Timing tool, split duration from onset

(Version AFNI_23.3.02 'Septimius Severus')
I'm fairly new to AFNI and working to create timing files with the timing tool where duration is not married to onset time. I've read through the timing tool help page but I'm not sure I saw anything that would achieve this. I've tried setting the duration with -stim_dur, thinking that a constant duration would be ignored and not used for modulation, but the output was still Onset:Duration.
Any advice?

timing_tool.py -fsl_timing_files nodm_class_run*.txt -write_timing nodm_class.1D -stim_dur 1
timing_tool.py -fsl_timing_files nodm_iti_run*.txt -write_timing nodm_iti.1D -stim_dur 1

Indeed, I see no such option. You are the first to seek it (and say so).
I will put that on "the list". In the meanwhile, use something like:

1dMarry -divorce nodm_class.1D


  • rick
1 Like

Thanks so much, Rick! Should I remove the -write_timing command? or just add what you've recommended?

Went ahead and ran it both ways
With the -write_timing command preceding 1dMarry -divorce nodm_class.1D there was too many commands.
Then ran as timing_tool.py -fsl_timing_files nodm_class_run*.txt 1dMarry -divorce nodm_class.1D
timing_tool.py -fsl_timing_files nodm_iti_run*.txt 1dMarry -divorce nodm_iti.1D

timing_tool.py -fsl_timing_files nodm_Mean_anticipation_*.txt  1dMarry -divorce nodm_Mean_anticipation.1D
timing_tool.py -fsl_timing_files nodm_Mean_feedback_run*.txt  1dMarry -divorce nodm_Mean_feedback.1D
timing_tool.py -fsl_timing_files nodm_Mean_response_run*.txt  1dMarry -divorce nodm_Mean_response.1D

timing_tool.py -fsl_timing_files nodm_Nice_anticipation_*.txt  1dMarry -divorce nodm_Nice_anticipation.1D
timing_tool.py -fsl_timing_files nodm_Nice_feedback_run*.txt  1dMarry -divorce nodm_Nice_feedback.1D
timing_tool.py -fsl_timing_files nodm_Nice_response_run*.txt  1dMarry -divorce nodm_Nice_response.1D

timing_tool.py -fsl_timing_files nodm_Unp_anticipation_run*.txt  1dMarry -divorce nodm_Unp_anticipation.1D
timing_tool.py -fsl_timing_files nodm_UnpMean_feedback_run*.txt  1dMarry -divorce nodm_UnpMean_feedback.1D
timing_tool.py -fsl_timing_files nodm_UnpMean_response_run*.txt  1dMarry -divorce nodm_UnpMean_response.1D
timing_tool.py -fsl_timing_files nodm_UnpNice_feedback_run*.txt  1dMarry -divorce nodm_UnpNice_feedback.1D
timing_tool.py -fsl_timing_files nodm_UnpNice_response_run*.txt  1dMarry -divorce nodm_UnpNice_response.1D

Output: ** option -fsl_timing_files has illegal dashed parameter: -divorce
--> maybe parameter is a mis-typed option?

Sorry. Just to clarify, the 1dMarry command would be run after the timing_tool.py command. It is not part of the same command.

  • rick
1 Like

For example, consider:

timing_tool.py -fsl_timing_files nodm_class_run*.txt -write_timing nodm_class.1D -stim_dur 1
1dMarry -divorce nodm_class.1D

The result would be multiple output files, one of which would be the pure stimulus timing.

  • rick

You're the man! With this input I got the results we were looking for:

timing_tool.py -fsl_timing_files nodm_class_run*.txt -write_timing nodm_class.1D -write_as_married
1dMarry -divorce nodm_class.1D

Only mini concern was that I got this message for each epoch/participant:

++ No filename given to get divorce results ==> using 'nodm_class.1D'

Tells me that afni is smarter than I am lol, but I don't know where in the input I was supposed to add the filename so it wouldn't have to search for it. Thanks for all the help!

  • Tejiri

I was typing this up as you sent the clarification, is it ok that I used the -write_as_married bit? I don't think we necessarily needed to change the duration time

The -write_as_married option forces output to be married. In your case, it should not be needed. It is too bad that I did not make that a yes/no option to force married or not.

The warning about "divorce results" is just because there isn't a second parameter given as an output file pattern, and so it uses the input one. Please feel free to add a divorce output name, such as nodm_divorce.

  • rick
1 Like