TMS location

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

Requirements

• 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.

How to use it

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).

The code uses the potpourri3d library to compute geodesic paths

• 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},
}

Please cite SimNIBS if you use this container

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.

[!WARNING] SimNIBS is a research tool. Clinical usage is not supported or advised. In particular, SimNIBS was not tested to give accurate results in the presence of pathological condition. See also https://simnibs.github.io/simnibs/

Other resources

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

About the container image

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.