Hi Durai
Yes, you can either fix the distortions using either blip-reversed b0s (see topup) or fieldmaps (see fugue).
Cheers
Stam
On 20 Feb 2014, at 19:02, Durai Arasan <[log in to unmask]> wrote:
> Hi FSL experts,
>
> I am trying to register a T1 structural image to b0 and FA images from a diffusion weighted scan (all within subject 6DOF) and getting poor alignment.
>
> I read in previous messages that the alignment is off at the genu of the CC and the orbital regions. I believe this is due to distortions in the b0 image.
>
> Are there any recommended ways to fix the distortion so I can use a 6DOF registration between b0 and T1. I really don't like affine for within subject registrations.
>
> Thank you
>
>
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