Does FSL/BET have options to extract everything inside skull/cortical bones that includes CSF also in peripheral gray matter regions? For example as below: background 0, skull 2 and everything inside the skull is 1.
I have tried running bet as following:
cmd = ['bet /media/banikr/DATA//5767/CT-MRI-5767_MR_norm.nii.gz /media/banikr//test/5767_MR_norm_bet.nii.gz -m -f 0.2259']
system(cmd)
which generates a binary mask that skips peripheral CSF.
Thanks in advance.
Rana Banik
Graduate Student