Week 3 session 1: Command line, modules and functions; FMRI artifacts

Recording

Week 3 session 1 recording

Schedule

• Again, towards the project.
• Bracketing Git, Github and working on your own computer.

Some background

You will need to have followed the installation instructions.

In particular, you are about to use your terminal application:

• Powershell on Windows
• Powshell on Mac

Modules and functions

We start with the laptop way.

• on_modules.

FMRI artifacts

• Principles of FMRI video
• Radiopedia article in MRI artifacts
• Common MRI artifacts and how to fix them

The above don’t focus much on fMRI (some coverage of susceptibility distortion), but here are some MRI quality control runs that show some interesting effects:

• Spin history artifact, motion spike, AP ghosting
• Ringing, bands in carpetplot
• Ghosting, possible hardware failure
• LR ghosting evident in background noise
• Hardware failures
• Electromagnetic spikes

For homework

Using Git

Watch the following two videos introducing Git in use, but relating what you see to the terms in the curious git tutorial from last week.

I’m referring to the “Git parable” in the videos, which is a similar introduction to the Curious Git tutorial from last week’s homework — but the two tutorials take a very similar track, so you can consider them interchangeable.

Introduction to the git working tree, repository and staging area from Matthew Brett on Vimeo.

The next video is a little out of date, in that the default branch name in Git has changed from “master” to “main”. You will likely find your copy of Git calls the default branch “main”. For “master” read “main” throughout.

The links between git commits, and git branches. from Matthew Brett on Vimeo.

Choosing a text editor

Your second job for this week is to assess and choose a text editor.

Here we a list of videos on choosing text editors:

• Edited version of Stéfan van der Walt on Emacs (16 minutes). You might prefer the full 24 minute version of the conversation here.
• Pamphile Roy on PyCharm (16 minutes).
• Edited version of Ilhan Polat on Spyder (14 minutes). You can also watch the 54 minute full conversation with Ilhan.
• Bhuvak Kalra on VSCode (16 minutes).
• Edited version of Paul Ivanov on Vim (15 minutes). You can watch the full 43 minute conversation with Paul Ivanov here. You might watch the full version if you interested in more on how you know when you have the right editor, how long it takes to get going with Vim.

Please take time for this task, and investigate your options.