allow brain extraction using FLIRT registration style
The use case here is relevant to clinical images with large lesions that confuse BET. fsl_anat already accepts a lesion mask for use during registration (both FLIRT and FNIRT based), but the --nononlinreg
option forces the use of BET for brain extraction which can fail with large lesions (for example chronic stroke on T1). It could be useful (and more robust) to use the linear registration and standard brain mask to brain extract these types of images, and use BET as a fallback method. Of course the linear registration will not be as precise as the FNIRT based brain extraction, but this could be robust in the presence of abnormal data.