Hello,

Sorry for being a bit slow on this.

To be sure, the stimulus times should be in seconds not milliseconds, though 7.8 and 134.0 look like seconds.

Those warnings suggests that all of the stimulus times seem to be in the first run. When you say the "times are stacked according to the order of runs", what does that imply about the times, are they offset from the beginning of each run (seems likely), or are they all offset from the beginning of the first run?

Let's assume each run is 200s long, for example. If the times looks like:

27.3
115.6
183.4
11.9
79.0
158.2

That would be giving offsets from the beginning of each respective run. It is also an invalid format for 3dDeconvolve.

The "global timing way" would be with times from the beginning of the first run, as with:

27.3
115.6
183.4
211.9
279.0
358.2

If you prefer times local to each run, then run times should be on a single row, as in:

27.3 115.6 183.4
11.9 79.0 158.2

Does that seem reasonable?


A separate question might be whether you would rather use afni_proc.py for the analysis, but we can leave that for another conversation. :)

- rick