3dretroicor wants cardiac pulse waveform data in a format like a "stim_file" input to 3dDeconvolve (i.e. something plottable with 1dplot). Fortunately, your list of R-wave times is like a "stim_times" input to 3dDeconvolve, and there just happens to be a tool for converting a stim_times data file to a stim_file format: timing_tool.py, e.g.
timing_tool.py -timing rwave.times.txt -timing_to_1D rwave.1D -tr 0.02 -stim_dur 0.001 -min_frac 0.01 -run_len 300
where rwave.times.txt is your list of R-wave times (all times in seconds, in one row--use 1dtranspose first if your numbers are in a column); rwave.1D is the 1D output; tr=0.02 for a simulated 50Hz sample rate (you can go faster if you like); duration 0.001 and fraction 0.01 are small numbers so the peaks are not smeared; and the run length is 300 seconds (change this to suit your run length).
This will generate a waveform with '1's at the R-wave times and '0's otherwise. Note that the default threshold for the pulse in 3dretroicor is 1, so you will need to either do something like "3dretroicor -threshold 0.5 ..." or modify the file again, e.g. 1deval -a rwave.1D -expr 'a*5' > rwave.fix.1D
