Hello Jesper,
Thank you for the reply
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.
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?
BW
Jay
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