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Hello, 

I am currently collecting diffusion data using a multishell protocol and has a few questions regarding preprocessing the data using topup and eddy. Here are the specs for my data: 

Siemens 3T Prisma, multiband acquisition, 64-channel head coil 

12 directions, 2 B0s (A>>P), b= 500 s/mm2
12 directions, 2 B0s (P>>A), b= 500 s/mm2

29 directions, 3 B0s (A>>P), b=1500 s/mm2
29 directions, 3 B0s (P>>A), b=1500 s/mm2

64 directions, 4 B0s (A>>P), b=3000 s/mm2
64 directions, 4 B0s (A>>P), b=3000 s/mm2

I hope to run eddy first and then popup and applytopup. 

For eddy, my initial question is whether I should combine all runs of my diffusion data (including the B0s) and then run eddy, or if eddy should be run on each run separately or each pair of runs. 

Similarly, should topup be run on concatenated B0s for all runs or should it be conducted on each pair of runs? 

In addition, to for the my_acq_param.txt file, I would like to confirm that the number of rows should correspond to the number of B0s and tat for any Siemens scanner, the first three values should be 0   +/-1   0 as noted in the popup faq. 

Thank you in advance for your guidance!
Cristina