Dear  All,

I am new to FSL. I have two dwi sets (70 volumes each, 10 initial/consecutive b0+60 dw images/set in different gradient directions on a sphere) acquired sequentially (set 1 first, then 2nd) in AP direction with reversed polarity. All data looks OK on visual inspection.

I want to use topup but I am not sure:

1. Should I use/combine the 1st b0 volumes in each data set to generate AP-PA files, or should I use all 10 b0 from each of the datasets (10-10) for the AP-PA, or should I discard a no of b0s from each set and use the others (5-5).

2. Whichever decision at no 1, is there a script that can be used/modified for my configuration?

Thank you,

Octavian