https://github.com/bast/tms-location
Code to visualize and locate points for transcranial magnetic stimulation (TMS).
Science Score: 36.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
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✓DOI references
Found 3 DOI reference(s) in README -
✓Academic publication links
Links to: ncbi.nlm.nih.gov -
○Committers with academic emails
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (14.7%) to scientific vocabulary
Repository
Code to visualize and locate points for transcranial magnetic stimulation (TMS).
Basic Info
Statistics
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 2
- Releases: 7
Metadata Files
README.md
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:
bash
$ ./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).
Authors
- Radovan Bast
- Per M. Aslaksen
- Bente S. Barge
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:
bibtex
@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.
Owner
- Name: Radovan Bast
- Login: bast
- Kind: user
- Location: Tromsø, Norway
- Company: @uit-no @neicnordic
- Website: https://bast.fr
- Repositories: 181
- Profile: https://github.com/bast
Theoretical chemist turned research software engineer. Leads @coderefinery.
GitHub Events
Total
- Create event: 5
- Release event: 2
- Issues event: 4
- Delete event: 2
- Issue comment event: 1
- Push event: 4
- Pull request event: 3
Last Year
- Create event: 5
- Release event: 2
- Issues event: 4
- Delete event: 2
- Issue comment event: 1
- Push event: 4
- Pull request event: 3
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 17
- Total pull requests: 8
- Average time to close issues: 22 days
- Average time to close pull requests: 22 minutes
- Total issue authors: 2
- Total pull request authors: 1
- Average comments per issue: 0.76
- Average comments per pull request: 0.0
- Merged pull requests: 7
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 1
- Pull requests: 3
- Average time to close issues: about 1 month
- Average time to close pull requests: about 1 hour
- Issue authors: 1
- Pull request authors: 1
- Average comments per issue: 0.0
- Average comments per pull request: 0.0
- Merged pull requests: 2
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- bast (16)
- peraslaksen (3)
Pull Request Authors
- bast (14)