Hi Bob,

You are right and somehow we took this idea from Waver and created the timing files. But surprisingly, the same script works on my linux machine and the same script on Andrew's linux machine reports the error as he wrote before.

Here is what it prints on my machine:

[srikanth@memphis Sub01]$ 3dDeconvolve -input S01_EP_TRDsNSI+tlrc.BRIK -mask S01_EP_BrainMask+tlrc. \
? -polort A \
? -nobout \
? -noFDR \
? -concat runs.1D \
? -num_stimts 6 \
? -stim_times 1 CS_minus_C_times_sub_1.txt 'TENT(0,15,7)' -stim_label 1 CS_minus_C \
? -stim_times 2 CS_minus_I_times_sub_1.txt 'TENT(0,15,7)' -stim_label 2 CS_minus_I \
? -stim_times 3 CS_plus_C_times_sub_1.txt 'TENT(0,15,7)' -stim_label 3 CS_plus_C \
? -stim_times 4 CS_plus_I_times_sub_1.txt 'TENT(0,15,7)' -stim_label 4 CS_plus_I \
? -stim_times 5 US_times_sub_1.txt 'TENT(0,15,7)' -stim_label 5 US \
? -stim_times 6 error_times_sub_1.txt 'TENT(0,15,7)' -stim_label 6 error \
? -iresp 1 ./CS_minus_C \
? -iresp 2 ./CS_minus_I \
? -iresp 3 ./CS_plus_C \
? -iresp 4 ./CS_plus_I \
? -iresp 5 ./US \
? -iresp 6 ./error \
? -xsave \
? -cbucket ./S01_TRDsNSI_deconv_betas \
? -x1D S01_TRDsNSI_deconv.x1D \
? -fout -tout -bucket ./S01_TRDsNSI_deconv
++ 3dDeconvolve: AFNI version=AFNI_2008_07_18_1710 (Nov 4 2008) [32-bit]
++ Authored by: B. Douglas Ward, et al.
++ current memory malloc-ated = 301641 bytes (about 302 thousand)
++ loading dataset S01_EP_TRDsNSI+tlrc.BRIK
++ current memory malloc-ated = 301641 bytes (about 302 thousand)
++ Imaging duration=280.0 s; Automatic polort=2
++ -stim_times using TR=2.5 s for stimulus timing conversion
++ -stim_times using TR=2.5 s for any -iresp output datasets
++ [you can alter the -iresp TR via the -TR_times option]
++ ** NOTE ** Will guess GLOBAL times if 1 time per line; LOCAL otherwise
++ ** GUESSED ** -stim_times 1 using LOCAL times
++ ** GUESSED ** -stim_times 2 using LOCAL times
++ ** GUESSED ** -stim_times 3 using LOCAL times
++ ** GUESSED ** -stim_times 4 using LOCAL times
++ ** GUESSED ** -stim_times 5 using LOCAL times
++ ** GUESSED ** -stim_times 6 using LOCAL times
++ Memory required for output bricks = 87782400 bytes (about 88 million)
++ Wrote matrix values to file S01_TRDsNSI_deconv.x1D
++ ========= Things you can do with the matrix file =========
++ (a) Linear regression with ARMA(1,1) modeling of serial correlation:

3dREMLfit -matrix S01_TRDsNSI_deconv.x1D -input S01_EP_TRDsNSI+tlrc.BRIK \
-mask S01_EP_BrainMask+tlrc. -Rbeta ./S01_TRDsNSI_deconv_betas_REML \
-fout -tout -Rbuck ./S01_TRDsNSI_deconv_REML -Rvar ./S01_TRDsNSI_deconv_REMLvar -verb

++ N.B.: 3dREMLfit command above written to file .REML_cmd
++ (b) Visualization/analysis of the matrix via ExamineXmat.R
++ (c) Synthesis of sub-model datasets using 3dSynthesize
++ ==========================================================
++ ----- Signal+Baseline matrix condition [X] (672x60): 14.4842 ++ VERY GOOD ++
++ ----- Signal-only matrix condition [X] (672x42): 7.27841 ++ VERY GOOD ++
++ ----- Baseline-only matrix condition [X] (672x18): 1 ++ VERY GOOD ++
++ ----- polort-only matrix condition [X] (672x18): 1 ++ VERY GOOD ++
++ +++++ Matrix inverse average error = 2.86816e-16 ++ VERY GOOD ++
++ Matrix setup time = 0.50 s
++ current memory malloc-ated = 93363978 bytes (about 93 million)
++ Calculations starting; elapsed time=0.801
++ voxel loop:0123456789.0123456789.0123456789.0123456789.0123456789.
++ Calculations finished; elapsed time=135.371
++ Wrote cbucket to ./S01_TRDsNSI_deconv_betas+tlrc.BRIK
++ Wrote bucket dataset into ./S01_TRDsNSI_deconv+tlrc.BRIK
++ Wrote iresp 3D+time dataset into ./CS_minus_C+tlrc.BRIK
++ Wrote iresp 3D+time dataset into ./CS_minus_I+tlrc.BRIK
++ Wrote iresp 3D+time dataset into ./CS_plus_C+tlrc.BRIK
++ Wrote iresp 3D+time dataset into ./CS_plus_I+tlrc.BRIK
++ Wrote iresp 3D+time dataset into ./US+tlrc.BRIK
++ Wrote iresp 3D+time dataset into ./error+tlrc.BRIK
++ #Flops=8.15071e+10 Average Dot Product=92.2079
[srikanth@memphis Sub01]$

Timing files have the same format on my machine too.

[srikanth@memphis Sub01]$ cat CS_minus_C_times_sub_1.txt
0.00:1.00 11.51:12.51 35.71:36.71 98.24:99.24 102.28:103.28 131.19:132.19 152.17:153.17 188.76:189.76 194.36:195.36 198.79:199.79 215.35:216.35 224.16:225.16 246.74:247.74 250.08:251.08
8.94:9.94 13.91:14.91 39.36:40.36 68.84:69.84 74.15:75.15 115.49:116.49 146.13:147.13 173.93:174.93 184.47:185.47 221.42:222.42 225.72:226.72 232.22:233.22 258.38:259.38
0.00:1.00 8.34:9.34 17.07:18.07 25.77:26.77 51.03:52.03 86.37:87.37 103.43:104.43 107.38:108.38 125.14:126.14 166.78:167.78 186.97:187.97 192.33:193.33 204.99:205.99 260.78:261.78
3.93:4.93 12.18:13.18 27.85:28.85 34.73:35.73 38.00:39.00 66.74:67.74 70.17:71.17 93.04:94.04 95.67:96.67 100.11:101.11 147.99:148.99 166.90:167.90 174.08:175.08 189.40:190.40
3.65:4.64 10.49:11.49 18.33:19.33 26.72:27.72 40.78:41.78 44.73:45.73 60.41:61.41 76.93:77.93 112.63:113.63 136.89:137.89 163.26:164.26 216.57:217.57 224.01:225.01 237.28:238.28
0.00:1.00 3.46:4.46 14.40:15.40 37.19:38.19 65.18:66.18 86.24:87.24 109.03:110.03 173.36:174.36 181.88:182.88 242.55:243.55 252.40:253.40 255.94:256.94
[srikanth@memphis Sub01]$

I am not sure why and how it worked on my machine.

Thanks,
Srikanth.