hands-on-brain-data

Denis Schluppeck, started Sept/Oct 2020.

This material provides some details for reproducing the animations / interactive examples I have used to for teaching in my 2nd year undergraduate lab in neuroimaging.

You could also used this as a starting point for learning a bit of scripting / programming for your own data analysis with #julialang with sample MRI data shown in class.

Getting set up

• install julia and pluto.jl as per excellent instructions in this youtube clip

• clone or download this repository:

cd ~
git clone https://github.com/schluppeck/hands-on-brain-data.git

# wait for it to download / clone and then change directory into it
cd hands-on-brain-data
# you can now look around at the files in this folder
ls
pwd # print working directory: where are you in the file hierarchy?

• Next, start the julia interpreter by double-clicking the app icon or start julia in the shell, if you have set it up. You can install dependencies at this point, but if you are going to run the notebooks with Pluto you can also do that from within that environment

Try and run the Pluto notebook you want to explore. The first time you run it, you will have to be a bit patient, as some additional packages may need to be installed)

# change directory to the folder with the downloaded files...
# using the ; changes the prompt to red / shell
;  
cd ~/hands-on-brain-data
# BACKSPACE to go back to the julia prompt
using Pluto

# for versions 1.9 onwards, the julia package manager will ask you if you
# want to install this package if you don't already have it... say [y]

Pluto.run()
# and open specific notebook in browser

A good place to start is the notebook what_are_images.jl. Load it, Click Run Notebook code at the top of the page... the first time you do this, it may take 30s to a minute to update packages.... you can look at the Status (by clicking the status button at the bottom right... this will show you progress of what's happening. Second time aroud, the code will run much faster).

Additional resources

• If you scroll to the bottom of the Pluto launch window, you can also find some Featured Notebooks which are a good place to find your feet with julia and Pluto.

• Grant Sanderson has a brilliant video explaining images, etc. in the second class of this MIT OpenCourseWare lecture, which is part of a whole course on Computational Thinking.

Enjoy!

update notes

You can use this snippet of code to get rid of Pluto.jl Manifest.toml update warnings

begin
    using Pkg 
    Pkg.upgrade_manifest()
    Pkg.resolve()
end