub-02_T1w.nii.gz | ||
|
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| 6 directories, 9 files | ||
| ``` |
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| { | ||
| "Name": "Phenotype guidelines example dataset 1", | ||
| "BIDSVersion": "1.11.1", | ||
| "DatasetType": "raw", | ||
| "License": "CC0", | ||
| "Authors": [ | ||
| "Arshitha Basavaraj", | ||
| "Eric Earl", | ||
| "Sebastian Urchs", | ||
| "Samuel Guay", | ||
| "Dustin Moraczewski" | ||
| ], | ||
| "AdditionalValidation": ["Phenotype"] | ||
| } |
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| { | ||
| "participant_id": { | ||
| "Description": "Participant identifier." | ||
| }, | ||
| "sex": { | ||
| "Description": "Sex assigned at birth.", | ||
| "Levels": { | ||
| "m": "Male", | ||
| "f": "Female" | ||
| } | ||
| }, | ||
| "age": { | ||
| "Description": "Age of the participant.", | ||
| "Units": "years" | ||
| }, | ||
| "ethnicity": { | ||
| "LongName": "ETHNICITY_1", | ||
| "Description": "Ethnicity:", | ||
| "Levels": { | ||
| "0": "Not Hispanic or Latino", | ||
| "1": "Hispanic or Latino", | ||
| "2": "Unknown" | ||
| } | ||
| }, | ||
| "race": { | ||
| "LongName": "RACE_1", | ||
| "Description": "Race:", | ||
| "Levels": { | ||
| "1": "American Indian/Alaska Native", | ||
| "2": "Asian", | ||
| "3": "Hawaiian/Pacific Islander", | ||
| "4": "Black/African American", | ||
| "5": "White/Caucasian", | ||
| "6": "Multiple race", | ||
| "7": "Unknown" | ||
| } | ||
| }, | ||
| "education": { | ||
| "LongName": "EDUCATION", | ||
| "Description": "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" | ||
| } | ||
| }, | ||
| "marital_status": { | ||
| "LongName": "MARITAL_STATUS", | ||
| "Description": "Marital Status:", | ||
| "Levels": { | ||
| "1": "Single/Never married", | ||
| "2": "Married or living with someone as if married", | ||
| "3": "Divorced or annulled", | ||
| "4": "Separated", | ||
| "5": "Widowed", | ||
| "6": "Other" | ||
| } | ||
| } | ||
| } |
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| participant_id sex age ethnicity race education marital_status | ||
| sub-01 m 22 0 4 1 1 | ||
| sub-02 f 63 0 3 2 3 |
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| { | ||
| "MeasurementToolMetadata": { | ||
| "Description": "Adverse Childhood Experience Questionnaire for Adults" | ||
| }, | ||
|
Contributor
There was a problem hiding this comment. are we doing that fun dance again of mixing in description of columns and additional metadata? All of that could be avoided if we followed somewhat established approach for any I really do not get why there is ongoing brewing of some non-BIDS-like cocktail in BEP036. Related issues backrefs: |
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| "participant_id": { | ||
| "Description": "OpenNeuro ID of the subject." | ||
| }, | ||
| "b_ace_q1": { | ||
| "LongName": "ACE_HUMILIATE_HURT (question ID 176435)", | ||
| "Description": "1. Did a parent or other adult in the household often swear at you, insult you, put you down, or humiliate you, or act in a way that made you afraid that you might be physically hurt?", | ||
| "Levels": { | ||
| "1": "Yes", | ||
| "0": "No" | ||
| } | ||
| }, | ||
| "b_ace_q2": { | ||
| "LongName": "ACE_INJURE (question ID 176436)", | ||
| "Description": "2. Did a parent or other adult in the household often push, grab, slap, or throw something at you or ever hit you so hard that you had marks or were injured? ", | ||
| "Levels": { | ||
| "1": "Yes", | ||
| "0": "No" | ||
| } | ||
| }, | ||
| "b_ace_q3": { | ||
| "LongName": "ACE_TOUCH_SEX_WAY (question ID 176437)", | ||
| "Description": "3. Did an adult or person at least 5 years older than you ever touch or fondle you or have you touch their body in a sexual way or try to or actually have oral, anal, or vaginal sex with you? ", | ||
| "Levels": { | ||
| "1": "Yes", | ||
| "0": "No" | ||
| } | ||
| }, | ||
| "b_ace_q4": { | ||
| "LongName": "ACE_NO_LOVE_SUPPORT (question ID 176438)", | ||
| "Description": "4. Did you often feel that no one in your family loved you or thought you were important or special or your family didn't look out for each other, feel close to each other, or support each other? ", | ||
| "Levels": { | ||
| "1": "Yes", | ||
| "0": "No" | ||
| } | ||
| }, | ||
| "b_ace_q5": { | ||
| "LongName": "ACE_PROTECT_CARE (question ID 176439)", | ||
| "Description": "5. Did you often feel that you didn't have enough to eat, had to wear dirty clothes, and had no one to protect you or your parents were too drunk or high to take care of you or take you to the doctor if you needed it?", | ||
| "Levels": { | ||
| "1": "Yes", | ||
| "0": "No" | ||
| } | ||
| }, | ||
| "tesi_s_165": { | ||
| "LongName": "ACE_SEPARATE_DIVORCE (question ID 176440)", | ||
| "Description": "6. Were your parents ever separated or divorced?", | ||
| "Levels": { | ||
| "1": "Yes", | ||
| "0": "No" | ||
| } | ||
| }, | ||
| "b_ace_q7": { | ||
| "LongName": "ACE_MOTHER_HURT (question ID 176441)", | ||
| "Description": "7. Was your mother or stepmother: Often pushed, grabbed, slapped, or had something thrown at her? or sometimes or often kicked, bitten, hit with a fist, or hit with something hard? or ever repeatedly hit over at least a few minutes or threatened with a gun or knife? ", | ||
| "Levels": { | ||
| "1": "Yes", | ||
| "0": "No" | ||
| } | ||
| }, | ||
| "b_ace_q8": { | ||
| "LongName": "ACE_LIVE_ALCOHOL_DRUGS (question ID 176442)", | ||
| "Description": "8. Did you live with anyone who was a problem drinker or alcoholic or who used street drugs? ", | ||
| "Levels": { | ||
| "1": "Yes", | ||
| "0": "No" | ||
| } | ||
| }, | ||
| "b_ace_q9": { | ||
| "LongName": "ACE_HOUSEHOLD_DEPRESS (question ID 176443)", | ||
| "Description": "9. Was a household member depressed or mentally ill or did a household member attempt suicide? ", | ||
| "Levels": { | ||
| "1": "Yes", | ||
| "0": "No" | ||
| } | ||
| }, | ||
| "ceahd15": { | ||
| "LongName": "ACE_HOUSEHOLD_PRISON (question ID 176444)", | ||
| "Description": "10. Did a household member go to prison?", | ||
| "Levels": { | ||
| "1": "Yes", | ||
| "0": "No" | ||
| } | ||
| } | ||
| } | ||
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| participant_id b_ace_q1 b_ace_q2 b_ace_q3 b_ace_q4 b_ace_q5 tesi_s_165 b_ace_q7 b_ace_q8 b_ace_q9 ceahd15 | ||
| sub-01 0 0 0 0 0 0 1 0 0 0 | ||
| sub-02 0 0 0 0 0 0 0 0 0 0 |
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| { | ||
| "Modality": "MR", | ||
| "MagneticFieldStrength": 3, | ||
| "ImagingFrequency": 127.697, | ||
| "Manufacturer": "GE", | ||
| "ManufacturersModelName": "DISCOVERY MR750", | ||
| "InstitutionName": "NIH FMRIF", | ||
| "DeviceSerialNumber": "000301496MR3T6MR", | ||
| "StationName": "fmrif3tb", | ||
| "BodyPartExamined": "BRAIN", | ||
| "PatientPosition": "HFS", | ||
| "ProcedureStepDescription": "MRI Brain", | ||
| "SoftwareVersions": "27\\LX\\MR Software release:DV26.0_R01_1725.a", | ||
| "MRAcquisitionType": "3D", | ||
| "SeriesDescription": "Accelerated Sagittal IR-FSPGR", | ||
| "ProtocolName": "ADNI3 FMRIF Enhanced Pro", | ||
| "ScanningSequence": "GR", | ||
| "SequenceVariant": "SS\\SP\\SK", | ||
| "ScanOptions": "FAST_GEMS\\EDR_GEMS\\FILTERED_GEMS\\ACC_GEMS\\IR_GEMS", | ||
| "ImageType": [ | ||
| "ORIGINAL", | ||
| "PRIMARY", | ||
| "OTHER" | ||
| ], | ||
| "SeriesNumber": 3, | ||
| "AcquisitionTime": "14:20:39.000000", | ||
| "AcquisitionNumber": 1, | ||
| "SliceThickness": 1.2, | ||
| "SpacingBetweenSlices": 1.2, | ||
| "SAR": 0.159922, | ||
| "EchoTime": 0.003036, | ||
| "RepetitionTime": 0.007348, | ||
| "SpoilingState": true, | ||
| "InversionTime": 0.4, | ||
| "FlipAngle": 11, | ||
| "CoilString": "32Ch Head", | ||
| "PercentPhaseFOV": 100, | ||
| "PercentSampling": 100, | ||
| "AcquisitionMatrixPE": 256, | ||
| "ReconMatrixPE": 256, | ||
| "ParallelReductionFactorInPlane": 1.72974, | ||
| "PixelBandwidth": 244.141, | ||
| "ImageOrientationPatientDICOM": [ | ||
| 0, | ||
| 1, | ||
| 0, | ||
| 0, | ||
| 0, | ||
| -1 | ||
| ], | ||
| "InPlanePhaseEncodingDirectionDICOM": "ROW", | ||
| "ConversionSoftware": "dcm2niix", | ||
| "ConversionSoftwareVersion": "v1.0.20211006", | ||
| "Dcm2bidsVersion": "2.1.6", | ||
| "AnatomicalLandmarkCoordinates": { | ||
| "NAS": [ | ||
| 96.99963391304016, | ||
| 217.00000713174342, | ||
| 132.00000993690617 | ||
| ], | ||
| "LPA": [ | ||
| 38.99985516548157, | ||
| 134.00001106030345, | ||
| 109.00000818113267 | ||
| ], | ||
| "RPA": [ | ||
| 151.99943243799208, | ||
| 132.00001115496755, | ||
| 109.00000818113267 | ||
| ] | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,72 @@ | ||
| { | ||
| "Modality": "MR", | ||
| "MagneticFieldStrength": 3, | ||
| "ImagingFrequency": 127.696, | ||
| "Manufacturer": "GE", | ||
| "ManufacturersModelName": "DISCOVERY MR750", | ||
| "InstitutionName": "NIH FMRIF", | ||
| "DeviceSerialNumber": "000301496MR3T6MR", | ||
| "StationName": "FMRI3tb", | ||
| "BodyPartExamined": "BRAIN", | ||
| "PatientPosition": "HFS", | ||
| "ProcedureStepDescription": "MRI Brain", | ||
| "SoftwareVersions": "27\\LX\\MR Software release:DV26.0_R03_1831.b", | ||
| "MRAcquisitionType": "3D", | ||
| "SeriesDescription": "ORIG Anat T1w MP-RAGE 1mm (ABCD)", | ||
| "ProtocolName": "ADNI3 FMRIF Enhanced Pro", | ||
| "ScanningSequence": "RM", | ||
| "SequenceVariant": "NONE", | ||
| "ScanOptions": "EDR_GEMS\\PROMO_GEMS\\ACC_GEMS\\IR_GEMS", | ||
| "ImageType": [ | ||
| "ORIGINAL", | ||
| "PRIMARY", | ||
| "OTHER" | ||
| ], | ||
| "SeriesNumber": 40003, | ||
| "AcquisitionTime": "15:33:5.000000", | ||
| "AcquisitionNumber": 1, | ||
| "SliceThickness": 1, | ||
| "SpacingBetweenSlices": 1, | ||
| "SAR": 0.121617, | ||
| "EchoTime": 0.00292, | ||
| "RepetitionTime": 0.006952, | ||
| "InversionTime": 1.06, | ||
| "FlipAngle": 8, | ||
| "CoilString": "32Ch Head", | ||
| "PercentPhaseFOV": 100, | ||
| "PercentSampling": 100, | ||
| "AcquisitionMatrixPE": 256, | ||
| "ReconMatrixPE": 256, | ||
| "ParallelReductionFactorInPlane": 2, | ||
| "ParallelReductionOutOfPlane": 2, | ||
| "PixelBandwidth": 244.141, | ||
| "ImageOrientationPatientDICOM": [ | ||
| 0, | ||
| 1, | ||
| 0, | ||
| 0, | ||
| 0, | ||
| -1 | ||
| ], | ||
| "InPlanePhaseEncodingDirectionDICOM": "ROW", | ||
| "ConversionSoftware": "dcm2niix", | ||
| "ConversionSoftwareVersion": "v1.0.20211006", | ||
| "Dcm2bidsVersion": "2.1.6", | ||
| "AnatomicalLandmarkCoordinates": { | ||
| "NAS": [ | ||
| 111.79899853515624, | ||
| 216.0946962158203, | ||
| 125.91931025390625 | ||
| ], | ||
| "LPA": [ | ||
| 36.48359853515625, | ||
| 138.14889621582032, | ||
| 92.27751025390626 | ||
| ], | ||
| "RPA": [ | ||
| 175.88069853515626, | ||
| 122.28609621582031, | ||
| 92.83361025390624 | ||
| ] | ||
| } | ||
| } |
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