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neurodatascience / nipoppy

Lightweight framework for neuroimaging-clinical data organization/processing
https://nipoppy.readthedocs.io/en/latest/
MIT License
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Add command to import a BIDS dataset into a Nipoppy dataset #233

Open michellewang opened 1 month ago

michellewang commented 1 month ago

Something like nipoppy import maybe? Or nipoppy init-from-bids?

It would:

  1. Move (or symlink?) the BIDS data to the Nipoppy BIDS directory (<DATASET_ROOT>/bids)
  2. Copy the sample global config to the appropriate directory
  3. Create a manifest from the BIDS dataset
    • participant_id: strip the sub- prefix from the BIDS subject
    • visit: strip the ses- prefix from the BIDS session
    • session: same as BIDS session
    • datatypes: either by crawling through the dataset to check the directories or using PyBIDS or bids2table

Need to decide:

  1. What do we do if the original BIDS dataset is cross-sectional (i.e. does not have sessions)?