[WIP] Examples dataset for Phenotype BEP

ds004129-pheno_segregated/.bidsignore

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+sub-*/*/asl
+sub*/*/fmap/*.bvec
+sub*/*/fmap/*.bval
+phenotype/

ds004129-pheno_segregated/CHANGES

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+1.0.0 2022-06-04
+  - Initial release (copy from ds003982 draft and phenotype.py segregate)

ds004129-pheno_segregated/LICENSE

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+.git/annex/objects/4P/2q/MD5E-s7047--3853e2a78a247145b4aa16667736f6de/MD5E-s7047--3853e2a78a247145b4aa16667736f6de

ds004129-pheno_segregated/dataset_description.json

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+{
+    "Name": "BIDS Phenotype Segregation Example Dataset",
+    "BIDSVersion": "1.7.0",
+    "DatasetType": "raw",
+    "License": "CC0",
+    "Authors": [
+        "Samuel Guay",
+        "Eric Earl",
+        "Hao-Ting Wang",
+        "Remi Gau",
+        "Dorota Jarecka",
+        "David Keator",
+        "Melissa Kline Struhl",
+        "Satra Ghosh",
+        "Louis De Beaumont",
+        "Adam G. Thomas"
+    ],
+    "Acknowledgements": "Many thanks to the first two authors' teams who allowed them to work on this among other tasks.",
+    "HowToAcknowledge": "Please cite the OHBM 2022 poster \"New guidelines for phenotypic data in Brain Imaging Data Structure (BIDS)\" and the paper (in review) \"The NIMH Healthy Research Volunteer Dataset: A comprehensive clinical, MRI, and MEG resource\".",
+    "Funding": [
+        "ZICMH002889",
+        "ZICMH002960",
+        "ZIAMH002783",
+        "ZIDMH00291"
+    ],
+    "EthicsApprovals": [
+        "For the data itself: NIH Institutional Review Board (Recruitment and Characterization of Healthy Research Volunteer for NIMH Intramural Studies NCT033046)"
+    ],
+    "ReferencesAndLinks": [
+        "https://nimhresearchvolunteer.ctss.nih.gov",
+        "https://github.com/nih-megcore/hv_protocol",
+        "doi:10.1016/j.psychres.2020.112822",
+        "doi:10.1101/2021.04.28.21256253",
+        "doi:10.1371/journal.pone.0184661",
+        "doi:10.1038/s41592-018-0235-4"
+    ],
+    "DatasetDOI": "doi:10.18112/openneuro.ds004129.v1.0.0"
+}

ds004129-pheno_segregated/participants.json

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+{
+  "participant_id": {
+    "Description": "OpenNeuro ID of the subject."
+  },
+  "age": {
+    "Description": "Participant's age in years. n/a means there was no response from participant though a response was possible. Question may have been skipped over by participant.",
+    "Units": "Years"
+  },
+  "sex": {
+    "Description": "Biological sex assigned at birth.",
+    "Levels": {
+      "male": "Male",
+      "female": "Female",
+      "n/a": "No response, meaning there was no response from participant though a response was possible. Question may have been skipped over by participant."
+    }
+  },
+  "handedness": {
+    "Description": "Handedness is decided based on Laterality Quotient ranges from the Edinburgh Handedness Inventory.  See Levels below for exact ranges.",
+    "Levels": {
+      "left": "Left-handedness (Laterality Quotient between -100 and -40)",
+      "ambidextrous": "Ambidexterity (Laterality Quotient between -40 and 40)",
+      "right": "Right-handedness (Laterality Quotient between 40 and 100)",
+      "n/a": "No data available for a response.  The question was not presented or asked to the participant."
+    }
+  },
+  "eligibility": {
+    "Description": "Eligibility for the study.",
+    "Levels": {
+      "0": "Ineligible",
+      "1": "Eligible"
+    }
+  },
+  "MRI": {
+    "Description": "Presence of Magnetic Resonance Imaging (MRI) data in data set.",
+    "Levels": {
+      "0": "Not Present",
+      "1": "Present"
+    }
+  },
+  "MEG": {
+    "Description": "Presence of Magnetoencephalography (MEG) data in data set.",
+    "Levels": {
+      "0": "Not Present",
+      "1": "Present"
+    }
+  },
+  "cbc_with_differential": {
+    "Description": "Presence of Complete Blood Count with Differential data in data set.",
+    "Levels": {
+      "0": "Not Present",
+      "1": "Present"
+    }
+  },
+  "vitamin_levels": {
+    "Description": "Presence of Vitamin Levels data in data set.",
+    "Levels": {
+      "0": "Not Present",
+      "1": "Present"
+    }
+  },
+  "other": {
+    "Description": "Presence of Other Panel data in data set.",
+    "Levels": {
+      "0": "Not Present",
+      "1": "Present"
+    }
+  },
+  "hematology": {
+    "Description": "Presence of Hematology Panel data in data set.",
+    "Levels": {
+      "0": "Not Present",
+      "1": "Present"
+    }
+  },
+  "blood_chemistry": {
+    "Description": "Presence of Blood Chemistry data in data set.",
+    "Levels": {
+      "0": "Not Present",
+      "1": "Present"
+    }
+  },
+  "acute_care": {
+    "Description": "Presence of Acute Care Panel data in data set.",
+    "Levels": {
+      "0": "Not Present",
+      "1": "Present"
+    }
+  },
+  "urinalysis": {
+    "Description": "Presence of Urinalysis data in data set.",
+    "Levels": {
+      "0": "Not Present",
+      "1": "Present"
+    }
+  },
+  "infectious_disease": {
+    "Description": "Presence of Infectious Disease Panel data in data set.",
+    "Levels": {
+      "0": "Not Present",
+      "1": "Present"
+    }
+  },
+  "urine_chemistry": {
+    "Description": "Presence of Urine Chemistry data in data set.",
+    "Levels": {
+      "0": "Not Present",
+      "1": "Present"
+    }
+  },
+  "lipid": {
+    "Description": "Presence of Lipid Panel data in data set.",
+    "Levels": {
+      "0": "Not Present",
+      "1": "Present"
+    }
+  },
+  "hepatic": {
+    "Description": "Presence of Hepatic Function Panel data in data set.",
+    "Levels": {
+      "0": "Not Present",
+      "1": "Present"
+    }
+  },
+  "scid5": {
+    "Description": "Presence of Structured Clinical Interview for DSM-5 Disorders (SCID-5) data in data set.",
+    "Levels": {
+      "0": "Not Present",
+      "1": "Present"
+    }
+  },
+  "whodas": {
+    "Description": "Presence of World Health Organization Disability Assessment Schedule 2.0 (WHODAS 2.0) data in data set.",
+    "Levels": {
+      "0": "Not Present",
+      "1": "Present"
+    }
+  },
+  "drug_use": {
+    "Description": "Presence of Drug Use Questionnaire data in data set.",
+    "Levels": {
+      "0": "Not Present",
+      "1": "Present"
+    }
+  },
+  "ehi": {
+    "Description": "Presence of Edinburgh Handedness Inventory (EHI) data in data set.",
+    "Levels": {
+      "0": "Not Present",
+      "1": "Present"
+    }
+  },
+  "kbit2_vas": {
+    "Description": "Presence of Kaufman Brief Intelligence Test 2nd Edition (KBIT-2) and Vocabulary Assessment Scale (VAS) data in data set.",
+    "Levels": {
+      "0": "Not Present",
+      "1": "Present"
+    }
+  },
+  "health_history_questions": {
+    "Description": "Presence of Health History Questions data in data set.",
+    "Levels": {
+      "0": "Not Present",
+      "1": "Present"
+    }
+  },
+  "perceived_health_rating": {
+    "Description": "Presence of Perceived Health Rating data in data set.",
+    "Levels": {
+      "0": "Not Present",
+      "1": "Present"
+    }
+  },
+  "ace": {
+    "Description": "Presence of Adverse Childhood Experiences (ACEs) data in data set.",
+    "Levels": {
+      "0": "Not Present",
+      "1": "Present"
+    }
+  },
+  "satisfaction": {
+    "Description": "Presence of Satisfaction Survey data in data set.",
+    "Levels": {
+      "0": "Not Present",
+      "1": "Present"
+    }
+  },
+  "demographics": {
+    "Description": "Presence of Demographics data in data set.",
+    "Levels": {
+      "0": "Not Present",
+      "1": "Present"
+    }
+  },
+  "bdi": {
+    "Description": "Presence of Beck Depression Inventory-II (BDI-II) data in data set.",
+    "Levels": {
+      "0": "Not Present",
+      "1": "Present"
+    }
+  },
+  "health_rating": {
+    "Description": "Presence of Health Rating data in data set.",
+    "Levels": {
+      "0": "Not Present",
+      "1": "Present"
+    }
+  },
+  "nih_toolbox": {
+    "Description": "Presence of National Institutes of Health (NIH) Toolbox Cognition Battery data in data set.",
+    "Levels": {
+      "0": "Not Present",
+      "1": "Present"
+    }
+  },
+  "audit": {
+    "Description": "Presence of Alcohol Use Disorders Identification Test (AUDIT) data in data set.",
+    "Levels": {
+      "0": "Not Present",
+      "1": "Present"
+    }
+  },
+  "figs": {
+    "Description": "Presence of Family Interview for Genetic Studies (FIGS) data in data set.",
+    "Levels": {
+      "0": "Not Present",
+      "1": "Present"
+    }
+  },
+  "mri_variables": {
+    "Description": "Presence of MRI Variables data in data set.",
+    "Levels": {
+      "0": "Not Present",
+      "1": "Present"
+    }
+  },
+  "clinical_variable_form": {
+    "Description": "Presence of Clinical Variable Form data in data set.",
+    "Levels": {
+      "0": "Not Present",
+      "1": "Present"
+    }
+  },
+  "mental_health_questions": {
+    "Description": "Presence of Mental Health Questions data in data set.",
+    "Levels": {
+      "0": "Not Present",
+      "1": "Present"
+    }
+  },
+  "bai": {
+    "Description": "Presence of Beck Anxiety Inventory (BAI) data in data set.",
+    "Levels": {
+      "0": "Not Present",
+      "1": "Present"
+    }
+  }
+}

ds004129-pheno_segregated/participants.tsv

@@ -0,0 +1,5 @@
+participant_id	age	sex	handedness	eligibility	MRI	MEG	ace	acute_care	audit	bai	bdi	blood_chemistry	cbc_with_differential	clinical_variable_form	demographics	drug_use	ehi	figs	health_history_questions	health_rating	hematology	hepatic	infectious_disease	kbit2_vas	lipid	mental_health_questions	mri_variables	nih_toolbox	other	perceived_health_rating	satisfaction	scid5	urinalysis	urine_chemistry	vitamin_levels	whodas
+sub-ON01016	21	male	right	1	1	0	0	1	1	1	1	1	1	1	1	1	1	0	1	1	0	1	0	1	0	1	0	1	1	1	0	1	0	1	0	1
+sub-ON18047	40	female	right	1	1	0	0	1	1	1	1	1	1	1	1	1	1	1	1	1	0	1	0	1	0	1	1	1	1	1	0	1	0	1	0	1
+sub-ON25939	43	male	right	1	1	1	0	1	1	1	1	1	1	1	1	1	1	1	1	1	0	1	0	1	0	1	1	1	1	1	0	0	0	1	0	1
+sub-ON66199	35	male	right	1	1	1	0	1	1	1	1	1	1	1	1	1	1	1	1	1	0	1	0	1	0	1	1	1	1	1	0	1	0	1	0	1