Usage: requirements

The plugin requires at least one EPI image acquired with phase-encoding direction anterior-posterior (A>>P) and one with phase-encoding direction posterior-anterior (P>>A) or left-right (LR) and right-left (RL) phase encoded, saved as an FMR (gradient-echo EPI, BOLD) or DMR project (spin-echo EPI, diffusion weighted data (DWI)). The images are supposed to be from the same session and should have the same dimensions. For DWI data, it is recommended to select the b=0 volumes for estimation of the voxel displacement map. COPE only accepts DMR/DWI data in DataStorageFormat 3 at the moment.

Usage: practical directions

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.

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Latest update of this page: 12 December 2022