Step 1: Preparation (1 Hour):

Before starting the training, you’ll need to set up your computer. Follow the instructions that match your operating system:

• Mac Users:
  • Change your default terminal language to Bash
  • How to Change the Default Shell to Bash on macOS
  • Why? Bash is the shell we’ll use to run commands in the terminal. This ensures everything works as expected.
• Windows Users:
  • Install Windows Subsystem for Linux (WSL), keeping the default Ubuntu settings
  • How to install Linux on Windows with WSL
  • Why? This creates a Linux-like environment where you can run Bash commands, just like on a Mac
• Everyone:
  • Install Anaconda
    • Anaconda Installation Instructions
    • Follow all steps, including verifying the installation with shasum. If you get stuck, this page has helpful videos:
      • Workshop Install Instructions
    • Why? Anaconda makes it easy to manage Python and install the tools we’ll use
  • Once these steps are done, bookmark this resource for later:
    • Shell Basics on the Lab Wiki

Step 2: Training (~18 hours total):

Now for the fun part! These self-paced lessons will introduce you to the basics of Bash and Python programming. Please complete these trainings in the order listed below, remembering that each training is self-paced and has multiple spots where you can pause and return later.

1. The Unix Shell (~2 hours):
   • The Unix Shell Training
   • Why? This will teach you how to navigate and manage files using the command line—a key skill for working with fMRI data
2. Programming with Python (~8 hours):
   • Programming with Python Training
   • Why? Python is the primary language we’ll use for data analysis. Focus on running the examples in Jupyter Notebook, learning to open it from the terminal
3. Plotting and Programming in Python (~8 hours):
   • Plotting and Programming in Python
   • Why? This builds on the Python basics and introduces data visualization, which is essential for analyzing and presenting fMRI data
4. File Permissions in Uni (~15 minutes):
   • Linux file permissions explained
   • Why? File permissions are core to the security model used by Linux systems. They determine who can access files and directories on a system and how. If you don't know how they work, you will not be able to work with files in a scientific computing environment.

Helpful Tips:

• Take Your Time: The time estimates are just guides—don’t worry if it takes longer. This isn’t about getting it perfect, just building a solid starting foundation.
• Feel Stuck? That’s completely normal when learning to program! If you run into issues, email me, or try Googling—it’s a skill you’ll use often. You can also ask ChatGPT to explain how code works. It's really good at that!
• What’s Next? Start with the preparation steps in the order listed. Once those are done, move on to ''The Unix Shell'' training.

Why this Matters:

This training will set you up for success in many aspects of the lab where we work on neuroimaging and/or behavioral data. Learning Bash and Python will help you access and analyze data effectively. These skills will also be a huge asset for your ongoing future projects.