Oh, thank you for looking at this (and the other one) during weekend!

This is an NHP dataset which gives me a lot of trouble with EPI-anat alignment. Like I said in the other post, I am basically following MACAQUE_DEMO_REST so I am going to standard (NMT2.1) space, using animal_warper, now possibly adding another anat step, as described in the other post.

At some point, I spent a lot of time tuning epi-anat alignment (but using MIN_OUTLIER) but even in relatively successful attempts, one or two epi dsets would fail to align. And these were different dsets depending on the parameters, so it wasn't that I had two completely bad datasets. Daniel Glen suggested using EPI[0] for epi-anat alignement, with the logic that a pre-steady state image has better contrast. I should also have said that the EPIs are collected with MION, which changes contrast compared to regular EPIs.

This worked fine (well, better than before), so I used EPI[0] for volreg and EPI-anat alignement.

Just recently I had a thought that maybe EPI[0] is good for anat but not ideal for volreg,

In afni_proc help I found

The entire purpose of -align_epi_ext_dset is for the case where the
user might want to align the anat to a different volume than what is
used for the EPI (e.g. align anat to a pre-steady state TR but the EPI
to a steady state one).

and

The user might want to align to an EPI volume that is not in the
processing stream in the case where there is not sufficient EPI
contrast left after the magnetization has reached a steady state.
Perhaps volume 0 has sufficient contrast for alignment, but is not
appropriate for analysis. In such a case, the user may elect to
align to volume 0, while excluding it from the analysis as part of
the first volumes removed in -tcat_remove_first_trs.

- which is exactly what I had in mind. So I decided to try that. But then I started having doubts about the "missing link" between the epi[0] volume and the MIN_OUTLIER volume, I could not find an answer in the documentation, so I thought I'd ask here.