Thank you for this advice! I am using realtime_receiver.py from the AFNI distribution, installed in a NeuroDebian virtual machine running on a Windows machine (my institution won't let us use a non-Windows computer). I haven't heard of Vinai's version before. I tried setting AFNI_REALTIME_SHOW_TIMES as an env var and also used the -show_comm_times option in realtime_reciever.py. (Didn't realize I could do that!) The output shows the same strange lag, which tells me this is happening very early in the process, probably before it even gets to my python script (which is only checking the txt output from realtime_receiver. Here's a snippet from the Terminal below. Notice that TRs 1517-1519 are about 1 second off from each other, as one would hope, but then TR 1520 is happening 18 seconds after TR 1519. This lag goes away at the next TR, and recurs every 40 TRs exactly. I think the 40 TRs might be less important than the fact that the recurrence is periodic. I've now settled on using the same parameters and code every single time I run this and it's always 40 TRs. I think the past periodicity of 13-14 TRs had to do with me running slightly different code, though I have no idea why it does that.
Anyway, does this all collectively suggest that whatever is happening is happening at the AFNI part of the process?
This output was from running the script on archival data, not an active scan collection, so I assume the DICOMs should all be theoretically readable by Dimon. Not sure if that addresses your thought about DICOMs being "fully populated"?
-- comm time for TR 1517 @ 2021-04-12 18:45:15 (offset 1968.405)
++ recv motion: -0.00382 -0.11792 -0.12733 -0.14060 -0.04923 0.26249
++ recv 2 extras: 10034 10839.1
-- comm time for TR 1518 @ 2021-04-12 18:45:16 (offset 1969.205)
++ recv motion: -0.00621 -0.14899 -0.11283 -0.18226 -0.05892 0.27353
++ recv 2 extras: 10025.5 10828.3
-- comm time for TR 1519 @ 2021-04-12 18:45:17 (offset 1970.004)
++ recv motion: -0.00009 -0.16126 -0.12406 -0.15230 -0.05375 0.26467
++ recv 2 extras: 10046.1 10834.1
-- comm time for TR 1520 @ 2021-04-12 18:45:35 (offset 1988.388)
++ recv motion: -0.01088 -0.11837 -0.11698 -0.16080 -0.05985 0.26724
++ recv 2 extras: 10038.4 10826.7
-- comm time for TR 1521 @ 2021-04-12 18:45:36 (offset 1989.195)
++ recv motion: -0.00532 -0.12996 -0.12133 -0.15647 -0.05469 0.26561
++ recv 2 extras: 10018.6 10820
-- comm time for TR 1522 @ 2021-04-12 18:45:37 (offset 1989.993)
++ recv motion: -0.00790 -0.14649 -0.11460 -0.16861 -0.05968 0.26739
++ recv 2 extras: 10021.7 10796
