Hi-

Can we see how the original EPI and anatomical data (no changes to obliquity) overlay when you run this command:

@djunct_overlap_check -ulay DSET_ANAT -olay DSET_EPI -prefix check_olap

? That should create 2 images: one with obliquity *ignored* (which will likely have poor overlap) and then one where all obliquity is applied (called *_DEOB*). The question will be, how well do the data overlap when obliquity is applied? If they overlap well, then great.

Let's start with that, before getting into the EPI-anatomical alignment failure. (And actually, your APQC HTML should contain essentially these images in the vorig section, but I would like to see as well before the deoblique-while-preserving-coordinate-origin, to be sure).

--pt