When scanning we collect 2 sets of anatomical images. One set of prescan normalized Anatomical images (T1w, T2w), and one set of non-normalized anatomical images. which one is suggested to be used when running through fmriprep.
Either one should work with fMRIPrep. For a sanity check you could run a subject through once with prescan normalization and once without and compare the reports produced.
Otherwise you could use both at the same time. fMRIPrep will average the anatomical images provided. BIDS setup for having both types in a directory might look something like: