Hi Hayriye-

You can use 3dresample to change the orientation:

3dresample -orient RPI -inset T1.nii.gz -prefix T1_RPI

You can combine the orient and resample by using the -master option as well (see help page here).

If you wanted to use the AFNI program align_epi_anat.py, there is no need to modify the T1 image to be the same orientation or resolution as the EPI. You could use it to coregister/align to the T1 and then warp the functional data to a template for use with one of the Atlases. One example taken from the help:

@auto_tlrc -base ~/abin/TT_N27+tlrc -input sb23_mpra+orig
align_epi_anat.py -anat sb23_mpra+orig -epi epi_r03+orig      \
-epi_base 6 -child_epi epi_r??+orig.HEAD    \
-ex_mode dry_run -epi2anat -suffix _altest  \
-tlrc_apar sb23_mpra_at+tlrc

Here the @auto_tlrc step finding the transform from the T1 to the N27 brain, and then align_epi_anat.py is taking care of the registration to T1 and warp to N27 standard space.