Hi,
I've had a look at this and the T1 structural image (highres) is not registering well with the fieldmap, probably because its initial orientation is so different. If you run fslreorient2std on the T1 structural, as well as on the fieldmap images, then I think this should fix the problem.
All the best,
Mark
On 19 Sep 2013, at 19:33, Benjamin Philip <[log in to unmask]> wrote:
> I'm having some strange problems with the BBR registration in a most recent attempt to do B0 unwarping. In the unwarping output, the "Unwarping shift map" is grossly mis-aligned; the image has been flipped and rotated in a variety of ways.
>
> I've fiddled with the brain extraction a great deal already, and also ran fslreorient2std on all input files. Notably, this problem isn't arising from the FEAT unwarping parameters: I've successfully gone through this process using many other images in the same study, including from other experiments involving the same day/session/participant/t1.
>
> I'm at a bit of a loss what else I can do to troubleshoot a bad BBR fieldmap registration. Hopefully someone else in here can help! I've shared some files, including the reg directory, fieldmap, and T1 files. (This has some updates and expansions since my last post on the topic.)
>
> https://www.dropbox.com/s/ipaejcthbey57w3/BphilipFieldmap.zip
>
>
> Thanks,
> Benjamin Philip
> University of Missouri
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