nipoppy.workflows.bids_conversion.BidsConversionRunner¶

class nipoppy.workflows.bids_conversion.BidsConversionRunner(dpath_root, pipeline_name, pipeline_version=None, pipeline_step=None, participant_id=None, session_id=None, simulate=False, fpath_layout=None, logger=None, dry_run=False)¶

Convert data to BIDS.

Parameters:

dpath_root (nipoppy.env.StrOrPathLike)
pipeline_name (str)
pipeline_version (Optional[str])
pipeline_step (Optional[str])
participant_id (str)
session_id (str)
simulate (bool)
fpath_layout (Optional[nipoppy.env.StrOrPathLike])
logger (Optional[logging.Logger])
dry_run (bool)

get_participants_sessions_to_run(participant_id, session_id)¶

Return participant-session pairs to run the pipeline on.

Parameters:

participant_id (Optional[str])
session_id (Optional[str])

run_cleanup(**kwargs)¶

Clean up after main BIDS conversion part is run.

Specifically: - Write updated doughnut file

run_single(participant_id, session_id)¶

Run BIDS conversion on a single participant/session.

Parameters:

participant_id (str)
session_id (str)

property dpaths_to_check: list[pathlib.Path]¶

Directory paths to create if needed during the setup phase.

Return type:: list[pathlib.Path]

name = 'bids_conversion'¶

property pipeline_config: nipoppy.config.pipeline.BidsPipelineConfig¶

Get the user config for the BIDS conversion pipeline.

Return type:: nipoppy.config.pipeline.BidsPipelineConfig

property pipeline_step_config: nipoppy.config.pipeline_step.BidsPipelineStepConfig¶

Get the config for the relevant step of the BIDS conversion pipeline.

Return type:: nipoppy.config.pipeline_step.BidsPipelineStepConfig