Dear Ana,
what does dti.nii contain? It should contain only the two b=0 with reversed PE, and the acqparams.txt should contain two rows where each row corresponds to a volume in --imain. Also, you should never run topup without a configuration file. We recommend --config=b02b0.cnf that is distributed with FSL.
There are lots of instructions at
http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/TOPUP
Jesper
On 12 Sep 2016, at 09:24, Ana E. <[log in to unmask]> wrote:
> Hello,
>
> I have some problems with popup command, I apply TOPUP with one complete acquisition (64 read-out directions) and only one anti-parallel B0 Volume to estimate the magnetic field.
>
> topup --imain=dti.nii --datain=acqparams.txt
>
> where acqparams.txt has:
> 0 -1 0 0.05
>
> But I obtained this error message:
>
> Topup: msg...: Mismatch between dti.nii and acqparams.txt
>
>
> I don't know what to do? Somebody could help me?? Thanks!
>
>
> Best regards,
>
> Ana.
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