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Dear Monika,

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.

Jesper

On 26 Sep 2014, at 17:38, Monika . <[log in to unmask]> wrote:

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