A small portion of cortex in a superior part in axial and coronal view is removed my T1 and T1-gd datasets after done a skull stripping with FSL. I tried to improve the BET quality through manipulating a coordination, fractional intensity and vertical gradient, but still I can’t recover the small portion of cortex. I applied a brain mask from the T2 imaging with a good quality of BET to both T1 and T1-gd imaging, and this method seems to work. However, this method seems not recommendable as T2 and T1 have a different modalities.
Therefore, Is there other method to improve the BET quality of both T1 and T1-gd imaging in FSL?