Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
https://github.com/schluppeck/hands-on-brain-data
getting started with data analysis with #julialang and sample MRI data
https://github.com/schluppeck/hands-on-brain-data
brains colormaps julia mri
Last synced: about 1 month ago
JSON representation
getting started with data analysis with #julialang and sample MRI data
- Host: GitHub
- URL: https://github.com/schluppeck/hands-on-brain-data
- Owner: schluppeck
- License: mit
- Created: 2020-09-24T19:24:52.000Z (over 4 years ago)
- Default Branch: master
- Last Pushed: 2023-11-07T14:15:36.000Z (about 1 year ago)
- Last Synced: 2023-11-07T15:26:38.976Z (about 1 year ago)
- Topics: brains, colormaps, julia, mri
- Language: Julia
- Homepage: https://schluppeck.github.io/hands-on-brain-data
- Size: 46.2 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# 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](https://www.youtube.com/watch?v=OOjKEgbt8AI&list=PLP8iPy9hna6Q2Kr16aWPOKE0dz9OnsnIJ&index=21&t=204s)
- clone or download this repository:
```bash
cd ~
git clone https://github.com/schluppeck/hands-on-brain-data.git
```
```bash
# 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)
```julia
# 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](https://www.youtube.com/watch?v=DGojI9xcCfg&list=PLP8iPy9hna6Q2Kr16aWPOKE0dz9OnsnIJ&index=2
), which is part of a whole course on [Computational Thinking](https://www.youtube.com/playlist?list=PLP8iPy9hna6Q2Kr16aWPOKE0dz9OnsnIJ).
Enjoy!
## update notes
You can use this snippet of code to get rid of `Pluto.jl` Manifest.toml update warnings
```julia
begin
using Pkg
Pkg.upgrade_manifest()
Pkg.resolve()
end
```