Dear Marek,
> I have a question about topup and problem with applytopup.
> 1. I would like to ensure that my exam protocol and post processing are correct. I have one sequence of multi b DWI in A>P phase dir. and second sequence with only b = 0 in P>A phase dir. My idea is run topup only to b = 0 images from both sequences and then run applytopup only to first sequence (multi b). Is this idea correct? I cannot do both b= 0 A>P and P>A in one sequence so some motion registration will be need.
You are right about combining the two b=0 and running topup on those. However I would suggest then running eddy (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/eddy) instead of applytopup. It does what applytopup does, but in addition it corrects for motion and eddy currents.
> 2. I did topup only to b = 0 images and the results looks good. But when I tried to run applytopup to multi b values sequences the error message appeared: “ Invalid combination od phase-encode vectors for least-squares restoration”. Could you help me how can I fix this error?
If you are determined to use applytopup instead of eddy you need to use the --method=jac. You need to use that as soon as you don’t have matched pairs for every diffusion gradient direction.
Jesper
> Thank you
> Marek
>
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