Hi Rick,

I've got another puzzling problem that may shed some light.

I've modified the 3dDeconvolve cmd in the original proc script to use a different stimtimes file and try a different response model (saved as a new script and chmod 777 newscript). This modified script copies the new stimtimes6.txt file into the stimuli directory (of a new subject folder) and uses it for the regular 3dDeconvolve. However, stats.REML_cmd looks for the old stimtimes.txt file. I tried both source stats.REML_cmd and ./stats.REML_cmd but neither worked.

Please see the original and modified 3ddeconvolve cmd below along with the terminal error message (and some history). The proc scripts are executed with tcsh -xef proc.csh |& tee out.log.txt.

Could it have something to do with the LD_LIBRARY_PATH? This is unset in my ~/.cshrc_master.

Thanks so much again!

Nic


### ORIGINAL PROC SCRIPT:
3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD \
-censor censor_${subj}_combined_2.1D \
-polort 3 \
-num_stimts 7 \
-stim_times 1 stimuli/stimtimes.txt 'TENT(9,45,7)' \
-stim_label 1 bh \
-stim_file 2 motion_demean.1D'[0]' -stim_base 2 -stim_label 2 roll \
-stim_file 3 motion_demean.1D'[1]' -stim_base 3 -stim_label 3 pitch \
-stim_file 4 motion_demean.1D'[2]' -stim_base 4 -stim_label 4 yaw \
-stim_file 5 motion_demean.1D'[3]' -stim_base 5 -stim_label 5 dS \
-stim_file 6 motion_demean.1D'[4]' -stim_base 6 -stim_label 6 dL \
-stim_file 7 motion_demean.1D'[5]' -stim_base 7 -stim_label 7 dP \
-iresp 1 iresp_bh.$subj \
-fout -tout -bout -vout -x1D X.xmat.1D -xjpeg X.jpg -xsave \
-x1D_uncensored X.nocensor.xmat.1D \
-errts errts.${subj} \
-bucket stats.$subj
...
# -- execute the 3dREMLfit script, written by 3dDeconvolve --
source stats.REML_cmd

### ASSOCIATED stats.REML_cmd
# 3dDeconvolve -input pb04.sub-01.r01.scale+tlrc.HEAD -censor censor_sub-01_combined_2.1D -polort 3 -num_stimts 7 -stim_times 1 stimuli/stimtimes.txt 'TENT(9,45,7)' -stim_label 1 bh -stim_file 2 'motion_demean.1D[0]' -stim_base 2 -stim_label 2 roll -stim_file 3 'motion_demean.1D[1]' -stim_base 3 -stim_label 3 pitch -stim_file 4 'motion_demean.1D[2]' -stim_base 4 -stim_label 4 yaw -stim_file 5 'motion_demean.1D[3]' -stim_base 5 -stim_label 5 dS -stim_file 6 'motion_demean.1D[4]' -stim_base 6 -stim_label 6 dL -stim_file 7 'motion_demean.1D[5]' -stim_base 7 -stim_label 7 dP -iresp 1 iresp_bh.sub-01 -fout -tout -bout -vout -x1D X.xmat.1D -xjpeg X.jpg -xsave -x1D_uncensored X.nocensor.xmat.1D -errts errts.sub-01 -bucket stats.sub-01

3dREMLfit -matrix X.xmat.1D -input pb04.sub-01.r01.scale+tlrc.HEAD \
-fout -tout -Rbuck stats.sub-01_REML -Rvar stats.sub-01_REMLvar \
-Rerrts errts.sub-01_REML -verb $*

#########

### MODIFIED PROC SCRIPT:
3dDeconvolve -input pb04.$subj.r*.scale+tlrc.HEAD \
-censor censor_${subj}_combined_2.1D \
-polort 3 \
-num_stimts 7 \
-stim_times 1 stimuli/stimtimes6.txt 'BLOCK(15,1)' \
-stim_label 1 bh \
-stim_file 2 motion_demean.1D'[0]' -stim_base 2 -stim_label 2 roll \
-stim_file 3 motion_demean.1D'[1]' -stim_base 3 -stim_label 3 pitch \
-stim_file 4 motion_demean.1D'[2]' -stim_base 4 -stim_label 4 yaw \
-stim_file 5 motion_demean.1D'[3]' -stim_base 5 -stim_label 5 dS \
-stim_file 6 motion_demean.1D'[4]' -stim_base 6 -stim_label 6 dL \
-stim_file 7 motion_demean.1D'[5]' -stim_base 7 -stim_label 7 dP \
-iresp 1 iresp_bh.$subj \
-fout -tout -bout -vout -x1D X.xmat.1D -xjpeg X.jpg -xsave \
-x1D_uncensored X.nocensor.xmat.1D \
-errts errts.${subj} \
-bucket stats.$subj
...
# -- execute the 3dREMLfit script, written by 3dDeconvolve --
#source stats.REML_cmd
./stats.REML_cmd

### ASSOCIATED stats.REML_cmd (which was sourced first but led to termination error and then tried running from current directory with same error)
# 3dDeconvolve -input pb04.sub-01.r01.scale+tlrc.HEAD -censor censor_sub-01_combined_2.1D -polort 3 -num_stimts 7 -stim_times 1 stimuli/stimtimes6.txt 'BLOCK(15,1)' -stim_label 1 bh -stim_file 2 'motion_demean.1D[0]' -stim_base 2 -stim_label 2 roll -stim_file 3 'motion_demean.1D[1]' -stim_base 3 -stim_label 3 pitch -stim_file 4 'motion_demean.1D[2]' -stim_base 4 -stim_label 4 yaw -stim_file 5 'motion_demean.1D[3]' -stim_base 5 -stim_label 5 dS -stim_file 6 'motion_demean.1D[4]' -stim_base 6 -stim_label 6 dL -stim_file 7 'motion_demean.1D[5]' -stim_base 7 -stim_label 7 dP -iresp 1 iresp_bh.sub-01 -fout -tout -bout -vout -x1D X.xmat.1D -xjpeg X.jpg -xsave -x1D_uncensored X.nocensor.xmat.1D -errts errts.sub-01 -bucket stats.sub-01

3dREMLfit -matrix X.xmat.1D -input pb04.sub-01.r01.scale+tlrc.HEAD \
-fout -tout -Rbuck stats.sub-01_REML -Rvar stats.sub-01_REMLvar \
-Rerrts errts.sub-01_REML -verb $*


###########################


### ERROR MESSAGE WITH A BIT OF HISTORY:
3dDeconvolve -input pb04.sub-01.r01.scale+tlrc.HEAD -censor censor_sub-01_combined_2.1D -polort 3 -num_stimts 7 -stim_times 1 stimuli/stimtimes6.txt BLOCK(15,1) -stim_label 1 bh -stim_file 2 motion_demean.1D[0] -stim_base 2 -stim_label 2 roll -stim_file 3 motion_demean.1D[1] -stim_base 3 -stim_label 3 pitch -stim_file 4 motion_demean.1D[2] -stim_base 4 -stim_label 4 yaw -stim_file 5 motion_demean.1D[3] -stim_base 5 -stim_label 5 dS -stim_file 6 motion_demean.1D[4] -stim_base 6 -stim_label 6 dL -stim_file 7 motion_demean.1D[5] -stim_base 7 -stim_label 7 dP -iresp 1 iresp_bh.sub-01 -fout -tout -bout -vout -x1D X.xmat.1D -xjpeg X.jpg -xsave -x1D_uncensored X.nocensor.xmat.1D -errts errts.sub-01 -bucket stats.sub-01
++ 3dDeconvolve: AFNI version=AFNI_17.3.00 (Oct 12 2017) [64-bit]
++ Authored by: B. Douglas Ward, et al.
++ current memory malloc-ated = 242,879 bytes (about 243 thousand [kilo])
++ loading dataset pb04.sub-01.r01.scale+tlrc.HEAD
++ current memory malloc-ated = 547,983,083 bytes (about 548 million [mega])
++ STAT automask has 516409 voxels (out of 570000 = 90.6%)
++ Skipping check for initial transients
++ Input polort=3; Longest run=360.0 s; Recommended minimum polort=3 ++ OK ++
++ -stim_times using TR=0.75 s for stimulus timing conversion
++ -stim_times using TR=0.75 s for any -iresp output datasets
++ [you can alter the -iresp TR via the -TR_times option]
++ ** -stim_times NOTE ** guessing GLOBAL times if 1 time per line; LOCAL otherwise
++ ** GUESSED ** -stim_times 1 using LOCAL times
++ Number of time points: 480 (before censor) ; 472 (after)
+ Number of parameters: 11 [10 baseline ; 1 signal]
++ Memory required for output bricks = 1,165,080,000 bytes (about 1.2 billion [giga])
++ Wrote matrix image to file X.jpg
++ Wrote matrix values to file X.xmat.1D
++ ========= Things you can do with the matrix file =========
++ (a) Linear regression with ARMA(1,1) modeling of serial correlation:

3dREMLfit -matrix X.xmat.1D -input pb04.sub-01.r01.scale+tlrc.HEAD \
-fout -tout -Rbuck stats.sub-01_REML -Rvar stats.sub-01_REMLvar \
-Rerrts errts.sub-01_REML -verb

++ 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] (472x11): 3.25564 ++ VERY GOOD ++
++ ----- Signal-only matrix condition [X] (472x1): 1 ++ VERY GOOD ++
++ ----- Baseline-only matrix condition [X] (472x10): 3.24366 ++ VERY GOOD ++
++ ----- stim_base-only matrix condition [X] (472x6): 2.91534 ++ VERY GOOD ++
++ ----- polort-only matrix condition [X] (472x4): 1.01643 ++ VERY GOOD ++
++ +++++ Matrix inverse average error = 2.82774e-15 ++ VERY GOOD ++
++ Matrix setup time = 1.23 s
++ current memory malloc-ated = 1,714,499,644 bytes (about 1.7 billion [giga])
++ Calculations starting; elapsed time=6.400
++ voxel loop:0123456789.0123456789.0123456789.0123456789.0123456789.
++ Calculations finished; elapsed time=73.502
++ Smallest FDR q [1 Full_Fstat] = 1.25893e-13
++ Smallest FDR q [3 Run#1Pol#0_Tstat] = 9.99997e-16
++ Smallest FDR q [5 Run#1Pol#1_Tstat] = 7.03598e-14
++ Smallest FDR q [7 Run#1Pol#2_Tstat] = 1.40764e-12
++ Smallest FDR q [9 Run#1Pol#3_Tstat] = 8.68626e-13
++ Smallest FDR q [11 bh#0_Tstat] = 1.25892e-13
++ Smallest FDR q [12 bh_Fstat] = 1.25893e-13
++ Smallest FDR q [14 roll#0_Tstat] = 2.24815e-13
++ Smallest FDR q [15 roll_Fstat] = 2.24812e-13
++ Smallest FDR q [17 pitch#0_Tstat] = 3.75758e-13
++ Smallest FDR q [18 pitch_Fstat] = 3.75754e-13
++ Smallest FDR q [20 yaw#0_Tstat] = 2.6817e-12
++ Smallest FDR q [21 yaw_Fstat] = 2.6817e-12
++ Smallest FDR q [23 dS#0_Tstat] = 3.75509e-13
++ Smallest FDR q [24 dS_Fstat] = 3.75505e-13
++ Smallest FDR q [26 dL#0_Tstat] = 1.21213e-12
++ Smallest FDR q [27 dL_Fstat] = 1.21213e-12
++ Smallest FDR q [29 dP#0_Tstat] = 2.27109e-13
++ Smallest FDR q [30 dP_Fstat] = 2.27113e-13
++ Wrote bucket dataset into ./stats.sub-01+tlrc.BRIK
+ created 19 FDR curves in bucket header
++ Wrote iresp 3D+time dataset into ./iresp_bh.sub-01+tlrc.BRIK
++ Wrote 3D+time dataset into ./errts.sub-01+tlrc.BRIK
++ #Flops=1.03043e+11 Average Dot Product=19.7981
if ( 0 != 0 ) then
1d_tool.py -show_cormat_warnings -infile X.xmat.1D
tee out.cormat_warn.txt
-- no warnings for correlation matrix (cut = 0.400) --
timing_tool.py -multi_timing stimuli/stimtimes.txt -tr 0.75 -warn_tr_stats
tee out.TENT_warn.txt
** failed to open 1D file 'stimuli/stimtimes.txt'
** A1D: failed to read data file stimuli/stimtimes.txt
** (multi) failed to read timing from 'stimuli/stimtimes.txt'