Too quick to reply:
B0s of eddy output are out of order only when using the Mac version of fslview, not the Linux version running on our cluster. This was the same with both Mac fslview 3.1.8 and 3.2.0.
Further, when using Mac fslview, the app will crash when trying to run the eddy output data in Movie Mode (but it doesn't crash running the eddy input data in Movie Mode - which is a much smaller file size). Here is the crash message:
fslview(52693,0xac0d4a28) malloc: *** mmap(size=4063232) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
So this doesn't seem to be an eddy-specific problem, but a problem related to the large file size and the Mac version of fslview.
Here's a download link to the eddy output data file if interested:
There are in total 1068 volumes, and the B0s are supposed to be at the positions (with the first volume=0):
0:10 267:277 534:544 801:811
>>I found out that the eddy output data was actually fine, it was just fslview showing the B0s at wrong positions, having
>>memory problems with the big data set, when the data was accessed remotely from our server. When I view a local copy of
>>the data or when I run fslview differently on the server it's fine. I'm really sorry having bothered you with this!