In order to register functional MRI data on to the high-resolution structural image, one first needs to extract the brain out of the structural image (aka skull stripping). I usually use BET tool (provided by FSL) for the same. However, it sometime takes forever to adjust parameters (f and g) to get the best results out. Especially, in cases where the lower half of structural image is noisy. To solve the problem and save time, I have found that pre-masking the structural images to standard space brain usually helps. So run this command before running your regular bet command will help,
standard_space_roi <input> <output> -b
Then run the BET command (usually with very liberal f-values) works beautifully, e.g.,
bet <input> <output> -f 0.15
Hope that helps!
neuroimager 