Python Library Documentation¶

SimNIBS main programming language is Python. Here you can see documentation for the main modules used in SimNIBS.

I/O Functions¶

`read_msh`	Reads a gmsh '.msh' file
`write_msh`	Writes a gmsh 'msh' file
`read_freesurfer_surface`	Function to read FreeSurfer surface files
`write_freesurfer_surface`	Writes a FreeSurfer surface Only the surfaces (triangles) are writen to the FreeSurfer surface file
`read_gifti_surface`	Reads a gifti surface
`read_curv`	Reads a freesurfer .curv file
`write_curv`	Writes a freesurfer .curv file
`read_stl`	Reads mesh surface in a .stl file
`write_geo_spheres`	Writes a .geo file with spheres in specified positions
`write_geo_text`	Writes a .geo file with text in specified positions

`Msh`	class to handle the meshes.
`Nodes`	class to handle the node information:
`Elements`	Mesh elements.
`NodeData`	Data (scalar, vector or tensor) defined in mesh nodes.
`ElementData`	Data (scalar, vector or tensor) defined in mesh elements.

`subject2mni_coords`	Warps a set of coordinates in subject space to MNI space
`mni2subject_coords`	Warps a set of coordinates in MNI space to subject space
`subject_atlas`	Loads a brain atlas based of the FreeSurfer fsaverage template

`templates`	Defines the Templates for file names used in SimNIBS
`get_atlas`	Loads a brain atlas based of the FreeSurfer fsaverage template
`SubjectFiles`	Class to find files for a given subject

`simulation.calc_B`	Calculates the magnetic field caused by a current density distribution J
`simulation.calc_fields`	Given a mesh and the electric potentials at the nodes, calculates the fields
`simulation.tdcs`	Simulates a tDCS electric potential.
`simulation.tdcs_neumann`	Simulates a tDCS electric potential using Neumann boundary conditions on the electrodes.
`simulation.tdcs_leadfield`	Simulates tDCS fields using Neumann boundary conditions and writes the output electric fields to an HDF5 file.
`simulation.tms_dadt`	Simulates a TMS electric potential from a dA/dt field.
`simulation.tms_coil`	Simulates TMS fields using a coil + matsimnibs + dIdt definition.
`simulation.tms_many_simulations`	Function for running a large amount of TMS simulations.
`simulation.electric_dipole`	Electric dipole simulations using the partial integration method