We are planning to use 'topup' to correct the diffusion data of postmortem brains acquired using segmented 3D EPI sequences. Since there are two phase encoding directions, I feel the distortion will not be confined to each axial slice (am I right that the distortion
will be at 45 degree from the axial slices?). So, my question is whether I could use "topup" to correct for the distortion between two averages of data with completely opposite two phase encoding directions? What other points that I need to pay attention to
when I am using "topup" to correct for such data?
having two phase encode directions may mean having distortions along two directions, but not necessarily. It depends on the specifics of how you acquired your data. Distortions "only" occur when you have multiple phase-encode steps following a single excitation.
If you have another phase-encode direction where the phase only changes between excitations you wouldn't get any distortions in that direction.
I'm assuming you have the frequency encode in the z-direction so as to avoid wrap-around of the neck/body? If so each shot will presumably consist of a "slice of k-space" in a direction that is parallel with the z-axis. If each shot is a "coronal slice
of k-space" your distortions would be in the left-right direction. If each shot is a "sagittal slice of k-space" they would be in the ant-post direction. So in either of those cases I think you would only see distortions in one direction.
Please get back to me if your acquisition is different from what I have assumed and let me know some more details so I can help you.
Jesper
Many thanks in advance!
Longchuan