Hi, Philipp-

There are a couple issues here. But the main one is that while the first few EPI volumes have good tissue contrast, they are "pre-steady state" and get removed (rightfully) during processing---the problem is that the remaining volumes have very poor tissue contrast, and so they provide little detail for the cost function to align well with the anatomical. You can see in the attached image---the top row volumes have recognizable EPI-like contrast (that is the [0]th volume, which is pre-steady state), while the bottom row has post-steady state, and has poor tissue contrast---the ventricles almost look dark, even, which might prove extra challenging for the lpc-based cost function.

The good news is that we can try another cost function, and also that they EPI and anatomical line up well to start (a good thing for helping alignment). I tried changing to the "nmi" cost function, and to not including "-giant_move" (to address those respective points in the previous sentence), and results looked pretty good. So please try changing this line:

-align_opts_aea -cost lpc+ZZ -giant_move \

to this:

-align_opts_aea -cost nmi \

in your afni_proc.py command.

--pt