nipoppy.workflows.ExtractionRunner¶

class nipoppy.workflows.ExtractionRunner(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_single(participant_id, session_id)¶

Run extractor on a single participant/session.

Parameters:

participant_id (str)
session_id (str)

property dpath_pipeline: pathlib.Path¶

Get the path to the derivatives directory associated with the extractor.

Return type:: pathlib.Path

property dpath_pipeline_idp: pathlib.Path¶

Return the path to the pipeline’s IDP directory.

Return type:: pathlib.Path

property dpath_pipeline_output: pathlib.Path¶

Return the path to the pipeline’s output directory.

Return type:: pathlib.Path

property dpaths_to_check: list[pathlib.Path]¶

Directory paths to create if needed during the setup phase.

Return type:: list[pathlib.Path]

name = 'extract'¶

property pipeline_config: nipoppy.config.pipeline.ExtractionPipelineConfig¶

Get the user config for the extraction pipeline.

Return type:: nipoppy.config.pipeline.ExtractionPipelineConfig

property pipeline_step_config: nipoppy.config.pipeline_step.ExtractionPipelineStepConfig¶

Get the config for the relevant step of the extraction pipeline.

Return type:: nipoppy.config.pipeline_step.ExtractionPipelineStepConfig

property proc_pipeline_info: nipoppy.config.pipeline.PipelineInfo¶

Get info about the first processing pipeline associated with extractor.

Also make sure the it is in the config as a processing pipeline.

Return type:: nipoppy.config.pipeline.PipelineInfo