From b0d15b9c505efd11efa57024126afe4d9b741f3f Mon Sep 17 00:00:00 2001 From: Arshitha Date: Thu, 29 Aug 2024 17:06:46 -0400 Subject: [PATCH 1/6] adding 2 example datasets for bep036 --- pheno001/README.md | 28 ++++++ pheno001/participants.json | 37 ++++++++ pheno001/participants.tsv | 3 + pheno001/phenotype/ace.json | 95 +++++++++++++++++++ pheno001/phenotype/ace.tsv | 4 + pheno001/phenotype/demographics.json | 67 +++++++++++++ pheno001/phenotype/demographics.tsv | 4 + pheno001/sub-01/anat/sub-01_T1w.json | 0 pheno001/sub-01/anat/sub-01_T1w.nii.gz | 0 pheno001/sub-02/anat/sub-02_T1w.json | 0 pheno001/sub-02/anat/sub-02_T1w.nii.gz | 0 pheno002/README.md | 38 ++++++++ pheno002/participants.json | 37 ++++++++ pheno002/participants.tsv | 3 + pheno002/phenotype/ace.json | 95 +++++++++++++++++++ pheno002/phenotype/ace.tsv | 3 + pheno002/phenotype/demographics.json | 64 +++++++++++++ pheno002/phenotype/demographics.tsv | 3 + pheno002/sessions.json | 15 +++ pheno002/sessions.tsv | 5 + .../sub-01/ses-01/anat/sub-01_ses-01_T1w.json | 0 .../ses-01/anat/sub-01_ses-01_T1w.nii.gz | 0 .../sub-01/ses-02/anat/sub-01_ses-02_T1w.json | 0 .../ses-02/anat/sub-01_ses-02_T1w.nii.gz | 0 .../sub-02/ses-01/anat/sub-02_ses-01_T1w.json | 0 .../ses-01/anat/sub-02_ses-01_T1w.nii.gz | 0 .../sub-02/ses-02/anat/sub-02_ses-02_T1w.json | 0 .../ses-02/anat/sub-02_ses-02_T1w.nii.gz | 0 28 files changed, 501 insertions(+) create mode 100644 pheno001/README.md create mode 100644 pheno001/participants.json create mode 100644 pheno001/participants.tsv create mode 100644 pheno001/phenotype/ace.json create mode 100644 pheno001/phenotype/ace.tsv create mode 100644 pheno001/phenotype/demographics.json create mode 100644 pheno001/phenotype/demographics.tsv create mode 100644 pheno001/sub-01/anat/sub-01_T1w.json create mode 100644 pheno001/sub-01/anat/sub-01_T1w.nii.gz create mode 100644 pheno001/sub-02/anat/sub-02_T1w.json create mode 100644 pheno001/sub-02/anat/sub-02_T1w.nii.gz create mode 100644 pheno002/README.md create mode 100644 pheno002/participants.json create mode 100644 pheno002/participants.tsv create mode 100644 pheno002/phenotype/ace.json create mode 100644 pheno002/phenotype/ace.tsv create mode 100644 pheno002/phenotype/demographics.json create mode 100644 pheno002/phenotype/demographics.tsv create mode 100644 pheno002/sessions.json create mode 100644 pheno002/sessions.tsv create mode 100644 pheno002/sub-01/ses-01/anat/sub-01_ses-01_T1w.json create mode 100644 pheno002/sub-01/ses-01/anat/sub-01_ses-01_T1w.nii.gz create mode 100644 pheno002/sub-01/ses-02/anat/sub-01_ses-02_T1w.json create mode 100644 pheno002/sub-01/ses-02/anat/sub-01_ses-02_T1w.nii.gz create mode 100644 pheno002/sub-02/ses-01/anat/sub-02_ses-01_T1w.json create mode 100644 pheno002/sub-02/ses-01/anat/sub-02_ses-01_T1w.nii.gz create mode 100644 pheno002/sub-02/ses-02/anat/sub-02_ses-02_T1w.json create mode 100644 pheno002/sub-02/ses-02/anat/sub-02_ses-02_T1w.nii.gz diff --git a/pheno001/README.md b/pheno001/README.md new file mode 100644 index 000000000..ec128cce5 --- /dev/null +++ b/pheno001/README.md @@ -0,0 +1,28 @@ +# BEP036 example dataset 01: 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 +| |-- 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 + +6 directories, 11 files + +``` + +**NOTE**: There is no sessions file in this dataset since both phenotype and imaging data were collected at the same single session. diff --git a/pheno001/participants.json b/pheno001/participants.json new file mode 100644 index 000000000..baedfc44c --- /dev/null +++ b/pheno001/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/pheno001/participants.tsv b/pheno001/participants.tsv new file mode 100644 index 000000000..a4f634e2f --- /dev/null +++ b/pheno001/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/pheno001/phenotype/ace.json b/pheno001/phenotype/ace.json new file mode 100644 index 000000000..ac6c0e9b8 --- /dev/null +++ b/pheno001/phenotype/ace.json @@ -0,0 +1,95 @@ +{ + "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." + } + }, + "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?", + "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/pheno001/phenotype/ace.tsv b/pheno001/phenotype/ace.tsv new file mode 100644 index 000000000..1585fc41f --- /dev/null +++ b/pheno001/phenotype/ace.tsv @@ -0,0 +1,4 @@ +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 diff --git a/pheno001/phenotype/demographics.json b/pheno001/phenotype/demographics.json new file mode 100644 index 000000000..4099b1b04 --- /dev/null +++ b/pheno001/phenotype/demographics.json @@ -0,0 +1,67 @@ +{ + "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." + } + }, + "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": { + "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/pheno001/phenotype/demographics.tsv b/pheno001/phenotype/demographics.tsv new file mode 100644 index 000000000..260297d06 --- /dev/null +++ b/pheno001/phenotype/demographics.tsv @@ -0,0 +1,4 @@ +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 diff --git a/pheno001/sub-01/anat/sub-01_T1w.json b/pheno001/sub-01/anat/sub-01_T1w.json new file mode 100644 index 000000000..e69de29bb diff --git a/pheno001/sub-01/anat/sub-01_T1w.nii.gz b/pheno001/sub-01/anat/sub-01_T1w.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/pheno001/sub-02/anat/sub-02_T1w.json b/pheno001/sub-02/anat/sub-02_T1w.json new file mode 100644 index 000000000..e69de29bb diff --git a/pheno001/sub-02/anat/sub-02_T1w.nii.gz b/pheno001/sub-02/anat/sub-02_T1w.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/pheno002/README.md b/pheno002/README.md new file mode 100644 index 000000000..eb6cc011c --- /dev/null +++ b/pheno002/README.md @@ -0,0 +1,38 @@ +# BEP036 example dataset 02: two sessions, one imaging-only session + +This dataset has two sessions but only the first session includes both phenotype and imaging data. The second session only contains imaging data. The file tree is as follows: + +```bash +pheno002 +|-- README.md +|-- participants.json +|-- participants.tsv +|-- phenotype +| |-- ace.json +| |-- ace.tsv +| |-- demographics.json +| `-- demographics.tsv +|-- sessions.json +|-- sessions.tsv +|-- sub-01 +| |-- ses-01 +| | `-- anat +| | |-- sub-01_ses-01_T1w.json +| | `-- sub-01_ses-01_T1w.nii.gz +| `-- ses-02 +| `-- anat +| |-- sub-01_ses-02_T1w.json +| `-- sub-01_ses-02_T1w.nii.gz +`-- sub-02 + |-- ses-01 + | `-- anat + | |-- sub-02_ses-01_T1w.json + | `-- sub-02_ses-01_T1w.nii.gz + `-- ses-02 + `-- anat + |-- sub-02_ses-02_T1w.json + `-- sub-02_ses-02_T1w.nii.gz + +12 directories, 17 files + +``` diff --git a/pheno002/participants.json b/pheno002/participants.json new file mode 100644 index 000000000..baedfc44c --- /dev/null +++ b/pheno002/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/pheno002/participants.tsv b/pheno002/participants.tsv new file mode 100644 index 000000000..a4f634e2f --- /dev/null +++ b/pheno002/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/pheno002/phenotype/ace.json b/pheno002/phenotype/ace.json new file mode 100644 index 000000000..6aa2e48a9 --- /dev/null +++ b/pheno002/phenotype/ace.json @@ -0,0 +1,95 @@ +{ + "participant_id": { + "Description": "OpenNeuro ID of the subject." + }, + "session_id": { + "Description": "ID assigned to participant's visit.", + "Levels": { + "01": "First phenotype assessment and imaging visit.", + "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?", + "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/pheno002/phenotype/ace.tsv b/pheno002/phenotype/ace.tsv new file mode 100644 index 000000000..7fa296f94 --- /dev/null +++ b/pheno002/phenotype/ace.tsv @@ -0,0 +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 diff --git a/pheno002/phenotype/demographics.json b/pheno002/phenotype/demographics.json new file mode 100644 index 000000000..9fa9ac10d --- /dev/null +++ b/pheno002/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": { + "01": "First phenotype assessment and imaging visit.", + "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": { + "m": "Male", + "f": "Female" + } + }, + "race": { + "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": { + "Description": "6. Ethnicity:", + "Levels": { + "0": "Not Hispanic or Latino", + "1": "Hispanic or Latino", + "2": "Unknown" + } + }, + "education": { + "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": { + "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/pheno002/phenotype/demographics.tsv b/pheno002/phenotype/demographics.tsv new file mode 100644 index 000000000..2b345be16 --- /dev/null +++ b/pheno002/phenotype/demographics.tsv @@ -0,0 +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 diff --git a/pheno002/sessions.json b/pheno002/sessions.json new file mode 100644 index 000000000..e3662afba --- /dev/null +++ b/pheno002/sessions.json @@ -0,0 +1,15 @@ +{ + "participant_id": { + "Description": "OpenNeuro ID of the subject." + }, + "session_id": { + "Description": "ID assigned to participant's visit.", + "Levels": { + "01": "First phenotype assessment and imaging visit.", + "02": "Second imaging only visit." + } + }, + "acq_time": { + "Description": "Date and/or time of acquisition." + } +} diff --git a/pheno002/sessions.tsv b/pheno002/sessions.tsv new file mode 100644 index 000000000..89efe4da0 --- /dev/null +++ b/pheno002/sessions.tsv @@ -0,0 +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 diff --git a/pheno002/sub-01/ses-01/anat/sub-01_ses-01_T1w.json b/pheno002/sub-01/ses-01/anat/sub-01_ses-01_T1w.json new file mode 100644 index 000000000..e69de29bb diff --git a/pheno002/sub-01/ses-01/anat/sub-01_ses-01_T1w.nii.gz b/pheno002/sub-01/ses-01/anat/sub-01_ses-01_T1w.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/pheno002/sub-01/ses-02/anat/sub-01_ses-02_T1w.json b/pheno002/sub-01/ses-02/anat/sub-01_ses-02_T1w.json new file mode 100644 index 000000000..e69de29bb diff --git a/pheno002/sub-01/ses-02/anat/sub-01_ses-02_T1w.nii.gz b/pheno002/sub-01/ses-02/anat/sub-01_ses-02_T1w.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/pheno002/sub-02/ses-01/anat/sub-02_ses-01_T1w.json b/pheno002/sub-02/ses-01/anat/sub-02_ses-01_T1w.json new file mode 100644 index 000000000..e69de29bb diff --git a/pheno002/sub-02/ses-01/anat/sub-02_ses-01_T1w.nii.gz b/pheno002/sub-02/ses-01/anat/sub-02_ses-01_T1w.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/pheno002/sub-02/ses-02/anat/sub-02_ses-02_T1w.json b/pheno002/sub-02/ses-02/anat/sub-02_ses-02_T1w.json new file mode 100644 index 000000000..e69de29bb diff --git a/pheno002/sub-02/ses-02/anat/sub-02_ses-02_T1w.nii.gz b/pheno002/sub-02/ses-02/anat/sub-02_ses-02_T1w.nii.gz new file mode 100644 index 000000000..e69de29bb From 0e60f773f8473e69bd0f17e535be7a7ea846816c Mon Sep 17 00:00:00 2001 From: Arshitha Date: Fri, 30 Aug 2024 14:05:28 -0400 Subject: [PATCH 2/6] adding a dataset ; minor changes to existing datasets --- pheno001/participants.json | 2 +- pheno001/participants.tsv | 2 +- pheno001/phenotype/ace.json | 3 - pheno001/phenotype/ace.tsv | 7 +- pheno001/phenotype/demographics.json | 3 - pheno001/phenotype/demographics.tsv | 7 +- pheno002/phenotype/ace.json | 3 - pheno002/phenotype/ace.tsv | 6 +- pheno002/phenotype/demographics.json | 4 - pheno002/phenotype/demographics.tsv | 6 +- pheno002/sessions.json | 4 + pheno002/sessions.tsv | 10 +- pheno003/README.md | 32 +++++++ pheno003/participants.json | 37 ++++++++ pheno003/participants.tsv | 3 + pheno003/phenotype/ace.json | 92 +++++++++++++++++++ pheno003/phenotype/ace.tsv | 4 + pheno003/phenotype/demographics.json | 64 +++++++++++++ pheno003/phenotype/demographics.tsv | 4 + pheno003/sessions.json | 16 ++++ pheno003/sessions.tsv | 4 + .../anat/sub-01_ses-baseline_T1w.json | 0 .../anat/sub-01_ses-baseline_T1w.nii.gz | 0 .../anat/sub-02_ses-baseline_T1w.json | 0 .../anat/sub-02_ses-baseline_T1w.nii.gz | 0 25 files changed, 279 insertions(+), 34 deletions(-) create mode 100644 pheno003/README.md create mode 100644 pheno003/participants.json create mode 100644 pheno003/participants.tsv create mode 100644 pheno003/phenotype/ace.json create mode 100644 pheno003/phenotype/ace.tsv create mode 100644 pheno003/phenotype/demographics.json create mode 100644 pheno003/phenotype/demographics.tsv create mode 100644 pheno003/sessions.json create mode 100644 pheno003/sessions.tsv create mode 100644 pheno003/sub-01/ses-baseline/anat/sub-01_ses-baseline_T1w.json create mode 100644 pheno003/sub-01/ses-baseline/anat/sub-01_ses-baseline_T1w.nii.gz create mode 100644 pheno003/sub-02/ses-baseline/anat/sub-02_ses-baseline_T1w.json create mode 100644 pheno003/sub-02/ses-baseline/anat/sub-02_ses-baseline_T1w.nii.gz diff --git a/pheno001/participants.json b/pheno001/participants.json index baedfc44c..e31a2dcde 100644 --- 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 index a4f634e2f..7c89b50cd 100644 --- 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 index ac6c0e9b8..cdb90410b 100644 --- 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 index 1585fc41f..12b51bdb1 100644 --- 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 index 4099b1b04..20edad26f 100644 --- 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 index 260297d06..ac7f13831 100644 --- 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 index 6aa2e48a9..2d33163f3 100644 --- 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 index 7fa296f94..157d52b1c 100644 --- 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 index 9fa9ac10d..e36dc2632 100644 --- 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 index 2b345be16..aa99ea314 100644 --- 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 index e3662afba..aa732ed28 100644 --- 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 index 89efe4da0..47317e012 100644 --- 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 new file mode 100644 index 000000000..752e23964 --- /dev/null +++ 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 new file mode 100644 index 000000000..baedfc44c --- /dev/null +++ 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 new file mode 100644 index 000000000..a4f634e2f --- /dev/null +++ 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 new file mode 100644 index 000000000..c8d360842 --- /dev/null +++ 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 new file mode 100644 index 000000000..6256759a3 --- /dev/null +++ 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 new file mode 100644 index 000000000..805e6c8eb --- /dev/null +++ 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 new file mode 100644 index 000000000..90e7a004d --- /dev/null +++ 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 new file mode 100644 index 000000000..bd15a5b7d --- /dev/null +++ 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 new file mode 100644 index 000000000..52b2cd938 --- /dev/null +++ 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 new file mode 100644 index 000000000..e69de29bb 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 new file mode 100644 index 000000000..e69de29bb 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 new file mode 100644 index 000000000..e69de29bb 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 new file mode 100644 index 000000000..e69de29bb From 588b644431ac847ee0e9c16b68148604fa0549e0 Mon Sep 17 00:00:00 2001 From: Arshitha Basavaraj Date: Fri, 30 Aug 2024 15:59:54 -0400 Subject: [PATCH 3/6] Update pheno002/sessions.tsv Co-authored-by: Eric Earl --- pheno002/sessions.tsv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pheno002/sessions.tsv b/pheno002/sessions.tsv index 47317e012..022b9fda4 100644 --- a/pheno002/sessions.tsv +++ b/pheno002/sessions.tsv @@ -1,4 +1,4 @@ -participant_id session_id age_at_visit acq_time +participant_id session_id age acq_time sub-01 01 22 1975-02-08 sub-01 02 24 1977-04-01 sub-02 01 63 1975-02-09 From 85dcd26835c6d8b8efe741026c2e62f4560c9683 Mon Sep 17 00:00:00 2001 From: Arshitha Basavaraj Date: Fri, 30 Aug 2024 16:00:10 -0400 Subject: [PATCH 4/6] Update pheno003/sessions.json Co-authored-by: Eric Earl --- pheno003/sessions.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pheno003/sessions.json b/pheno003/sessions.json index bd15a5b7d..0b2c04f06 100644 --- a/pheno003/sessions.json +++ b/pheno003/sessions.json @@ -9,7 +9,7 @@ "followup": "Second phenotype data collection visit." } }, - "age_at_visit": { + "age": { "Description": "Age of the participant at the time of the visit.", "Units": "years" } From b3efe27bd7e27b00ee1c82238b2e1c82343f8d27 Mon Sep 17 00:00:00 2001 From: Arshitha Basavaraj Date: Fri, 30 Aug 2024 16:00:22 -0400 Subject: [PATCH 5/6] Update pheno002/sessions.json Co-authored-by: Eric Earl --- pheno002/sessions.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pheno002/sessions.json b/pheno002/sessions.json index aa732ed28..af80c0899 100644 --- a/pheno002/sessions.json +++ b/pheno002/sessions.json @@ -9,7 +9,7 @@ "02": "Second imaging only visit." } }, - "age_at_visit": { + "age": { "Description": "Age of the participant at the time of the visit.", "Units": "years" }, From 0792d1f374b429d74fcfbce95b3ddf380de8a963 Mon Sep 17 00:00:00 2001 From: Arshitha Basavaraj Date: Fri, 30 Aug 2024 16:00:38 -0400 Subject: [PATCH 6/6] Update pheno003/sessions.tsv Co-authored-by: Eric Earl --- pheno003/sessions.tsv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pheno003/sessions.tsv b/pheno003/sessions.tsv index 52b2cd938..ce30a1091 100644 --- a/pheno003/sessions.tsv +++ b/pheno003/sessions.tsv @@ -1,4 +1,4 @@ -participant_id session_id age_at_visit +participant_id session_id age sub-01 baseline 22 sub-01 followup 24 sub-02 baseline 63