I assume you are aligning all the EPI datasets to the single anatomical dataset with a series of align_epi_anat.py commands. If so, you should use the "-master_epi" option to set the master_epi dataset to be the anatomical dataset or "BASE" and set the output resolution to be some dimension like 3 mm with "-master_epi_dxyz 3". The "-giant_move" default assumes these kinds of large movements and sets the output resolution to be the minimum dimension of the input EPI dataset. You can do that with "MIN_DXYZ". Review the "-master_xxxx" option part of the align_epi_anat.py help for more information.