I've used the following command
align_epi_anat.py -anat SN01_S2_EXP_MP_S_oblique+orig -epi SN01_S2_ALL_EP+orig -epi_base 0

Kept getting error message. It's either complaining that it can't strip the skull. But the I've used 3dSkullStrip -input SN01_S2_EXP_MP+orig -prefix SN01_S2_EXP_MP_S+orig to remove the skull and use this new file as the input for align_epi_anat.py

** Critical 3dSkullStrip (SUMA_3dSkullStrip.c:2495):
Failed to allocate for fvec.
Oh misery.
** ERROR: Could not strip skull

or

** FATAL ERROR: Can't read file 'SN01_S2_EXP_MP_S_al_a2e_only_mat.aff12.1D'
#++ Combining anat to epi and oblique transformations
#Script is running (command trimmed):
3dAllineate -base __tt_SN01_S2_EXP_EP_tsh_vr_ts_rs_ns_al+orig -1Dmatrix_apply SN01_S2_EXP_MP_S_al_mat.aff12.1D -prefix SN01_S2_EXP_MP_S_al -input SN01_S2_EXP_MP_S+orig -master SOURCE
++ 3dAllineate: AFNI version=AFNI_2008_07_18_1710 (Jul 24 2008) [32-bit]
++ Authored by: Emperor Zhark
** FATAL ERROR: Can't read -1Dmatrix_apply 'SN01_S2_EXP_MP_S_al_mat.aff12.1D'
#**ERROR Could not square a circle (3dAllineate could not align anat to epi)
Traceback (most recent call last):
File "/home/yangming/abin/align_epi_anat.py", line 1725, in ?
ps.anat_alnd, ps.anat_alndwt = \
TypeError: unpack non-sequence