uber_subject.py Remove TRs, compensate in stimfile?

AFNI Message Board
1

Hello,

If I am going to be removing the first 4 TRs per run, do I have to account for this timing difference in my StimFiles or is it already incorporated in the script?

Thanks

2

From the help for afni_proc.py:


    TIMING FILE NOTE: ~2~

    One issue that the user must be sure of is the timing of the stimulus
    files (whether -regress_stim_files or -regress_stim_times is used).

    The 'tcat' step will remove the number of pre-steady-state TRs that the
    user specifies (defaulting to 0).  The stimulus files, provided by the
    user, must match datasets that have had such TRs removed (i.e. the stim
    files should start _after_ steady state has been reached).

https://afni.nimh.nih.gov/pub/dist/doc/program_help/afni_proc.py.html

In other words, you have to adjust the timing files yourself.

3

I forgot to mention that the AFNI program timing_tool.py can manipulate stimulus timing files for you, including adding/subtracting values from a given file.
https://afni.nimh.nih.gov/pub/dist/doc/program_help/timing_tool.py.html