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
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:
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.