Programming Languages Compared

Of the 700+ programming languages, there are four (below) you are likely to encounter and/or want to learn more about.

With the exception of Matlab, these are all open-source.

Bash: You have already worked with Bash commands in Google Cloud Shell. You can create a simple script by putting commands into a text file and running the text file as a program! Bash is not a sophisticated programming language, but it does have control structures, and is very useful for setting up pipelines of command line tools. I use it frequently to create directory structures and run neuroimaging programs. In subsequent lessons and practicums you'll look into Bash scripting in more detail.

Bash scripts may have no extension, or the extension *.sh.

Warning!

If you are a Windows user, you need to set up WSL2 to access Bash!

Python is a general-purpose programming language. There are many versions of Python and its libraries, and because they can overwrite and conflict with one another, it is better not to install Python programs directly on your operating system! In addition, most operating systems use some Python internally, so you want to be really careful not to overwrite Python installations that your operating system depends on! In another lesson, we'll talk about how to work safely with Python tools using Conda.

Python scripts have the extension *.py.

Matlab is an excellent language for image and signal processing, but it is terrible for text manipulation! It is an expensive commercial product, but the U of A pays for a license which gives you free access to Matlab and a huge number of its toolboxes. Matlab has a very nice development environment, and some important neuroimaging packages are written in Matlab (SPM, CONN, GIFT etc.). In a later practicum, you'll learn more about Matlab.

Matlab scripts have the extension *.m.

R is an excellent tool for statistics and data wrangling. It has a nice Integrated Development Environment: R-studio, and many of you have probably encountered it already. Although it can handle matrices, it cannot handle big matrices as well as Matlab and Python.

R scripts have the extension *.R.

Note

Expect to see only one programming language per script! In a later lesson, you'll learn why matrix manipulation is so important to neuroimaging.

The University of Arizona provides substantial support for learning R and Python. See also the Data Science Institute.

Watch this 4.5-minute video clip

Programming 2 (45-minutes)