SimNIBS

The main goal of SimNIBS is to calculate electric fields caused by Transcranial Electrical Stimulation (TES) and Transcranial Magnetic Stimulation (TMS).

The pipeline is divided in three parts:

1. Automatic segmentation of MRI images and meshing to create individualized head models
2. Calculation of electric fields through the Finite Element Method (FEM)
3. Post-processing of results for further analysis.

Build Status

Linux	Windows	MacOS

Getting Started

SimNIBS runs on 64bit Windows, Linux and MacOS machines. Please visit the SimNIBS website for instructions on how to download and install SimNIBS.

Installation for development

After cloning the repository (for all platforms except arm64 Macs):

conda env create -f environment_.yml -n <name_of_my_environment>
conda activate <name_of_my_environment>
python -m pip install --editable .
python simnibs/cli/link_external_progs.py

NOTE

Currently on arm64 Macs it is only possible to build by creating an x86_64 environment. To do so, replace the first command above with:

conda env create -f environment_.yml -n <name_of_my_environment> --platform osx-64

If the --platform argument is not available in your version of conda, use

CONDA_SUBDIR=osx-64 conda env create -f environment_.yml -n <name_of_my_environment>
conda env config vars set CONDA_SUBDIR=osx-64 -n <name_of_my_environment>

The latter command ensures that new packages are also installed from the osx-64 subdir in this environment.

Authors

Please see the SimNIBS website for a complete list of contributors.

3rd Party Files

We have included code or binaries from the following project to this repository:

• Gmsh
• meshfix
• CAT12
• PETSc
• HYPRE
• MPICH
• MSMPI
• CYGWIN
• pygpc
• PyPardiso
• PyPardiso
• PyPardiso
• CGAL
• Mmg
• FMM3D

For a full list of files and licenses, please see the 3RD-PARTY.md file