Setting our censoring threshold to FD > 0.9 removed very few frames; less than 2% in most runs, and never more than 12%. I wondered if such a modest amount of censoring would have a noticeable impact, but it looks like it did (which is a bit of a reminder of GLM sensitivity, but that's another issue).
Here's an example person. In the Stroop task for this person 1 frame was censored in the Bas session, 15 in the Pro, and 0 in the Rea. There are more than 1000 frames in each session, so this is not many ant all. The acquisition was with the MB4 paradigm, so we have a pair of runs (AP - PA encoding) for the task each session. Here are motion and FD traces for the person, the Pro session (highest censoring); this is a pretty good set of traces, with the biggest spikes censored at FD > 0.9 (red x).
Now, here are F-statistic images for the same task and person, for the sustained ("block") effect from a GLM. The no-censoring image is first, followed by the with-censoring image. The first row for each is the Bas session, followed by Pro, then Rea; the color scaling is the same in each.
The third (Rea) row is identical in the two images: no censoring (so they better match, since each session went into a separate GLM). The top rows (Bas) look very similar, though the peak values (rng in upper right) vary slightly. The second row (Pro), with the 15 censored frames, varies quite a bit between the two. I found the area marked with the blue arrows particularly interesting: the white matter is much brighter in the no-censoring version, and this white-matter pattern isn't present in the other (less spiky motion) runs, and looks very much like an artifact (not BOLD-ish); particularly the k=44 slice.
Similar effects are seen in the TENTs: high-motion people and sessions tend to have spikier (and less HRF-like) shapes, which is ameliorated a bit by the censoring. There seems to be a bit less ringing with censoring, as well. So, while these are preliminary, qualitative assessments, I'm encouraged that this small amount of censoring may be sensible.