Mark,
Good to see that you got in on this post, will probably make things much
easier. Basically, I was told to align the fieldmap to the DTI B0 image
BEFORE applying the correction.
The pipeline now is: apply eddy-correction to non-BETed DTI data, BET both
fieldmap and DTI, register fieldmap to B0 (have tried 3 dof and 6-dof), then
apply fieldmap. Again, registering the fieldmap to the DTI B0 produces
artifacts. Additionally, using non-BETed fieldmap and DTI data produces
horrendous results.
I am wondering if the DTI data should be registered to the fieldmap instead.
However, I am assuming this would add unwanted smoothing.
Thank you.
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