User Guide

The EEGPrep user guide is organized around real research workflows: load data, understand the dataset structure, work in the GUI and console together, script repeatable steps, review artifacts and components, manage plugins, and run group-level analyses.

Recommended path: run the quick start with sample_data/eeglab_data.set, read the Concepts Guide, then repeat the same workflow with the GUI and eegprep-console open side by side.

Getting Started

• Installation
• Quick Start
• Concepts Guide
• EEGLAB Migration Notes

GUI, Console, and Scripts

• GUI and Console Together
• GUI Tutorials
• Interactive Console
• Agent-Friendly EEGPrep CLI
• Scripting Workflows
• MNE-Python Integration

Preprocessing and Review

• Preprocessing Pipeline
• ICA, ICLabel, Rejection, and Visual Diagnostics
• EEGBrowser Workflows
• BIDS Workflow
• Large-Dataset Storage

Group and Plugin Workflows

• STUDY Workflows
• Bundled Plugins and Extensions
• External Extensions
• Installing Extensions
• Using Installed Extensions
• Startup and Extension Loading
• Required Package Format
• pop_* History and Console Rules
• Package Data, Optional Dependencies, and Large Files
• Trust Levels and States
• Catalog Schema
• Catalog Submission Checks
• Extension Curation and Catalog Policy

Admin, Help, and Development

• GUI and Help Menus
• Configuration
• Visual Parity Testing
• Advanced Topics

Common Entry Points

Task	GUI path	Console or Python call
Load a tutorial dataset	File > Load existing dataset	EEG = pop_loadset("sample_data/eeglab_data.set")
Inspect channel data	Plot > Channel data (scroll)	eegplot(EEG) or pop_eegplot(EEG)
Filter data	Tools > Filter the data	pop_eegfiltnew(EEG, locutoff=1, hicutoff=40)
Run headless agent workflows	Not applicable	eegprep pipeline plan preprocess.yaml --json
Resample data	Tools > Change sampling rate	pop_resample(EEG, 64)
Run clean_rawdata	Tools > Reject data using Clean Rawdata and ASR	pop_clean_rawdata(EEG, BurstCriterion=20)
Run ICA	Tools > Decompose data by ICA	pop_runica(EEG, icatype="picard", gui=False)
Label components	Tools > Classify components using ICLabel	pop_iclabel(EEG, "default")
Create a STUDY	File > Create study > Using all loaded datasets	pop_study(None, ALLEEG, name="My study")
Manage extensions	File > Manage EEGPrep extensions	plugin_menu(show=False)

Help Coverage

Every implemented GUI Help button and pophelp topic uses EEGPrep-owned Markdown resources packaged under src/eegprep/resources/help. Missing help is a packaging error; runtime code does not fall back to the vendored EEGLAB reference tree.