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Stage Folders under derivatives/

AutoCleanEEG writes numbered stage folders directly under bids/derivatives/. These are dynamically generated — only the steps you enable and configure for export will appear. For example, if you skip ICA or don’t export filtering outputs, the corresponding step folder (08_ica/ or 03_filter/) won’t exist in your run.

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Example Layout

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How It Works

  • Step numbering reflects the pipeline order.
  • Exported steps only: If you request export after filtering but not after trimming, you’ll see 03_filter/ but not 04_trim/.
  • Flexible granularity: This lets you save just the checkpoints you care about (for inspection or debugging), while avoiding unnecessary disk usage.

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Step Highlights

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ICA Export Format

The ICA stage is exported in both EEGLAB (.set) and MNE (.fif) formats.
This is a special case:
  • In EEGLAB, ICA weights are stored directly inside the .set dataset.
  • In MNE-Python, ICA weights are stored separately from the EEG data (the .fif ICA file).
This separation allows you to:
  • Reapply ICA weights later to the same dataset.
  • Redo component artifact removal and continue the pipeline from that point (feature coming soon).

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Why It Matters

  • Customizable exports: You decide which steps produce saved files.
  • Debug-friendly: Inspect any stage of the pipeline without re-running the entire process.
  • Storage-aware: Avoid large intermediate folders by disabling exports for steps you don’t need.
Stage folders are optional checkpoints. You can enable or disable exports per step in your task configuration. Once validated, these folders can be safely deleted to reclaim space.