I don't use the @RetinoProc script, but that one or the @SUMA_AlignToExperiment should both produce anatomical datasets that are aligned to the particular subject data. The datasets are aligned using 3dWarpDrive. You should check that the data is aligned by overlaying the aligned anatomical with the subject's dataset for that session. Usually with the -nifti option, there would be little need for an extra alignment, and you could potentially skip that step. One somewhat esoteric caveat is if the MRI anatomical dataset used as input for Freesurfer has an odd number of voxels in any direction, then the output MRI dataset is slightly misaligned from the input. In any case, the EPI dataset should be aligned to your subject's anatomical dataset.