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];

  • target_direction: None/[] or (3x1) list/array (Python/MATLAB) of floats, optional

    • Desctiption: Direction of the electric field to be optimized. If None (Python) or [] (MATLAB), will optimize the elctric field magnitude. Default: optimize field magnitude

    • Example: Python/MATLAB

    opt.target_direction = [1, 0, 0]

  • 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

  • method: ‘direct’ or ‘ADM’, optional

    • Description: Method to be used for the solution. Can be either a direct method, which will perform electric field simulations at each coil position or the Auxiliary Dipole Method (ADM, Gomez 2020), which uses reciprocity and the fast multipole method (FMM) to massively accelerate the optimization. The ADM method is only compatible with .ccd coil files

    • Default: direct