Question about using timing_tool.py to process timing files with modulator

AFNI Message Board
,
1

AFNI version info: 24.1.11

Greetings!
I'm following Reynolds' script to complete the PPI analysis. Everything seems to be going well. However, I've noticed that timing_tool.py doesn't seem to be able to properly handle time series files containing modulators when creating timing partition files:

timing_tool.py -timing $tfile                \
       -tr $TRup -stim_dur $stim_dur[$sind]   \
       -run_len $run_lens                     \
       -min_frac 0.3                          \
       -timing_to_1D $timing_prefix.$sind2.$label \
       -per_run_file -show_timing

(Example of my time series file: option times * CR, EV)
1719393447673

Next, i found timing_pool. py seems to ignore '*' characters
(3dDeconvolve — AFNI, SUMA and FATCAT: v22.3.03)

As a beginner, I'm confused as to whether this means that the modulator is meaningless in PPI analysis, and that I only need to focus on the time series presented by the stimuli.

Or, should I replace or modify the timing_pool.py to produce my timing partition files.

If anyone has a suggestion, I would be very grateful!

2

Rick (@rickr) is the best person for this question, but he is currently unavailable until July 22.

As a side note, the reliability of PPI analysis is debatable. The assumed hemodynamic response is overly simplistic and fails to accommodate the variability observed across different brain regions.

Gang Chen

3

Thanks for your reply! Indeed, I should be cautious about PPI results. In the case of this problem, though, I eventually found a solution. Just need to add an option to the timing_pool.py command:

   timing_tool.py -timing $tfile                \
         -tr $TRup -stim_dur $stim_dur[$sind]   \
         -run_len $run_lens                     \
         -min_frac 0.3                          \
         -timing_to_1D $timing_prefix.$sind2.$label \
         -per_run_file -show_timing \
         -timing_to_1D_mods