afni.nimh.nih.gov

HI Afni gurus!

I am getting a Signal 11 (SIGSEGV) error when trying to run 3dDeconvolve (on only some of my subjects).

Here is my script with 3dDecon command.

for i in {1004..1004} #{1007..1008} {1012..1012} {1014..1014} {1023..1023} {1026..1028} # {1023..1023}
do

value=$(<../${i}/GLM_BASIC/scans.txt)
set $value

/home/bradley/bin/qexec2.R -q bigmem_16.q --mem=16G \
3dDeconvolve -force_TR 1.77 \
-local_times \
-input ../${i}/GLM_BASIC/$1 ../${i}/GLM_BASIC/$2 ../${i}/GLM_BASIC/$3 ../${i}/GLM_BASIC/$4 ../${i}/GLM_BASIC/$5 ../${i}/GLM_BASIC/$6 \
-xout -num_stimts 23 \
-GOFORIT \
-polort 5 \
-stim_times_IM 1 ${i}_study_scene_prev_correct.1D 'GAM' -stim_label 1 StudCor \
-stim_times_IM 2 ${i}_study_scene_prev_incorrect.1D 'GAM' -stim_label 2 StudIncor \
-stim_times_IM 3 ${i}_study_scene_prev_not_tested.1D 'GAM' -stim_label 3 Stud_nottested \
-stim_times_IM 4 ${i}_test_scene_delay_correct.1D 'GAM' -stim_label 4 delayCor \
-stim_times_IM 5 ${i}_test_scene_delay_incorrect.1D 'GAM' -stim_label 5 delayIncor \
-stim_times_IM 6 ${i}_test_scene_face_correct.1D 'GAM' -stim_label 6 faceCor \
-stim_times_IM 7 ${i}_test_scene_face_incorrect.1D 'GAM' -stim_label 7 faceIncor \
-stim_times_IM 8 ${i}_test_scene_prev_correct.1D 'GAM' -stim_label 8 prevCor \
-stim_times_IM 9 ${i}_test_scene_prev_incorrect.1D 'GAM' -stim_label 9 prevIncor \
-stim_times_IM 10 ${i}_study_scene_prev_NoGuess.1D 'GAM' -stim_label 10 StudGuess \
-stim_times_IM 11 ${i}_study_scene_prev_no_response.1D 'GAM' -stim_label 11 StudnoR \
-stim_times_IM 12 ${i}_test_scene_delay_NoGuess.1D 'GAM' -stim_label 12 delayGuess \
-stim_times_IM 13 ${i}_test_scene_delay_no_response.1D 'GAM' -stim_label 13 delaynoR \
-stim_times_IM 14 ${i}_test_scene_face_NoGuess.1D 'GAM' -stim_label 14 faceGuess \
-stim_times_IM 15 ${i}_test_scene_face_no_response.1D 'GAM' -stim_label 15 facenoR \
-stim_times_IM 16 ${i}_test_scene_prev_NoGuess.1D 'GAM' -stim_label 16 prevGuess \
-stim_times_IM 17 ${i}_test_scene_prev_no_response.1D 'GAM' -stim_label 17 prevnoR \
-stim_file 18 ../${i}/epi/MotionFile_allruns.1D'[0]' -stim_base 18 -stim_label 18 roll \
-stim_file 19 ../${i}/epi/MotionFile_allruns.1D'[1]' -stim_base 19 -stim_label 19 pitch \
-stim_file 20 ../${i}/epi/MotionFile_allruns.1D'[2]' -stim_base 20 -stim_label 20 yaw \
-stim_file 21 ../${i}/epi/MotionFile_allruns.1D'[3]' -stim_base 21 -stim_label 21 dS \
-stim_file 22 ../${i}/epi/MotionFile_allruns.1D'[4]' -stim_base 22 -stim_label 22 dL \
-stim_file 23 ../${i}/epi/MotionFile_allruns.1D'[5]' -stim_base 23 -stim_label 23 dP \
-x1D ${i}.xmat.1D -xjpeg ${i}.jpg \
-fout -tout -bucket ${i}_bc_stats4FC_syn -cbucket ${i}.cstats
done


And here is the output (more P_1396_0319163057487458.cmd.e961578):

++ '-stim_times_IM 1 1004_study_scene_prev_correct.1D' will have 42 regressors
++ '-stim_times_IM 2 1004_study_scene_prev_incorrect.1D' will have 16 regressors
++ '-stim_times_IM 3 1004_study_scene_prev_not_tested.1D' will have 192 regressors
++ '-stim_times_IM 4 1004_test_scene_delay_correct.1D' will have 42 regressors
++ '-stim_times_IM 5 1004_test_scene_delay_incorrect.1D' will have 16 regressors
++ '-stim_times_IM 6 1004_test_scene_face_correct.1D' will have 42 regressors
++ '-stim_times_IM 7 1004_test_scene_face_incorrect.1D' will have 16 regressors
++ '-stim_times_IM 8 1004_test_scene_prev_correct.1D' will have 42 regressors
++ '-stim_times_IM 9 1004_test_scene_prev_incorrect.1D' will have 16 regressors
++ '-stim_times_IM 10 1004_study_scene_prev_NoGuess.1D' will have 37 regressors
*+ WARNING: '-stim_times_IM 11' didn't read any good times from file '1004_study_scene_prev_no_response.1D'
++ '-stim_times_IM 11 1004_study_scene_prev_no_response.1D' will have 0 regressors
++ '-stim_times_IM 12 1004_test_scene_delay_NoGuess.1D' will have 37 regressors
*+ WARNING: '-stim_times_IM 13' didn't read any good times from file '1004_test_scene_delay_no_response.1D'
++ '-stim_times_IM 13 1004_test_scene_delay_no_response.1D' will have 0 regressors
++ '-stim_times_IM 14 1004_test_scene_face_NoGuess.1D' will have 37 regressors
*+ WARNING: '-stim_times_IM 15' didn't read any good times from file '1004_test_scene_face_no_response.1D'
++ '-stim_times_IM 15 1004_test_scene_face_no_response.1D' will have 0 regressors
++ '-stim_times_IM 16 1004_test_scene_prev_NoGuess.1D' will have 37 regressors
*+ WARNING: '-stim_times_IM 17' didn't read any good times from file '1004_test_scene_prev_no_response.1D'
++ '-stim_times_IM 17 1004_test_scene_prev_no_response.1D' will have 0 regressors
++ 3dDeconvolve: AFNI version=AFNI_2011_12_21_1014 (Aug 31 2012) [64-bit]
++ Authored by: B. Douglas Ward, et al.
++ current memory malloc-ated = 455,053 bytes (about 455 thousand)
++ loading dataset ../1004/GLM_BASIC/../epi/rscan01.nii ../1004/GLM_BASIC/../epi/rscan02.nii ../1004/GLM_BASIC/../epi/rscan03.nii ../1004/GLM_BASIC/../epi/rscan04.nii ../1004/GLM_BASIC/../epi
/rscan05.nii ../1004/GLM_BASIC/../epi/rscan06.nii
++ current memory malloc-ated = 515,197 bytes (about 515 thousand)
++ forcibly using TR=1.7700 seconds for -input dataset
++ Auto-catenated input datasets treated as multiple imaging runs
++ Auto-catenated datasets start at: 0 346 692 1038 1384 1730
++ STAT automask has 183823 voxels (out of 762300 = 24.1%)
++ Skipping check for initial transients
++ Input polort=5; Longest run=612.4 s; Recommended minimum polort=5 ++ OK ++
++ -stim_times using TR=1.77 s for stimulus timing conversion
++ -stim_times using TR=1.77 s for any -iresp output datasets
++ [you can alter the -iresp TR via the -TR_times option]
++ -stim_times_IM 1 using LOCAL times
++ -stim_times_IM 2 using LOCAL times
++ -stim_times_IM 3 using LOCAL times
++ -stim_times_IM 4 using LOCAL times
++ -stim_times_IM 5 using LOCAL times
++ -stim_times_IM 6 using LOCAL times
++ -stim_times_IM 7 using LOCAL times
++ -stim_times_IM 8 using LOCAL times
++ -stim_times_IM 9 using LOCAL times
++ -stim_times_IM 10 using LOCAL times
*+ WARNING: -stim_times_IM 11 has all times equal to '*' ?!?!
++ -stim_times_IM 11 using LOCAL times
*+ WARNING: !! '-stim_times_IM 11' file '1004_study_scene_prev_no_response.1D' has no good stimulus time values
++ -stim_times_IM 12 using LOCAL times
*+ WARNING: -stim_times_IM 13 has all times equal to '*' ?!?!
++ -stim_times_IM 13 using LOCAL times
*+ WARNING: !! '-stim_times_IM 13' file '1004_test_scene_delay_no_response.1D' has no good stimulus time values
++ -stim_times_IM 14 using LOCAL times
*+ WARNING: -stim_times_IM 15 has all times equal to '*' ?!?!
++ -stim_times_IM 15 using LOCAL times
*+ WARNING: !! '-stim_times_IM 15' file '1004_test_scene_face_no_response.1D' has no good stimulus time values
++ -stim_times_IM 16 using LOCAL times
*+ WARNING: -stim_times_IM 17 has all times equal to '*' ?!?!
++ -stim_times_IM 17 using LOCAL times
*+ WARNING: !! '-stim_times_IM 17' file '1004_test_scene_prev_no_response.1D' has no good stimulus time values
++ Number of time points: 2076 (no censoring)
+ Number of parameters: 614 [42 baseline ; 572 signal]
++ Memory required for output bricks = 3,799,303,200 bytes (about 3.8 billion)

Fatal Signal 11 (SIGSEGV) received
Last STATUS: extract xgood matrix
init_indep_var_matrix
calculate_results
3dDeconvolve main
Bottom of Debug Stack
** AFNI version = AFNI_2011_12_21_1014 Compile date = Aug 31 2012
** [[Precompiled binary linux_openmp_64: Aug 31 2012]]
** Program Abort **
** 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.
*** MCW_malloc post-corruption! serial=853005 size=10197312 source=matrix.c line#225
<- init_indep_var_matrix <- calculate_results <- 3dDeconvolve main
[[ Called from source=debugtrace.h line#148 ]]

Seeing as it's the same thing but an error for only some subjects I don't really know where to start. Any help you can offer would be much appreciated.

Thank you very much!
Kirk