crash with 3dttest++ and covariate

AFNI Message Board
1

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?

2

Hello,

I do not think you can use sub-brick selectors for the covariates file, since it is not necessarily a numerical file.

If you want to extract the first 2 columns, consider running awk first, as in:

awk '{print $1, $2}' covariate35_new.txt > covariates_2.txt
  • rick
3

Hi Rick,
actually I have run the same script on another computer and it worked. Also on the other computer (a MacBook Pro) the ETAC calculation works where on my other computer it fails. I think I’m out of memory dsepite the tact I use 8 CPU…

4

That covariate file has a column of nan’s. It would be worth removing that and seeing if it helps (as it should not be useful in the regression anyway).

Do you have any of the screen text that appears just before the crash? That might make the context more clear. You can also run ‘top’ while this is going, and track memory usage against how much you have.

  • rick