Code to visualize and locate points for trans-cranial magnetic stimulation (TMS).

• You need mesh data generated by https://github.com/bast/MRI-extract-surfaces.
• You need an installation of Apptainer (e.g. following the quick installation). Alternatively, SingularityCE should also work.

First download the container image (ending with *.sif) from here: https://github.com/bast/tms-location/releases

Make the image executable and then point the container image to the directory where you have the mesh data:

$ ./tms-location.sif /path/to/ernie_data

Then open the browser at the URL shown in the terminal (typically http://127.0.0.1:8050).

• Radovan Bast
• Per M. Aslaksen
• Bente S. Barge

• https://github.com/nmwsharp/potpourri3d
• https://nmwsharp.com/research/flip-geodesics/

If you use this code, please cite their paper:

@article{sharp2020flipout,
  author = {Sharp, Nicholas and Crane, Keenan},
  title = {You Can Find Geodesic Paths in Triangle Meshes by Just Flipping Edges},
  journal = {ACM Trans. Graph.},
  volume = {39},
  number = {6},
  year = {2020},
  publisher = {ACM},
  address = {New York, NY, USA},
}

I am not affiliated with SimNIBS but this container uses SimNIBS under the hood.

When you publish results based on SimNIBS, please cite Thielscher, A., Antunes, A. and Saturnino, G.B. (2015), Field modeling for transcranial magnetic stimulation: a useful tool to understand the physiological effects of TMS? IEEE EMBS 2015, Milano, Italy.

• https://kathleenhupfeld.com/mni-template-coordinate-systems/
• https://clinicalresearcher.org/F3/calculate.php
• https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2882797/

To build the image, I have used this wonderful guide as starting point and inspiration.

I find it important that everybody can verify how the container image was built. And you can! You can inspect the definition file and all scripts which are all part of this repository.