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Hello all, 

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


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