Hi, Yash-
Glad that the first set of issues got sorted.
Re. you questions about removing TRs and the offset:
You included this option in the afni_proc.py command:
-tcat_remove_first_trs 2
Therefore, the first 2 TRs from each time series will be removed at the very start of processing. This kind of step is often done to remove pre-steady state signal. If you don't have pre-steady state signals in your EPIs, then you might not need to include this. However, if you do include this option, then yes, you must adjust your timing files (assuming that at present, they are counting t=0s from the start of your input EPIs).
And yes, your timing file information must be in units of seconds, so you have to adjust them by the amount of time that removing 2 TRs would be. If TR=2s, then removing 2 TRs would require you to adjust the timing values back by 4s.
And indeed, timing_tool.py should be able to help you, for example following this example (for your own time offset):
Example 2. subtract 12 seconds from each stimulus time ~2~
For example, subtract 12 seconds 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
--pt
