Contributors and Funding¶
Current Contributors¶
- Oula Puonti
Main author of charm and of simnibs 4.0 in general (4.0)
Debugging and maintenance across the complete code.
New MNI head mesh (2.1)
- Kristoffer H. Madsen
Debugging and maintenance across the complete code.
Cross-platform building (4.0)
New html-based viewer (4.0)
Ccd to nifti conversion (4.0)
New TMS coil models (4.0)
I/O function for Softaxic (4.0)
MNI transformation (2.1)
Fast I/O for gmsh-meshes in python (2.0)
Pre-calculated A-fields for TMS in the pipeline using nifti volume files (2.0)
- Jesper D. Nielsen
Contributions to the segmentation functions in charm (4.0)
Main author of the headreco pipeline, now discontinued (2.1)
Update to charm to optionally use FreeSurfer surfaces (4.1)
- Konstantin Weise
First version of the TMS optimization (3.1)
UQ functionality (3.0)
Integration of mmg to improve tetrahedral mesh quality (4.1)
- Thomas Knoesche
Help with the UQ functionality (3.0)
- Ole Numssen
I/O functions for Localite and Brainsight (4.0)
First version of the TMS optimization (3.1)
- Torge H. Worbs
Integration of mmg to improve tetrahedral mesh quality (4.1)
- Merle Diedrichsen
Update of electrode meshing to improve tetrahedral quality at the electrode edges (4.1)
Former Contributors¶
- Maria Drakaki
Main contributor to the new TMS coil models (4.0)
- Fang Cao
Code testing and updating to python 3.9 (4.0)
- Guilherme B. Saturnino
- Main contributor to many SimNIBS features:
TES optimiaztion algorithms (3.1, 3.2)
Installation procedure (3.0, 3.2)
Documentation (3.0, 3.1 and 3.2)
Fast FEM code (3.0)
(together with K. Weise) UQ functionality (3.0)
New python core (2.1)
GUI (2.0)
Electrode modeling for TES (2.0)
Bug-fixing
Meshing part of charm (4.0)
- Hassan Yazdanian and Kim Knudsen
Magnetic Field Calculations (3.2)
- Luis J. Gomez, Moritz Dannhauer, and Angel V. Peterchev; Duke University, Durham, North Carolina, U.S.A.
Auxiliary Dipole Method (ADM) TMS optimization (3.2)
- Andre Antunes
Main contributor to the FEM pipeline in SimNIBS 2.0
Implementation of a range of post-processing programs in SimNIBS 2.0
- Andreas Bungert
Testing of the new FEM pipeline in SimNIBS 2.0
- Alex Opitz
Implementation of first diffusion-to-conductivity mapping approach
Co-contributor to many other parts in SimNIBS 1.0
Testing and validation of the new FEM calculations for tDCS in SimNIBS 2.0
- Mirko Windhoff
Main contributor to SimNIBS 1.0
Acknowledgements¶
SimNIBS integrates free software for Neuroimaging, computer graphics and FEM calculations into one coherent pipeline:
charm uses Samseg (Oula Puonti, Koen Van Leemput) from FreeSurfer as segmentation backend, CGAL for meshing, Mmg for improving the mesh quality, a modified version of MeshFix by Marco Attene for surface fixing, and functions from CAT12 from the Structural Brain Mapping Group (University of Jena) for GM central surface estimation
We use Gmsh by Christophe Geuzaine and Jean-François Remacle for visualization.
dwi2cond uses FSL from the FMRIB Center (Oxford University).
FEM code introduced in version 3.0 relies on PETSc and Hypre.
Thanks for Konstantin Weise for giving us access to an early version of his software, pygpc.
Thanks for Luis Gomez for providing a python version of his ADM TMS optimization package.
Institutions¶
Versions 2.1, 3 and 4 have been developed at the Danish Research Center for Magnetic Resonance (Copenhagen, Denmark) and the Technical University of Denmark (Kgs Lyngby, Denmark), in collaboration with external partners.
Version 1.0 was created at the Max-Planck Institute for Biological Cybernetics (Tübingen, Germany).
Version 2.0 was developed in all three institutions
Funding Sources¶
We would like to thank our funding sources
