I had a question as to how to integrate fsl's topup command for correcting B0 distortion with freesurfer's boundary-based registration. I am working with high-resolution epi data (0.8mm isotropic) with a reduced FOV and am trying to register it to an MP2RAGE structural scan that I've already run through free surfer's recon-all. When I use the BBR command it works perfectly fine but when I try to add the topup field map it fails, returning this error "MRIvol2surfVSM: vsm dimension mismatch 1".

the field map was generated using two reverse phase encoded SE-EPI volumes with the same resolution and field of view as the GE-EPI BOLD data I am trying to register.