Dear Khoi,
>
> 1. topup with both AP and PA scans
yes, typically it is enough to pick just one b0 volume for each PE-direction. It is important that the first volume of your input to topup is also the first volume of your input to eddy.
> 2. eddy with topup results
Yes, you pass the name you specified as --out for topup as the parameter for --topup for eddy.
>
> Some suggested pipelines (i.e. the HCP) use eddy_combine after the above steps but I find little to no detailed description on what is its role. My guess is it just corrects (balances) the intensity between AP and PA scans but does not alter any structural details. Does it just simply average the corrected AP and PA scans or fit a sophisticated model instead? And it is necessary to include it in the pipeline or it is deprecated?
It just averages the corresponding AP and PA scans. It was only done so as to reduce the execution time of the subsequent bedpost step. I wouldn’t necessarily recommend doing it.
Jesper
>
> Any suggestion would be much appreciated.
>
> Sincerely,
> Khoi
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