Coordinates in SimNIBS¶
Coordinates in SimNIBS are always world coordinates in subject space. Coordinates are given in millimiters and along x, y and z axis.
Voxel to SimNIBS Coordinates¶
The head meshing procedures create a NifTI file called
m2m_subID/T1fs_conform.nii.gz. This file contains a transformed T1 image of the subject, with the world coordinates used by SimNIBS.
During head meshing, SimNIBS calculates 6 degrees-of-freedom, 12 degrees-of-freedom and non-linear MNI transformations. They are stored in the
SimNIBS uses these transformations when transforming simulation results to MNI space (see the Simulation Options Window and map_to_mni attribute).
Command line Utilities¶
SimNIBS has several command line utilities to transform data and coordinates between MNI and Subject space
Python and MATLAB Functionas¶
We also provide Python and MATLAB interfaces to transform coordinates between MNI and Subject Space. Those have the signature
mni2subject_coords(coords_mni, subdir, transformation_type)
coords_mniis a set of coordinates in MNI space
subdiris the subject segmentation directory, for example
transformation_typeis the type of transformation, can be
And equivalently to