1

Prerequisites

  • AutocleanEEG Pipeline (see Installation)
  • Download our Resting EEG example dataset from Zenodo
2

Check Workspace Location

By default, AutocleanEEG Pipeline creates a workspace folder named Autoclean-EEG inside your Documents folder.
  • Verify the workspace location:
% autocleaneeg-pipeline workspace show

      AutocleanEEG Pipeline Workspace                                             
          Current configuration                                      

  ✓ Workspace ~/Documents/Autoclean-EEG                              
          💾 Free space 472.9 GB
To open the workspace in your file explorer try:autocleaneeg-pipeline workspace explore
3

List Tasks

List available tasks in your workspace:
autocleaneeg-pipeline task list
AutocleanEEG task list showing built-in and custom tasks
Task creation can be entirely custom and complex, incorporating Python, R, or MATLAB code. For this guide, we’re using a simple built-in task to get you started quickly.
4

Copy Task

Copy the built-in RestingState_Basic task and rename it for our tutorial:
autocleaneeg-pipeline task copy RestingState_Basic RestingState_Tutorial
This creates a custom copy that you can modify without affecting the original built-in task.
5

Set Active Task

Set the copied task as your active task:
autocleaneeg-pipeline task set
Select the number corresponding to RestingState_Tutorial from the displayed list.
6

Set Input File

Set the input EEG file for processing:
autocleaneeg-pipeline input set
Copy and paste the full path to your downloaded example file when prompted.
You can also set a folder path for batch processing multiple files at once.
7

Confirm Configuration

Verify that workspace, task, and input are all properly configured:
autocleaneeg-pipeline
This displays your current pipeline configuration and confirms everything is set correctly.
8

Run Pipeline

Start the processing pipeline:
autocleaneeg-pipeline process
Confirm the details when prompted and type yes to start the pipeline running.
9

View Outputs

When processing is complete, explore the generated outputs:
autocleaneeg-pipeline workspace explore
This opens your workspace folder to view the processed results and quality control outputs.
The next sections go over outputs in detail, including BIDS compliance, subject reports, processing logs, and intermediate pipeline steps.