Hello AFNI connoisseurs,
I am facing an error when running the 3dTcat function through Compute Canada resources.
I have a set of arrays which all correspond to number based nifti files that I’d like to merge together.
The command I run is the following, and the $file_paths variable is a list of all files that I’d like to have merged (see image for the artistic aspect of echo $file_path)
xvfb-run -a vglrun -d egl 3dTcat
-prefix Temp.nii
Zero_dataset.nii
“$file_paths”
The error I get from the sbatch output text file is:
++ 3dTcat: AFNI version=AFNI_23.0.04 (Feb 13 2023) [64-bit]
Fatal Signal 11 (SIGSEGV) received
3dTcat main
Bottom of Debug Stack
** AFNI version = AFNI_23.0.04 Compile date = Feb 13 2023
** [[Precompiled binary linux_centos_7_64: Feb 13 2023]]
** 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.
** Crash log is appended to file /home/coopapap/.afni.crashlog
++ 3dTstat: AFNI version=AFNI_23.0.04 (Feb 13 2023) [64-bit]
++ Authored by: KR Hammett & RW Cox
e[7m** FATAL ERROR:e[0m Can’t open dataset Temp.nii
** Program compile date = Feb 13 2023
rm: cannot remove ‘Temp.nii’: No such file or directory
Processing SMN…
++ 3dTcat: AFNI version=AFNI_23.0.04 (Feb 13 2023) [64-bit]
And when I go to the crash log I get the following:
------ CRASH LOG ------------------------------**
Fatal Signal 11 (SIGSEGV) received
… recent internal history …
++++++++mri_free [8]: {ENTRY (file=mri_free.c line=49) from THD_delete_datablock {19 ms}
mri_free – call killpurge {19 ms}
+++++++++mri_killpurge [9]: {ENTRY (file=mri_purger.c line=259) from mri_free {19 ms}
mri_killpurge – check if im==NULL ptr=0x21da810
mri_killpurge – can’t killpurge NULL fname! {19 ms}
---------mri_killpurge [9]: EXIT} (file=mri_purger.c line=270) to mri_free {19 ms}
mri_free – free im {19 ms}
--------mri_free [8]: EXIT} (file=mri_free.c line=69) to THD_delete_datablock {19 ms}
THD_delete_datablock – free brick_ stuff {19 ms}
THD_delete_datablock – KILL_KILL {19 ms}
THD_delete_datablock – free attributes {19 ms}
-------THD_delete_datablock [7]: EXIT} (file=thd_delete.c line=122) to THD_delete_3dim_dataset {19 ms}
THD_delete_3dim_dataset – KILL_KILL {19 ms}
------THD_delete_3dim_dataset [6]: EXIT} (file=thd_delete.c line=179) to THD_is_dataset {19 ms}
-----THD_is_dataset [5]: EXIT} (file=thd_opendset.c line=407) to init_global_atlas_list {19 ms}
+++++invert_affine [5]: {ENTRY (file=thd_atlas.c line=2026) from init_global_atlas_list {19 ms}
-----invert_affine [5]: EXIT} (file=thd_atlas.c line=2049) to init_global_atlas_list {19 ms}
+++++invert_affine [5]: {ENTRY (file=thd_atlas.c line=2026) from init_global_atlas_list {19 ms}
-----invert_affine [5]: EXIT} (file=thd_atlas.c line=2049) to init_global_atlas_list {19 ms}
+++++invert_affine [5]: {ENTRY (file=thd_atlas.c line=2026) from init_global_atlas_list {19 ms}
-----invert_affine [5]: EXIT} (file=thd_atlas.c line=2049) to init_global_atlas_list {19 ms}
+++++invert_affine [5]: {ENTRY (file=thd_atlas.c line=2026) from init_global_atlas_list {19 ms}
-----invert_affine [5]: EXIT} (file=thd_atlas.c line=2049) to init_global_atlas_list {19 ms}
----init_global_atlas_list [4]: EXIT} (file=thd_ttatlas_query.c line=2234) to THD_open_one_dataset {19 ms}
++++THD_3dim_from_ROIstring [4]: {ENTRY (file=thd_ttatlas_query.c line=8411) from THD_open_one_dataset {19 ms}
+++++ROI_String_Decode [5]: {ENTRY (file=thd_ttatlas_query.c line=3654) from THD_3dim_from_ROIstring {19 ms}
-----ROI_String_Decode [5]: EXIT} (file=thd_ttatlas_query.c line=3690) to THD_3dim_from_ROIstring {19 ms}
----THD_3dim_from_ROIstring [4]: EXIT} (file=thd_ttatlas_query.c line=8419) to THD_open_one_dataset {19 ms}
++++THD_patch_brickim [4]: {ENTRY (file=thd_loaddblk.c line=1267) from THD_open_one_dataset {19 ms}
----THD_patch_brickim [4]: EXIT} (file=thd_loaddblk.c line=1269) to THD_open_one_dataset {19 ms}
—THD_open_one_dataset [3]: EXIT} (file=thd_opendset.c line=359) to 3dTcat main {19 ms}
…
3dTcat main
** AFNI compile date = Feb 13 2023
** [[Precompiled binary linux_centos_7_64: Feb 13 2023]]
** Program Crash **
Can you provide any assistance?
