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Practice and theory of brain imaging

Week 4 session 1: Indexing and four dimensions

Recording

Week 4 session 1 recording

Schedule and plan

  • More on four dimensions
  • Modules and functions

Indexing and four dimensions

Homework

There is a well-done video on Git and Github on YouTube, link below.

Here are a few notes before you watch the video.

The video concentrates on the use of Git / Github for programmers, but all the same things apply to scientists and academics writing collaborative projects and papers.

It starts very basic, but bear with, it quickly gets on the specific stuff we have not covered elsewhere, on using Git with Github.

The author is using the old-style default branch naming in Git, where the default branch is called master. The default branch, for modern Git, is now called main. Just read main for master throughout.

I would set up your Github account with an SSH key following the Github instructions before you start the video. Although the video suggests that having no passphrase for your SSH key is OK, we would not recommend that. We suggest you do in fact have a reasonably long (but memorable) SSH key passphrase.

The video starts using the terminal from within VSCode. The author says this later, but this is just the same as using terminal outside VSCode, so if you are not using VSCode, just type the same commands in the terminal. In fact, I would recommend using the terminal outside VSCode even if you are using VSCode, at least at first.

The video uses the -m flag to git commit to provide a commit message and maybe a description. We suggest you don’t do that, and you set up your editor to work with Git, so when you type git commit, Git will open your editor for you to type a message. See below for how to do this.

Setting your default editor for Git

The usual default editor for Git is Vim, so if you want that, you don’t need to change anything. If you don’t then:

The video

The video is Git and Github for Beginners.

After the video

To make sure you understand most of the material in the video, do the following:

  • Fork the repository at https://github.com/nipraxis/first-pull-request using the “Fork” button towards the top right.
  • Clone your fork of this repository to your computer.
  • Make and checkout a new branch called spm-funcs-fixes.
  • Make the changes given in the instructions at the top of the spm_funcs.py file.
  • git add these changes, then git commit the changes.
  • Push the changes from this branch up to your fork. Make sure you are pushing the new branch.
  • Do a Pull request from this new branch to the original (base) repository master branch at https://github.com/nipraxis/first-pull-request
  • We will review your pull request!

The Markdown tutorial

Markdown is the standard way of writing nicely formatted text on many platforms, including on Github, and in the Jupyter notebook. You will see it in many places, and you will find yourself using it often — for example, in Jupyter text cells. Get used to writing Markdown by doing the Markdown tutorial.

Voxel exercise