🧠
BRIDGE Lab Documentation
  • BRIDGE Lab Documentation
  • 📘General
    • About Us
    • Onboarding
      • First Steps
      • Research Specialist Training
      • Project Coordinator Training
    • Misc
      • How to do misc things
      • Burning Scans to a Disc
      • Setting Up Meetings in the Conference Room
      • Printing
    • Imaging Glossary
  • 🖇️Admin
    • Ourday
    • Training
    • Regulatory
    • Social Media
    • REDCap
      • Archiving REDCap Projects
  • 🖥️Tech
    • Setting Up Meetings in the Conference Room
    • Effective Troubleshooting
    • Remote Work Resources
    • Arthur
    • Servers
      • Connecting to an External Server
    • Bash 101
      • What is Bash?
      • Bash Examples
      • How to add elements to your bash profile
    • git and Github
  • 🩻Image Acquisition
    • ViSTa
  • 🗃️Data Organization
    • BIDs Data Formatting
    • MRI Data Organization
  • 🖼️Image Analysis
    • Image QC
      • Raw Data QC
        • Diffusion QC
        • T1/T2 QC
        • ViSTa QC
        • Spectroscopy QC
      • PyDesigner QC
    • Project Lifecycle
    • General Concepts
    • Raw Data
    • Preprocessing
      • Denoising UNI MP2RAGE Images
      • PyDesigner
      • ViSTa
    • Native Space Analysis
      • TractSeg
        • TractSeg + Within-Subject Registration
      • Segmentation
        • LST
        • Freesurfer
        • NOMIS
    • Registration
      • DTI-TK
      • TBSS
      • Coordinate Systems
    • Other Pipelines
    • Archiving
  • 📊Data Viz and Stats
    • Plotting in R
  • 📚Imaging Library
Powered by GitBook
On this page
  1. Tech
  2. Bash 101

What is Bash?

Last updated 1 year ago

Note: This is only relevant if you are working on a Mac or Linux system or using a Windows Subsystem for Linux (WSL)

What is bash and why should I use it?

When you open your Terminal on a Mac, what you see is a bash shell. This bash shell is an interface to your operating system. From here, you can input commands to access files or programs on your computer. Doing this will accomplish the same task as double clicking to open a program and then using the graphical user interface (GUI) of the program to interface with it. The main difference is that by using the Mac Terminal, you will interface with programs and files via the command line (CLI) instead of a GUI.

Being able to use bash is essential for most image analysis techniques discussed within this collective of documentation. For example, programs like Freesurfer and FSL become significantly more versatile by interfacing with them via bash. Plus, bash allows you to quickly move, delete, rename, copy, or otherwise reorganize long lists of files very quickly (along with many other convenient perks).

.

It will be helpful to get familiar with bash quickly by opening the Terminal and trying out some simple commands.

🖥️
Here is a quick list of common, useful bash commands