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claudio_gentili
December 09, 2019 02:21PM
Hi all,
I'm trying to use 3dttest++ using bricks from a dataset as covariate. However I have this crash:
** 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=9099 bytes=29391779
** Crash log is appended to file /home/utente/.afni.crashlog

the afni.crasholog reports:

*********------ CRASH LOG ------------------------------***********
Fatal Signal 11 (SIGSEGV) received
.......... recent internal history .........................................
+++++AFNI_process_environ [5]: {ENTRY (file=afni_environ.c line=112) from THD_load_datablock
++++++AFNI_suck_file [6]: {ENTRY (file=afni_environ.c line=25) from AFNI_process_environ
------AFNI_suck_file [6]: EXIT} (file=afni_environ.c line=30) to AFNI_process_environ
-----AFNI_process_environ [5]: EXIT} (file=afni_environ.c line=132) to THD_load_datablock
+++++THD_alloc_datablock [5]: {ENTRY (file=thd_loaddblk.c line=852) from THD_load_datablock
THD_alloc_datablock -- trying to malloc sub-bricks
-----THD_alloc_datablock [5]: EXIT} (file=thd_loaddblk.c line=890) to THD_load_datablock
THD_load_datablock -- reading from BRIK file
+++++AFNI_process_environ [5]: {ENTRY (file=afni_environ.c line=112) from THD_load_datablock
++++++AFNI_suck_file [6]: {ENTRY (file=afni_environ.c line=25) from AFNI_process_environ
------AFNI_suck_file [6]: EXIT} (file=afni_environ.c line=30) to AFNI_process_environ
-----AFNI_process_environ [5]: EXIT} (file=afni_environ.c line=132) to THD_load_datablock
THD_load_datablock -- data has been read in
----THD_load_datablock [4]: EXIT} (file=thd_loaddblk.c line=839) to THD_dset_to_vectim
THD_dset_to_vectim -- create index list
THD_dset_to_vectim -- ignore==0 --> extracting all at once
++++THD_extract_many_arrays [4]: {ENTRY (file=thd_dsetto1D.c line=551) from THD_dset_to_vectim
+++++THD_load_datablock [5]: {ENTRY (file=thd_loaddblk.c line=133) from THD_extract_many_arrays
++++++AFNI_process_environ [6]: {ENTRY (file=afni_environ.c line=112) from THD_load_datablock
+++++++AFNI_suck_file [7]: {ENTRY (file=afni_environ.c line=25) from AFNI_process_environ
-------AFNI_suck_file [7]: EXIT} (file=afni_environ.c line=30) to AFNI_process_environ
------AFNI_process_environ [6]: EXIT} (file=afni_environ.c line=132) to THD_load_datablock
++++++AFNI_process_environ [6]: {ENTRY (file=afni_environ.c line=112) from THD_load_datablock
+++++++AFNI_suck_file [7]: {ENTRY (file=afni_environ.c line=25) from AFNI_process_environ
-------AFNI_suck_file [7]: EXIT} (file=afni_environ.c line=30) to AFNI_process_environ
------AFNI_process_environ [6]: EXIT} (file=afni_environ.c line=132) to THD_load_datablock
-----THD_load_datablock [5]: EXIT} (file=thd_loaddblk.c line=150) to THD_extract_many_arrays
----THD_extract_many_arrays [4]: EXIT} (file=thd_dsetto1D.c line=638) to THD_dset_to_vectim
THD_dset_to_vectim -- setting parameters in vectim header
THD_dset_to_vectim -- VECTIM_scan()
---THD_dset_to_vectim [3]: EXIT} (file=thd_dset_to_vectim.c line=117) to 3dttest++ main
............................................................................
** Command line was:
3dttest++ -mask mask_res35_GM50_anat+tlrc -setA subects s1 /media/DATA1/impuls/task_results/subject_results/group.healthy/subj.sub/sub_1.results/stats.sub_1.resamp4+tlrc s2 /media/DATA1/impu
ls/task_results/subject_results/group.healthy/subj.sub/sub_2.results/stats.sub_2.resamp4+tlrc s3 /media/DATA1/impuls/task_results/subject_results/group.healthy/subj.sub/sub_3.results/stats.s
ub_3.resamp4+tlrc s4 /media/DATA1/impuls/task_results/subject_results/group.healthy/subj.sub/sub_4.results/stats.sub_4.resamp4+tlrc s5 /media/DATA1/impuls/task_results/subject_results/group.
healthy/subj.sub/sub_5.results/stats.sub_5.resamp4+tlrc s6 /media/DATA1/impuls/task_results/subject_results/group.healthy/subj.sub/sub_6.results/stats.sub_6.resamp4+tlrc s7 /media/DATA1/impu
ls/task_results/subject_results/group.healthy/subj.sub/sub_7.results/stats.sub_7.resamp4+tlrc s8 /media/DATA1/impuls/task_results/subject_results/group.healthy/subj.sub/sub_8.results/stats.s
ub_8.resamp4+tlrc s9 /media/DATA1/impuls/task_results/subject_results/group.healthy/subj.sub/sub_9.results/stats.sub_9.resamp4+tlrc s10 /media/DATA1/impuls/task_results/subject_results/group
.healthy/subj.sub/sub_10.results/stats.sub_10.resamp4+tlrc s11 /media/DATA1/impuls/task_results/subject_results/group.healthy/subj.sub/sub_11.results/stats.sub_11.resamp4+tlrc s12 /media/DAT
A1/impuls/task_results/subject_results/group.healthy/subj.sub/sub_12.results/stats.sub_12.resamp4+tlrc s13 /media/DATA1/impuls/task_results/subject_results/group.healthy/subj.sub/sub_13.resu
lts/stats.sub_13.resamp4+tlrc s14 /media/DATA1/impuls/task_results/subject_results/group.healthy/subj.sub/sub_14.results/stats.sub_14.resamp4+tlrc s15 /media/DATA1/impuls/task_results/subjec
t_results/group.healthy/subj.sub/sub_15.results/stats.sub_15.resamp4+tlrc s17 /media/DATA1/impuls/task_results/subject_results/group.healthy/subj.sub/sub_17.results/stats.sub_17.resamp4+tlrc
s18 /media/DATA1/impuls/task_results/subject_results/group.healthy/subj.sub/sub_18.results/stats.sub_18.resamp4+tlrc s19 /media/DATA1/impuls/task_results/subject_results/group.healthy/subj.
sub/sub_19.results/stats.sub_19.resamp4+tlrc s20 /media/DATA1/impuls/task_results/subject_results/group.healthy/subj.sub/sub_20.results/stats.sub_20.resamp4+tlrc s21 /media/DATA1/impuls/task
_results/subject_results/group.healthy/subj.sub/sub_21.results/stats.sub_21.resamp4+tlrc s22 /media/DATA1/impuls/task_results/subject_results/group.healthy/subj.sub/sub_22.results/stats.sub_
22.resamp4+tlrc s23 /media/DATA1/impuls/task_results/subject_results/group.healthy/subj.sub/sub_23.results/stats.sub_23.resamp4+tlrc s24 /media/DATA1/impuls/task_results/subject_results/grou
p.healthy/subj.sub/sub_24.results/stats.sub_24.resamp4+tlrc s31 /media/DATA1/impuls/task_results/subject_results/group.healthy/subj.sub/sub_31.results/stats.sub_31.resamp4+tlrc s32 /media/DA
TA1/impuls/task_results/subject_results/group.healthy/subj.sub/sub_32.results/stats.sub_32.resamp4+tlrc s33 /media/DATA1/impuls/task_results/subject_results/group.healthy/subj.sub/sub_33.res
ults/stats.sub_33.resamp4+tlrc s34 /media/DATA1/impuls/task_results/subject_results/group.healthy/subj.sub/sub_34.results/stats.sub_34.resamp4+tlrc s35 /media/DATA1/impuls/task_results/subje
ct_results/group.healthy/subj.sub/sub_35.results/stats.sub_35.resamp4+tlrc s36 /media/DATA1/impuls/task_results/subject_results/group.healthy/subj.sub/sub_36.results/stats.sub_36.resamp4+tlr
c s25 /media/DATA1/impuls/task_results/subject_results/group.healthy/subj.sub/sub_25.results/stats.sub_25.resamp4+tlrc s26 /media/DATA1/impuls/task_results/subject_results/group.healthy/subj
.sub/sub_26.results/stats.sub_26.resamp4+tlrc s27 /media/DATA1/impuls/task_results/subject_results/group.healthy/subj.sub/sub_27.results/stats.sub_27.resamp4+tlrc s28 /media/DATA1/impuls/tas
k_results/subject_results/group.healthy/subj.sub/sub_28.results/stats.sub_28.resamp4+tlrc s29 /media/DATA1/impuls/task_results/subject_results/group.healthy/subj.sub/sub_29.results/stats.sub
_29.resamp4+tlrc s30 /media/DATA1/impuls/task_results/subject_results/group.healthy/subj.sub/sub_30.results/stats.sub_30.resamp4+tlrc -covariates 'covariate35_new.txt[0,1]' -prefix task4_DMN
............................................................................
3dttest++ main
** Command line was:
3dttest++ -mask mask_res35_GM50_anat+tlrc -setA subects s1 /media/DATA1/impuls/task_results/subject_results/group.healthy/subj.sub/sub_1.results/stats.sub_1.resamp4+tlrc s2 /media/DATA1/impu
ls/task_results/subject_results/group.healthy/subj.sub/sub_2.results/stats.sub_2.resamp4+tlrc s3 /media/DATA1/impuls/task_results/subject_results/group.healthy/subj.sub/sub_3.results/stats.s
ub_3.resamp4+tlrc s4 /media/DATA1/impuls/task_results/subject_results/group.healthy/subj.sub/sub_4.results/stats.sub_4.resamp4+tlrc s5 /media/DATA1/impuls/task_results/subject_results/group.
healthy/subj.sub/sub_5.results/stats.sub_5.resamp4+tlrc s6 /media/DATA1/impuls/task_results/subject_results/group.healthy/subj.sub/sub_6.results/stats.sub_6.resamp4+tlrc s7 /media/DATA1/impu
ls/task_results/subject_results/group.healthy/subj.sub/sub_7.results/stats.sub_7.resamp4+tlrc s8 /media/DATA1/impuls/task_results/subject_results/group.healthy/subj.sub/sub_8.results/stats.s
ub_8.resamp4+tlrc s9 /media/DATA1/impuls/task_results/subject_results/group.healthy/subj.sub/sub_9.results/stats.sub_9.resamp4+tlrc s10 /media/DATA1/impuls/task_results/subject_results/group
.healthy/subj.sub/sub_10.results/stats.sub_10.resamp4+tlrc s11 /media/DATA1/impuls/task_results/subject_results/group.healthy/subj.sub/sub_11.results/stats.sub_11.resamp4+tlrc s12 /media/DAT
A1/impuls/task_results/subject_results/group.healthy/subj.sub/sub_12.results/stats.sub_12.resamp4+tlrc s13 /media/DATA1/impuls/task_results/subject_results/group.healthy/subj.sub/sub_13.resu
lts/stats.sub_13.resamp4+tlrc s14 /media/DATA1/impuls/task_results/subject_results/group.healthy/subj.sub/sub_14.results/stats.sub_14.resamp4+tlrc s15 /media/DATA1/impuls/task_results/subjec
t_results/group.healthy/subj.sub/sub_15.results/stats.sub_15.resamp4+tlrc s17 /media/DATA1/impuls/task_results/subject_results/group.healthy/subj.sub/sub_17.results/stats.sub_17.resamp4+tlrc
s18 /media/DATA1/impuls/task_results/subject_results/group.healthy/subj.sub/sub_18.results/stats.sub_18.resamp4+tlrc s19 /media/DATA1/impuls/task_results/subject_results/group.healthy/subj.
sub/sub_19.results/stats.sub_19.resamp4+tlrc s20 /media/DATA1/impuls/task_results/subject_results/group.healthy/subj.sub/sub_20.results/stats.sub_20.resamp4+tlrc s21 /media/DATA1/impuls/task
_results/subject_results/group.healthy/subj.sub/sub_21.results/stats.sub_21.resamp4+tlrc s22 /media/DATA1/impuls/task_results/subject_results/group.healthy/subj.sub/sub_22.results/stats.sub_
22.resamp4+tlrc s23 /media/DATA1/impuls/task_results/subject_results/group.healthy/subj.sub/sub_23.results/stats.sub_23.resamp4+tlrc s24 /media/DATA1/impuls/task_results/subject_results/grou
p.healthy/subj.sub/sub_24.results/stats.sub_24.resamp4+tlrc s31 /media/DATA1/impuls/task_results/subject_results/group.healthy/subj.sub/sub_31.results/stats.sub_31.resamp4+tlrc s32 /media/DA
TA1/impuls/task_results/subject_results/group.healthy/subj.sub/sub_32.results/stats.sub_32.resamp4+tlrc s33 /media/DATA1/impuls/task_results/subject_results/group.healthy/subj.sub/sub_33.res
ults/stats.sub_33.resamp4+tlrc s34 /media/DATA1/impuls/task_results/subject_results/group.healthy/subj.sub/sub_34.results/stats.sub_34.resamp4+tlrc s35 /media/DATA1/impuls/task_results/subje
ct_results/group.healthy/subj.sub/sub_35.results/stats.sub_35.resamp4+tlrc s36 /media/DATA1/impuls/task_results/subject_results/group.healthy/subj.sub/sub_36.results/stats.sub_36.resamp4+tlr
c s25 /media/DATA1/impuls/task_results/subject_results/group.healthy/subj.sub/sub_25.results/stats.sub_25.resamp4+tlrc s26 /media/DATA1/impuls/task_results/subject_results/group.healthy/subj
.sub/sub_26.results/stats.sub_26.resamp4+tlrc s27 /media/DATA1/impuls/task_results/subject_results/group.healthy/subj.sub/sub_27.results/stats.sub_27.resamp4+tlrc s28 /media/DATA1/impuls/tas
k_results/subject_results/group.healthy/subj.sub/sub_28.results/stats.sub_28.resamp4+tlrc s29 /media/DATA1/impuls/task_results/subject_results/group.healthy/subj.sub/sub_29.results/stats.sub
_29.resamp4+tlrc s30 /media/DATA1/impuls/task_results/subject_results/group.healthy/subj.sub/sub_30.results/stats.sub_30.resamp4+tlrc -covariates 'covariate35_new.txt[0,1]' -prefix task4_DMN
** AFNI compile date = Jul 27 2017
** [[Precompiled binary linux_ubuntu_16_64: Jul 27 2017]]
** Program Crash **


Am I out of memory?
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Subject Author Posted

crash with 3dttest++ and covariate

claudio_gentili December 09, 2019 02:21PM

Re: crash with 3dttest++ and covariate

rick reynolds December 10, 2019 03:38PM

Re: crash with 3dttest++ and covariate

claudio_gentili December 11, 2019 10:47AM

Re: crash with 3dttest++ and covariate

rick reynolds December 13, 2019 10:14AM