Hi --pt,
If we go back to what we have done here:
[afni.nimh.nih.gov]

# --------------------- for obliquity and center of mass of EPI

3dcalc \
    -a       ${dset_bold}        \
    -expr    'a'                         \
    -prefix  ${dset_bold_deob}

# purge obliquity info, and apply shifts so BOLD dset overlays anat dset well
3drefit                               \
    -deoblique                        \
    ${dset_bold_deob}

3dCM                                  \
    -set 0 0 0                        \
    ${dset_bold_deob}

#### Recenter the

It has work fine with the full dataset one of the cohort of monkey! thank you!

However, we have different orientation of the FOV between the anat and the func for another group of monkey due to a different coil.

This difference of orientation is lost in the header when I previously change the center of my images and they are not aligned anymore when I do:
(they were aligned with the other monkeys)

EPI '-dsets ..' dset(s)
# also, move the EPI to be centered (approximately) on that new spot,
# so the WARP dset doesn't have to stretch too far
@Align_Centers                       \
    -cm                              \
    -base a00_deob_ns_RECEN.nii.gz   \
    -dset LONGER_e00_deob.nii        \
    -prefix LONGER_e00_deob_RECEN.nii

That's why I am trying to refit/resemble these images before.
I also tried
3drefit func -duporigin anat
and it didn't work =(

thanks again