BrainGrowth
Table of Contents
Introduction
This repository contains the work during the PhD of Xiaoyu WANG, titled "Brain development analysis using MRI and physical modeling".
Requirements
All scripts were coded in python 2.7, but they are compatible to python 3.7.
Python packages and versions
- enum34==1.1.6
- funcsigs==1.0.2
- llvmlite==0.24.0
- nibabel==2.5.1
- numba==0.39.0
- numpy==1.17.2
- numpy-stl==2.10.1
- python-utils==2.3.0
- scikit-learn==0.21.3
- scipy==1.3.1
- singledispatch==3.4.0.3
- six==1.12.0
- Vapory==0.1.1
- mpmath==1.0.0
- os
- trimesh
- slam
The file called requirements.txt helps to install all the python libraries.
- Using pip:
pip install -r requirements.txt
Configuration of Parameters and Run
simulation.py
Example of dynamic simulations of a neo-Hookean solid with a tangential differential growth.
python simulation.py -i './data/sphere5.mesh' -o './res/sphere5' -t 0.042 -g 1.829
i: path of input maillage
o: path of output
t: cortical thickness
g: relative growth rate
Running a demo
In simulation.py, there are certain parameters should be set manually:
a: average mesh spacing
For sphere5.mesh:
a = 0.01
Input mesh image， output dynamic process
