Coordinates in SimNIBS

Definitions

Coordinates in SimNIBS are always world coordinates in subject space. Coordinates are given in millimiters and along x, y and z axis.

The origin and the alignment of the axes can vary in head models ran with headreco. In head models ran with mri2mesh, the coordinates are based on the conform coordinate system based on FreeSurfer.

Voxel to SimNIBS Coordinates

The head meshing procedures create a NifTI file called m2m_subID/T1fs_conform.nii.gz. This file contains the input T1 image of the subject with a header such that the world coordinates reflect those used by SimNIBS.

Please notice that mri2mesh changes the header compared to the original T1 input image, while headreco does not change it by default.

MNI Transformations

During head meshing, SimNIBS calculates 6 degrees-of-freedom, 12 degrees-of-freedom and non-linear MNI transformations. They are stored in the m2m_subID/toMNI/ folder. SimNIBS uses these transformations when transforming simulation results to MNI space (see the Simulation Options Window and map_to_mni attribute) as well as in the command line utilities