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Hi, Yes, the brain extracted fieldmap image is mainly used for masking (as well as an initial registration). As long as the brain extracted image looks OK and your final unwarping result looks good then this is fine. All the best, Mark From: FSL - FMRIB's Software Library <[log in to unmask]<mailto:[log in to unmask]>> on behalf of Pavel Hok <[log in to unmask]<mailto:[log in to unmask]>> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]<mailto:[log in to unmask]>> Date: Friday, 29 April 2016 14:39 To: "[log in to unmask]<mailto:[log in to unmask]>" <[log in to unmask]<mailto:[log in to unmask]>> Subject: [FSL] B0 unwarping in EPI - BET settings Dear FSL Experts, could you please confirm that it is ok to run BET on my magnitude fieldmap image (for FUGUE in FEAT) with the -B option (i.e., bias field correction)? The unwarping results in FEAT look ok, so I assume this brain-extracted image serves just as a brain mask. Thanks! Kind regards Pavel Hok fMRI Lab Olomouc BIC Frankfurt am Main