> 1. Even though i estimated the susceptibility field first using the TOPUP tool and then pass the result from that into the --topup parameter of EDDY, it does not perform the susceptibility distortion correction at all. Hence the merging is also going wrong despite using --resamp=lsr and --fep options.
that is strange. I have not heard of that problem before. Can you please send me (to my personal email) the --index file and the --acqp files.
> 2. Afetr performing eddy, you have suggested the average of two b-vectors as one possible solution. If one diffusion-weighted image (say the first in AP scan ) was corrected for 10 degrees of rotation and the corresponding diffusion-weighted image (say the first in PA scan ) is corrected for 20 degrees. Why would the average of two rotated vectors be valid for the merged diffusion-weighted image (say the first in PA scan )? in our example, the average rotation is 15 degrees, and its not a valid rotation for the merged diffusion-weighted image.
> Would it be more correct if the b-vectors of AP and PA separately, and then calculate diffusion parameter maps (eg FA). And then use topup to merge both FA_AP and FA_PA maps? Would it be possible to correct FA maps using applytopup using distortion field calculated on b0 maps?
If you see a 20 degree rotation you will have big problems with different susceptibility fields for the two scans, so data like that will have lots of problems besides rotating bvecs. For more normal rotations (up to a couple of degrees) it has quite small effects and an average is probably close enough.
At the moment you cannot correct FA maps using applytopup since it will always do a Jacobian modulation of your images. You will have to decide what you see as more important, rotating bvecs or doing a better job of correcting distortions.