Thank you. This is how I have been basically working, with the exception that we are still scanning subjects for the project. I have been happy with AW results in all monkeys (they all have their anat scans done), and with AP results from one monkey. Once I started expanding to another monkey (we have full functional datasets from 2, just starting another 2), things started going sideways, epi-anat would fail for specific sessions or runs of that second monkey (and on HPC only)

One of the ideas that Daniel suggested to solve that was to use MDEFTs acquired during functional sessions as anat. Before that, I was using MPRAGEs which were acquired separately (and in another scanner). So my first step was, OK, but will these MDEFTs align to the template, this is why went back to AW, and they did not. (both the EPI's and MDEFTs are oblique and partial which apparently causes a lot of problems, plus these are monkeys with huge muscles and surface coils which makes skull-stripping within epi-anat alignment a challenge too).

I am going to sort out the environment variables first (after I figure out which of them means what), and then I will make a step back and ensure I am working from the same versions of the template and the source files on both systems. I was pretty sure they were identical, but maybe a difference crept in.

As for random seeding explaining different alignment results, I thought about that too - but then repeated runs converged to a (visually) identical solution on each system, different between the systems.