Thank you very much Jesper for your reply.
1) I had actually already run eddy without slice-to-volume option earlier. It seems like vast majority of the volumes do not have any outliers in my case. Only a few volumes have some outliers.
2) In my case, I see this error when I use the --slspec option (even when slice-to-volume registration is not done). I just tested that eddy_cuda only with the compulsory inputs (with no extra options) works fine. But when I add "--slspec=slspec.txt", I get this error.
Can somehow incorrect slspec.txt cause this error? This (Siemens) data was reconstructed without mosaic (I cannot get it with mosaic anymore). And I read somewhere that slice timings might not be accurate without mosaic option? Can this be related?
Thank you,
-Baran
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