Dear Simon,
>
> We are trying to use the combination of topup and eddy to correct for susceptibility distortions and eddy currents/movements in our diffusion data. We acquired one set of volumes with phase-encoding R>>L consisting of 7 b=0 volumes and 60 gradient-weighted volumes. We also acquired one single b=0 volume with phase-encoding L>>R. The attached screenshot shows our diffusion data before (on the left) and after (on the right) running topup and eddy. In this case the uncorrected data appears to be less distorted than the corrected data. What might be the cause of this problem?
I would need to see the commands you used and the contents of your --acqp and --index file to have a chance of diagnosing what went wrong.
One thing though, are you certain the PE is R->L and L->R? Looking at the before figure it looks more like an A->P image to me. The pile up of intensity posterior to the ear-canals in particular makes it look like that.
Jesper
>
> Kind regards,
>
> Simon Baker
> Brain & Mental Health Laboratory
> Institute of Cognitive & Clinical Neuroscience
> Monash University
>
> <before_after.png>
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