> ## Documentation Index
> Fetch the complete documentation index at: https://docs.autocleaneeg.org/llms.txt
> Use this file to discover all available pages before exploring further.

# Raw Subject Folders in BIDS

> Explore the per-subject structure (`sub-<ID>`) created when raw data are converted into BIDS format.

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
```

<Tip>
  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.
</Tip>

### 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](https://bids-standard.github.io/bids-validator/) and read by tools like MNE-BIDS or EEGLAB-BIDS.
* **Traceability**: Original input → standardized BIDS copy → cleaned derivatives.

<Info>
  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`.
</Info>