TDCSLEADFIELD¶
Describes the simulations for a Leadfield. Required for optimization
Initialization¶
Python
from simnibs import sim_struct tdcs_lf = sim_struct.TDCSLEADFIELD()
MATLAB
tdcs_lf = sim_struct('TDCSLEADFIELD');
Attributes¶
fnamehead: string (Python)/character array (MATLAB)
Desctiption Name of head mesh file (
subID.mshfile)Example: Python/MATLAB
tdcs_lf.fnamehead = 'ernie.msh'
pathfem: string (Python)/character array (MATLAB)
Desctiption Name of output folder
Example: Python/MATLAB
tdcs_lf.pathfem = 'tdcs_leadfield/'
field: ‘E’ or ‘J’, optional
Description: Whether to calculate the electric field ‘E’ or current density ‘J’.
Default: ‘E’
eeg_cap: string (Python)/character array (MATLAB), optional
Description: Name of .csv file with EEG electrode positions.
Default: Automatically finds the file
subpath/eeg_positions/EEG10-10_UI_Jurak_2007.csvbased on fnamehead or subpathNote: Only needs to be set by the user if not using the standard .csv cap file.
interpolation: ‘middle gm’, None/[], or list/cell array of strings (Python/MATLAB), optional. Default: ‘middle gm’
Description: Where to interpolate fields
‘middle_gm’: Interpolate fields in the middle Gray Matter surface obtained from the head segmentation. Default value
None/[]: Do not interpolate the field anywhere, just store it in the region defined by the tissues attribute.
list/cell array of strings: List of mesh files in ‘.stl’, ‘.gii’, ‘.off’ or ‘.msh’ format. The files will be loaded and the fields will be interpolated at the mesh nodes.
Default: ‘middle_gm’
Note
Does not work for headreco models ran with the
--no-catoption.
tissues: list (python) or array (MATLAB), optional
Description: Tissues numbers of where to record the electric field, in addition to interpolate. Mixing surfaces and volumes is not allowed.
Default: [1006] (i.e. eye surfaces)
Example: Python
# Example: Record electric fields in gray and white matter tdcs_lf.tissues = [1, 2]
interpolation_tissue: list (python) or array (MATLAB), optional
Description: Tissues numbers to use as a base for the interpolation procedure. Nodes in the interpolated surfaces outside of the region defined by interpolation_tissue will be extrapolated using nearest neighbor. Ignored if interpolation is set to None/[]. Must correspond to a volume.
Default: [2] (i.e. gray matter surface)
electrode: ELECTRODE structure, list/array of ELECTRODE structures, or None/’none’ optional
Description: Electrodes to be used. Typically small round electrodes. There are 3 ways to set this variable:
ELECTRODE structure: Use the same electrode shape for each electrode defined in the cap
list of ELECTRODE structures: Each electrode in the cap file will have the shape of the corresponding entry in the list
list of ELECTRODE structures and eeg_cap set to None (Python only): will use the centre and pos_ydir attributes of the electrodes to place them. This allows to set up electrodes on your own, without using a eeg cap provided by SimNIBS.
None(Python) or ‘none’ (MATLAB): Use point electrodes located at the surface nodes closest to the electrode center
Default: Use 1 x 1cm round electrodes with 4mm thickness
cond: list/array of COND structures (Python/MATLAB), optional
anisotropy_type: ‘scalar’, ‘vn’, ‘dir’ or ‘mc’, optional
aniso_maxratio: float
aniso_maxcond: float
fname_tensor:string (Python)/character array (MATLAB), optional
Description: Name of NIfTI file with conductivity tensors
Default: Automatically finds the file
d2c_subID/dti_results_T1space/DTI_conf_tensor.nii.gzbased on fnamehead.Note: Only needed for simulations with anisotropic conductivities. And only needs to be set by the user if a file other than the above is to be used.
solver_options: string (pytohn) / character array (MATLAB)
