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Data organization

Nipoppy docs are moving

Nipoppy is undergoing a major refactor to move from scripts to a command-line interface (CLI) and Python API. The new documentation website (work in progress) can be found at

If you are using the (soon-to-be legacy) scripts from Nipoppy 0.1.0, this is still the correct place to be. But we encourage you to check out the new website!

Data organization

An Nipoppy dataset consists of a specific directory structure to organize MRI and tabular data.


  • tabular
    • contains manifest.csv
    • demographics: contains demographic data (e.g. age, sex)
    • assessments: contains clinical assessments (e.g. MoCA)
  • downloads: data dumps from remote data-stores (e.g. LONI)
  • scratch: space for un-organized data and wrangling
  • dicom: participant-level dicom dirs
  • bids: BIDS formatted dataset
  • derivatives: output of processing pipelines (e.g. fmriprep, mriqc)
  • proc: space for config and log files of the processing pipelines
  • backups: data backup space (tars)
  • releases: data releases (symlinks)