OK, there was a bug in the qform output in MRtrix3, which was discussed at length in this thread, and I was hoping was fixed with this commit on April 22. If your install is older than that, there is a good chance updating might fix it (git pull && ./build). However, it might be that the fix I’d committed didn’t actually completely address the issue - the original problem seemed to persist in that thread, although I was unable to reproduce it. If updating doesn’t fix it, it would be good if I could have access to the data to investigate further.
So this would address the discrepancy between the qform and the storm in the output, which sounds like the problem. The RAI code in ITKsnap matches what fslhd reports, and gets the wrong inferior-superior direction in the output. The most likely explanation is that ITKsnap is reading the (incorrect) qform and ignoring the sform (MRtrix3 uses the sform preferentially)…
By the way, I notice that earlier on, I used LAS to describe what ITKsnap refers to as RPI, etc. The issue is that I expect for example L to mean ‘towards the left’, whereas ITKsnap expects it to mean ‘from left to right’ - the exact opposite. I’m not sure who’s right here - probably not me… But the point is there’s no disagreement, at least as far as the input image is concerned. The problem really seems to be confined to the incorrect qform…