This repository contains the work during the PhD of Xiaoyu WANG, titled "Brain development analysis using MRI and physical modeling".
All scripts were coded in python 2.7, but they are compatible to python 3.7 (tested on the version 3.7.3).
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
Example of dynamic simulations of a neo-Hookean solid with a tangential differential growth.
python simulation.py -i './data/sphere5.mesh' -o './res/sphere5' -hc 'whole' -t 0.042 -g 1.829 -gm 'global'
i: path of input maillage
o: path of output
hc: whole or half geometry
t: cortical thickness
g: relative growth rate
gm: global or regional growth
In simulation.py, there are certain parameters should be set manually:
a: average mesh spacing
For sphere5.mesh:
a = 0.01
Wang, X., Lefèvre, J., Bohi, A. et al. The influence of biophysical parameters in a biomechanical model of cortical folding patterns. Sci Rep 11, 7686 (2021). https://doi.org/10.1038/s41598-021-87124-y