Configuration Guide

AutoClean uses a YAML configuration file to control pipeline behavior. This guide explains all available configuration options.

Basic Configuration

Here's a minimal configuration example:

task: resting_eyesopen
eeg_system: biosemi64
input_file: /path/to/your/eeg/file.bdf

Environment Variables

AutoClean requires two environment variables:

AUTOCLEAN_DIR: Root directory for output files
AUTOCLEAN_CONFIG: Path to your configuration YAML file

You can set these in your .env file or export them directly:

export AUTOCLEAN_DIR=/path/to/output
export AUTOCLEAN_CONFIG=config.yml

Configuration Options

Required Settings

Option	Description	Type	Example
`task`	Processing task type	string	`resting_eyesopen`
`eeg_system`	EEG system montage	string	`biosemi64`
`input_file`	Path to input EEG file	string	`/path/to/file.bdf`

Optional Settings

Option	Description	Default	Type
`line_freq`	Power line frequency	60.0	float
`resample_freq`	Resampling frequency	250	integer
`ref_type`	Reference type	`average`	string
`crop_start`	Start time for cropping	0	float
`crop_end`	End time for cropping	None	float

Advanced Configuration

Bad Channel Detection

bad_channel_criteria:
  deviation_threshold: 3.0
  correlation_threshold: 0.4
  line_noise_threshold: 4.0

ICA Settings

ica_settings:
  n_components: 20
  random_state: 42
  method: 'fastica'

Artifact Rejection

artifact_rejection:
  amplitude_threshold: 100
  gradient_threshold: 25
  muscle_threshold: 3.0

Configuration File Location

The configuration file can be placed anywhere, but it's recommended to keep it in your project root directory. The location must be specified in the AUTOCLEAN_CONFIG environment variable.