Please note that this is a clear violation of the DICOM standard: Philips MUST NOT include derived images in the same series as the raw data. They are a professional company and you should contact them and ask them to stand behind their conformance statement. I do not have a Philips system, so I can not replicate your problem, but if you send my personal email a link to a sample image, I might be able to come up with a simple solution. By the way, I would also consider increasing the number of B=0 volumes in your acquisition (or acquire a separate series of B=0 images):
 https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/eddy#If_you_haven.27t_already_acquired_your_data
 http://www.mccauslandcenter.sc.edu/crnl/tools/advanced-dti