adding a dataset ; minor changes to existing datasets

Arshitha · Arshitha · commit 0e60f773f847 · 2024-08-30T14:05:28.000-04:00
diff --git a/pheno001/participants.json b/pheno001/participants.json
@@ -9,7 +9,7 @@
       "f": "Female"
     }
   },
-  "age": {
+  "age_at_visit": {
     "Description": "Age of the participant.",
     "Units": "years"
   },
diff --git a/pheno001/participants.tsv b/pheno001/participants.tsv
@@ -1,3 +1,3 @@
-participant_id	sex	age	MRI	ace	demographics
+participant_id	sex	age_at_visit	MRI	ace	demographics
 sub-01	m	22	1	1	1
 sub-02	f	63	1	1	1
diff --git a/pheno001/phenotype/ace.json b/pheno001/phenotype/ace.json
@@ -9,9 +9,6 @@
       "followup": "Second in-person visit."
     }
   },
-  "age_at_visit": {
-    "Description": "Age of the participant at the time of 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?",
diff --git a/pheno001/phenotype/ace.tsv b/pheno001/phenotype/ace.tsv
@@ -1,4 +1,3 @@
-participant_id	age_at_visit	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	22	0	0	0	0	0	0	1	0	0	0
-sub-01	24	1	0	0	1	0	1	0	0	0	0
-sub-02	63	0	0	0	0	0	0	0	0	0	0
+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
diff --git a/pheno001/phenotype/demographics.json b/pheno001/phenotype/demographics.json
@@ -9,9 +9,6 @@
       "onlineFollowup": "Online follow-up visit after 1 year of first in-person visit."
     }
   },
-  "age_at_visit": {
-    "Description": "1. What is your current age?"
-  },
   "gender": {
     "Description": "2. What sex were you assigned at birth, on your original birth certificate?",
     "Levels": {
diff --git a/pheno001/phenotype/demographics.tsv b/pheno001/phenotype/demographics.tsv
@@ -1,4 +1,3 @@
-participant_id	age_at_visit	gender	race	ethnicity	education	marital_status
-sub-01	22	m	3	0	4	1
-sub-01	24	m	3	0	4	1
-sub-02	63	f	6	0	3	2
+participant_id	gender	race	ethnicity	education	marital_status
+sub-01	m	3	0	4	1
+sub-02	f	6	0	3	2
diff --git a/pheno002/phenotype/ace.json b/pheno002/phenotype/ace.json
@@ -9,9 +9,6 @@
       "02": "Second imaging only visit."
     }
   },
-  "age_at_visit": {
-    "Description": "Age of the participant at the time of 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?",
diff --git a/pheno002/phenotype/ace.tsv b/pheno002/phenotype/ace.tsv
@@ -1,3 +1,3 @@
-participant_id	session_id	age_at_visit	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	01	22	0	0	0	0	0	0	1	0	0	0
-sub-02	01	63	0	0	0	0	0	0	0	0	0	0
+participant_id	session_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	01	0	0	0	0	0	0	1	0	0	0
+sub-02	01	0	0	0	0	0	0	0	0	0	0
diff --git a/pheno002/phenotype/demographics.json b/pheno002/phenotype/demographics.json
@@ -9,10 +9,6 @@
       "02": "Second imaging only visit."
     }
   },
-  "age_at_visit": {
-    "Description": "1. What is your current age?",
-    "Units": "years"
-  },
   "gender": {
     "Description": "2. What sex were you assigned at birth, on your original birth certificate?",
     "Levels": {
diff --git a/pheno002/phenotype/demographics.tsv b/pheno002/phenotype/demographics.tsv
@@ -1,3 +1,3 @@
-participant_id	session_id	age_at_visit	gender	race	ethnicity	education	marital_status
-sub-01	01	22	1	3	0	4	1
-sub-02	01	63	2	6	0	3	2
+participant_id	session_id	gender	race	ethnicity	education	marital_status
+sub-01	01	m	3	0	4	1
+sub-02	01	f	6	0	3	2
diff --git a/pheno002/sessions.json b/pheno002/sessions.json
@@ -9,6 +9,10 @@
       "02": "Second imaging only visit."
     }
   },
+  "age_at_visit": {
+    "Description": "Age of the participant at the time of the visit.",
+    "Units": "years"
+  },
   "acq_time": {
     "Description": "Date and/or time of acquisition."
   }
diff --git a/pheno002/sessions.tsv b/pheno002/sessions.tsv
@@ -1,5 +1,5 @@
-participant_id	session_id	acq_time
-sub-01	01	1975-02-08
-sub-01	02	n/a
-sub-02	01	1975-02-09
-sub-02	02	n/a
+participant_id	session_id	age_at_visit	acq_time
+sub-01	01	22	1975-02-08
+sub-01	02	24	1977-04-01
+sub-02	01	63	1975-02-09
+sub-02	02	65	1977-03-29
diff --git a/pheno003/README.md b/pheno003/README.md
@@ -0,0 +1,32 @@
+# BEP036 example dataset 03: Two sessions with one phenotype-only session
+
+This dataset contains imaging data from the baseline session and phenotypic data from baseline and followup sessions. The file tree is as follows:
+
+```bash
+pheno003
+|-- README.md
+|-- participants.json
+|-- participants.tsv
+|-- phenotype
+|   |-- ace.json
+|   |-- ace.tsv
+|   |-- demographics.json
+|   `-- demographics.tsv
+|-- sessions.json
+|-- sessions.tsv
+|-- sub-01
+|   `-- ses-baseline
+|       `-- anat
+|           |-- sub-01_ses-baseline_T1w.json
+|           `-- sub-01_ses-baseline_T1w.nii.gz
+`-- sub-02
+    `-- ses-baseline
+        `-- anat
+            |-- sub-02_ses-baseline_T1w.json
+            `-- sub-02_ses-baseline_T1w.nii.gz
+
+8 directories, 13 files
+
+```
+
+
diff --git a/pheno003/participants.json b/pheno003/participants.json
@@ -0,0 +1,37 @@
+{
+  "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"
+  },
+  "MRI": {
+    "Description": "Does the participant have an MRI?",
+    "Levels": {
+      "1": "Yes",
+      "0": "No"
+    }
+  },
+  "ace": {
+    "Description": "Does the participant have Adverse Childhood Experience (ACE) survey data?",
+    "Levels": {
+      "1": "Yes",
+      "0": "No"
+    }
+  },
+  "demographics": {
+    "Description": "Does the participant have demographics survey data?",
+    "Levels": {
+      "1": "Yes",
+      "0": "No"
+    }
+  }
+}
diff --git a/pheno003/participants.tsv b/pheno003/participants.tsv
@@ -0,0 +1,3 @@
+participant_id	sex	age	MRI	ace	demographics
+sub-01	m	22	1	1	1
+sub-02	f	63	1	1	1
diff --git a/pheno003/phenotype/ace.json b/pheno003/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 imaging and phenotype data collection visit.",
+      "followup": "Second phenotype data collection 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"
+    }
+  }
+}
diff --git a/pheno003/phenotype/ace.tsv b/pheno003/phenotype/ace.tsv
@@ -0,0 +1,4 @@
+participant_id	session_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	baseline	0	0	0	0	0	0	1	0	0	0
+sub-01	followup	1	0	0	1	0	1	0	0	0	0
+sub-02	baseline	0	0	0	0	0	0	0	0	0	0
diff --git a/pheno003/phenotype/demographics.json b/pheno003/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": {
+      "baseline": "First imaging and phenotype data collection visit.",
+      "followup": "Second phenotype data collection visit."
+    }
+  },
+  "sex": {
+    "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"
+    }
+  }
+}
diff --git a/pheno003/phenotype/demographics.tsv b/pheno003/phenotype/demographics.tsv
@@ -0,0 +1,4 @@
+participant_id	session_id	sex	race	ethnicity	education	marital_status
+sub-01	baseline	m	3	0	4	1
+sub-01	followup	m	3	0	4	1
+sub-02	baseline	f	6	0	3	2
diff --git a/pheno003/sessions.json b/pheno003/sessions.json
@@ -0,0 +1,16 @@
+{
+  "participant_id": {
+    "Description": "OpenNeuro ID of the subject."
+  },
+  "session_id": {
+    "Description": "ID assigned to participant's visit.",
+    "Levels": {
+      "baseline": "First imaging and phenotype data collection visit.",
+      "followup": "Second phenotype data collection visit."
+    }
+  },
+  "age_at_visit": {
+    "Description": "Age of the participant at the time of the visit.",
+    "Units": "years"
+  }
+}
diff --git a/pheno003/sessions.tsv b/pheno003/sessions.tsv
@@ -0,0 +1,4 @@
+participant_id	session_id	age_at_visit
+sub-01	baseline	22
+sub-01	followup	24
+sub-02	baseline	63
diff --git a/pheno003/sub-01/ses-baseline/anat/sub-01_ses-baseline_T1w.json b/pheno003/sub-01/ses-baseline/anat/sub-01_ses-baseline_T1w.json
diff --git a/pheno003/sub-01/ses-baseline/anat/sub-01_ses-baseline_T1w.nii.gz b/pheno003/sub-01/ses-baseline/anat/sub-01_ses-baseline_T1w.nii.gz
diff --git a/pheno003/sub-02/ses-baseline/anat/sub-02_ses-baseline_T1w.json b/pheno003/sub-02/ses-baseline/anat/sub-02_ses-baseline_T1w.json
diff --git a/pheno003/sub-02/ses-baseline/anat/sub-02_ses-baseline_T1w.nii.gz b/pheno003/sub-02/ses-baseline/anat/sub-02_ses-baseline_T1w.nii.gz

Original file line number	Diff line number	Diff line change
`@@ -9,7 +9,7 @@`
`9`	`9`	`"f": "Female"`
`10`	`10`	`}`
`11`	`11`	`},`
`12`		`- "age": {`
	`12`	`+ "age_at_visit": {`
`13`	`13`	`"Description": "Age of the participant.",`
`14`	`14`	`"Units": "years"`
`15`	`15`	`},`