Hi Rick,
Thanks for your quick response! Here are the outputs:

out.3dD.001
cmd.3dd.001: No such file or directory.

-- have 2 stim and 2 runs, prefix = stim_times.001
-- run_time : 240 240
-- num_reps : 15 15
-- stim_dur : 2 2
-- max_consec : 3 3
-- pre_stim_rest=0, post_stim_rest=0, seed=1234567.0
min_rest=2, max_rest=0, offset=0, t_gran=4, t_digits=1
labels are: first, second

++ creating timing...
++ init random with seed 1234567
-- make_rand_timing: nruns = 1
rtime, offset, tinit, tfinal = 240, 0, 0, 0
reps_list = [15, 15]
sdur_list = 2 2
tgran = 4.0000, verb = 4

++ total time = 240.0, (stim = 60.0, rest = 180.0)
init rest = 0.0, end rest = 0.0, min rest = 2.0
total ISI = 180.0, rand ISI = 120.0
rand ISI rest time = 30 intervals of 4.000 seconds

-- limited events reps = [15, 15], max = [3, 3]
-- have 0 events to insert
== clist (0-based) [[-1, 0], [1, 1], [0, 1], [1, 1], [0, 1], [1, 2], [0, 1], [1, 3], [0, 2], [1, 3], [0, 3], [1, 3], [0, 3], [1, 1], [0, 3], [1, 1], [0, 1]]
== elist (1-based) [2, 1, 2, 1, 2, 2, 1, 2, 2, 2, 1, 1, 2, 2, 2, 1, 1, 1, 2, 2, 2, 1, 1, 1, 2, 1, 1, 1, 2, 1]
-- end make_random_timing() --
++ stim list[1][0] = 12 24 56 76 84 112 116 128 160 164 180 200 224 228 236
++ stim list[2][0] = 8 20 36 44 60 64 72 88 92 96 136 148 152 192 232
-- make_rand_timing: nruns = 1
rtime, offset, tinit, tfinal = 240, 0, 0, 0
reps_list = [15, 15]
sdur_list = 2 2
tgran = 4.0000, verb = 4

++ total time = 240.0, (stim = 60.0, rest = 180.0)
init rest = 0.0, end rest = 0.0, min rest = 2.0
total ISI = 180.0, rand ISI = 120.0
rand ISI rest time = 30 intervals of 4.000 seconds

-- limited events reps = [15, 15], max = [3, 3]
-- have 0 events to insert
== clist (0-based) [[-1, 0], [1, 1], [0, 3], [1, 2], [0, 1], [1, 3], [0, 3], [1, 2], [0, 2], [1, 1], [0, 1], [1, 2], [0, 2], [1, 1], [0, 2], [1, 3], [0, 1]]
== elist (1-based) [2, 1, 1, 1, 2, 2, 1, 2, 2, 2, 1, 1, 1, 2, 2, 1, 1, 2, 1, 2, 2, 1, 1, 2, 1, 1, 2, 2, 2, 1]
-- end make_random_timing() --
++ stim list[1][0] = 8 12 16 36 52 64 80 96 112 140 152 172 180 188 236
++ stim list[2][0] = 0 20 24 40 44 48 84 88 132 144 148 176 196 220 228
--------- final list ---------
++ stim list[1][0] = 12 24 56 76 84 112 116 128 160 164 180 200 224 228 236
++ stim list[1][1] = 8 12 16 36 52 64 80 96 112 140 152 172 180 188 236
++ stim list[2][0] = 8 20 36 44 60 64 72 88 92 96 136 148 152 192 232
++ stim list[2][1] = 0 20 24 40 44 48 84 88 132 144 148 176 196 220 228
writing timing file: stim_times.001_01_first.1D
writing timing file: stim_times.001_02_second.1D
min, max stim times are: 0.0, 236.0
saving 3dD command to file 'sample.3dd.command.001'...

# -------------------------------------------------------
# create 3dDeconvolve -nodata command

3dDeconvolve \
-nodata 120 4.000 \
-polort 2 \
-concat '1D: 0 60' \
-num_stimts 2 \
-stim_times 1 stim_times.001_01_first.1D 'BLOCK(2,1)' \
-stim_label 1 first \
-stim_times 2 stim_times.001_02_second.1D 'BLOCK(2,1)' \
-stim_label 2 second \
-num_glt 1 \
-gltsym 'SYM: first -second' -glt_label 1 first-second \
-x1D X.xmat.1D

# compute the sum of non-baseline regressors
3dTstat -sum -prefix sum_ideal.1D X.xmat.1D'[6..$]'

# consider plotting the SUM below non-polort regressors
# command: 1dplot -xlabel Time -ynames SUM - sum_ideal.1D X.xmat.1D'[6..$]'


ISI statistics :

data min mean max stdev
----------- ------- ------- ------- -------
pre-rest 0.000 4.000 8.000 5.657
post-rest 2.000 2.000 2.000 0.000

run #0 ISI 2.000 5.862 22.000 4.955
run #1 ISI 2.000 6.138 22.000 5.805

all runs ISI 2.000 6.000 22.000 5.351

ISI #0 : 2 6 2 10 6 10 2 2 6 2 6 2 2 2 14 2 10 6 10 2 6 2 14 10 6 22 2 2 2
ISI #1 : 6 2 2 2 2 10 2 2 2 2 10 14 2 2 6 14 18 6 2 2 2 18 2 2 6 6 22 6 6

sorted ISI #0 : 2 2 2 2 2 2 2 2 2 2 2 2 2 2 6 6 6 6 6 6 6 10 10 10 10 10 14 14 22
sorted ISI #1 : 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 6 6 6 6 6 6 6 10 10 14 14 18 18 22