Dear Joyce,
>
> Thank you so much for your help and problem solved!I have a silly questions though: you have mentioned my MRI and DTI data don't have same dimensions. Then, why I could register them perfectly using FLIRT? Thanks!
the various registration tools (FLIRT, FNIRT etc.) in FSL “know about space”, and are use to transform images from one space to another. That means that other tools like for example dtfit don’t need to know about them, and instead they just assume that the various images have been put in the same space by one of the registration tools. So in this case dtifit just assumed that the --data and the --mask was in the same space.
However, as I said, it really ought to check it and produce a clear error message if they are not.
Jesper
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