Hi FreeSurfers,

I just processed a dataset using FreeSurfer (the base created from the norm.mgz volumes of a longitudinal study) and noticed that the labels for the cerebellum are causing an incorrect segmentation towards the inferior of the cortex. Further, labels for cerebellum, brain stem and the fourth ventricle can be found outside the brain mask (see attached screenshot).

Note that input was not a full head scan, but an already skull stripped brain only image, i.e., also without cerebellum and brain stem.

Does FreeSurfer not work with such input data? Must the cerebellum be present?

Thanks, Andreas