Dear FreeSurfer experts

I did brainstem segmentation using BrainstemSubstructure method. Then after segmentation, I aligned all my segmented brainstem to Talairach coordinates using transform=$SUBJECTS_DIR/$s/mri/transforms/talairach.xfm.

Alignment seems to be fine. But the boundary of the aligned brainstem looks distorted with different other colors. Why does the boundary look like this? and how can I improve this?

I have attached the image of brainstem after alignment.

Thanks in advance.

Regards