3dvolreg fatal signal

AFNI Message Board
1

Hello,
I just saw this message today when running 3dvolreg on ubuntu 16.06. I updated my AFNI and it still exists. I found the same problem with an old version and the most updated version of AFNI on a cluster which runs redhat 7.

Fatal Signal 11 (SIGSEGV) received
3dvolreg main
Bottom of Debug Stack
** Command line was:
3dvolreg -prefix NULL -1Dmatrix_save …/preprocessed/sub-MSC09/EPI/glasslexical_run-02/…/preprocessed/sub-MSC09/EPI/glasslexical_run-02/sub-MSC09_ses-func08_task-glasslexical_run-02_bold_motion.aff12.1D -1Dfile …/preprocessed/sub-MSC09/EPI/glasslexical_run-02/…/preprocessed/sub-MSC09/EPI/glasslexical_run-02/sub-MSC09_ses-func08_task-glasslexical_run-02_bold_motion.txt -base 0 …/preprocessed/sub-MSC09/EPI/glasslexical_run-02/sub-MSC09_ses-func08_task-glasslexical_run-02_bold_t.nii.gz
** AFNI version = AFNI_18.0.13 Compile date = Feb 6 2018
** [[Precompiled binary linux_openmp_64: Feb 6 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 /home/mingbo/.afni.crashlog

I searched for some old posts and the suggestion there. Here are some outputs for the suggested commands in those posts:

which 3dvolreg
/home/mingbo/abin/3dvolreg

which 3dvolreg.afni
/usr/local/freesurfer/bin/3dvolreg.afni

But on the cluster which also had this problem, I actually did not load freesurfer and therefore the second output is that it cannot find 3dvolreg.afni in its path – 3dvolreg still crashes.

2

Hi Mingbo,

Would you please send me email (might be better than
the message board) showing the following command
and their output? You should be able to get my address
by clicking on my name.

ldd ~/abin/3dvolreg
afni_system_check.py -check_all
3dvolreg -help | head

Also, note that we actually have Ubuntu 16 binaries
and CentOS 7 binaries. But still, this crash is strange.

Thanks,

  • rick
3

It was my fault. I put wrong output directory for the motion parameter files.

4

Sorry, that will be more clearly reported in the future.

  • rick