The BIDS Validator is a tool that checks if a dataset is compliant with the BIDS standard. The validator is available for use within several different environments to best suit individual user preferences and use cases, those versions are:
A web browser based version
Command line version
Docker based version
A python library installable via pip
Instructions to install and use these versions can be found within the quickstart guide at the BIDS Validator repository.
Data Privacy and Confidentiality
Please note that the web app is entirely browser(not server) based. As such, there is no file uploading as part of the validation.
The BIDS Validator can be found at http://bids-standard.github.io/bids-validator/. It requires that you use the Chrome or Firefox browser, since those are the only ones in which you can select a whole folder rather than individual files.
You can then choose the folder that you wish to validate
Types of Feedback¶
This response indicates that your dataset is not BIDS compliant. Try following the suggestions listed to make the appropriate corrections
This response indicates that your dataset is BIDS compliant, but there are some non-critical problems (such as optional fields missing, or differences between participants)
This response indicates that your folder contains a valid BIDS Dataset!
Command Line Version¶
Verifying a BIDS compliant data set¶
After installation with npm using the CLI is trivial. Locate a bids data set similar to the one below:
user@host:~/bids-examples$ tree sub001/ sub001/ ├── dataset_description.json ├── participants.json ├── participants.tsv ├── README └── sub-01 ├── ses-baseline │ ├── anat │ │ ├── sub-01_ses-baseline_T1w.json │ │ └── sub-01_ses-baseline_T1w.nii.gz │ └── pet │ ├── sub-01_ses-baseline_pet.json │ └── sub-01_ses-baseline_pet.nii.gz └── ses-intervention ├── anat │ ├── sub-01_ses-intervention_T1w.json │ └── sub-01_ses-intervention_T1w.nii.gz └── pet ├── sub-01_ses-intervention_task-eyes_events.json ├── sub-01_ses-intervention_task-eyes_events.tsv ├── sub-01_ses-intervention_task-eyes_pet.json └── sub-01_ses-intervention_task-eyes_pet.nii.gz
Now simply point the bids validator at the folder path of the subject(s) in question:
user@host:~/bids-examples$ bids-validator sub001
Types of Feedback¶
As is the case w/ the browser or any version of the validator follow the
messages and correct until bids-validator returns 0 errors after running.
user@host:~/bids-examples$ bids-validator sub001 firstname.lastname@example.org 1: [ERR] Invalid JSON file. The file is not formatted according the schema. (code: 55 - JSON_SCHEMA_VALIDATION_ERROR) ./sub-01/ses-baseline/pet/sub-01_ses-baseline_pet.json Evidence: should have property InjectedRadioactivityUnits when property InjectedRadioactivity is present ./sub-01/ses-baseline/pet/sub-01_ses-baseline_pet.json Evidence: should have required property 'InjectedMassUnits' ... ... ... and 3 more files having this issue (Use --verbose to see them all). Please visit https://neurostars.org/search?q=JSON_SCHEMA_VALIDATION_ERROR for existing conversations about this issue. Summary: Available Tasks: Available Modalities: 14 Files, 5.72MB T1w 1 - Subject pet 2 - Sessions events If you have any questions, please post on https://neurostars.org/tags/bids.
As stated with the browser version above, one may elect to ignore warnings, but the information provided via the validator should help to pinpoint where and how to resolve some of these warnings. When in doubt consult the BIDS Spec
user@host:~/bids-examples$ bids-validator sub001/ email@example.com 1: [WARN] Tabular file contains custom columns not described in a data dictionary (code: 82 - CUSTOM_COLUMN_WITHOUT_DESCRIPTION) ./sub-01/func/sub-01_task-balloonanalogrisktask_run-01_events.tsv ... ... ... and 38 more files having this issue (Use --verbose to see them all). Please visit https://neurostars.org/search?q=CUSTOM_COLUMN_WITHOUT_DESCRIPTION for existing conversations about this issue. Summary: Available Tasks: Available Modalities: 134 Files, 411.53KB balloon analog risk task T1w 16 - Subjects inplaneT2 1 - Session bold events If you have any questions, please post on https://neurostars.org/tags/bids.
Pass go and collect 200 dollars, the data set in question passes validation.
user@host:~/bids-examples$ bids-validator sub001 firstname.lastname@example.org This dataset appears to be BIDS compatible. Summary: Available Tasks: Available Modalities: 12 Files, 218.75KB T1w 1 - Subject pet 1 - Session blood If you have any questions, please post on https://neurostars.org/tags/bids