Just to add my 2 cents on this issue:
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We all agree high correction factors outside the brain are not problematic in and of themselves, and that if you want to check for correct operation, the only place that matters is within the brain.
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Nonetheless, I think Ben’s point is valid: if there are high intensity regions outside the mask, it may be indicative of issues with the procedure, so it’s worth checking that everything has worked OK – especially if the bias field wasn’t too bad to begin with. So rather than ignoring them completely, treat them merely as an invitation to double-check your data.
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Following this discussion, I’ve had a look into the effect of the mask on
mtnormalise, and I have to admit that it is indeed a lot more sensitive to the mask than I’d appreciated… Based on this, I think we should at the very least update our documentation to recommend the use of a very conservative mask for this particular step.