Coarse vs fine smoothing in Patch Motion?


Looking at the log file for Patch Motion, in the “rigid motion correction” section, there is a plot with 3 series - one for raw shifts, one for shifts with coarse smoothing, and one for shifts with fine smoothing.

The shifts with fine smoothing look like a consistently worse fit to the raw data than the “coarse” smoothing. None of these curves seem to change when I alter the “calibrated smoothing parameter”.

What is the difference between these two smoothing parameters, and is this something worth tweaking parameters to fix?

Hi @olibclarke, thanks for asking - how did you determine that the “fine” fit is worse?
The coarse and fine in this case refer to the resolution at which motion estimation is done - we first do “coarse” fitting at low resolution to help get large motions correct (especially important when there is a lot of motion or tilted data etc) and then do fine fitting after with higher resolution signal.
Can you try to adjust the “maximum alignment resolution” and see how that changes the results?

Thanks for the repy @apunjani! Well - I don’t know that it is worse, but it is certainly systematically different from the “coarse” fit, and for some of the mics really dramatically different. That makes sense re using the lower res data. I haven’t tried altering the alignment res, but certainly increasing the B-factor to 2000 makes the “fine” fit more similar to the coarse one (and actually doing that the CTF fits estimated by Patch CTF were very slightly better).

All these params only apply to the initial rigid whole frame fit, right? not the subsequent patch-based fit?