Command Line Basics for AutoClean#

Don’t worry - you don’t need to be a programmer to use AutoClean! This guide will teach you the few simple commands you need to know.

🖥️ What is the Command Line?#

The command line (also called “terminal”, “command prompt”, or “shell”) is a way to give instructions to your computer by typing text commands instead of clicking buttons.

Why use it? - It’s actually faster once you learn a few commands - AutoClean can process your data automatically - You can repeat the same analysis easily - It works the same way on Windows, Mac, and Linux

🚀 Opening the Command Line#

Windows: 1. Press Windows key + R 2. Type cmd and press Enter 3. A black window opens - this is your command prompt

Mac: 1. Press Command + Space to open Spotlight 2. Type terminal and press Enter 3. A window opens - this is your terminal

Linux: 1. Press Ctrl + Alt + T 2. Or search for “Terminal” in your applications

📁 Basic Navigation#

These commands help you move around your computer:

See where you are:

# Windows
cd

# Mac/Linux
pwd

See what files are in your current folder:

# Windows
dir

# Mac/Linux
ls

Change to a different folder:

# Go to your Documents folder
cd Documents

# Go to a specific folder
cd "path/to/your/folder"

# Go back to the previous folder
cd ..

Pro tip: Use quotes around folder names that have spaces!

🧠 AutoClean Commands You Need to Know#

Once AutoClean is installed, you only need to remember these commands:

1. Check if AutoClean is working:

autoclean version

This should show you the AutoClean version number.

2. Set up your workspace (first time only):

autoclean setup

This runs a clean setup wizard that creates your personal AutoClean workspace in Documents/Autoclean-EEG.

3. See what tasks are available:

# Built-in tasks only
autoclean list-tasks

# Include your custom tasks too
autoclean list-tasks --include-custom

This shows all the processing workflows you can use.

4. Process your data:

autoclean process RestingEyesOpen my_data_file.raw

Replace “RestingEyesOpen” with your task name and “my_data_file.raw” with your actual file.

5. Manage your custom tasks:

# Add a custom task
autoclean task add my_custom_task.py

# List your custom tasks
autoclean task list

# Remove a custom task
autoclean task remove MyTaskName

6. Check your results:

autoclean config show

This shows where your results are saved.

🎯 Step-by-Step: Your First Analysis#

Let’s walk through processing your first EEG file:

Step 1: Open the command line (see instructions above)

Step 2: Navigate to your data folder

If your EEG files are in Documents/EEG_Data:

cd Documents/EEG_Data

Step 3: Check what files are there

# Windows
dir

# Mac/Linux
ls

You should see your .raw, .set, or other EEG files listed.

Step 4: Process your data

autoclean process RestingEyesOpen subject001.raw

Replace “subject001.raw” with your actual filename.

Step 5: Wait for processing to complete

You’ll see messages showing the progress. When it’s done, you’ll see “Processing completed successfully!”

Step 6: Check your results

autoclean config show

This tells you where to find your processed data and reports.

📋 Common File and Folder Names#

Your data files might be named like: - subject001.raw - participant_01_rest.set - data_session1.eeg - sub-01_task-rest_eeg.raw

Folder paths you might use: - Documents/Research/EEG_Data - Desktop/Experiment_Data - C:ResearchSubject_Data (Windows) - /Users/yourname/Research (Mac)

🆘 What If Something Goes Wrong?#

“Command not found” error: This means AutoClean isn’t installed properly. Try:

pip install autocleaneeg

“File not found” error: Check that you’re in the right folder and the filename is correct:

# See what files are available
dir    # Windows
ls     # Mac/Linux

“Permission denied” error: Try running the command as administrator (Windows) or with sudo (Mac/Linux).

AutoClean seems stuck: - Wait a few minutes - EEG processing takes time - Press Ctrl+C to cancel if needed - Check the error messages for clues

💡 Helpful Tips#

Use Tab completion: Start typing a filename and press Tab - the computer will try to complete it for you!

Use the up arrow: Press the up arrow key to repeat your last command.

Copy and paste: - Windows: Right-click to paste - Mac: Cmd+V to paste - Linux: Ctrl+Shift+V to paste

Keep a cheat sheet: Write down the commands you use most often until you memorize them.

🎉 You’re Ready!#

That’s all you need to know! With these few commands, you can: - Navigate to your data - Process EEG files with AutoClean - Find your results

The command line becomes easier with practice. Start with these basics and gradually learn more as needed.

Next steps: - Try the Python-Based EEG Processing tutorial - Learn about Understanding AutoClean Results - Explore Creating a Custom Task for your research