Dear Ines,
> Dear Jasper,
>
> Apologies for the missing information. I have used the following eddy commands line:
>
> eddy --imain=dti_base --mask=mask_hifi_mask --acqp=acqparams.txt --index=index.txt --bvecs=dti_base.bvec --bvals=dti_base.bval –-topup=my_topup_results --data_is_shelled --repol --out=eddy_corrected_data –-verbose
how did you create the 4D image that you used as input to topup? My advice is to always put the first b=0 file from the full diffusion data (dti_base) as the first volume since that is what guarantees alignment between the field (and mask) from topup and your data.
Also, did you look at your --iout images to check that topup had worked well?
Jesper
>
> Please let me know if there is any other info you may need.
>
> Thanks,
> Ines
>
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