Contributors and Funding

Current Contributors

• Axel Thielscher

  • Project coordination

  • Debugging and maintenance across the complete code.

  • Meshing part of charm (4.0)

  • New TMS coil models (4.0)

  • dwi2cond (2.1)

  • Example dataset ernie (2.1)

• 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)

• Maria Drakaki

  • Main contributor to the new TMS coil models (4.0)

• Fang Cao

  • Code testing and updating to python 3.9 (4.0)

• Konstantin Weise

  • First version of the TMS optimization (3.1)

  • UQ functionality (3.0)

• 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)

Former Contributors

• 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, and also a modified version of MeshFix by Marco Attene, functions from CAT12 from the Structural Brain Mapping Group (University of Jena)

• 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