# AutocleanEEG Pipeline > Automated EEG Software ## Docs - [Basic Concepts](https://docs.autocleaneeg.org/basics.md): Understand the three pillars and how they fit together. - [CLI Themes](https://docs.autocleaneeg.org/customizations/cli-themes.md) - [Advanced: Flagged Runs & Output Routing](https://docs.autocleaneeg.org/customizations/flagged-outputs.md): Control whether flagged runs move into FLAGGED_* directories and whether final files are produced. - [Advanced: Persistent State (setup.json)](https://docs.autocleaneeg.org/customizations/persistent-state.md): How AutocleanEEG saves your defaults across runs and where to find them. - [Advanced: User‑Defined Variables in Tasks](https://docs.autocleaneeg.org/customizations/task-variables.md): Define custom variables in your task config and access them safely via `self.settings`. - [Setting Up Your Workspace](https://docs.autocleaneeg.org/essentials/workspace-cli.md): Create and set up your AutoClean EEG workspace folder - [Running Your Data](https://docs.autocleaneeg.org/input/batch_run.md): Learn how to set your input folder and run batch EEG preprocessing with AutoCleanEEG. - [Exploring the BIDS Folder](https://docs.autocleaneeg.org/outputs/bids_overview.md): Understand the structure and files created in the `bids/` folder, including metadata, subject folders, and processed outputs. - [Derivatives Overview](https://docs.autocleaneeg.org/outputs/derivatives_overview.md): Learn how AutoCleanEEG stores processed outputs in the BIDS derivatives folder, including metadata, intermediate files, and subject-level results. - [Exports Folder](https://docs.autocleaneeg.org/outputs/exports.md): Learn about the task‑root exports folder that collects EEG‑only final datasets and convenience logs. - [Derivatives: Stage Folders](https://docs.autocleaneeg.org/outputs/intermediate_steps.md): Learn how AutoCleanEEG writes numbered stage folders under derivatives for step-by-step inspection. - [LLM Reports (Optional)](https://docs.autocleaneeg.org/outputs/llm_reports.md): Opt-in AI-generated summaries from pipeline runs, written under task-root reports. - [Logs, Reports, and Metadata](https://docs.autocleaneeg.org/outputs/metadata_logs.md): Understand the task‑root logs, reports, and metadata artifacts generated by AutoCleanEEG, including the ICA control sheet and QA images. - [AutoCleanEEG Workspace](https://docs.autocleaneeg.org/outputs/open_workspace.md): Learn how to navigate and understand the AutoCleanEEG workspace structure - [Understanding the Processing Log](https://docs.autocleaneeg.org/outputs/processing_log.md): Learn how to interpret the CSV report generated by each pipeline run - [Report chat](https://docs.autocleaneeg.org/outputs/report_chat.md) - [Raw Subject Folders in BIDS](https://docs.autocleaneeg.org/outputs/subject_folders.md): Explore the per-subject structure (`sub-`) created when raw data are converted into BIDS format. - [Derivatives: Subject-Specific Reports](https://docs.autocleaneeg.org/outputs/subject_reports.md): Explore the per-subject reports, logs, and visualizations generated by AutoCleanEEG for quality control. - [Task Output Layout](https://docs.autocleaneeg.org/outputs/task_output_layout.md): Overview of the per‑task folder structure: BIDS inputs/derivatives, exports, logs, QA, reports, ICA, and combined logs. - [Independent Component Analysis (ICA)](https://docs.autocleaneeg.org/pipeline-steps/ica.md): Understand how AutocleanEEG uses ICA to identify and remove artifacts like eye blinks, muscle activity, and heartbeat from EEG data. - [How ICVision Works](https://docs.autocleaneeg.org/pipeline-steps/icvision.md): Understanding the vision-based approach to ICA component classification - [Pipeline Reference](https://docs.autocleaneeg.org/pipeline-steps/overview.md): Overview of how methods are organized in AutoCleanEEG, how to extend them, and how we approach documentation during development. - [Run segment rejection peer review](https://docs.autocleaneeg.org/pipeline-steps/run-segment-rejection-peer-review.md) - [Artifact and Epoching Steps](https://docs.autocleaneeg.org/pipeline-steps/steps.md): Functions that label and clean artifacts and create analysis-ready epochs. - [Running an AutocleanEEG Pipeline](https://docs.autocleaneeg.org/pipeline_tutorial.md): Configure a workspace, select a task, and run reproducible EEG preprocessing with clear quality-control (QC) outputs. - [System Architecture](https://docs.autocleaneeg.org/system-architecture.md): Overview of the modular architecture enabling reproducible EEG preprocessing - [Task Management](https://docs.autocleaneeg.org/tasks/task-management.md): Comprehensive guide to creating, managing, and working with AutocleanEEG processing tasks. - [How the Task Class Works](https://docs.autocleaneeg.org/tasks/task_class.md): Understand how AutoCleanEEG Task classes transform MNE objects step by step, enabling powerful and customizable preprocessing workflows. - [Flexibility of the Task Class](https://docs.autocleaneeg.org/tasks/task_flexibility.md): See how the Task class enables branching, custom functions, and integration with Python or MATLAB to adapt pipelines for any experimental design. - [Task Library & Online Registry](https://docs.autocleaneeg.org/tasks/task_library_overview.md): Understand the built-in task library, GitHub registry, and how to keep your templates up to date. - [Task Library Walkthrough](https://docs.autocleaneeg.org/tasks/task_library_walkthrough.md): Step-by-step guide for syncing and installing official templates. - [Introduction to Task Files](https://docs.autocleaneeg.org/tasks/tasks_intro.md): Learn how Task files define your preprocessing pipeline in AutoCleanEEG Pipeline - [TaskWizard: Online Task Builder](https://docs.autocleaneeg.org/tasks/taskwizard.md): Generate custom AutoCleanEEG task files through an intuitive web interface - [Welcome to the AutocleanEEG Pipeline!](https://docs.autocleaneeg.org/welcome.md): Automated EEG Processing Software ## Optional - [TaskWizard](https://taskwizard.autocleaneeg.org/) - [Community](https://github.com/cincibrainlab/autocleaneeg_pipeline/discussions) - [Issues](https://github.com/cincibrainlab/autocleaneeg_pipeline/issues)