Get the MNI coordination from warped anatomy using cs_convert function

Hi all,
I have simple question.
when i use cs_convert function (e.g. P_mni = cs_convert(sMri, 'scs', 'mni', P_scs); ), P_mni is empty. So i check the sMri.NCS.R and .T. These file are also empty.
sMri is exported from warped anatomy. because i didn't get MRI i warped the default anatomy data using digitized data when i review raw file.

could you give me some advice?


Indeed, the MNI transformation is not available on warped MRIs. The non-linear deformation field from the MNI template to the digitized head surface is not kept, and after the computation of the warped anatomy, there is no way to get it back. This could be improved, for sure.

But there is a much easier way to deal with the correspondance with MNI space: the warped surfaces are exactly the same as the original MNI152 surfaces, matching vertex by vertex. If you want the MNI coordinates of vertex #i of the warped surface, just read the original MNI surface and get the coordinates of vertex #i. You should be able to project easily scouts and source maps between warped and template surfaces with the menus in the Surface tab.

Hi Francois,

Thank you for your always polite explanation.