We are using afni_proc’s volreg to align data to MIN_OUTLIER. We do not want to remove the first two time points of each run with 3dTcat. At the same time, we want the 3dToutcount to ignore the first 2 time points in its calculations. Is there an option in afni_proc that would let us ignore the first 2 time points in 3dToutcount. As it stands, we generate the afni_proc code and modify it for each subject so that 3dToutcount uses ‘[2…$]’. We are hoping to not have to do this for every participant.
I think the option -tcat_remove_first_trs in afni_proc.py is what you are looking for
Since you want to apply ‘2…$’ in 3dToutcount, rather than removing 2 time points and you and Cesar noted, I will assume there are stimulus events at the beginning of the run that you do not want to manage after they get chopped off, or something similar.
The difficulty with applying ‘2…$’ for computation of MIN_OUTLIERS (or for censoring), is that the results will be 2 time points (per run) off from the rest of the script. So the MIN_OUTLIER would not actually be correct, nor would the outlier censoring, if applied.
There would be much more to adjust in the proc script to account for missing those time points.
Are you trying to preserve early stim events?
Is there another reason you are trying this?