I have ABIDE-II NYU dwi datasets.The SIemens allegra data had 2 runs of dwi and also the fieldmap magnitude(2 different echo times) and associated phasemap image.I was planning to use FUGUE  followed by dti_preprocess command.

However,the orientations of the dwi runs and the fieldmap images appear to be different(Screen-shots attached,also confirmed using the ´fslorient´ command).Kindly suggest a workaround with this issue.

Regards,

Archith Rajan

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