In SPM the image origin needs to be approximately equivalent to the origin of the template. If it is too far off the registration steps can’t cope.
MANTiS includes a simple tool to set the origin based on centre of mass. This tool is derived from an equivalent function in the VBM8 package and should be applied to brain extracted images. It is available via the batch interface and can be combined with the brain extraction tool.
This is an optional step if tissue classification doesn’t appear to make sense. It is usually safe to apply it. The tool is available via the batch interface: