Fatal Signal 11 (SIGSEGV) fat_proc_select_vols

AFNI Message Board
1

Hi there,

When I try to run fat_proc_select_vols, this error message repeats until I terminate the command:

Fatal Signal 11 (SIGSEGV) received
SUMA_PauseForUserDisco
prompt_popup
Bottom of Debug Stack
** AFNI version = AFNI_18.1.05 Compile date = Apr 18 2018
** [[Precompiled binary macosx_10.7_local: Apr 18 2018]]
** 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 /Users/cunninghamca2/.afni.crashlog
/Users/cunninghamca2/abin/@djunct_dwi_selector.bash: line 86: [: : integer expression expected
/Users/cunninghamca2/abin/@djunct_dwi_selector.bash: line 120: [: : integer expression expected
/Users/cunninghamca2/abin/@djunct_dwi_selector.bash: line 151: [: : integer expression expected
Warning: Fatal Error:
_XmGetDefaultDisplay cannot be used prior to VendorS.Initialize, returns NULL

Any help would be greatly appreciated!

Catherine

2

Hi, Catherine-

Can you please copy+paste the exact command you are running?

Thanks,
pt

3

Hi Catherine,

It seems likely that you may need to set up DYLD_LIBRARY_PATH
for tcsh. Perhaps you have set it for and are using bash, but it
not done for tcsh.

Would you please run suma from both shells, and see if it starts?
So start a bash shell and run suma, then start tcsh and run suma.
Then you can exit from both shells, or close the window.

bash
suma
tcsh
suma

Thanks,

  • rick
4

Hello,

Here’s the command:

set path_P_ss = data_proc/S01

fat_proc_select_vols
-in_dwi $path_P_ss/dwi_00/ap.nii.gz
-in_img $path_P_ss/dwi_00/ap_sepscl.sag.png
-prefix $path_P_ss/dwi_01/dwi_sel_ap

fat_proc_select_vols
-in_dwi $path_P_ss/dwi_00/pa.nii.gz
-in_img $path_P_ss/dwi_00/pa_sepscl.sag.png
-in_bads $path_P_ss/dwi_01/dwi_sel_ap_bads.txt
-prefix $path_P_ss/dwi_01/dwi_sel_both

Thanks!

Catherine

5

Hi Rick,

Suma starts both times for me without a problem.

Catherine

6

Hi there,

I’m still getting this error when I try to run the command:

set path_B_ss = data_basic/S01
set path_P_ss = data_proc/S01

fat_proc_select_vols
-in_dwi $path_P_ss/dwi_00/ap.nii.gz
-in_img $path_P_ss/dwi_00/ap_sepscl.sag.png
-prefix $path_P_ss/dwi_01/dwi_sel_ap

fat_proc_select_vols
-in_dwi $path_P_ss/dwi_00/pa.nii.gz
-in_img $path_P_ss/dwi_00/pa_sepscl.sag.png
-in_bads $path_P_ss/dwi_01/dwi_sel_ap_bads.txt
-prefix $path_P_ss/dwi_01/dwi_sel_both

I’m able to run suma from both shells, and Rick you were kind enough to fix the library issues I was having before. But this error still remains despite that. I’d appreciate any help or suggestions.

Thanks very much!

Catherine

7

Hmm, are you running this as a script, or directly in the terminal?

–pt

8

I’m running it as a script.

9

Hi Catherine

To be positive, you would please post the error messages?

Thanks,

  • rick