nipoppy.workflows.bids_conversion

Workflow for convert command.

Module Contents

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)

Bases: nipoppy.workflows.runner.PipelineRunner

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)

dpaths_to_check()

Directory paths to create if needed during the setup phase.

Return type:

list[pathlib.Path]

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])

pipeline_config()

Get the user config for the BIDS conversion software.

Return type:

nipoppy.config.pipeline.BidsPipelineConfig

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)