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.

example animation

Getting set up

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

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