simnibs.simulation.calc_B

simnibs.simulation.calc_B(J, n_voxels, affine, calc_res=2.0, mask=False)

Calculates the magnetic field caused by a current density distribution J

Parameters
  • J (simnibs.msh.ElementData) – ElementData field with the current density field

  • n_voxels (list or tuple) – number of voxels in x, y, and z directions for the output B

  • affine (ndarray) – A 4x4 matrix specifying the transformation from voxels to xyz for the output B

  • calc_res (float (optional)) – Resolution of the space used for the FFT calculations, in mm. Default: 2

  • mask (bool (optional)) – Wether to mask the resul using the mesh. Default: False

Returns

  • B (ndarray) – numpy array of size n_voxesx3 with the magnetic field

  • Reference

  • ———-

  • Yazdanian, H., Saturnino, G. B., Thielscher, A., & Knudsen, K. (2020).

  • Fast evaluation of the Biot-Savart integral using FFT for electrical conductivity imaging.

  • Journal of Computational Physics, 109408.

  • https (//doi.org/10.1016/j.jcp.2020.109408)

Example

Load a simulation result with a ‘J’ field can calculate B in an ROI Defined by a nifti file >>> import simnibs >>> import nibabel >>> simulation_J = simnibs.read_msh(‘simulation_result_with_J.msh’) >>> reference_nifti = nibabel.load(‘reference.nii) >>> B = simnibs.simulation.calc_B(simulation_J.field[‘J’], reference_nifti.shape, reference_nifti.affine)