using uber_subject.py one can select to remove a number of TRs from the beginning of each run. For instance, in the YouTube AFNI tutorials it is recommended to remove 2TRs. While in the corresponding script generated by the GUI and in the tutorials there are warnings that the time files should be adjusted to reflect the removal of the xTRs, I couldn’t find any example in this regard and how exactly this should be done is not clear to me. Say that we focus our discussion on the AV1_vis.txt and AV2_aud.txt timing files that are associated with the standard AFNI analysis example. Can anyone write what these files should be when I’m removing say 3TR’s. What should the actual numbers in these files be?
Thank you so much!
You could use 3dcalc or 1deval to adjust the timing of a dataset, but it’s easiest with timing_tool.py. Here’s example 2 from the help:
Example 2. Subtract 12 seconds from each stimulus time (to offset TRs
dropped prior to the magnetization steady state).
timing_tool.py -timing stimesB_01_houses.1D \ -add_offset -12.0 \ -write_timing stimesB1_offset12.1D
To be clear, the tutorials do not recommend removing 2 time points.
It is important to remove the time points before the scanner reaches
a magnetization steady state, but how many that is depends on the
scanner setup, so we cannot say what you should do.
Many scanners even throw out those time points automatically.
It is up to you to be sure that the stimulus timing files match
the timing of the EPI data. If that is messed up, the analysis is
probably garbage, so be sure. It is something that you only have
to figure once (per scanner and protocol).
As for how to do it, yes timing_tool.py is the way to go,
particularly with local timing files (many times per row/run).