Hi,
Sorry about the delay in replying.
This is nothing to be concerned about. It comes from using periodic boundary conditions for the spline interpolation and is dealt with through masking of the non-PE directions in eddy and applytopup. The important thing is that the —iout output from topup is just intended as a visual check of what topup has been up to, so therefore no masking is applied there.
These periodic boundary conditions for the PE direction are necessary as in many cases the brain does not fit inside the FOV for both blip-directions so it is more a rule than an exception that the brain wraps around.
As long as your final output is fine then you don't need to worry about this in the --iout output from topup.
All the best,
Mark
On 11 Aug 2014, at 16:57, Kasper Winther <[log in to unmask]> wrote:
> Dear all,
> when running topup using the following command:
> topup --imain=pref0aref0.nii.gz --datain=aq_param.txt --out=my_topup_results --fout=my_field --iout=my_unwarped_images --config=b02b0.cnf
> I experienced that the top slice in the unwarped images contain a slice that should have been at the bottom (please see attached unwarped.jpg). Likewise, the fieldcoeff image also contain a slice in the top, which looks like it belongs to the bottom of the image.
> When I use eddy to unwarp other images the output looks ok, that is, without the strange top-slice. Does anyone know why this happens and should I be worried about this? The input images (pref0aref0.nii.gz) looks ok.
>
> Thanks,
> Kasper
> <unwarped.jpg>
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