Dear Jan,
>
> "terminate called after throwing an instance of 'NEWMAT::IndexException'
>
> Could you give me any advices where this error comes from, because I coud not find more information about it in the internet.
that particular error message is not very helpful. It comes from the linear algebra library we are using, and all it says is that topup attempted to index outside of a vector or matrix.
>
> I am using a 4D dataset with different b0 images (blip up and blip down). Because those images just consist of one slice, I merged each image with itself in z-direction to receive 2 slices. Otherwise I received a subsampling error because of an odd number in slice direction.
> The acq_param.txt file also fits to my data [0 1 0 0.62 ; 0 -1 0 0.62]
> The b02b0.cnf file is just copyed from the fsl directory.
topup hasn’t really been designed to work with 2D data. In the past I have had some success with doing what you have done in the z-direction, but so that I get a larger number of slices. I would suggest trying with 16. Note that with 2D data you can never correct for out-of-plane movement, and that your data will only be corrected for in-plane translations and the in-plane rotation.
Note also that your readout time is unrealistically large. Typical values are on the order ~0.05s.
Jesper
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> I am using the latest version of fsl -5.0.9
>
> Maybe you can help me with my problem.
>
> Best greetings from germany and also a happy new year 2017!
>
> Jan Rüdiger Schüre
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