SimNIBS 2.0 Tutorials

TMS Simulation

- Open a terminal instance. If SimNIBS is properly installed you should get the message:

setting up paths for SimNIBS 2.0.1

SIMNIBSDIR /path/to/simnibs/folder

- Start the SimNIBS Graphical User Interface by typing simnibs_gui in the terminal.

- The following window should appear:

- Click on “Browse” next to the highlighted area in order to select a head model “.msh” file When selected, the model will appear in the right-hand side

- For setting up a TMS simulation, click on “Add TMS Poslist”

- Select a coil file by clicking on “Browse” above the table

- For selecting the coil position, click twice in the “Position” column. Click twice in the model for selecting the coil center position, and twice again for selecting the coil handle direction

- If you selected a nifti (.nii.gz) coil file, you can preview the magnetic vector potential (dA/dt)

you can also view it in gray matter

- Click in “Run” for starting the simulation

- When the simulation is finished, this message will appear

- You can open the final results using Gmsh, which is included In your SimNIBS installation. I order to open it, type gmsh <file_name> In the Terminal.

- In the Left-hand side of the screen in gmsh, you can select which field to visualize

- In Tools→Visibility, you can select the tissue you want to see: 1 for WM, 2 for GM, 3 for CSF, 4 for Bone, and 5 for Scalp

- In Tools→Options→Mesh, you can select to turn the mesh surfaces and volumes visualization on and off. We recommend turning both off for better visualizing the fields

- In Tools→Options→View, you can change the field display proprieties

- In Tools→Clipping, you can clip the model