> ## 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.

# AutoCleanEEG Workspace

> Learn how to navigate and understand the AutoCleanEEG workspace structure

The **AutoCleanEEG workspace** is your centralized hub for all pipeline activities, containing tasks, outputs, logs, and configuration files. This organized structure ensures your research is reproducible, traceable, and easy to manage across multiple projects and collaborators.

<Note>
  The workspace is designed to support multiple concurrent projects. Output folders are named after the tasks you run, and reruns automatically create timestamped backups to preserve previous results.
</Note>

## Workspace Structure

```
Autoclean-EEG/
├── process_log.txt         (command history and system events)
├── pipeline.db             (run database and metadata)   
├── tasks/                  (task definitions and configurations)
│   ├── RestingState_Basic.py
│   ├── RestingStateTutorial.py
│   └── custom_task.py
└── output/                 (processing results and outputs)
    ├── RestingStateTutorial/               (task-specific output folder)
    │   ├── bids/                           (BIDS-compliant inputs & derivatives) 
    │   ├── exports/                        (EEG-only final datasets + convenience logs/CSVs)
    │   ├── reports/                        (run_reports: PDFs, per-file CSVs, JSON summaries)
    │   ├── logs/                           (single pipeline.log)
    │   ├── qa/                             (fastplot PNGs + qa_manifest.csv)
    │   ├── ica/                            (ICA FIF + ica_control_sheet.csv)
    │   └── preprocessing_log.csv           (combined task-level processing log)
    └── RestingStateTutorial_2025-09-04/    (automatic backup from rerun)
```

### Key Components

* **`tasks/`** - Contains your task definitions, both built-in and custom tasks you create
* **`output/`** - Stores all processing results, organized by task name
* **`process_log.txt`** - System-wide command history and pipeline events
* **`pipeline.db`** - SQLite database tracking all runs, parameters, and results

## Opening the Workspace Folder

By default, the workspace is created as **`Autoclean-EEG`** inside your **Documents** directory.

To open the workspace directly from the terminal, run:

```bash theme={null}
autocleaneeg-pipeline workspace explore
```

This command will:

* Locate your active workspace.
* Launch your system’s file explorer at that location:

  * **macOS** → Finder
  * **Linux** → Nautilus (or your system’s default file manager)
  * **Windows** → File Explorer

## Workspace Management

### Multiple Projects

The workspace supports running multiple tasks and projects simultaneously. Each task creates its own output folder, allowing you to:

* Compare results across different preprocessing approaches
* Maintain separate configurations for different studies
* Archive completed projects without affecting active work

### Backup System

AutoCleanEEG automatically preserves your work:

* Reruns create timestamped backup folders (`TaskName_YYYY-MM-DD/`)
* Previous results are never overwritten
* Compare parameters and outcomes across different runs

## Next Steps

* **Browse Tasks** - Explore the `tasks/` folder to see available processing pipelines
* **Review Outputs** - Check the `output/` folder for BIDS inputs/derivatives, and task‑root `exports/`, `reports/`, `qa/`, and `ica/`
* **Examine Logs** - Use `process_log.txt` and run-specific logs for troubleshooting
* **Database Queries** - Access `pipeline.db` for detailed run metadata and batch analysis