Flooding_brains

Creating mesmerizing brain animations by playing with geodesic distances.

Dependencies

Package	Tested version
Python	3.7.6
NumPy	1.17.2
Nibabel	2.2.1
PyVista	0.30.1
LayNii	2.1.0 (in devel)
ffmpeg	4.3.1

This project is developed using Debian 10 operating system.

Installation

Flooding brains project is just a script compilation for now. Therefore make sure to install each dependency to be able run the scripts.

Beginner's guide

1. Change directory to where your scripts are stored. For example you can use the scripts directory that comes with this repository: cd /path/to/flooding/brains/scripts

Prepare inputs for animation

2. Get borders from a segmentation file by running python prep-flooding_step-01_borders.py.
3. Get points on the borders by running: python prep-flooding_step-02_points.py.
4. Get geodesic distances from the points on the borders by running: python prep-flooding_step-03_distances.py

Create animation frames

5. Run python anim-flooding_step-1_prep.py to find a nice viewing angle.
6. Run python anim-flooding_step-2_render.py for generating animation frames (png).

Compile frames into a movie

7. Run bash movie-flooding_compile.sh to convert the frames into movies (mp4).

What comes next?

Feel free to read, edit and augment all the example scripts to generate different animations.

Support

Please use the GitHub issues for questions.

License

This project is licensed under MIT.