Hi, Irene-

that looks a bit different than what was happening in the first case in this thread-- though the solution might be the same. Please see my new reply to that thread.

Basically, my guess is that your dset starts out far from overlapping on the template dset; you can check this with:

3dcopy  ${T1_data} test_copy.nii
3drefit -space TLRC test_copy.nii

... and then overlay that dset on your base (MNI152_2009_template_SSW.nii.gz)

In your particular case, I think this happens because of purging the obliquity information with "-deoblique_refitly".

You could deoblique your anatomical with 3drefit, and then use a similar @Align_Centers command to what I used above. Note that removing the obliquity information might mean that your anatomical and EPI don't align well...

Does your anatomical dset actually have obliquity? What is the output of:

3dWarp -disp_obl_xform_only -deoblique ${T1_data}

?

--pt