Add pheno004 example dataset

.github/workflows/validate_datasets.yml

@@ -15,6 +15,10 @@ concurrency:
   group: ${{ github.ref }}
   cancel-in-progress: true
 
+defaults:
+  run:
+    shell: bash
+
 jobs:
   build:
     strategy:
@@ -47,23 +51,20 @@ jobs:
       if: matrix.bids-validator == 'stable'
       run: |
           deno install -Agf -n bids-validator jsr:@bids/validator
-      shell: bash
 
     - name: Install BIDS validator (main)
       if: matrix.bids-validator == 'main'
       run: |
         # If unmerged validator PRs are needed for testing, you can use
         # https://github.com/<FORK>/bids-validator/raw/<BRANCH>/bids-validator/src/bids-validator.ts
         deno install -Agf https://github.com/bids-standard/bids-validator/raw/deno-build/bids-validator.js
-      shell: bash
 
     - name: Install BIDS validator (dev)
       if: matrix.bids-validator == 'dev'
       run: |
         git clone -b dev https://github.com/bids-standard/bids-validator/ ../bids-validator
         cd ../bids-validator
         deno compile -A -o $HOME/.deno/bin/bids-validator src/bids-validator.ts
-      shell: bash
 
     - name: Install BIDS validator (legacy)
       if: "matrix.bids-validator == 'legacy'"
@@ -78,7 +79,6 @@ jobs:
         echo "node\n----"; node --version
         echo "npm\n----"; npm --version
         echo "bids-validator"; bids-validator --version
-      shell: bash
 
     - name: Check that no large files are present
       if: "matrix.bids-validator == 'stable'"
@@ -93,28 +93,32 @@ jobs:
             echo "$found"
             exit 1;
         fi
-      shell: bash
 
     - name: Skip legacy validation for post-legacy datasets
-      run: for DS in mrs_* dwi_deriv; do touch $DS/.SKIP_VALIDATION; done
+      run: for DS in mrs_* dwi_deriv pheno004; do touch $DS/.SKIP_VALIDATION; done
       if: matrix.bids-validator == 'legacy'
-      shell: bash
 
-    - name: Skip stable validation for datasets with unreleased features
-      run: for DS in dwi_deriv; do touch $DS/.SKIP_VALIDATION; done
+    - name: Skip stable validation for datasets with unreleased validator features
+      # Replace ${EMPTY} with dataset patterns, when this is needed
+      # Reset to "for DS in ${EMPTY}; ..." after a validator release
+      run: for DS in ${EMPTY}; do touch $DS/.SKIP_VALIDATION; done
+      if: matrix.bids-validator == 'stable'
+
+    - name: Skip main validation for datasets with unreleased spec features
+      # Replace ${EMPTY} with dataset patterns, when this is needed
+      # Reset to "for DS in ${EMPTY}; ..." after a spec release
+      run: for DS in dwi_deriv pheno004; do touch $DS/.SKIP_VALIDATION; done
       if: matrix.bids-validator != 'dev'
-      shell: bash
 
     - name: Set BIDS_SCHEMA variable for dev version
       if: matrix.bids-validator == 'dev'
       # When proposing new features, schema changes may be necessary.
       # 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--2044.org.readthedocs.build/en/2044/schema.json >> $GITHUB_ENV
 
     - name: Validate all BIDS datasets using bids-validator
       run: |
         cat ./run_tests.sh
         ./run_tests.sh
-      shell: bash

pheno004/README.md

@@ -0,0 +1,23 @@
+# BEP036 example dataset 04: One imaging-only, one phenotypic-only, and one with both imaging and phenotypic data
+
+This dataset contains imaging data and phenotypic data from one subject, only imaging data for another subject, and only phenotypic data for a third subject. Phenotype and imaging data were collected at the same session. The file tree is as follows:
+
+```ascii
+📦pheno004
+ ┣ 📂phenotype
+ ┃ ┣ 📜ace.json
+ ┃ ┣ 📜ace.tsv
+ ┃ ┣ 📜demographics.json
+ ┃ ┗ 📜demographics.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
+ ┣ 📜participants.json
+ ┣ 📜participants.tsv
+ ┗ 📜README.md
+```

pheno004/dataset_description.json

@@ -0,0 +1,12 @@
+{
+    "Name": "Mixed Phenotype+Participants",
+    "BIDSVersion": "1.11.0",
+    "License": "CC0",
+    "Authors": [
+        "Eric Earl",
+        "Arshitha Basavaraj",
+        "Samuel Guay",
+        "Sebastian Urchs"
+    ],
+    "Acknowledgements": "Acknowledgements"
+}

pheno004/participants.json

@@ -0,0 +1,16 @@
+{
+  "participant_id": {
+    "Description": "OpenNeuro ID of the subject."
+  },
+  "sex": {
+    "Description": "Sex assigned at birth.",
+    "Levels": {
+      "m": "Male",
+      "f": "Female"
+    }
+  },
+  "age": {
+    "Description": "Age of the participant.",
+    "Units": "years"
+  }
+}

pheno004/participants.tsv

@@ -0,0 +1,4 @@
+participant_id	sex	age
+sub-01	m	22
+sub-02	f	63
+sub-03	f	47

pheno004/phenotype/ace.json

@@ -0,0 +1,92 @@
+{
+  "participant_id": {
+    "Description": "OpenNeuro ID of the subject."
+  },
+  "session_id": {
+    "Description": "ID assigned to participant's visit.",
+    "Levels": {
+      "baseline": "First in-person visit.",
+      "followup": "Second in-person visit."
+    }
+  },
+  "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"
+    }
+  }
+}

pheno004/phenotype/ace.tsv

@@ -0,0 +1,3 @@
+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-03	0	0	0	0	0	0	0	0	0	0

pheno004/phenotype/demographics.json

@@ -0,0 +1,64 @@
+{
+  "participant_id": {
+    "Description": "OpenNeuro ID of the subject."
+  },
+  "session_id": {
+    "Description": "ID assigned to participant's visit.",
+    "Levels": {
+      "onlineScreening": "First online screening visit.",
+      "onlineFollowup": "Online follow-up visit after 1 year of first in-person visit."
+    }
+  },
+  "gender": {
+    "Description": "2. What sex were you assigned at birth, on your original birth certificate?",
+    "Levels": {
+      "m": "Male",
+      "f": "Female"
+    }
+  },
+  "race": {
+    "LongName": "RACE_1, first endorsement",
+    "Description": "5. Race: (Check all that apply)",
+    "Levels": {
+      "1": "American Indian/Alaska Native",
+      "2": "Asian",
+      "3": "Hawaiian/Pacific Islander",
+      "4": "Black/African American",
+      "5": "White/Caucasian",
+      "6": "Multiple race",
+      "7": "Unknown"
+    }
+  },
+  "ethnicity": {
+    "LongName": "ETHNICITY_1 (question ID 140032)",
+    "Description": "6. Ethnicity:",
+    "Levels": {
+      "0": "Not Hispanic or Latino",
+      "1": "Hispanic or Latino",
+      "2": "Unknown"
+    }
+  },
+  "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"
+    }
+  },
+  "marital_status": {
+    "LongName": "MARITAL_STATUS (question ID 7171)",
+    "Description": "11. 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"
+    }
+  }
+}

pheno004/phenotype/demographics.tsv

@@ -0,0 +1,3 @@
+participant_id	gender	race	ethnicity	education	marital_status
+sub-01	m	3	0	4	1
+sub-03	f	6	0	3	2

pheno004/sub-01/anat/sub-01_T1w.json

@@ -0,0 +1,63 @@
+{
+    "Modality": "MR",
+    "MagneticFieldStrength": 3,
+    "ImagingFrequency": 127.695727,
+    "Manufacturer": "GE",
+    "ManufacturersModelName": "DISCOVERY MR750",
+    "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": "[XT-ID:17-M-0181] ADNI3",
+    "ScanningSequence": "RM",
+    "SequenceVariant": "NONE",
+    "ScanOptions": "EDR_GEMS\\PROMO_GEMS\\ACC_GEMS\\IR_GEMS",
+    "PulseSequenceName": "mprage",
+    "ImageType": [
+        "ORIGINAL",
+        "PRIMARY",
+        "OTHER"
+    ],
+    "SeriesNumber": 40003,
+    "AcquisitionTime": "12:43:16.000000",
+    "AcquisitionNumber": 1,
+    "SliceThickness": 1,
+    "SpacingBetweenSlices": 1,
+    "SAR": 0.115406,
+    "EchoTime": 0.00292,
+    "RepetitionTime": 0.006952,
+    "InversionTime": 1.06,
+    "FlipAngle": 8,
+    "ShimSetting": [
+        3,
+        -2,
+        -13
+    ],
+    "PrescanReuseString": "TG/s2,RN/s1",
+    "CoilString": "32Ch Head",
+    "PercentPhaseFOV": 100,
+    "PercentSampling": 100,
+    "AcquisitionMatrixPE": 256,
+    "ReconMatrixPE": 256,
+    "ParallelReductionFactorInPlane": 2,
+    "ParallelReductionFactorOutOfPlane": 2,
+    "PixelBandwidth": 244.141,
+    "ImageOrientationPatientDICOM": [
+        0,
+        1,
+        0,
+        0,
+        0,
+        -1
+    ],
+    "InPlanePhaseEncodingDirectionDICOM": "ROW",
+    "BidsGuess": [
+        "anat",
+        "_acq-EFGRE3Dp2_run-40003_T1w"
+    ],
+    "ConversionSoftware": "dcm2niix",
+    "ConversionSoftwareVersion": "v1.0.20240202",
+    "Dcm2bidsVersion": "3.1.1"
+}