Adding some follow-up information to this thread
before forgetting completely (it was resolved via
email)...

The image flipping is indeed because of acquiring
alternating phase encoding directions each time
point. Such volumes are easy to separate using
-num_chan 2 (in this case).

The -sort_method geme_index option would not
be appropriate for this data, but rather the default
sorting applied via -dicom_org, which ends up
applying 'RIN', the Image Instance Number.

Aside from the first image in each directory having
a different name (upload.dcm) than the others, this
scan was 28 images from one point in the run, and
150 images from another. Combining that with
multi-echo data made it a little challenging for Dimon
and other software to deal with.

- rick