No please don't worry about it. I simply appended it into the proc.SUBJ file as such:

1dBport -nodata $nt 2.5 -band 0.008 0.07 -invert -nozero > rm.bpass.1D
1d_tool.py -infile rm.bpass.1D -pad_into_many_runs $run $#runs -set_run_lengths $tr_counts \
-write bpass.r$run.1D

The execution however is taking a long time on my practice subject. I am afraid it may be stalled out here:

++ N.B.: 3dREMLfit command above written to file stats.REML_cmd
++ (b) Visualization/analysis of the matrix via ExamineXmat.R
++ (c) Synthesis of sub-model datasets using 3dSynthesize
++ ==========================================================
++ Wrote matrix values to file X.nocensor.xmat.1D
++ ----- Signal+Baseline matrix condition [X] (861x661): 61.5911 ++ GOOD ++
++ ----- Signal-only matrix condition [X] (861x14): 1.51395 ++ VERY GOOD ++
++ ----- Baseline-only matrix condition [X] (861x647): 60.7251 ++ GOOD ++
++ ----- stim_base-only matrix condition [X] (861x623): 55.8368 ++ GOOD ++
++ ----- polort-only matrix condition [X] (861x24): 1.05807 ++ VERY GOOD ++

If this seems suspicious to you let me know. I am leaving the regression to see if it runs overnight but not sure what comes next if it hasn't progressed. Granted this could be because the tsch -xef states " + Number of parameters: 661 [647 baseline ; 14 signal] "

~`Dane