It can be good to place the run with the opposite phase encoding direction closest to the acquisition of the anatomy.
For very long sessions with multiple runs: if the anatomy is at the end or at the beginning, then there is too much motion; therefore, it is recommended to plan anatomy in the middle.
The question "at what point in preprocessing the EPI distortion correction should it be applied" has occurred regularly, and the answer by experts seems to be that it does not really matter, as long as the distortion correction is applied before spatial smoothing (if any).
For one session, only one VDM needs to be estimated; then apply that single VDM to the several ((intra-session) motion corrected) runs.
Latest update of this page: 12 December 2022