Standardize Input Names Across PET prep piplines

openneuropet / petdeface

A nipype implementation of an anatomical MR and PET defacing pipeline for BIDS datasets

https://petdeface.readthedocs.io

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Open bendhouseart opened 5 hours ago

bendhouseart commented 5 hours ago

PET pipelines should follow BIDS app naming conventions and formatting:

use positional arguments over flagged arguments for bids_dir, output_dir and participant_level
subjects should be referred to participants/subjects uniformly across apps.

See nipreps guide, petprep_hmc, and petprep_extract_tacs for examples both conforming and non-conforming.

bendhouseart commented 5 hours ago

@mnoergaard are we sticking with --flags or moving over to positional args as outlined above?