TMSLIST

Describes a set of TMS simulations.

Initialization

• Python

  from simnibs import sim_struct
  s = sim_struct.SESSION()
  tms_list = s.add_tmslist()
  

• MATLAB

  s = sim_struct('SESSION');
  s.poslist{1} = sim_struct('TMSLIST');
  

Attributes

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

  • Description: Name of coil file. Coil files come in two types

    • .nii.gz files: NIfTI files with sampled magnetic vector potentials. Recommended, allows for faster simulations. (Madsen et al., 2015)

    • .ccd files: Text files that describe the coil as a set of magnetic dipoles. Simulations with this type of coil are slower. (Thielscher and Kammer, 2004)

  • Examples: Python/MATLAB

    Select the SimNIBS model for the Magstim 70mm figure-of-eight coil

    tmslist.fnamecoil = fullfile('legacy_and_other','Magstim_70mm_Fig8.ccd');
    

  • Note: When using a coil provided by SimNIBS you only need to use the file name. If using some other coil file, please use the full path.

  • References: Madsen et al., 2015, Thielscher and Kammer, 2004

• pos: list/array of POSITION structures (Python/MATLAB)

  • Description: List of coil positions for the simulations

  • Examples: See the documentation for the POSITION strucure.

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

  Follow this link.

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

  Follow this link.

• aniso_maxratio: float

  Follow this link.

• aniso_maxcond: float

  Follow this link.

• solver_options: string (pytohn) / character array (MATLAB)

  Follow this link.

Examples

• Set up a simulation with a coil over C3, pointing posteriorly. See the documentation on SESSION and the POSITION structures for more information.

  • Python

  from simnibs import sim_struct, run_simnibs
  # Create a SESSION structure
  S = sim_struct.SESSION()
  # Select the head mesh
  S.fnamehead = 'ernie.msh'
  # add a TMSLIST to the SESSION
  tms = S.add_tmslist()
  # Select the coil from those available in the ccd-coils subfolder
  tms.fnamecoil = os.path.join('legacy_and_other','Magstim_70mm_Fig8.ccd')
  # Add a new position
  pos = tms.add_position()
  # Place the coil over C3
  pos.centre = 'C3'
  # Point the coil towards CP3
  pos.pos_ydir = 'CP3'
  #  4 mm distance between coil and head
  pos.distance = 4
  

  • MATLAB

  % Create a SESSION structure
  S = sim_struct('SESSION');
  % Select the head mesh
  S.fnamehead = 'ernie.msh';
  % Add a TMSLIST to the SESSION
  S.poslist{1} = sim_struct('TMSLIST');
  % Select the coil from those available in the ccd-coils subfolder
  S.poslist{1}.fnamecoil = fullfile('legacy_and_other','Magstim_70mm_Fig8.ccd');
  % Place the coil over C3
  S.poslist{1}.pos(1).centre = 'C3';
  % Point the coil towards CP3
  S.poslist{1}.pos(1).pos_ydir = 'CP3';
  %  4 mm distance between coil and head
  S.poslist{1}.pos(1).distance = 4;