kESI

Kernel based curent source density estimation using FEM models of conductivity.

Basic structure

src/kesi - contains a very barebones kESI framewo rk

extras - contains tutorials and snakemake file which is used to do everything - from mesh segmentation to FEM elements to leadfield and CSD calculations. Refer to SNAKEMAKE_README.md.

Installation

You need to use conda to install the appropriate dependencies defined in enviroment_*.yml files, * stands for different Python versions. To install kESI for Python 3.10 use:

conda env create -f enviroment_3.10.yml

Activate kesi_310 enviroment:

conda activate kesi_310

afterwards use pip to install the kESI package:

pip install .

Additionally, kESI requires gmsh for mesh generation and FEM segmentation. You'll have to install it from your package manager for example Ubuntu:

sudo apt install gmsh

Kesi will be available in this conda enviroment.