Jesper and Mareike,
Thank you both for your responses.
>If you run eddy_correct first it will correct for the movements (as
>well as eddy current-induced distortions) and all the images will be
>in the same space. That means that you will only have to register the
>fieldmap to one of the images (e.g. the average of your b=0 images),
>and then it can be applied to all of them.
However, I do have a question for Jesper. What do you mean by registering
the fieldmap to the AVERAGE of my B0 IMAGES? I thought I would just have to
register the fieldmap to the DTI B0 for that subject. Also, I imagine that
in order to register to a B0 image I would have to make the 4D DTI files
into 3D, then do an fslmaths command (not sure which one) for the registration?
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