a tool that allows interactive visualization of the TMS-induced effects over tractography data.
- Free software: 3-clause BSD license
- Documentation: (COMING SOON!) https://KulikovaSofya.github.io/StimVis_TMS.
Before installation of the StimVis please make sure that all dependencies have been installed:
- Install the latest version of SimNIBS as described here: https://simnibs.github.io/simnibs/build/html/installation/conda.html
Install other packages by printing at the command line:
$ pip install numpy $ pip install dipy $ pip install fury $ pip install vtkplotter
Then you can install the StimVis by printing at the command line:
$ pip install stimvis_01 | Running StimVis |
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To run StimVis first navigate to the stimvis directory and then run the tms_stimulation.py file at the command line: |
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You will be asked to specify 4 input files and the output directory: |
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Example: ./Example_data/tracts.trk |
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Example: ./Example_data/T1fs_conform.nii.gz |
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Example: ./Example_data/dti_fa.nii |
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Example: ./Example_data/subject.msh |
And finally, the output directory that will contain the resulting files with the TMS-induced effects |
Example: /Example_data/Output |
Once all input data is co-registered to each other (please, be patient as this may take a while) an interactive scene will open to visualize in 3D the tractography streamlines superimposed on T1-weighted images. |
By clicking at a particular location within a horizontal plane you can select the position of the stimulating coil and then press the big red button to start the calculations. |
As soon as the calculations are finished the total TMS effect will be shown over the streamlines in a color-coded manner. Also the calculated effects will be saved in a text file |
output_directory/stimulation_at_pos<selected coil position>/subject_effective_field.txt |
via pickle.dump() in a form of a numpy array. |
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| Sample Data |
Sample data to test StimVis could be downloaded with this link: https://drive.google.com/drive/folders/1H86xzAhA7VS0i8sNdIzoO5BWQrCa_qyu?usp=sharing
===== Reproducibility Runs ===== Provisional CodeOcean Compute Capsule's DOI is 10.24433/CO.4813589.v1
===== Acknowledgements ===== This project has been supported by Russian Science Foundation №18-75-00034.