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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 Sadia Research Student
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