Transforms fields in mesh files to nifti files.

Usage example

  1. Open a simulation results folder. For the following, it is assumed that you ran a TDCS simulation on ernie.

  2. Run

msh2nii ernie_TDCS_1_scalar.msh ../m2m_ernie/T1.nii.gz ernie_TDCS_1

  1. This will create one file for each data field in the mesh, e.g. ernie_TDCS_1_E.nii.gz, ernie_TDCS_1_J.nii.gz, ernie_TDCS_1_magnE.nii.gz, and ernie_TDCS_1_magnJ.nii.gz

  2. The files are in the same coordinate space as the ../m2m_ernie/T1.nii.gz file

Further notes

  • Type msh2nii -h for more information and options.

  • This tool performs an equivalent function to selecting the Interpolate to a nifti volume option in the GUI or set map_to_vol to true in the SESSION structure.

  • Can also be used to create tissue masks with the --create_masks argument (one binary mask per tissue).

  • Using the --create_label argument will create an image with the tissue labels in the mesh.