Dear Mark,
I got an email from you on this topic (7 July) suggesting that I could either use fslswapdim or fslreorient2std.
Since I'm using FSL 4.1.4, I applied fslswapdim. (command was: fslswapdim in x -y z out)
The labels of the original stacks were all correct in FSLView, so there is no reason why I should
flip the y axis. But it resolved the registration problems, though.
Reading your response I get the impression that this is not the
right way to do. My feeling is that the orientation is not causing
these problems but fsl_reg.
Ed
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