afni.nimh.nih.gov

Dear AFNI experts,

[I should have checked the data more detail. Thus, this issue was solved. Thank you. :) ]


I'm trying to conduct the 3dDeconvolve.
The data which I used is the concatenated pre-processed data (i.e. concatenated two runs; also I concatenated motion part too.)
The problem is, there were no issues in other subjects data, but only one subject data had an issue.
The error message was shown below.

** AFNI version = AFNI_17.0.04  Compile date = Jul 26 2009
** [[Precompiled binary linux_xorg7_64: Jul 26 2009]]
** Program Death **
** If you report this crash to the AFNI message board,
** please copy the error messages EXACTLY, and give
** the command line you used to run the program, and
** any other information needed to repeat the problem.
** You may later be asked to upload data to help debug.
** Memory usage: chunks=1531 bytes=1429465
** Crash log is appended to file /home/hdw/.afni.crashlog

** FATAL ERROR: Can't read input file 'X.nocensor.xmat.1D[1]'
** Program compile date = Jul 26 2009
** FATAL ERROR: Can't read input file 'X.nocensor.xmat.1D[2]'
** Program compile date = Jul 26 2009
** FATAL ERROR: Can't read input file 'X.nocensor.xmat.1D[3]'
** Program compile date = Jul 26 2009
** FATAL ERROR: Can't read input file 'X.nocensor.xmat.1D[4]'
** Program compile date = Jul 26 2009
** FATAL ERROR: Can't read input file 'X.nocensor.xmat.1D[5]'
** Program compile date = Jul 26 2009
** FATAL ERROR: Can't read input file 'X.nocensor.xmat.1D[6]'
** Program compile date = Jul 26 2009
** FATAL ERROR: Can't read input file 'X.nocensor.xmat.1D[7]'
** Program compile date = Jul 26 2009
** FATAL ERROR: Can't read input file 'X.nocensor.xmat.1D[8]'
** Program compile date = Jul 26 2009
** FATAL ERROR: Can't read input file 'X.nocensor.xmat.1D[9]'
** Program compile date = Jul 26 2009
** FATAL ERROR: Can't read input file 'X.nocensor.xmat.1D[10]'
** Program compile date = Jul 26 2009
** FATAL ERROR: Can't read input file 'X.nocensor.xmat.1D[11]'
** Program compile date = Jul 26 2009
** FATAL ERROR: Can't read input file 'X.nocensor.xmat.1D[12]'
** Program compile date = Jul 26 2009
** FATAL ERROR: Can't read input file 'X.nocensor.xmat.1D[13]'
** Program compile date = Jul 26 2009
** FATAL ERROR: Can't read input file 'X.nocensor.xmat.1D[14]'
** Program compile date = Jul 26 2009
** FATAL ERROR: Can't read input file 'X.nocensor.xmat.1D[15]'
** Program compile date = Jul 26 2009
** FATAL ERROR: Can't read input file 'X.nocensor.xmat.1D[16]'
** Program compile date = Jul 26 2009
** FATAL ERROR: Can't read input file 'X.nocensor.xmat.1D[17]'
** Program compile date = Jul 26 2009
** FATAL ERROR: Can't read input file 'X.nocensor.xmat.1D[18]'
** Program compile date = Jul 26 2009
** FATAL ERROR: Can't read input file 'X.nocensor.xmat.1D[19]'
** Program compile date = Jul 26 2009
** FATAL ERROR: Can't read input file 'X.nocensor.xmat.1D[20]'
** Program compile date = Jul 26 2009
** FATAL ERROR: Can't read input file 'X.nocensor.xmat.1D[21]'
** Program compile date = Jul 26 2009
** FATAL ERROR: Can't read input file 'X.nocensor.xmat.1D[22]'
** Program compile date = Jul 26 2009
** FATAL ERROR: Can't read input file 'X.nocensor.xmat.1D[23]'
** Program compile date = Jul 26 2009
** FATAL ERROR: Can't read input file 'X.nocensor.xmat.1D[24]'
** Program compile date = Jul 26 2009
** FATAL ERROR: Can't read input file 'X.nocensor.xmat.1D[25]'
** Program compile date = Jul 26 2009
** FATAL ERROR: Can't read input file 'X.nocensor.xmat.1D[26]'
** Program compile date = Jul 26 2009
** FATAL ERROR: Can't read input file 'X.nocensor.xmat.1D[27]'
** Program compile date = Jul 26 2009
** FATAL ERROR: Can't read input file 'X.nocensor.xmat.1D[28]'
** Program compile date = Jul 26 2009
** FATAL ERROR: Can't read input file 'X.nocensor.xmat.1D[29]'
** Program compile date = Jul 26 2009
** FATAL ERROR: Can't read input file 'X.nocensor.xmat.1D[30]'
** Program compile date = Jul 26 2009
** FATAL ERROR: Can't read input file 'X.nocensor.xmat.1D[31]'
** Program compile date = Jul 26 2009
** FATAL ERROR: Can't read input file 'X.nocensor.xmat.1D[32]'
** Program compile date = Jul 26 2009
** FATAL ERROR: Can't read input file 'X.nocensor.xmat.1D[33]'
** Program compile date = Jul 26 2009
** FATAL ERROR: Can't read input file 'X.nocensor.xmat.1D[34]'
** Program compile date = Jul 26 2009
** FATAL ERROR: Can't read input file 'X.nocensor.xmat.1D[35]'
** Program compile date = Jul 26 2009
** FATAL ERROR: Can't read input file 'X.nocensor.xmat.1D[36]'
** Program compile date = Jul 26 2009
** FATAL ERROR: Can't read input file 'X.nocensor.xmat.1D[37]'
** Program compile date = Jul 26 2009
** FATAL ERROR: Can't read input file 'X.nocensor.xmat.1D[38]'
** Program compile date = Jul 26 2009
** FATAL ERROR: Can't read input file 'X.nocensor.xmat.1D[39]'
** Program compile date = Jul 26 2009
** FATAL ERROR: Can't read input file 'X.nocensor.xmat.1D[40]'
** Program compile date = Jul 26 2009
++ WARNING: file /home/hdw/.afni.log is now 214663711 (215 million [mega]) bytes long!
++ 3dTstat: AFNI version=AFNI_17.0.04 (Jul 26 2009) [64-bit]
++ Authored by: KR Hammett & RW Cox
** Can't read 1D dataset file /media/hdw/DATA/ercig_afni/s16/rcig/sat/concatenate_scaled_prep_from_two_runs/X.nocensor.xmat.1D[1d_tool.py
*+ WARNING: THD_open_tcat: can't open dataset /media/hdw/DATA/ercig_afni/s16/rcig/sat/concatenate_scaled_prep_from_two_runs/X.nocensor.xmat.1D[1d_tool.py
*+ WARNING: THD_open_tcat: can't open dataset -infile
** THD_open_1D(/media/hdw/DATA/ercig_afni/s16/rcig/sat/concatenate_scaled_prep_from_two_runs/X.nocensor.xmat.1D): can't open file
*+ WARNING: THD_open_tcat: can't open dataset /media/hdw/DATA/ercig_afni/s16/rcig/sat/concatenate_scaled_prep_from_two_runs/X.nocensor.xmat.1D
*+ WARNING: THD_open_tcat: can't open dataset -show_indices_interest]
** FATAL ERROR: Can't open dataset /media/hdw/DATA/ercig_afni/s16/rcig/sat/concatenate_scaled_prep_from_two_runs/X.nocensor.xmat.1D[1d_tool.py -infile /media/hdw/DATA/ercig_afni/s16/rcig/sat/concatenate_scaled_prep_from_two_runs/X.nocensor.xmat.1D -show_indices_interest]
** Program compile date = Jul 26 2009
** FATAL ERROR: Can't read input file '/media/hdw/DATA/ercig_afni/s16/rcig/sat/concatenate_scaled_prep_from_two_runs/X.nocensor.xmat.1D[1d_tool.py -infile /media/hdw/DATA/ercig_afni/s16/rcig/sat/concatenate_scaled_prep_from_two_runs/X.nocensor.xmat.1D -show_indices_interest]'
** Program compile date = Jul 26 2009

The command line is (it's long...),

3dDeconvolve -input pb07.s16.scale+tlrc.HEAD -censor motion_s16_censor.1D -polort 0 -num_stimts 46 -stim_times 1 /media/hdw/DATA/ercig_afni/onset_time/fixntr_tsk5_blk1.txt 'WAV(15)' -stim_label 1 fixntr_run1tsk5_blk1 -stim_times 2 /media/hdw/DATA/ercig_afni/onset_time/fixntr_tsk5_blk2.txt 'WAV(15)' -stim_label 2 fixntr_run1tsk5_blk2 -stim_times 3 /media/hdw/DATA/ercig_afni/onset_time/fixntr_tsk5_blk3.txt 'WAV(15)' -stim_label 3 fixntr_run1tsk5_blk3 -stim_times 4 /media/hdw/DATA/ercig_afni/onset_time/fixntr_tsk5_blk4.txt 'WAV(15)' -stim_label 4 fixntr_run1tsk5_blk4 -stim_times 5 /media/hdw/DATA/ercig_afni/onset_time/fixntr_tsk5_blk5.txt 'WAV(15)' -stim_label 5 fixntr_run1tsk5_blk5 -stim_times 6 /media/hdw/DATA/ercig_afni/onset_time/fixsmk_tsk5_blk1.txt 'WAV(15)' -stim_label 6 fixsmk_run1tsk5_blk1 -stim_times 7 /media/hdw/DATA/ercig_afni/onset_time/fixsmk_tsk5_blk2.txt 'WAV(15)' -stim_label 7 fixsmk_run1tsk5_blk2 -stim_times 8 /media/hdw/DATA/ercig_afni/onset_time/fixsmk_tsk5_blk3.txt 'WAV(15)' -stim_label 8 fixsmk_run1tsk5_blk3 -stim_times 9 /media/hdw/DATA/ercig_afni/onset_time/fixsmk_tsk5_blk4.txt 'WAV(15)' -stim_label 9 fixsmk_run1tsk5_blk4 -stim_times 10 /media/hdw/DATA/ercig_afni/onset_time/fixsmk_tsk5_blk5.txt 'WAV(15)' -stim_label 10 fixsmk_run1tsk5_blk5 -stim_times 11 /media/hdw/DATA/ercig_afni/onset_time/ntr_tsk5_blk1.txt 'WAV(15)' -stim_label 11 ntr_run1tsk5_blk1 -stim_times 12 /media/hdw/DATA/ercig_afni/onset_time/ntr_tsk5_blk2.txt 'WAV(15)' -stim_label 12 ntr_run1tsk5_blk2 -stim_times 13 /media/hdw/DATA/ercig_afni/onset_time/ntr_tsk5_blk3.txt 'WAV(15)' -stim_label 13 ntr_run1tsk5_blk3 -stim_times 14 /media/hdw/DATA/ercig_afni/onset_time/ntr_tsk5_blk4.txt 'WAV(15)' -stim_label 14 ntr_run1tsk5_blk4 -stim_times 15 /media/hdw/DATA/ercig_afni/onset_time/ntr_tsk5_blk5.txt 'WAV(15)' -stim_label 15 ntr_run1tsk5_blk5 -stim_times 16 /media/hdw/DATA/ercig_afni/onset_time/smk_tsk5_blk1.txt 'WAV(15)' -stim_label 16 smk_run1tsk5_blk1 -stim_times 17 /media/hdw/DATA/ercig_afni/onset_time/smk_tsk5_blk2.txt 'WAV(15)' -stim_label 17 smk_run1tsk5_blk2 -stim_times 18 /media/hdw/DATA/ercig_afni/onset_time/smk_tsk5_blk3.txt 'WAV(15)' -stim_label 18 smk_run1tsk5_blk3 -stim_times 19 /media/hdw/DATA/ercig_afni/onset_time/smk_tsk5_blk4.txt 'WAV(15)' -stim_label 19 smk_run1tsk5_blk4 -stim_times 20 /media/hdw/DATA/ercig_afni/onset_time/smk_tsk5_blk5.txt 'WAV(15)' -stim_label 20 smk_run1tsk5_blk5 -stim_times 21 /media/hdw/DATA/ercig_afni/onset_time_concat/fixntr_tsk1_blk1.txt 'WAV(15)' -stim_label 21 fixntr_run2tsk1_blk1 -stim_times 22 /media/hdw/DATA/ercig_afni/onset_time_concat/fixntr_tsk1_blk2.txt 'WAV(15)' -stim_label 22 fixntr_run2tsk1_blk2 -stim_times 23 /media/hdw/DATA/ercig_afni/onset_time_concat/fixntr_tsk1_blk3.txt 'WAV(15)' -stim_label 23 fixntr_run2tsk1_blk3 -stim_times 24 /media/hdw/DATA/ercig_afni/onset_time_concat/fixntr_tsk1_blk4.txt 'WAV(15)' -stim_label 24 fixntr_run2tsk1_blk4 -stim_times 25 /media/hdw/DATA/ercig_afni/onset_time_concat/fixntr_tsk1_blk5.txt 'WAV(15)' -stim_label 25 fixntr_run2tsk1_blk5 -stim_times 26 /media/hdw/DATA/ercig_afni/onset_time_concat/fixsmk_tsk1_blk1.txt 'WAV(15)' -stim_label 26 fixsmk_run2tsk1_blk1 -stim_times 27 /media/hdw/DATA/ercig_afni/onset_time_concat/fixsmk_tsk1_blk2.txt 'WAV(15)' -stim_label 27 fixsmk_run2tsk1_blk2 -stim_times 28 /media/hdw/DATA/ercig_afni/onset_time_concat/fixsmk_tsk1_blk3.txt 'WAV(15)' -stim_label 28 fixsmk_run2tsk1_blk3 -stim_times 29 /media/hdw/DATA/ercig_afni/onset_time_concat/fixsmk_tsk1_blk4.txt 'WAV(15)' -stim_label 29 fixsmk_run2tsk1_blk4 -stim_times 30 /media/hdw/DATA/ercig_afni/onset_time_concat/fixsmk_tsk1_blk5.txt 'WAV(15)' -stim_label 30 fixsmk_run2tsk1_blk5 -stim_times 31 /media/hdw/DATA/ercig_afni/onset_time_concat/ntr_tsk1_blk1.txt 'WAV(15)' -stim_label 31 ntr_run2tsk1_blk1 -stim_times 32 /media/hdw/DATA/ercig_afni/onset_time_concat/ntr_tsk1_blk2.txt 'WAV(15)' -stim_label 32 ntr_run2tsk1_blk2 -stim_times 33 /media/hdw/DATA/ercig_afni/onset_time_concat/ntr_tsk1_blk3.txt 'WAV(15)' -stim_label 33 ntr_run2tsk1_blk3 -stim_times 34 /media/hdw/DATA/ercig_afni/onset_time_concat/ntr_tsk1_blk4.txt 'WAV(15)' -stim_label 34 ntr_run2tsk1_blk4 -stim_times 35 /media/hdw/DATA/ercig_afni/onset_time_concat/ntr_tsk1_blk5.txt 'WAV(15)' -stim_label 35 ntr_run2tsk1_blk5 -stim_times 36 /media/hdw/DATA/ercig_afni/onset_time_concat/smk_tsk1_blk1.txt 'WAV(15)' -stim_label 36 smk_run2tsk1_blk1 -stim_times 37 /media/hdw/DATA/ercig_afni/onset_time_concat/smk_tsk1_blk2.txt 'WAV(15)' -stim_label 37 smk_run2tsk1_blk2 -stim_times 38 /media/hdw/DATA/ercig_afni/onset_time_concat/smk_tsk1_blk3.txt 'WAV(15)' -stim_label 38 smk_run2tsk1_blk3 -stim_times 39 /media/hdw/DATA/ercig_afni/onset_time_concat/smk_tsk1_blk4.txt 'WAV(15)' -stim_label 39 smk_run2tsk1_blk4 -stim_times 40 /media/hdw/DATA/ercig_afni/onset_time_concat/smk_tsk1_blk5.txt 'WAV(15)' -stim_label 40 smk_run2tsk1_blk5 -stim_file 41 'motion_s16_demean.1D[0]' -stim_base 41 -stim_label 41 roll -stim_file 42 'motion_s16_demean.1D[1]' -stim_base 42 -stim_label 42 pitch -stim_file 43 'motion_s16_demean.1D[2]' -stim_base 43 -stim_label 43 yaw -stim_file 44 'motion_s16_demean.1D[3]' -stim_base 44 -stim_label 44 dS -stim_file 45 'motion_s16_demean.1D[4]' -stim_base 45 -stim_label 45 dL -stim_file 46 'motion_s16_demean.1D[5]' -stim_base 46 -stim_label 46 dP -gltsym 'SYM: smk_run1tsk5_blk1 +smk_run1tsk5_blk2 +smk_run1tsk5_blk3 +smk_run1tsk5_blk4      +smk_run1tsk5_blk5 +smk_run2tsk1_blk1 +smk_run2tsk1_blk2 +smk_run2tsk1_blk3 +smk_run2tsk1_blk4      +smk_run2tsk1_blk5' -glt_label 1 smk -gltsym 'SYM: fixsmk_run1tsk5_blk1 +fixsmk_run1tsk5_blk2 +fixsmk_run1tsk5_blk3      +fixsmk_run1tsk5_blk4 +fixsmk_run1tsk5_blk5 +fixsmk_run2tsk1_blk1 +fixsmk_run2tsk1_blk2      +fixsmk_run2tsk1_blk3 +fixsmk_run2tsk1_blk4 +fixsmk_run2tsk1_blk5' -glt_label 2 smkfix -gltsym 'SYM: smk_run1tsk5_blk1 +smk_run1tsk5_blk2 +smk_run1tsk5_blk3 +smk_run1tsk5_blk4      +smk_run1tsk5_blk5 +smk_run2tsk1_blk1 +smk_run2tsk1_blk2 +smk_run2tsk1_blk3 +smk_run2tsk1_blk4      +smk_run2tsk1_blk5 -fixsmk_run1tsk5_blk1 -fixsmk_run1tsk5_blk2 -fixsmk_run1tsk5_blk3      -fixsmk_run1tsk5_blk4 -fixsmk_run1tsk5_blk5 -fixsmk_run2tsk1_blk1 -fixsmk_run2tsk1_blk2      -fixsmk_run2tsk1_blk3 -fixsmk_run2tsk1_blk4 -fixsmk_run2tsk1_blk5' -glt_label 3 s_sfix -gltsym 'SYM: ntr_run1tsk5_blk1 +ntr_run1tsk5_blk2 +ntr_run1tsk5_blk3 +ntr_run1tsk5_blk4      +ntr_run1tsk5_blk5 +ntr_run2tsk1_blk1 +ntr_run2tsk1_blk2 +ntr_run2tsk1_blk3 +ntr_run2tsk1_blk4      +ntr_run2tsk1_blk5' -glt_label 4 ntr -gltsym 'SYM: fixntr_run1tsk5_blk1 +fixntr_run1tsk5_blk2 +fixntr_run1tsk5_blk3      +fixntr_run1tsk5_blk4 +fixntr_run1tsk5_blk5 +fixntr_run2tsk1_blk1 +fixntr_run2tsk1_blk2      +fixntr_run2tsk1_blk3 +fixntr_run2tsk1_blk4 +fixntr_run2tsk1_blk5' -glt_label 5 ntrfix -gltsym 'SYM: ntr_run1tsk5_blk1 +ntr_run1tsk5_blk2 +ntr_run1tsk5_blk3 +ntr_run1tsk5_blk4      +ntr_run1tsk5_blk5 +ntr_run2tsk1_blk1 +ntr_run2tsk1_blk2 +ntr_run2tsk1_blk3 +ntr_run2tsk1_blk4      +ntr_run2tsk1_blk5 -fixntr_run1tsk5_blk1 -fixntr_run1tsk5_blk2 -fixntr_run1tsk5_blk3      -fixntr_run1tsk5_blk4 -fixntr_run1tsk5_blk5 -fixntr_run2tsk1_blk1 -fixntr_run2tsk1_blk2      -fixntr_run2tsk1_blk3 -fixntr_run2tsk1_blk4 -fixntr_run2tsk1_blk5' -glt_label 6 n_nfix -gltsym 'SYM: smk_run1tsk5_blk1 +smk_run1tsk5_blk2 +smk_run1tsk5_blk3 +smk_run1tsk5_blk4      +smk_run1tsk5_blk5 +smk_run2tsk1_blk1 +smk_run2tsk1_blk2 +smk_run2tsk1_blk3 +smk_run2tsk1_blk4      +smk_run2tsk1_blk5 -ntr_run1tsk5_blk1 -ntr_run1tsk5_blk2 -ntr_run1tsk5_blk3      -ntr_run1tsk5_blk4 -ntr_run1tsk5_blk5 -ntr_run2tsk1_blk1 -ntr_run2tsk1_blk2 -ntr_run2tsk1_blk3      -ntr_run2tsk1_blk4 -ntr_run2tsk1_blk5' -glt_label 7 smk_ntr -gltsym 'SYM: smk_run1tsk5_blk1 +smk_run1tsk5_blk2 +smk_run1tsk5_blk3 +smk_run1tsk5_blk4      +smk_run1tsk5_blk5 +smk_run2tsk1_blk1 +smk_run2tsk1_blk2 +smk_run2tsk1_blk3 +smk_run2tsk1_blk4      +smk_run2tsk1_blk5 -fixsmk_run1tsk5_blk1 -fixsmk_run1tsk5_blk2 -fixsmk_run1tsk5_blk3      -fixsmk_run1tsk5_blk4 -fixsmk_run1tsk5_blk5 -fixsmk_run2tsk1_blk1 -fixsmk_run2tsk1_blk2      -fixsmk_run2tsk1_blk3 -fixsmk_run2tsk1_blk4 -fixsmk_run2tsk1_blk5 -ntr_run1tsk5_blk1 -ntr_run1tsk5_blk2      -ntr_run1tsk5_blk3 -ntr_run1tsk5_blk4 -ntr_run1tsk5_blk5 -ntr_run2tsk1_blk1 -ntr_run2tsk1_blk2      -ntr_run2tsk1_blk3 -ntr_run2tsk1_blk4 -ntr_run2tsk1_blk5 +fixntr_run1tsk5_blk1      +fixntr_run1tsk5_blk2 +fixntr_run1tsk5_blk3 +fixntr_run1tsk5_blk4 +fixntr_run1tsk5_blk5      +fixntr_run2tsk1_blk1 +fixntr_run2tsk1_blk2 +fixntr_run2tsk1_blk3 +fixntr_run2tsk1_blk4 +fixntr_run2tsk1_blk5' -glt_label 8 ssf_nnf -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -errts errts.s16 -bucket stats.s16

When I check the data, it seems that they couldn't read the stimulus file (the .txt file).
Thus, I double checked the path, but I couldn't solve that problem.

I also tried to save stimulus files in the same path which the command script located, but it also doesn't work.

Therefore, may I ask you how to solve this issue?
Thank you for reading, and thank you in advance.

Regards,
DaWoon Heo



Edited 2 time(s). Last edit at 08/14/2017 05:37AM by dawoon.