[Freesurfer] Clarification about "Per-Run" Motion Correction and Registration in Preproc-Sess

Hello,

A few quick questions about the "Per-Run" option in preproc-sess. I understand that in this option, each run's images are registered to the middle timepoint of that run, rather than the first timepoint of the first run. I was wondering, though:

1) Why is this the preferred option instead of per-session? 2) If motion-correction is only done internally to each run, then wouldn't between-run motion throw things off if you wanted to do a GLM spanning the whole scanning session (although I assume it'd be fine for single-run GLMs)? What ensures that the images line up properly between runs?

Thank you very much,

JohnMark