Visualizing Results

This tutorial comes after the tutorial on Setting up and Running Simulations. Please be sure to complete it before going further.

Visualizing Results in Gmsh

Gmsh is a powerful program for 3D visualization. However, it has somewhat steep learning curve. For this reason, in SimNIBS 3.0 we now write the .opt files with basic visualization configurations. Here we will give a walk-through of a few useful features in Gmsh.

Note

Gmsh is distributed together with SimNIBS, you don’t need to install it separately

Starting Gmsh

Gmsh automatically opens when a simulation is finished. Alternatively, you can start Gmsh by double clicking in the ernie_TDCS_1_scalar.msh file or typing in the terminal

gmsh ernie_TDCS_1_scalar.msh

The following window will appear

../_images/tutorial_gmshinit.png

There, we see the gray matter surface with the norm of the electric field (normE) ploted, as well as the electrode currents. You can rotate the model with the left mouse button, translate it with the right button, and zoom with the mouse wheel

Selecting Where to Visualize

To visualize another surface, such as while matter

  1. Go to ToolsVisibility

../_images/tutorial_gmshvisibility.png

select Elementary entities

../_images/tutorial_elementaryentities.png

  1. Select surfaces and volumes to be visualized. In SimNIBS, we have defined

    1: White Matter volume

    2: Gray Matter volume

    3: Cerebrospinal Fluid (CSF) volume

    4: Skull volume

    5: Skin volume

    6: Eye volumes (headreco models only)

    101+: Electrode rubber layer volume

    501+: Electrode Gel / Sponge volume

    The corresponding surfaces have the number 1000 + volume value. For example, 1002 corresponds to the gray matter surface. The only exception are the electrode contacts, numbered 2100+. You can select multiple surfaces or volumes by holding Ctrl. Selecting 1001 and clicking in Apply, we can see the white matter surface

../_images/tutorial_gmshwmfield.png

Selecting What to Visualize

You can select the field to be visualized by checking the boxes in the left of the Gmsh window

../_images/tutorial_gmshnorme.png

To visualize the surfaces or volumes without any field, go to Tools -> Options -> Mesh and click on Surface Faces or Volume Faces

../_images/tutorial_gmshdeselecsurf.png

Changing the Scale

To change the scale of a field visualization ToolsOptionsView [N] and change the Min and Max values

../_images/tutorial_gmshview.png

Exporting an Image

To create an image, go to File -> Export (or press Ctrl+E)and type in a file name with a .png or .jpg extension.

Other Functionalities

We recommend users to explore the many functionalities of Gmsh. One can, for example, produce the image bellow by selecting the Volume 2 for visualization an clipping the model in ToolsClipping

../_images/tutorial_gmshclip.png

Visualizing Results in MATLAB

To visualize results in MATLAB, add the <SIMNIBS_INSTALL_DIR>/matlab/ folder to your MATLAB path. Afterwards, type

mesh_get_simulation_result

or use

mesh_show_surface

to have more control over the visualization.

Further Reading

For more information on visualization and simulation output, please see the SimNIBS 2.1 tutorial paper.