ENH: Add example datasets corresponding to BEP020 #478
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I'll work on the other dataset later this week. |
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quick thing: unless there is a good reason for it, maybe let's try to have just one or 2 subejcts per dataset. |
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See here for an example on how to test with the schema from the eyetracking BEP: 6e79b9e |
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@julia-pfarr we've got some errors: 2025-01-15T10:52:27.5811168Z �[31m[ERROR] NOT_INCLUDED Files with such naming scheme are not part of BIDS specification. This error is most commonly caused by typos in file names that make them not BIDS compatible. Please consult the specification and make sure your files are named correctly. If this is not a file naming issue (for example when including files not yet covered by the BIDS specification) you should include a ".bidsignore" file in your dataset (see https://github.com/bids-standard/bids-validator#bidsignore for details). Please note that derived (processed) data should be placed in /derivatives folder and source data (such as DICOMS or behavioural logs in proprietary formats) should be placed in the /sourcedata folder.�[39m
2025-01-15T10:52:27.5814716Z /task-rest_physioevents.json
2025-01-15T10:52:27.5815092Z /sub-01/ses-01/func/sub-01_ses-01_task-rest_run-02_recording-eye1_physioevents.tsv.gz
2025-01-15T10:52:27.5815532Z
2025-01-15T10:52:27.5815624Z 3 more files with the same issue
2025-01-15T10:52:27.5815778Z
2025-01-15T10:52:27.5816190Z �[36m Please visit https://neurostars.org/search?q=NOT_INCLUDED for existing conversations about this issue.�[39m
2025-01-15T10:52:27.5816657Z
2025-01-15T10:52:27.5817370Z �[31m[ERROR] JSON_SCHEMA_VALIDATION_ERROR Invalid JSON sidecar file. The sidecar is not formatted according the schema.�[39m
2025-01-15T10:52:27.5818045Z �[31mStartTime�[39m
2025-01-15T10:52:27.5818412Z /sub-01/ses-01/func/sub-01_ses-01_task-rest_run-01_recording-eye1_physio.json - must be number
2025-01-15T10:52:27.5819165Z /sub-01/ses-01/func/sub-01_ses-01_task-rest_run-02_recording-eye1_physio.json - must be number
2025-01-15T10:52:27.5819550Z
2025-01-15T10:52:27.5819635Z 2 more files with the same issue
2025-01-15T10:52:27.5820008Z
2025-01-15T10:52:27.5820496Z �[36m Please visit https://neurostars.org/search?q=JSON_SCHEMA_VALIDATION_ERROR for existing conversations about this issue.�[39m
2025-01-15T10:52:27.5820936Z
2025-01-15T10:52:27.5821281Z �[31m[ERROR] SIDECAR_WITHOUT_DATAFILE A json sidecar file was found without a corresponding data file�[39m
2025-01-15T10:52:27.5821700Z /task-rest_events.json
2025-01-15T10:52:27.5821835Z
2025-01-15T10:52:27.5822247Z �[36m Please visit https://neurostars.org/search?q=SIDECAR_WITHOUT_DATAFILE for existing conversations about this issue.�[39m
2025-01-15T10:52:27.5822659Z
2025-01-15T10:52:27.5822663Z
2025-01-15T10:52:27.5822958Z �[35mSummary:�[39m �[35mAvailable Tasks:�[39m �[35mAvailable Modalities:�[39m
2025-01-15T10:52:27.5823397Z 50 Files, 40.4 kB rest MRI
2025-01-15T10:52:27.5823756Z 2 - Subjects 1 - Sessions
2025-01-15T10:52:27.5824005Z
2025-01-15T10:52:27.5824292Z �[36m If you have any questions, please post on https://neurostars.org/tags/bids.�[39m
2025-01-15T10:52:27.5824580Z
2025-01-15T10:52:27.5825096Z Validating dataset eyetracking2/: Running bids-validator eyetracking2 --config /home/runner/work/bids-examples/bids-examples/schemaconfig.json --ignoreNiftiHeaders
2025-01-15T10:52:27.8557449Z strict mode: missing type "array" for keyword "maxItems" at "#/properties/ScreenResolution/anyOf/0/items" (strictTypes)
2025-01-15T10:52:27.8560249Z strict mode: missing type "array" for keyword "minItems" at "#/properties/ScreenResolution/anyOf/0/items" (strictTypes)
2025-01-15T10:52:27.8563341Z strict mode: missing type "array" for keyword "maxItems" at "#/properties/ScreenSize/anyOf/0/items" (strictTypes)
2025-01-15T10:52:27.8564630Z strict mode: missing type "array" for keyword "minItems" at "#/properties/ScreenSize/anyOf/0/items" (strictTypes)
2025-01-15T10:52:27.9015902Z �[33m[WARNING] TSV_ADDITIONAL_COLUMNS_UNDEFINED A TSV file has extra columns which are not defined in its associated JSON sidecar�[39m
2025-01-15T10:52:27.9016841Z �[33msub-01�[39m
2025-01-15T10:52:27.9017152Z /participants.tsv
2025-01-15T10:52:27.9017333Z
2025-01-15T10:52:27.9018149Z �[36m Please visit https://neurostars.org/search?q=TSV_ADDITIONAL_COLUMNS_UNDEFINED for existing conversations about this issue.�[39m
2025-01-15T10:52:27.9018697Z
2025-01-15T10:52:27.9019115Z �[33m[WARNING] UNKNOWN_BIDS_VERSION The BIDSVersion field of 'dataset_description.json' does not match a known release.
2025-01-15T10:52:27.9019656Z The BIDS Schema used for validation may be out of date.
2025-01-15T10:52:27.9020197Z �[39m
2025-01-15T10:52:27.9020405Z /dataset_description.json
2025-01-15T10:52:27.9020562Z
2025-01-15T10:52:27.9021252Z �[36m Please visit https://neurostars.org/search?q=UNKNOWN_BIDS_VERSION for existing conversations about this issue.�[39m
2025-01-15T10:52:27.9021676Z
2025-01-15T10:52:27.9022032Z �[33m[WARNING] SIDECAR_KEY_RECOMMENDED A data file's JSON sidecar is missing a key listed as recommended.�[39m
2025-01-15T10:52:27.9022487Z �[33mInstructions�[39m
2025-01-15T10:52:27.9022886Z /sub-01/beh/sub-01_task-FreeView_run-01_events.tsv
2025-01-15T10:52:27.9023191Z /sub-01/beh/sub-01_task-FreeView_run-02_events.tsv
2025-01-15T10:52:27.9023375Z
2025-01-15T10:52:27.9023466Z 2 more files with the same issue
2025-01-15T10:52:27.9023620Z
2025-01-15T10:52:27.9023734Z �[33mTaskDescription�[39m
2025-01-15T10:52:27.9023994Z /sub-01/beh/sub-01_task-FreeView_run-01_events.tsv
2025-01-15T10:52:27.9024288Z /sub-01/beh/sub-01_task-FreeView_run-02_events.tsv
2025-01-15T10:52:27.9024468Z
2025-01-15T10:52:27.9024547Z 2 more files with the same issue
2025-01-15T10:52:27.9024696Z
2025-01-15T10:52:27.9024793Z �[33mCogAtlasID�[39m
2025-01-15T10:52:27.9025022Z /sub-01/beh/sub-01_task-FreeView_run-01_events.tsv
2025-01-15T10:52:27.9025299Z /sub-01/beh/sub-01_task-FreeView_run-02_events.tsv
2025-01-15T10:52:27.9025480Z
2025-01-15T10:52:27.9025558Z 2 more files with the same issue
2025-01-15T10:52:27.9025700Z
2025-01-15T10:52:27.9025799Z �[33mCogPOID�[39m
2025-01-15T10:52:27.9026009Z /sub-01/beh/sub-01_task-FreeView_run-01_events.tsv
2025-01-15T10:52:27.9026287Z /sub-01/beh/sub-01_task-FreeView_run-02_events.tsv
2025-01-15T10:52:27.9026471Z
2025-01-15T10:52:27.9026555Z 2 more files with the same issue
2025-01-15T10:52:27.9026698Z
2025-01-15T10:52:27.9026838Z �[33mInstitutionalDepartmentName�[39m
2025-01-15T10:52:27.9027104Z /sub-01/beh/sub-01_task-FreeView_run-01_events.tsv
2025-01-15T10:52:27.9027381Z /sub-01/beh/sub-01_task-FreeView_run-02_events.tsv
2025-01-15T10:52:27.9027557Z
2025-01-15T10:52:27.9027641Z 2 more files with the same issue
2025-01-15T10:52:27.9027783Z
2025-01-15T10:52:27.9027893Z �[33mSoftwareVersions�[39m
2025-01-15T10:52:27.9028207Z /sub-01/beh/sub-01_task-FreeView_run-02_recording-eye1_physio.tsv.gz
2025-01-15T10:52:27.9028611Z /sub-01/beh/sub-01_task-FreeView_run-01_recording-eye2_physio.tsv.gz
2025-01-15T10:52:27.9028844Z
2025-01-15T10:52:27.9028923Z 6 more files with the same issue
2025-01-15T10:52:27.9029072Z
2025-01-15T10:52:27.9029170Z �[33mTaskName�[39m
2025-01-15T10:52:27.9029432Z /sub-01/beh/sub-01_task-FreeView_run-02_recording-eye1_physio.tsv.gz
2025-01-15T10:52:27.9029992Z /sub-01/beh/sub-01_task-FreeView_run-01_recording-eye2_physio.tsv.gz
2025-01-15T10:52:27.9030232Z
2025-01-15T10:52:27.9030309Z 6 more files with the same issue
2025-01-15T10:52:27.9030457Z
2025-01-15T10:52:27.9030892Z �[36m Please visit https://neurostars.org/search?q=SIDECAR_KEY_RECOMMENDED for existing conversations about this issue.�[39m
2025-01-15T10:52:27.9031306Z
2025-01-15T10:52:27.9031750Z �[31m[ERROR] PARTICIPANT_ID_MISMATCH Participant labels found in this dataset did not match the values in participant_id column
2025-01-15T10:52:27.9032253Z found in the participants.tsv file.
2025-01-15T10:52:27.9032498Z �[39m
2025-01-15T10:52:27.9032661Z /participants.tsv
2025-01-15T10:52:27.9032782Z
2025-01-15T10:52:27.9033206Z �[36m Please visit https://neurostars.org/search?q=PARTICIPANT_ID_MISMATCH for existing conversations about this issue.�[39m
2025-01-15T10:52:27.9033637Z
2025-01-15T10:52:27.9033832Z �[31m[ERROR] TSV_COLUMN_MISSING A required column is missing�[39m
2025-01-15T10:52:27.9034171Z �[31mparticipant_id�[39m
2025-01-15T10:52:27.9034444Z /participants.tsv - Column 0 (starting from 0) not found.
2025-01-15T10:52:27.9034741Z /participants.tsv
2025-01-15T10:52:27.9034852Z
2025-01-15T10:52:27.9035249Z �[36m Please visit https://neurostars.org/search?q=TSV_COLUMN_MISSING for existing conversations about this issue.�[39m
2025-01-15T10:52:27.9035642Z
2025-01-15T10:52:27.9038189Z �[31m[ERROR] NOT_INCLUDED Files with such naming scheme are not part of BIDS specification. This error is most commonly caused by typos in file names that make them not BIDS compatible. Please consult the specification and make sure your files are named correctly. If this is not a file naming issue (for example when including files not yet covered by the BIDS specification) you should include a ".bidsignore" file in your dataset (see https://github.com/bids-standard/bids-validator#bidsignore for details). Please note that derived (processed) data should be placed in /derivatives folder and source data (such as DICOMS or behavioural logs in proprietary formats) should be placed in the /sourcedata folder.�[39m
2025-01-15T10:52:27.9040796Z /task-FreeView_physioevents.json
2025-01-15T10:52:27.9041147Z /sub-01/beh/sub-01_task-FreeView_run-01_recording-eye1_physioevents.tsv.gz
2025-01-15T10:52:27.9041416Z
2025-01-15T10:52:27.9041496Z 7 more files with the same issue
2025-01-15T10:52:27.9041645Z
2025-01-15T10:52:27.9042041Z �[36m Please visit https://neurostars.org/search?q=NOT_INCLUDED for existing conversations about this issue.�[39m
2025-01-15T10:52:27.9042427Z
2025-01-15T10:52:27.9042820Z �[31m[ERROR] JSON_SCHEMA_VALIDATION_ERROR Invalid JSON sidecar file. The sidecar is not formatted according the schema.�[39m
2025-01-15T10:52:27.9043307Z �[31mStartTime�[39m
2025-01-15T10:52:27.9043626Z /sub-01/beh/sub-01_task-FreeView_run-02_recording-eye1_physio.json - must be number
2025-01-15T10:52:27.9044118Z /sub-01/beh/sub-01_task-FreeView_run-01_recording-eye2_physio.json - must be number
2025-01-15T10:52:27.9044402Z
2025-01-15T10:52:27.9044486Z 6 more files with the same issue
2025-01-15T10:52:27.9044631Z
2025-01-15T10:52:27.9045057Z �[36m Please visit https://neurostars.org/search?q=JSON_SCHEMA_VALIDATION_ERROR for existing conversations about this issue.�[39m
2025-01-15T10:52:27.9045487Z
2025-01-15T10:52:27.9045492Z
2025-01-15T10:52:27.9045774Z �[35mSummary:�[39m �[35mAvailable Tasks:�[39m �[35mAvailable Modalities:�[39m
2025-01-15T10:52:27.9046197Z 34 Files, 15.8 kB FreeView beh
2025-01-15T10:52:27.9046558Z 2 - Subjects 1 - Sessions
2025-01-15T10:52:27.9046785Z
2025-01-15T10:52:27.9047050Z �[36m If you have any questions, please post on https://neurostars.org/tags/bids.�[39m |
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@oesteban I think I fixed all the errors in the two datasets. Could you check again for both? (v2.0.5 for the OpenNeuro one). My validation shows ok (except the naming scheme part for the physioevents files) |
This was referenced Jan 23, 2025
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Adds example data to complement bids-standard/bids-specification#1128.
cc/ @mszinte, @julia-pfarr, @Remi-Gau