Establishing a reliable correspondence between lesioned brains and a template is challenging using current normalization techniques. The optimum procedure has not been conclusively established, and a critical dichotomy is whether to use input data sets which contain skull signal, or whether skull signal should be removed. Here we provide a first investigation into whether clinical fMRI benefits from skull stripping, based on data from a presurgical language localization task. Brain activation changes related to deskulled/not-deskulled input data are determined in the context of very recently developed (New Segment, Unified Segmentation) and standard normalization approaches. Analysis of structural and functional data demonstrates that skull stripping improves language localization in MNI space - particularly when used in combination with the New Segment normalization technique.