Hi Ian,
1. If the -global_times option is used first (in which case, ALL stim files should be global), then they will be read as global. Without that, 3dDeconvolve would warn about "times outside the range ..." and "unusable times follow".
And plotting those vectors from the X-matrix should show events going to the end.
Note that -global_times (or -local_times) should precede all relevant input timing files.
2. Yes, alt+z vs alt+z2 is almost a 1/2 TR difference in every slice time. It would be highly preferable to correct that (3drefit -TR) and reprocess. The mistake should not have a huuuge effect, but you won't want to leave it.
- rick
