Thanks so much for the reply.
Yes, afni_proc did correct process and transformed the data. However, my original epi dataset is 2x2x2.2 mm and 100x100x37 dimension. afni_proc (i.e., 3dAllineate) resamples data to 2x2x2 mm and 128x128x128 dimension, which dramatically increase file size and change the resolution and matrix of the data. I just want to align epi to T1 but without changing the resolution and matrix size—namely, no resampling data. Is that possible? It seems possible only when epi and anat are very close. Unfortunately my epi data and anat T1 deviate significantly, so I can not use -master epi.

Ruyuan