Dear Matthias,
To get the coordinates of the FreeSurfer regions, and I suppose also the thalamic subnuclei, you can check the command “mri_segcentroids” in Freesurfer and add the appropriate flags.
In addition, you can also look into the Freesurfer forum for answers related to this topic or post a question yourself in case you have problems when using the command above.
I hope this helps.
Best wishes,
Anna