Dear AFNI message board,
I am running 3dDeconvolve with event-related design. I am wondering if you could help with finding where the error might be. Looking forward to your response.
AFNI version info (afni -ver): AFNI_20.2.16 (Sep 1 2020) [64-bit]
3-doDecon.sh file:
if ( $#argv > 0 ) then
set subj = $argv[1]
else
set subj = sub-002
endif
3dDeconvolve -input r*_scale.nii \
# -censor motion_${subj}_censor.1D \
-mask full_mask.nii \
-polort 3 \
-num_stimts 39 \
-stim_times_AM2 1 stimuli2/name.1D 'BLOCK(2,1)' \
-stim_label 1 name \
-stim_times_AM2 2 stimuli2/nulltrial.1D 'BLOCK(2,1)' \
-stim_label 2 nulltrial \
-stim_times_AM2 3 stimuli2/word.1D 'BLOCK(2,1)' \
-stim_label 3 word \
-stim_file 4 trans_x_run1.txt'[0]' -stim_base 4 -stim_label 4 trans_x_01 \
-stim_file 5 trans_y_run1.txt'[0]' -stim_base 5 -stim_label 5 trans_y_01 \
-stim_file 6 trans_z_run1.txt'[0]' -stim_base 6 -stim_label 6 trans_z_01 \
-stim_file 7 rot_x_run1.txt'[0]' -stim_base 7 -stim_label 7 rot_x_01 \
-stim_file 8 rot_y_run1.txt'[0]' -stim_base 8 -stim_label 8 rot_y_01 \
-stim_file 9 rot_z_run1.txt'[0]' -stim_base 9 -stim_label 9 rot_z_01 \
-stim_file 10 trans_x_run2.txt'[0]' -stim_base 10 -stim_label 10 trans_x_02 \
-stim_file 11 trans_y_run2.txt'[0]' -stim_base 11 -stim_label 11 trans_y_02 \
-stim_file 12 trans_z_run2.txt'[0]' -stim_base 12 -stim_label 12 trans_z_02 \
-stim_file 13 rot_x_run2.txt'[0]' -stim_base 13 -stim_label 13 rot_x_02 \
-stim_file 14 rot_y_run2.txt'[0]' -stim_base 14 -stim_label 14 rot_y_02 \
-stim_file 15 rot_z_run2.txt'[0]' -stim_base 15 -stim_label 15 rot_z_02 \
-stim_file 16 trans_x_run3.txt'[0]' -stim_base 16 -stim_label 16 trans_x_03 \
-stim_file 17 trans_y_run3.txt'[0]' -stim_base 17 -stim_label 17 trans_y_03 \
-stim_file 18 trans_z_run3.txt'[0]' -stim_base 18 -stim_label 18 trans_z_03 \
-stim_file 19 rot_x_run3.txt'[0]' -stim_base 19 -stim_label 19 rot_x_03 \
-stim_file 20 rot_y_run3.txt'[0]' -stim_base 20 -stim_label 20 rot_y_03 \
-stim_file 21 rot_z_run3.txt'[0]' -stim_base 21 -stim_label 21 rot_z_03 \
-stim_file 22 trans_x_run4.txt'[0]' -stim_base 22 -stim_label 22 trans_x_04 \
-stim_file 23 trans_y_run4.txt'[0]' -stim_base 23 -stim_label 23 trans_y_04 \
-stim_file 24 trans_z_run4.txt'[0]' -stim_base 24 -stim_label 24 trans_z_04 \
-stim_file 25 rot_x_run4.txt'[0]' -stim_base 25 -stim_label 25 rot_x_04 \
-stim_file 26 rot_y_run4.txt'[0]' -stim_base 26 -stim_label 26 rot_y_04 \
-stim_file 27 rot_z_run4.txt'[0]' -stim_base 27 -stim_label 27 rot_z_04 \
-stim_file 28 trans_x_run5.txt'[0]' -stim_base 28 -stim_label 28 trans_x_05 \
-stim_file 29 trans_y_run5.txt'[0]' -stim_base 29 -stim_label 29 trans_y_05 \
-stim_file 30 trans_z_run5.txt'[0]' -stim_base 30 -stim_label 30 trans_z_05 \
-stim_file 31 rot_x_run5.txt'[0]' -stim_base 31 -stim_label 31 rot_x_05 \
-stim_file 32 rot_y_run5.txt'[0]' -stim_base 32 -stim_label 32 rot_y_05 \
-stim_file 33 rot_z_run5.txt'[0]' -stim_base 33 -stim_label 33 rot_z_05 \
-stim_file 34 trans_x_run6.txt'[0]' -stim_base 34 -stim_label 34 trans_x_06 \
-stim_file 35 trans_y_run6.txt'[0]' -stim_base 35 -stim_label 35 trans_y_06 \
-stim_file 36 trans_z_run6.txt'[0]' -stim_base 36 -stim_label 36 trans_z_06 \
-stim_file 37 rot_x_run6.txt'[0]' -stim_base 37 -stim_label 37 rot_x_06 \
-stim_file 38 rot_y_run6.txt'[0]' -stim_base 38 -stim_label 38 rot_y_06 \
-stim_file 39 rot_z_run6.txt'[0]' -stim_base 39 -stim_label 39 rot_z_06 \
-jobs 8 \
-gltsym 'SYM: word -nulltrial' \
-glt_label 1 word-nulltrial \
-gltsym 'SYM: word -name' \
-glt_label 2 word-name \
-gltsym 'SYM: name -nulltrial' \
-glt_label 3 name-nulltrial \
-fout -tout -x1D X.xmat.1D -xjpeg X.jpg \
-x1D_uncensored X.nocensor.xmat.1D \
-fitts fitts.$subj \
-errts errts.${subj} \
-bucket stats.$subj
terminal:
tcsh 3-doDecon.sh sub-002
++ '-stim_times_AM2 1 stimuli2/name.1D' has 1 auxiliary values per time point
++ '-stim_times_AM2 1 stimuli2/name.1D' will have 2 regressors
++ '-stim_times_AM2 2 stimuli2/nulltrial.1D' has 1 auxiliary values per time point
++ '-stim_times_AM2 2 stimuli2/nulltrial.1D' will have 2 regressors
++ '-stim_times_AM2 3 stimuli2/word.1D' has 1 auxiliary values per time point
++ '-stim_times_AM2 3 stimuli2/word.1D' will have 2 regressors
++ 3dDeconvolve: AFNI version=AFNI_20.2.16 (Sep 1 2020) [64-bit]
++ Authored by: B. Douglas Ward, et al.
++ loading dataset r1_scale.nii r2_scale.nii r3_scale.nii r4_scale.nii r5_scale.nii r6_scale.nii
++ Auto-catenated input datasets treated as multiple imaging runs
++ Auto-catenated datasets start at: 0 218 436 654 872 1090
++ Skipping check for initial transients
++ Input polort=3; Longest run=327.0 s; Recommended minimum polort=3 ++ OK ++
++ -stim_times using TR=1.5 s for stimulus timing conversion
++ -stim_times using TR=1.5 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_AM2 1 using LOCAL times
++ '-stim_times_AM2 1' average amplitude#1=6.26923
++ ** GUESSED ** -stim_times_AM2 2 using LOCAL times
++ '-stim_times_AM2 2' average amplitude#1=6.07692
++ ** GUESSED ** -stim_times_AM2 3 using LOCAL times
++ '-stim_times_AM2 3' average amplitude#1=5.93506
------------------------------------------------------------
GLT matrix from 'SYM: word -nulltrial':
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -1 -1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
------------------------------------------------------------
GLT matrix from 'SYM: word -name':
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -1 -1 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
------------------------------------------------------------
GLT matrix from 'SYM: name -nulltrial':
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 -1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
++ Number of time points: 1308 (no censoring)
+ Number of parameters: 66 [60 baseline ; 6 signal]
++ total shared memory needed = 10,487,886,380 bytes (about 10 billion)
++ mmap() memory allocated: 10,487,886,380 bytes (about 10 billion)
Killed