datahipy.bids.validation module

Functions for validating BIDS datasets.

datahipy.bids.validation.add_bidsignore_validation_rule(bids_dir, rule)

Create/update a bidsignore file to ignore specific files by the BIDS Validator.

Parameters

bids_dirstr

Path to the BIDS dataset.

rulestr

Rule to add to the bidsignore file, e.g. “**/_ct.” to ignore all CT files.

datahipy.bids.validation.get_bids_validator_output_info(bids_dir, bids_schema_version=None)

Run the bids-validator on the dataset with the specified schema version and the option to ignore subject consistency.

Parameters

bids_dirstr

Path to the BIDS dataset.

bids_schema_versionstr

BIDS schema version to use for the validation. (e.g. “v1.7.0”)

Returns

bids_validator_output_infodict

Dictionary containing the bids-validator output to be integrated in the dataset content to be indexed.

datahipy.bids.validation.validate_bids_dataset(container_dataset_path, *args)

Validate a BIDS dataset using the BIDS Validator.

Parameters

container_dataset_pathstr

Path to the BIDS dataset

argslist

List of options to pass to the bids-validator. Can be used to ignore warnings (["--ignoreWarnings"]) or nifti headers (["--ignoreNiftiHeaders"]) or to skip checking that any given file for one subject is present for all other subjects (["--ignoreSubjectConsistency"]) or to use a specific BIDS schema (["-s", "v1.6.0"])

Returns

outputdict

Output of the bids-validator as a dictionary.

return_codeint

Return code of the bids-validator.