Hi Emily,
That notion of interleaved should refer to how the actual
slices are stored in the mosaic. If the EPI volumes look
correct when viewed in afni, then that -sinter option should
not be a worry.
Given that the volumes are now stored correctly on disk,
the alt+z only affects how they are processed during a
3dTshift operation, say, to deal with timing of individual
slices.
Note that you should have the option to use Dimon, e.g.
Dimon -gert_create_dataset -infile_prefix /Volumes/HaleDepo/STRESSSPGRREST_150816/${subject}/REST2/M
From there you could consider options like -dicom_org
and -save_details, if you wanted to.
- rick