afni.nimh.nih.gov

There seem to be 2 issues then. One is that the
sform_code/qform_code values are 2 (which has become
ambiguous because of improper usage). To treat those
as orig space, set AFNI_NIFTI_VIEW to orig (in your
.afnirc file, or perhaps the shell).

Also, if the TR is 1.0 s for some reason (i.e. it is
incorrect), fix it before proceeding.

What does "3dinfo 4D_TE1.nii" show, for example?
Does it show "Time step = 1.00000s"?

If so, just fix it: 3drefit -TR 2 4D_TE1.nii .

- rick