[BEP036] Example datasets

.github/workflows/validate_datasets.yml

@@ -107,7 +107,7 @@ jobs:
         fi
 
     - name: Skip legacy validation for post-legacy datasets
-      run: for DS in mrs_* dwi_deriv pet006 pheno004 volume_timing; do touch $DS/.SKIP_VALIDATION; done
+      run: for DS in mrs_* dwi_deriv pet006 pheno00* volume_timing; do touch $DS/.SKIP_VALIDATION; done
       if: matrix.bids-validator == 'legacy'
 
     - name: Skip stable validation for datasets with unreleased validator features
@@ -119,7 +119,7 @@ jobs:
     - 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
+      run: for DS in dwi_deriv pheno00*; do touch $DS/.SKIP_VALIDATION; done
       if: matrix.bids-validator != 'dev'
 
     - name: Set BIDS_SCHEMA variable for dev version
@@ -128,7 +128,7 @@ 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--2123.org.readthedocs.build/en/2123/schema.json >> $GITHUB_ENV
 
     - name: Validate all BIDS datasets using bids-validator
       run: |

pheno001/README.md

@@ -0,0 +1,25 @@
+# Pheno001 example dataset: One session with imaging and phenotypic data
+
+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:
+
+```bash
+pheno001
+|-- README.md
+|-- participants.json
+|-- participants.tsv
+|-- phenotype
+|   |-- ace.json
+|   `-- ace.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
+
+6 directories, 9 files
+```
+
+**NOTE**: There is no sessions file in this dataset since both phenotype and imaging data were collected at the same single session.

pheno001/dataset_description.json

@@ -0,0 +1,13 @@
+{
+	"Name": "Phenotype guidelines example dataset 1",
+	"BIDSVersion": "1.10.1",
+	"DatasetType": "raw",
+	"License": "CC0",
+	"Authors": [
+		"Arshitha Basavaraj",
+		"Eric Earl",
+		"Sebastian Urchs",
+		"Samuel Guay"
+	],
+	"AdditionalValidation": "Phenotype"
+}

pheno001/participants.json

@@ -0,0 +1,61 @@
+{
+	"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"
+		}
+	}
+}

pheno001/participants.tsv

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

pheno001/phenotype/ace.json

@@ -0,0 +1,85 @@
+{
+  "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"
+    }
+  }
+}

pheno001/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-02	0	0	0	0	0	0	0	0	0	0

pheno001/sub-01/anat/sub-01_T1w.json

@@ -0,0 +1,72 @@
+{
+    "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
+        ]
+    }
+}

pheno001/sub-02/anat/sub-02_T1w.json

@@ -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
+        ]
+    }
+}