The current segmentation approach https://freesurfer.net/fswiki/ThalamicNuclei seems to have been superceded by a couple other approaches:
https://freesurfer.net/fswiki/ThalamicNucleiDTI
including a Bayesian one and a CNN..
I am thinking it may be useful to swap in the CNN version (likely the most computationally efficient option)..