you need to cut both volumes down to 72x72x48, and then it would work. You can use fslroi for that. Just make sure that the voxel size is identical for both cases, otherwise it won’t work.
Yes, you are right, the error comes from fslmerge. I checked image dimensions for the images I want to merge in order to run topup. B0 has dim1 74 dim2 72 dim3 48 whereas B0flipped has dim1 72 dim2 74 dim3 48.
Can I still use these images to run eddy? Is this a problem that the diffusion volumes are acquired in anterior-posterior phase encoding and B0flipped is acquired in right-left phase encoding direction?