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Dear SPM experts;

I have a clinical fMRI data in which some of the superior slices of functional images are missing. (That is due to the technician's slipping the FOV downwards as the subjects have atrophies in their brains.) However, the structural images contain whole brain volume. How would that affect co-registration step where I try to co-register the structural images to the mean EPI of the subject? Should I consider using a mask for structural images before this step? 

Thank you for your help