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@Hyedryn Hyedryn commented Jan 20, 2023

Provide a fix for #50

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Currently fmriprep-rodents consider that the collect_data function of niworkflows has the following header:

def collect_data( bids_dir, participant_label, task=None, echo=None, bids_validate=True, bids_filters=None, )

Indeed, when calling collect_data, the task and echo parameters are not defined explicitly:
subject_data = collect_data( config.execution.layout, subject_id, config.execution.task_id, config.execution.echo_idx, bids_filters=config.execution.bids_filters, )[0]

However, the header of the collect_data function of niworkflows has the optional parameter session_id before the optional parameter task.
def collect_data( bids_dir, participant_label, session_id=Query.OPTIONAL, task=None, echo=None, bids_validate=True, bids_filters=None, )

When calling collect_data, the task and echo parameters should thus be defined explicitly:
subject_data = collect_data( config.execution.layout, subject_id, task=config.execution.task_id, echo=config.execution.echo_idx, bids_filters=config.execution.bids_filters, )[0]

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