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Dear Jasper, 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? Thank you, Monika 2014-09-26 21:41 GMT+08:00 Jesper Andersson <[log in to unmask]> : > Dear Monika, > > > > > I want to use eddy distortion correction of dsi data. We acquired > diffusion volumes in A>P phase encoding direction and an additional B0 in > R>L. I tried to run Topup on the B0 volumes but got an error message saying > "error in size-match along non-concatenated dimension". > > That doesn’t sound like an error message I recognise from topup. Are you > sure that doesn’t come from fslmerge (for example if you have a script that > prepares the data for you that calls fslmerge)? > > Jesper > > > > > > Any help on this will be greatly appreciated. > > > > Thank you, > > Monika >