TMSoptimize

Describes a TMS optimization problem

Initialization

  • Python

    from simnibs import opt_struct
    opt = opt_struct.TMSoptimize()
    

  • MATLAB

    opt = opt_struct('TMSoptimize');
    

Attributes

  • fnamehead: string (Python)/character array (MATLAB)

    • Desctiption: Name of head mesh file (subID.msh file)

    • Example: Python/MATLAB

    opt.fnamehead = 'ernie.msh'
    

  • pathfem: string (Python)/character array (MATLAB)

    • Desctiption: Name of output folder

    • Example: Python/MATLAB

    opt.pathfem = 'tms_optimization/'
    

  • fnamecoil: string (Python)/ character array (MATLAB)

  • target: (3x1) list/array (Python/MATLAB) of floats

    • Desctiption: Position of optimization target. Please see Coordinates in SimNIBS for more information and how to obtain coordinates in SimNIBS

    • Example: Python/MATLAB

    opt.target = '[-43.4, -20.7, 83.4]'
    

  • cond: list/array of COND structures (Python/MATLAB), optional

  • anisotropy_type: ‘scalar’, ‘vn’, ‘dir’ or ‘mc’, optional

  • aniso_maxratio: float, optional

  • aniso_maxcond: float, optional

  • target_size: float, optional

    • Description: Radius of target area, in mm.

    • Default: 5

  • tissues: list/array (Python/MATLAB) of ints, optional

    • Description: Tissues where the target is defined.

    • Default: [2] (Gray matter volume)

  • centre: (3x1) list/array (Python/MATLAB) of floats, optional

    • Description: Position in scalp to use as a reference for the search space.

    • Default: target projected to the scalp

  • pos_ydir: (3x1) list/array (Python/MATLAB) of floats, optional

    • Description: Reference position for the coil Y axis, with respect to the pos variable

    • Default: Search positions in a 360 degrees radius.

  • distance: float, optional

    • Description: Distance from coil to scalp, in mm.

    • Default: 4

  • didt: float, optional

    • Description: Coil dI/dt value, in A/s.

    • Default: 1e6

  • search_radius float, optional

    • Description: Radius of search area, in mm.

    • Default: 20

  • spatial_resolution: float, optional

    • Description: Space between coil positions, in mm.

    • Default: 5

  • angle_resolution: float, optional

  • Description: Space between two coil angles, in degrees

  • Default: 30

  • search_angle: float, optional

    • Description: Range of angles to use in search, in degrees.

    • Default: 360

  • open_in_gmsh: bool, optional

    • Description: Wether to open the results in gmsh

    • Default: True

  • solver_options: str, optional

    • Description: Options for the FEM matrix solver. Leave empty to use the CG+AMG solver, use a string to be passed to PETSc or set solver_options='pardiso' to use the MKL Pardiso direct solver

    • Default: Use the CG solver with the AMG preconditioner