Dear Andrew,
>
> We are running Eddy on a large number of our DWI scans, which have already been collected. They do not have the opposite phase encoding required to run topup as-is, but we have collected fieldmap images. It appears that topup estimates the fieldmap/bias, and then applies some processing on that estimation, which can be passed on to Eddy. I was wondering if instead of estimating the fieldmap, whether we could use our own collected fieldmaps, with some additional processing? Is there a better alternative, given our acquisition?
at the moment it is not possible to use “traditional” fieldmaps with eddy. It is something that we might implement in future releases. Even if we did we would still strongly recommend using topup (blip-up-blip-down based) fieldmaps with the first input volume to topup being identical to the first b0 in the diffusion data set passed to eddy. That will “automatically” give a very good registration between the fieldmap and the diffusion data, something which isn’t otherwise trivial.
Jesper
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> Note, this might be a duplicate of this, but I didn't see any responses:
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> https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=FSL;e2733c54.1411
>
> Thanks!
>
> Andy
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