Hi there,
>
> I'm trying to run the new topup tool on 2 b=0 DW images acquired with perpendicular phase encoding directions:
it's been a long time since I tested it on perpendicular directions. It is possible I have introduced some bug that affects that. I'll test on some data I have sitting around and get back to you.
meanwhile I suggest you test running it also with the b02b0.cnf config file. It seems from below you are running it without a configuration file.
Also, when you don't put the correct readout time in (you are using 1 below) you might get into trouble with eddy later on (I put a check for "reasonable readout" in eddy but not in topup, stupidly) so I suggest you use e.g. 0.1 instead (just to so you have it in a realistic range).
Jesper
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