stimulus timing file

AFNI Message Board
1

Dear AFNI experts,

I’m totally new in afni. Here are some questions about how to write truly stimulus timing file and I really hope you can help me. Thanks a lot!

My experiments is slow event-related design. There are 8 runs and 11 types of stimulus conditions in a scanning session, each run consisted of 24 trials (1 trial=14s). However, the number of stimulus condition is different in each run, even there are not the condition in some runs.

For example, in the FT3.txt, there are not the third condition in the second run and the fifth run. And The warning message I keep getting is: ** warning for local stim_times format of file FT03.txt, - 6 rows does not match 8 runs. Therefore, what is the right way to write these stimulus timing files ?

Thanks a lot in advance.

% cat FT03.txt

32 46 242

46 60 130 144 298
158

60 102 242
158 256
228

2

Hello,

AFNI stimulus timing files, in their simple form have

  • one stimulus class per file
  • one row per run
  • runs without events can be shown using 2 space-separated astericks

Assuming the blank rows in FT03.txt are runs without
events, and assuming the ‘32 46 242’ line is the first
run (else it would seem like 9 runs) the timing file
could look like:

32 46 242
* *
46 60 130 144 298
158
* *
60 102 242
158 256
228
  • rick
3

Thanks for your help!

Best regards,
Jiaxin Li

4

I have a question i would like to add to this thread. When you add these asterisks to denote the absence of all conditions for a given run does that run get ignored entirely or is it incorporated into baseline BOLD signal for comparison against ones modelled conditions?

5

Those asterisks are essentially a place-holder to include the run in the (local) timing file, even though there were no events of a particular condition.
If all conditions had no events for some run, yes, that run would still be included in the analysis (for the regressors of no interest).

  • rick