diff --git a/.github/workflows/validate_datasets.yml b/.github/workflows/validate_datasets.yml index ae9db3cd5..f471966fb 100644 --- a/.github/workflows/validate_datasets.yml +++ b/.github/workflows/validate_datasets.yml @@ -148,7 +148,7 @@ 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 ${EMPTY}; do touch $DS/.SKIP_VALIDATION; done + run: for DS in pheno00{1,2,3,5,6}; do touch $DS/.SKIP_VALIDATION; done if: matrix.bids-validator != 'dev' - name: Set BIDS_SCHEMA variable for dev version @@ -157,7 +157,7 @@ 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: Set BIDS_SCHEMA variable for dev-prs version if: matrix.bids-validator == 'dev-prs' && env.SPEC_PR != '' diff --git a/pheno001/README.md b/pheno001/README.md new file mode 100644 index 000000000..403dc5eee --- /dev/null +++ b/pheno001/README.md @@ -0,0 +1,23 @@ +# 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 +| |-- tool-ACE_phenotype.json +| `-- tool-ACE_phenotype.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 +``` diff --git a/pheno001/dataset_description.json b/pheno001/dataset_description.json new file mode 100644 index 000000000..2e106ab7f --- /dev/null +++ b/pheno001/dataset_description.json @@ -0,0 +1,14 @@ +{ + "Name": "Phenotype guidelines example dataset 1", + "BIDSVersion": "1.11.1", + "DatasetType": "raw", + "License": "CC0", + "Authors": [ + "Arshitha Basavaraj", + "Eric Earl", + "Sebastian Urchs", + "Samuel Guay", + "Dustin Moraczewski" + ], + "AdditionalValidation": ["Phenotype"] +} \ No newline at end of file diff --git a/pheno001/participants.json b/pheno001/participants.json new file mode 100644 index 000000000..1584a3a00 --- /dev/null +++ b/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" + } + } +} \ No newline at end of file diff --git a/pheno001/participants.tsv b/pheno001/participants.tsv new file mode 100644 index 000000000..2f0f2f24e --- /dev/null +++ b/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 diff --git a/pheno001/phenotype/tool-ACE_phenotype.json b/pheno001/phenotype/tool-ACE_phenotype.json new file mode 100644 index 000000000..8b917fe49 --- /dev/null +++ b/pheno001/phenotype/tool-ACE_phenotype.json @@ -0,0 +1,88 @@ +{ + "MeasurementToolMetadata": { + "Description": "Adverse Childhood Experience Questionnaire for Adults" + }, + "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" + } + } +} \ No newline at end of file diff --git a/pheno001/phenotype/tool-ACE_phenotype.tsv b/pheno001/phenotype/tool-ACE_phenotype.tsv new file mode 100644 index 000000000..12b51bdb1 --- /dev/null +++ b/pheno001/phenotype/tool-ACE_phenotype.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 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..c8ecf9b9e --- /dev/null +++ b/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 + ] + } +} \ No newline at end of file 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..98008d4c6 --- /dev/null +++ b/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 + ] + } +} \ No newline at end of file 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..38044760d --- /dev/null +++ b/pheno002/README.md @@ -0,0 +1,35 @@ +# Pheno002 example dataset: 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 +| |-- tool-ACE_phenotype.json +| |-- tool-ACE_phenotype.tsv +| |-- tool-Demographics_phenotype.json +| `-- tool-Demographics_phenotype.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, 15 files +``` diff --git a/pheno002/dataset_description.json b/pheno002/dataset_description.json new file mode 100644 index 000000000..670a8c91c --- /dev/null +++ b/pheno002/dataset_description.json @@ -0,0 +1,14 @@ +{ + "Name": "Phenotype guidelines example dataset 2", + "BIDSVersion": "1.11.1", + "DatasetType": "raw", + "License": "CC0", + "Authors": [ + "Arshitha Basavaraj", + "Eric Earl", + "Sebastian Urchs", + "Samuel Guay", + "Dustin Moraczewski" + ], + "AdditionalValidation": ["Phenotype"] +} \ No newline at end of file diff --git a/pheno002/participants.json b/pheno002/participants.json new file mode 100644 index 000000000..ab234fd4a --- /dev/null +++ b/pheno002/participants.json @@ -0,0 +1,61 @@ +{ + "participant_id": { + "Description": "Unique participant identifier." + }, + "sex": { + "Description": "Sex assigned at birth.", + "Levels": { + "m": "Male", + "f": "Female" + } + }, + "age": { + "Description": "Age of the participant.", + "Units": "years" + }, + "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" + } + }, + "ethnicity": { + "LongName": "ETHNICITY_1", + "Description": "Ethnicity:", + "Levels": { + "0": "Not Hispanic or Latino", + "1": "Hispanic or Latino", + "2": "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" + } + } +} \ No newline at end of file diff --git a/pheno002/participants.tsv b/pheno002/participants.tsv new file mode 100644 index 000000000..e98399da7 --- /dev/null +++ b/pheno002/participants.tsv @@ -0,0 +1,3 @@ +participant_id sex age race ethnicity education marital_status +sub-01 m 22 3 0 4 1 +sub-02 f 63 6 0 3 2 \ No newline at end of file diff --git a/pheno002/phenotype/tool-ACE_phenotype.json b/pheno002/phenotype/tool-ACE_phenotype.json new file mode 100644 index 000000000..80166e80e --- /dev/null +++ b/pheno002/phenotype/tool-ACE_phenotype.json @@ -0,0 +1,99 @@ +{ + "IndexColumns": [ + "participant_id", + "session_id" + ], + "MeasurementToolMetadata": { + "Description": "Adverse Childhood Experience Questionnaire for Adults" + }, + "participant_id": { + "Description": "OpenNeuro ID of the subject." + }, + "session_id": { + "Description": "ID assigned to participant's visit.", + "Levels": { + "ses-01": "First phenotype assessment and imaging visit.", + "ses-02": "Second imaging only 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/tool-ACE_phenotype.tsv b/pheno002/phenotype/tool-ACE_phenotype.tsv new file mode 100644 index 000000000..a460e7be0 --- /dev/null +++ b/pheno002/phenotype/tool-ACE_phenotype.tsv @@ -0,0 +1,3 @@ +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 ses-01 0 0 0 0 0 0 1 0 0 0 +sub-02 ses-01 0 0 0 0 1 0 0 0 0 0 diff --git a/pheno002/phenotype/tool-Demographics_phenotype.json b/pheno002/phenotype/tool-Demographics_phenotype.json new file mode 100644 index 000000000..721eb5281 --- /dev/null +++ b/pheno002/phenotype/tool-Demographics_phenotype.json @@ -0,0 +1,19 @@ +{ + "IndexColumns": [ + "participant_id", + "session_id" + ], + "participant_id": { + "Description": "Unique participant identifier." + }, + "session_id": { + "Description": "ID assigned to participant's visit.", + "Levels": { + "ses-01": "First phenotype assessment and imaging visit.", + "ses-02": "Second imaging only visit." + } + }, + "acq_time": { + "Description": "Date and/or time of acquisition." + } +} \ No newline at end of file diff --git a/pheno002/phenotype/tool-Demographics_phenotype.tsv b/pheno002/phenotype/tool-Demographics_phenotype.tsv new file mode 100644 index 000000000..75678316c --- /dev/null +++ b/pheno002/phenotype/tool-Demographics_phenotype.tsv @@ -0,0 +1,5 @@ +participant_id session_id acq_time +sub-01 ses-01 1975-02-08 11:37:09 +sub-01 ses-02 1977-04-01 09:00:57 +sub-02 ses-01 1975-02-09 13:50:30 +sub-02 ses-02 1977-03-29 10:25:04 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..c8ecf9b9e --- /dev/null +++ b/pheno002/sub-01/ses-01/anat/sub-01_ses-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 + ] + } +} \ No newline at end of file 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..c8ecf9b9e --- /dev/null +++ b/pheno002/sub-01/ses-02/anat/sub-01_ses-02_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 + ] + } +} \ No newline at end of file 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..33856df0d --- /dev/null +++ b/pheno002/sub-02/ses-01/anat/sub-02_ses-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 + ] + } +} \ No newline at end of file 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..98008d4c6 --- /dev/null +++ b/pheno002/sub-02/ses-02/anat/sub-02_ses-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 + ] + } +} \ No newline at end of file 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 diff --git a/pheno003/README.md b/pheno003/README.md new file mode 100644 index 000000000..5265a7cdf --- /dev/null +++ b/pheno003/README.md @@ -0,0 +1,28 @@ +# Pheno003 example dataset: 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 +| |-- tool-ACE_phenotype.json +| |-- tool-ACE_phenotype.tsv +| |-- tool-Demographics_phenotype.json +| `-- tool-Demographics_phenotype.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, 11 files + +``` diff --git a/pheno003/dataset_description.json b/pheno003/dataset_description.json new file mode 100644 index 000000000..78638db53 --- /dev/null +++ b/pheno003/dataset_description.json @@ -0,0 +1,14 @@ +{ + "Name": "Phenotype guidelines example dataset 3", + "BIDSVersion": "1.11.1", + "DatasetType": "raw", + "License": "CC0", + "Authors": [ + "Arshitha Basavaraj", + "Eric Earl", + "Sebastian Urchs", + "Samuel Guay", + "Dustin Moraczewski" + ], + "AdditionalValidation": ["Phenotype"] +} \ No newline at end of file diff --git a/pheno003/participants.json b/pheno003/participants.json new file mode 100644 index 000000000..0ae7d23bf --- /dev/null +++ b/pheno003/participants.json @@ -0,0 +1,12 @@ +{ + "participant_id": { + "Description": "Unique participant identifier." + }, + "sex": { + "Description": "Sex assigned at birth.", + "Levels": { + "m": "Male", + "f": "Female" + } + } +} \ No newline at end of file diff --git a/pheno003/participants.tsv b/pheno003/participants.tsv new file mode 100644 index 000000000..bbb87c397 --- /dev/null +++ b/pheno003/participants.tsv @@ -0,0 +1,3 @@ +participant_id sex +sub-01 m +sub-02 f diff --git a/pheno003/phenotype/tool-ACE_phenotype.json b/pheno003/phenotype/tool-ACE_phenotype.json new file mode 100644 index 000000000..59f817061 --- /dev/null +++ b/pheno003/phenotype/tool-ACE_phenotype.json @@ -0,0 +1,99 @@ +{ + "IndexColumns": [ + "participant_id", + "session_id" + ], + "MeasurementToolMetadata": { + "Description": "Adverse Childhood Experience Questionnaire for Adults" + }, + "participant_id": { + "Description": "OpenNeuro ID of the subject." + }, + "session_id": { + "Description": "ID assigned to participant's visit.", + "Levels": { + "ses-baseline": "First imaging and phenotype data collection visit.", + "ses-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/tool-ACE_phenotype.tsv b/pheno003/phenotype/tool-ACE_phenotype.tsv new file mode 100644 index 000000000..411b1865e --- /dev/null +++ b/pheno003/phenotype/tool-ACE_phenotype.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 ses-baseline 0 0 0 0 0 0 1 0 0 0 +sub-01 ses-followup 1 0 0 1 0 1 0 0 0 0 +sub-02 ses-baseline 0 0 0 0 0 0 0 0 0 0 diff --git a/pheno003/phenotype/tool-Demographics_phenotype.json b/pheno003/phenotype/tool-Demographics_phenotype.json new file mode 100644 index 000000000..6734c8833 --- /dev/null +++ b/pheno003/phenotype/tool-Demographics_phenotype.json @@ -0,0 +1,20 @@ +{ + "IndexColumns": [ + "participant_id", + "session_id" + ], + "participant_id": { + "Description": "Unique participant identifier." + }, + "session_id": { + "Description": "ID assigned to participant's visit.", + "Levels": { + "ses-baseline": "First imaging and phenotype data collection visit.", + "ses-followup": "Second phenotype data collection visit." + } + }, + "age": { + "Description": "Age of the participant.", + "Units": "years" + } +} \ No newline at end of file diff --git a/pheno003/phenotype/tool-Demographics_phenotype.tsv b/pheno003/phenotype/tool-Demographics_phenotype.tsv new file mode 100644 index 000000000..7c6c5c576 --- /dev/null +++ b/pheno003/phenotype/tool-Demographics_phenotype.tsv @@ -0,0 +1,4 @@ +participant_id session_id age +sub-01 ses-baseline 22 +sub-01 ses-followup 24 +sub-02 ses-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..c8ecf9b9e --- /dev/null +++ b/pheno003/sub-01/ses-baseline/anat/sub-01_ses-baseline_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 + ] + } +} \ No newline at end of file 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..98008d4c6 --- /dev/null +++ b/pheno003/sub-02/ses-baseline/anat/sub-02_ses-baseline_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 + ] + } +} \ No newline at end of file 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 diff --git a/pheno004/README.md b/pheno004/README.md index 0491b65d2..ddbd68936 100644 --- a/pheno004/README.md +++ b/pheno004/README.md @@ -1,14 +1,12 @@ -# BEP036 example dataset 04: One imaging-only, one phenotypic-only, and one with both imaging and phenotypic data +# Pheno004 example dataset: 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 + ┃ ┣ 📜tool-ACE_phenotype.json + ┃ ┗ 📜tool-ACE_phenotype.tsv ┣ 📂sub-01 ┃ ┗ 📂anat ┃ ┃ ┣ 📜sub-01_T1w.json diff --git a/pheno004/dataset_description.json b/pheno004/dataset_description.json index 17c712a0d..36b89991b 100644 --- a/pheno004/dataset_description.json +++ b/pheno004/dataset_description.json @@ -1,12 +1,15 @@ { - "Name": "Mixed Phenotype+Participants", - "BIDSVersion": "1.11.0", - "License": "CC0", - "Authors": [ - "Eric Earl", - "Arshitha Basavaraj", - "Samuel Guay", - "Sebastian Urchs" - ], - "Acknowledgements": "Acknowledgements" + "Name": "Mixed Phenotype+Participants", + "BIDSVersion": "1.11.1", + "DatasetType": "raw", + "License": "CC0", + "Authors": [ + "Eric Earl", + "Arshitha Basavaraj", + "Sebastian Urchs", + "Samuel Guay", + "Dustin Moraczewski" + ], + "Acknowledgements": "Acknowledgements", + "AdditionalValidation": ["Phenotype"] } \ No newline at end of file diff --git a/pheno004/participants.json b/pheno004/participants.json index 8408853fd..ab234fd4a 100644 --- a/pheno004/participants.json +++ b/pheno004/participants.json @@ -1,16 +1,61 @@ { - "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" - } -} + "participant_id": { + "Description": "Unique participant identifier." + }, + "sex": { + "Description": "Sex assigned at birth.", + "Levels": { + "m": "Male", + "f": "Female" + } + }, + "age": { + "Description": "Age of the participant.", + "Units": "years" + }, + "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" + } + }, + "ethnicity": { + "LongName": "ETHNICITY_1", + "Description": "Ethnicity:", + "Levels": { + "0": "Not Hispanic or Latino", + "1": "Hispanic or Latino", + "2": "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" + } + } +} \ No newline at end of file diff --git a/pheno004/participants.tsv b/pheno004/participants.tsv index a5c7696c6..809a720df 100644 --- a/pheno004/participants.tsv +++ b/pheno004/participants.tsv @@ -1,4 +1,4 @@ -participant_id sex age -sub-01 m 22 -sub-02 f 63 -sub-03 f 47 +participant_id sex age race ethnicity education marital_status +sub-01 m 22 3 0 4 1 +sub-02 f 63 6 0 3 2 +sub-03 f 47 2 1 2 3 diff --git a/pheno004/phenotype/demographics.json b/pheno004/phenotype/demographics.json deleted file mode 100644 index 20edad26f..000000000 --- a/pheno004/phenotype/demographics.json +++ /dev/null @@ -1,64 +0,0 @@ -{ - "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" - } - } -} diff --git a/pheno004/phenotype/demographics.tsv b/pheno004/phenotype/demographics.tsv deleted file mode 100644 index 4e5a30396..000000000 --- a/pheno004/phenotype/demographics.tsv +++ /dev/null @@ -1,3 +0,0 @@ -participant_id gender race ethnicity education marital_status -sub-01 m 3 0 4 1 -sub-03 f 6 0 3 2 diff --git a/pheno004/phenotype/ace.json b/pheno004/phenotype/tool-ACE_phenotype.json similarity index 94% rename from pheno004/phenotype/ace.json rename to pheno004/phenotype/tool-ACE_phenotype.json index cdb90410b..80d6e07d9 100644 --- a/pheno004/phenotype/ace.json +++ b/pheno004/phenotype/tool-ACE_phenotype.json @@ -1,14 +1,10 @@ { + "MeasurementToolMetadata": { + "Description": "Adverse Childhood Experience Questionnaire for Adults" + }, "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?", diff --git a/pheno004/phenotype/ace.tsv b/pheno004/phenotype/tool-ACE_phenotype.tsv similarity index 100% rename from pheno004/phenotype/ace.tsv rename to pheno004/phenotype/tool-ACE_phenotype.tsv diff --git a/pheno005/README.md b/pheno005/README.md new file mode 100644 index 000000000..05707c085 --- /dev/null +++ b/pheno005/README.md @@ -0,0 +1,28 @@ +# Pheno005 example dataset: Two multi-run sessions with one imaging-only session + +This dataset contains imaging and phenotypic data with multiple runs from the baseline session and phenotypic data from followup sessions. The file tree is as follows: + +```bash +pheno005 +|-- README.md +|-- participants.json +|-- participants.tsv +|-- phenotype +| |-- tool-ACE_phenotype.json +| |-- tool-ACE_phenotype.tsv +| |-- tool-Demographics_phenotype.json +| `-- tool-Demographics_phenotype.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, 11 files + +``` diff --git a/pheno005/dataset_description.json b/pheno005/dataset_description.json new file mode 100644 index 000000000..793af6545 --- /dev/null +++ b/pheno005/dataset_description.json @@ -0,0 +1,14 @@ +{ + "Name": "BEP036 example dataset 05: Two multi-run sessions with one imaging-only session.", + "BIDSVersion": "1.11.1", + "DatasetType": "raw", + "License": "CC0", + "Authors": [ + "Arshitha Basavaraj", + "Eric Earl", + "Sebastian Urchs", + "Samuel Guay", + "Dustin Moraczewski" + ], + "AdditionalValidation": ["Phenotype"] +} \ No newline at end of file diff --git a/pheno005/participants.json b/pheno005/participants.json new file mode 100644 index 000000000..bae56d0f1 --- /dev/null +++ b/pheno005/participants.json @@ -0,0 +1,57 @@ +{ + "participant_id": { + "Description": "Unique participant identifier." + }, + "sex": { + "Description": "Sex assigned at birth.", + "Levels": { + "m": "Male", + "f": "Female" + } + }, + "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" + } + }, + "ethnicity": { + "LongName": "ETHNICITY_1", + "Description": "Ethnicity:", + "Levels": { + "0": "Not Hispanic or Latino", + "1": "Hispanic or Latino", + "2": "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" + } + } +} \ No newline at end of file diff --git a/pheno005/participants.tsv b/pheno005/participants.tsv new file mode 100644 index 000000000..75e9deb45 --- /dev/null +++ b/pheno005/participants.tsv @@ -0,0 +1,3 @@ +participant_id sex race ethnicity education marital_status +sub-01 m 3 0 4 1 +sub-02 f 6 0 3 2 diff --git a/pheno005/phenotype/tool-ACE_phenotype.json b/pheno005/phenotype/tool-ACE_phenotype.json new file mode 100644 index 000000000..a81c47c46 --- /dev/null +++ b/pheno005/phenotype/tool-ACE_phenotype.json @@ -0,0 +1,110 @@ +{ + "IndexColumns": [ + "participant_id", + "session_id", + "run_id" + ], + "MeasurementToolMetadata": { + "Description": "Adverse Childhood Experience Questionnaire for Adults" + }, + "participant_id": { + "Description": "OpenNeuro ID of the subject." + }, + "session_id": { + "Description": "ID assigned to participant's visit.", + "Levels": { + "ses-baseline": "First imaging and phenotype data collection visit.", + "ses-followup": "Second phenotype data collection visit." + } + }, + "run_id": { + "Description": "Run index assigned to a given session.", + "Levels": { + "run-01": "First run of the session.", + "run-02": "Second run of the session." + } + }, + "acq_time": { + "Description": "Date and time of data acquisition in YYYY-MM-DD HH:MM:SS format." + }, + "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" + } + } +} \ No newline at end of file diff --git a/pheno005/phenotype/tool-ACE_phenotype.tsv b/pheno005/phenotype/tool-ACE_phenotype.tsv new file mode 100644 index 000000000..d3eaead6d --- /dev/null +++ b/pheno005/phenotype/tool-ACE_phenotype.tsv @@ -0,0 +1,6 @@ +participant_id session_id run_id acq_time 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 ses-baseline run-01 2001-01-05 10:05:23 0 0 0 0 0 0 1 0 0 0 +sub-01 ses-baseline run-02 2001-01-05 14:15:59 0 0 0 0 0 0 1 0 0 0 +sub-01 ses-followup run-01 2003-02-06 09:45:00 1 0 0 1 0 1 0 0 0 0 +sub-02 ses-baseline run-01 2001-01-13 12:04:08 1 0 0 0 0 0 0 0 0 0 +sub-02 ses-baseline run-02 2001-01-13 16:20:17 1 0 0 0 0 0 0 0 0 0 diff --git a/pheno005/phenotype/tool-Demographics_phenotype.json b/pheno005/phenotype/tool-Demographics_phenotype.json new file mode 100644 index 000000000..6734c8833 --- /dev/null +++ b/pheno005/phenotype/tool-Demographics_phenotype.json @@ -0,0 +1,20 @@ +{ + "IndexColumns": [ + "participant_id", + "session_id" + ], + "participant_id": { + "Description": "Unique participant identifier." + }, + "session_id": { + "Description": "ID assigned to participant's visit.", + "Levels": { + "ses-baseline": "First imaging and phenotype data collection visit.", + "ses-followup": "Second phenotype data collection visit." + } + }, + "age": { + "Description": "Age of the participant.", + "Units": "years" + } +} \ No newline at end of file diff --git a/pheno005/phenotype/tool-Demographics_phenotype.tsv b/pheno005/phenotype/tool-Demographics_phenotype.tsv new file mode 100644 index 000000000..7c6c5c576 --- /dev/null +++ b/pheno005/phenotype/tool-Demographics_phenotype.tsv @@ -0,0 +1,4 @@ +participant_id session_id age +sub-01 ses-baseline 22 +sub-01 ses-followup 24 +sub-02 ses-baseline 63 diff --git a/pheno005/sub-01/ses-baseline/anat/sub-01_ses-baseline_T1w.json b/pheno005/sub-01/ses-baseline/anat/sub-01_ses-baseline_T1w.json new file mode 100644 index 000000000..c8ecf9b9e --- /dev/null +++ b/pheno005/sub-01/ses-baseline/anat/sub-01_ses-baseline_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 + ] + } +} \ No newline at end of file diff --git a/pheno005/sub-01/ses-baseline/anat/sub-01_ses-baseline_T1w.nii.gz b/pheno005/sub-01/ses-baseline/anat/sub-01_ses-baseline_T1w.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/pheno005/sub-02/ses-baseline/anat/sub-02_ses-baseline_T1w.json b/pheno005/sub-02/ses-baseline/anat/sub-02_ses-baseline_T1w.json new file mode 100644 index 000000000..98008d4c6 --- /dev/null +++ b/pheno005/sub-02/ses-baseline/anat/sub-02_ses-baseline_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 + ] + } +} \ No newline at end of file diff --git a/pheno005/sub-02/ses-baseline/anat/sub-02_ses-baseline_T1w.nii.gz b/pheno005/sub-02/ses-baseline/anat/sub-02_ses-baseline_T1w.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/pheno006/README.md b/pheno006/README.md new file mode 100644 index 000000000..1e1a93ed6 --- /dev/null +++ b/pheno006/README.md @@ -0,0 +1,28 @@ +# Pheno006 example dataset: Two sessions with one imaging-only session. No sessions files + +This dataset contains the bare minimum of imaging and phenotypic data from the baseline session and phenotypic data from followup sessions. Note how these sessions files do not contain `acq_time`, which will trigger a warning in the validator under the `"AdditionalValidation": ["Phenotype"]` in the `dataset_description.json`. The file tree is as follows: + +```bash +pheno006 +|-- README.md +|-- participants.json +|-- participants.tsv +|-- phenotype +| |-- tool-ACE_phenotype.json +| |-- tool-ACE_phenotype.tsv +| |-- tool-Demographics_phenotype.json +| `-- tool-Demographics_phenotype.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, 11 files + +``` diff --git a/pheno006/dataset_description.json b/pheno006/dataset_description.json new file mode 100644 index 000000000..457891def --- /dev/null +++ b/pheno006/dataset_description.json @@ -0,0 +1,14 @@ +{ + "Name": "BEP036 example dataset 06: Two sessions with one imaging-only session. (No sessions file example)", + "BIDSVersion": "1.11.0", + "DatasetType": "raw", + "License": "CC0", + "Authors": [ + "Arshitha Basavaraj", + "Eric Earl", + "Sebastian Urchs", + "Samuel Guay", + "Dustin Moraczewski" + ], + "AdditionalValidation": ["Phenotype"] +} \ No newline at end of file diff --git a/pheno006/participants.json b/pheno006/participants.json new file mode 100644 index 000000000..a6968c8ac --- /dev/null +++ b/pheno006/participants.json @@ -0,0 +1,23 @@ +{ + "participant_id": { + "Description": "Unique participant identifier." + }, + "session_id": { + "Description": "ID assigned to participant's visit.", + "Levels": { + "ses-baseline": "First imaging and phenotype data collection visit", + "ses-followup": "Second phenotype data collection visit." + } + }, + "sex": { + "Description": "Biological sex of the participant.", + "Levels": { + "m": "Male", + "f": "Female" + } + }, + "age": { + "Description": "Age of the participant at the time of the visit.", + "Units": "years" + } +} \ No newline at end of file diff --git a/pheno006/participants.tsv b/pheno006/participants.tsv new file mode 100644 index 000000000..bbb87c397 --- /dev/null +++ b/pheno006/participants.tsv @@ -0,0 +1,3 @@ +participant_id sex +sub-01 m +sub-02 f diff --git a/pheno006/phenotype/tool-ACE_phenotype.json b/pheno006/phenotype/tool-ACE_phenotype.json new file mode 100644 index 000000000..700012e71 --- /dev/null +++ b/pheno006/phenotype/tool-ACE_phenotype.json @@ -0,0 +1,99 @@ +{ + "IndexColumns": [ + "participant_id", + "session_id" + ], + "MeasurementToolMetadata": { + "Description": "Adverse Childhood Experience Questionnaire for Adults" + }, + "participant_id": { + "Description": "Unique participant identifier." + }, + "session_id": { + "Description": "ID assigned to participant's visit.", + "Levels": { + "ses-baseline": "First imaging and phenotype data collection visit.", + "ses-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" + } + } +} \ No newline at end of file diff --git a/pheno006/phenotype/tool-ACE_phenotype.tsv b/pheno006/phenotype/tool-ACE_phenotype.tsv new file mode 100644 index 000000000..411b1865e --- /dev/null +++ b/pheno006/phenotype/tool-ACE_phenotype.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 ses-baseline 0 0 0 0 0 0 1 0 0 0 +sub-01 ses-followup 1 0 0 1 0 1 0 0 0 0 +sub-02 ses-baseline 0 0 0 0 0 0 0 0 0 0 diff --git a/pheno006/phenotype/tool-Demographics_phenotype.json b/pheno006/phenotype/tool-Demographics_phenotype.json new file mode 100644 index 000000000..9b674f386 --- /dev/null +++ b/pheno006/phenotype/tool-Demographics_phenotype.json @@ -0,0 +1,20 @@ +{ + "IndexColumns": [ + "participant_id", + "session_id" + ], + "participant_id": { + "Description": "Unique participant identifier." + }, + "session_id": { + "Description": "ID assigned to participant's visit.", + "Levels": { + "ses-baseline": "First imaging and phenotype data collection visit", + "ses-followup": "Second phenotype data collection visit." + } + }, + "age": { + "Description": "Age of the participant at the time of the visit.", + "Units": "years" + } +} \ No newline at end of file diff --git a/pheno006/phenotype/tool-Demographics_phenotype.tsv b/pheno006/phenotype/tool-Demographics_phenotype.tsv new file mode 100644 index 000000000..7c6c5c576 --- /dev/null +++ b/pheno006/phenotype/tool-Demographics_phenotype.tsv @@ -0,0 +1,4 @@ +participant_id session_id age +sub-01 ses-baseline 22 +sub-01 ses-followup 24 +sub-02 ses-baseline 63 diff --git a/pheno006/sub-01/ses-baseline/anat/sub-01_ses-baseline_T1w.json b/pheno006/sub-01/ses-baseline/anat/sub-01_ses-baseline_T1w.json new file mode 100644 index 000000000..c8ecf9b9e --- /dev/null +++ b/pheno006/sub-01/ses-baseline/anat/sub-01_ses-baseline_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 + ] + } +} \ No newline at end of file diff --git a/pheno006/sub-01/ses-baseline/anat/sub-01_ses-baseline_T1w.nii.gz b/pheno006/sub-01/ses-baseline/anat/sub-01_ses-baseline_T1w.nii.gz new file mode 100644 index 000000000..e69de29bb diff --git a/pheno006/sub-02/ses-baseline/anat/sub-02_ses-baseline_T1w.json b/pheno006/sub-02/ses-baseline/anat/sub-02_ses-baseline_T1w.json new file mode 100644 index 000000000..98008d4c6 --- /dev/null +++ b/pheno006/sub-02/ses-baseline/anat/sub-02_ses-baseline_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 + ] + } +} \ No newline at end of file diff --git a/pheno006/sub-02/ses-baseline/anat/sub-02_ses-baseline_T1w.nii.gz b/pheno006/sub-02/ses-baseline/anat/sub-02_ses-baseline_T1w.nii.gz new file mode 100644 index 000000000..e69de29bb