The vsm (voxel shift map) needs to be in the same voxel space as the fMRI (ie, it has to have the same voxel size, number of voxels, and the voxels must line up with the fMRI)
On 4/11/2024 8:11 PM, Gianluca Guglietti wrote:
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Hi,
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.
Any advice would be greatly appreciated!
Best,
Gianluca
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