dafni

UNIX

Some more details on how to use features of UNIX/bash that are particularly helpful for organising and processing data.

The people who make fsl have produced a collection of short videos that introduce some UNIX commands that are particularly helpful for running an FMRI data analysis with their tools.

For background, there is a really good online tutorial hosted at EE at University of Surrey. The terminal / shell.

You can also have a look at the brief online course at Software Carpentry, which looks really good.

Some basics

• only basics are needed for running FSL analysis
• lots of functionality is available through point-and-click
• but command line is helpful for organising (any) research data
• more complex analysis, e.g. freesurfer, require some working knowledge

Version control, git

My (very brief) presentation on version control with git as a markdown file or [as an HTML presentation], or PDF. This is what’s covered in the lab class.

Some really useful background is available in some brief videos produced by https://github.com

What is version control?

A really clear video explaing this in simple terms What is version control?

What is git

Have a look at the video on What is git

Get going with git

Finally, you can actually Get going with git, in particular check out
1:13min for configuring user.name and user.email - keeping in mind you’ll probably want to use a value for user.email that is your generic / non-university e-mail.

We don’t actually need to install this in the computer labs - but on your personal machines you might have to do this. You can use which git in the Terminal. If you get a valid path back, then you know it’s installed. You could also try git --version to find out which version you have installed on your machine.

Git basics

A slightly deeper look at git in the video about quick wins with git

History of my comands in shell 2023-02-21

ls -l
cd myFirstRepo
nano Readme.md 
ls
ls -l
more Readme.md
ls
git init
git status
git add Readme.md
git status
git commit
git status
git commit -m "this is the first commit. yay"
git status
git log