Raw Subject Folders in BIDS - AutocleanEEG Pipeline

Each participant has their own folder inside bids/. The pipeline begins by converting the original input files into BIDS-compliant format before any cleaning is applied. This ensures future steps follow the strict BIDS standard.

Example Layout

sub-451559/
├── sub-451559_scans.tsv
└── eeg/
    ├── sub-451559_task-tutorial_eeg.json
    ├── sub-451559_task-tutorial_eeg.vhdr
    ├── sub-451559_task-tutorial_eeg.vmrk
    ├── sub-451559_task-tutorial_eeg.eeg
    ├── sub-451559_task-tutorial_channels.tsv
    ├── sub-451559_task-tutorial_events.json
    ├── sub-451559_task-tutorial_events.tsv
    ├── sub-451559_space-XYZ_coordsystem.json
    └── sub-451559_space-XYZ_electrodes.tsv

These files are a direct conversion from the original inputs.
If you need to save disk space, you can safely delete them after processing, since they can always be regenerated from the raw recordings.

Key Files

File	Purpose
*`_scans.tsv`**	Records acquisition date/time for each data file.
*`_eeg.vhdr/.vmrk/.eeg`**	The BrainVision EEG file trio (header, markers, raw data). This is the converted raw EEG recording in BIDS format.
*`_eeg.json`**	Metadata describing acquisition parameters (sampling rate, reference, filters).
*`_channels.tsv`**	Channel list with type, name, and status (e.g., marked bad).
*`_events.tsv` / `_events.json`*	Event timing and event metadata.
*`_coordsystem.json`**	Coordinate system definition for electrode positions.
*`_electrodes.tsv`**	Electrode names and 3D positions.

Why BIDS First?

Standardization: Once in BIDS, every participant has the same predictable structure.
Interoperability: Outputs can be validated with the BIDS validator and read by tools like MNE-BIDS or EEGLAB-BIDS.
Traceability: Original input → standardized BIDS copy → cleaned derivatives.

The subject folder ID (e.g. sub-451559) may not match the original filename.
The mapping between recording filenames and subject IDs is tracked in participants.tsv.