Timing File and Slice Timing Question

Hi there AFNI team,

I have a couple of quick questions I was hoping to get clarification on.

  1. If a timing .txt file has all of the times listed (globally) from all 4 runs as a row instead of a column, will this still get appropriately interpreted by 3dDeconvolve? We use the “global_times” option as well.

  2. When using To3D to convert Dicom files to AFNI, we have thus far specified the slice timing acquisition pattern as “alt+z”. If it turns out the slice timing order should actually be “alt+z2”, would this have had significant effects on the resulting analysis? Specifically with 3dTshift and 3dDeconvolve.

Thank you,

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.

  1. 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

Thanks so much, Rick! I wanted to double-check the timing files because afni_proc.py gives me the error:

“**file has rows longer than 1
==BAD: file does not look like global stim times”

and I have to use “-test_stim_files no” to get around it, even though the timings are all in a single row. And I will definitely discuss the slice timing issue with our team.