Hi Gulhan,

Assuming the datasets had correct (if different) orientations
to begin with, then 3drefit is not an appropriate program to
use to change the orientation, 3dresample is.

What 3dresample does: changes the orientation on disk
to convert from one proper orientation to another.

What 3drefit does: alters the header, saying "ignore the
current orientation, it should really be this". In this case, the
data is unchanged on disk. This method is used to fix an
incorrect header.

When viewing data in afni, the orientation is disk does not
matter, *as long as it is correct*. It will be displayed correctly
in afni if afni knows the correct orientation.

So it is actually 3dinfo that does not matter. It says LPI
because you told it to say LPI (using 3drefit), not because
the volume is actually stored in LPI.

Does that help?

- rick