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Dan
September 18, 2022 02:27PM
I'm consistently encountering a 3dvolreg error for a subset (N=3) of my subjects, the crash log contents are provided here:

*********------ CRASH LOG ------------------------------***********
Fatal Signal 11 (SIGSEGV) received
.......... recent internal history .........................................
+++++++fft_shift2 [7]: {ENTRY (file=thd_shift2.c line=76) from apply_yshear {86793 ms}
-------fft_shift2 [7]: EXIT} (file=thd_shift2.c line=171) to apply_yshear {86793 ms}
+++++++fft_shift2 [7]: {ENTRY (file=thd_shift2.c line=76) from apply_yshear {86793 ms}
-------fft_shift2 [7]: EXIT} (file=thd_shift2.c line=171) to apply_yshear {86793 ms}
+++++++fft_shift2 [7]: {ENTRY (file=thd_shift2.c line=76) from apply_yshear {86793 ms}
-------fft_shift2 [7]: EXIT} (file=thd_shift2.c line=171) to apply_yshear {86793 ms}
+++++++fft_shift2 [7]: {ENTRY (file=thd_shift2.c line=76) from apply_yshear {86793 ms}
-------fft_shift2 [7]: EXIT} (file=thd_shift2.c line=171) to apply_yshear {86793 ms}
+++++++fft_shift2 [7]: {ENTRY (file=thd_shift2.c line=76) from apply_yshear {86793 ms}
-------fft_shift2 [7]: EXIT} (file=thd_shift2.c line=171) to apply_yshear {86793 ms}
+++++++fft_shift2 [7]: {ENTRY (file=thd_shift2.c line=76) from apply_yshear {86793 ms}
-------fft_shift2 [7]: EXIT} (file=thd_shift2.c line=171) to apply_yshear {86793 ms}
+++++++fft_shift2 [7]: {ENTRY (file=thd_shift2.c line=76) from apply_yshear {86793 ms}
-------fft_shift2 [7]: EXIT} (file=thd_shift2.c line=171) to apply_yshear {86793 ms}
+++++++fft_shift2 [7]: {ENTRY (file=thd_shift2.c line=76) from apply_yshear {86793 ms}
-------fft_shift2 [7]: EXIT} (file=thd_shift2.c line=171) to apply_yshear {86793 ms}
+++++++fft_shift2 [7]: {ENTRY (file=thd_shift2.c line=76) from apply_yshear {86793 ms}
-------fft_shift2 [7]: EXIT} (file=thd_shift2.c line=171) to apply_yshear {86793 ms}
+++++++fft_shift2 [7]: {ENTRY (file=thd_shift2.c line=76) from apply_yshear {86793 ms}
-------fft_shift2 [7]: EXIT} (file=thd_shift2.c line=171) to apply_yshear {86793 ms}
+++++++fft_shift2 [7]: {ENTRY (file=thd_shift2.c line=76) from apply_yshear {86793 ms}
-------fft_shift2 [7]: EXIT} (file=thd_shift2.c line=171) to apply_yshear {86793 ms}
+++++++fft_shift2 [7]: {ENTRY (file=thd_shift2.c line=76) from apply_yshear {86793 ms}
-------fft_shift2 [7]: EXIT} (file=thd_shift2.c line=171) to apply_yshear {86793 ms}
+++++++fft_shift2 [7]: {ENTRY (file=thd_shift2.c line=76) from apply_yshear {86793 ms}
-------fft_shift2 [7]: EXIT} (file=thd_shift2.c line=171) to apply_yshear {86793 ms}
+++++++fft_shift2 [7]: {ENTRY (file=thd_shift2.c line=76) from apply_yshear {86793 ms}
-------fft_shift2 [7]: EXIT} (file=thd_shift2.c line=171) to apply_yshear {86793 ms}
+++++++fft_shift2 [7]: {ENTRY (file=thd_shift2.c line=76) from apply_yshear {86793 ms}
-------fft_shift2 [7]: EXIT} (file=thd_shift2.c line=82) to apply_yshear {86793 ms}
+++++++fft_shift2 [7]: {ENTRY (file=thd_shift2.c line=76) from apply_yshear {86793 ms}
............................................................................
** Command line was:
3dvolreg -Fourier -twopass -1Dfile slice.1D -1Dmatrix_save slice.aff12.1D -prefix slice_volreg.nii.gz -zpad 4 -maxdisp1D slice_md.1D /N/scratch/dlevitas/fmriprep-20.2.0_temp/sub-43/fmriprep_wf/single_subject_43_wf/func_preproc_task_pacpal_run_6_wf/bold_std_trans_wf/bold_reference_wf/_std_target_MNI152NLin2009cAsym./gen_ref/slice.nii.gz
............................................................................
fft_shift2
apply_yshear
apply_3shear
THD_rota_vol
mri_3dalign_one
3dvolreg main
** Command line was:
3dvolreg -Fourier -twopass -1Dfile slice.1D -1Dmatrix_save slice.aff12.1D -prefix slice_volreg.nii.gz -zpad 4 -maxdisp1D slice_md.1D /N/scratch/dlevitas/fmriprep-20.2.0_temp/sub-43/fmriprep_wf/single_subject_43_wf/func_preproc_task_pacpal_run_6_wf/bold_std_trans_wf/bold_reference_wf/_std_target_MNI152NLin2009cAsym./gen_ref/slice.nii.gz
** AFNI compile date = Jan 31 2022
** [[Precompiled binary linux_centos_7_64: Jan 31 2022]]
** Program Crash **

For context, this is occurring while processing my dataset using fmriprep (version 20.2.0); however, I attempted to run the command on my linux server and am receiving the same error. I saw this similar post, but I can confirm that my 3dvolreg command comes from the AFNI (not Freesurfer) distribution: afni/22.0.04/3dvolreg

It's unclear to me why this only occurs for several subjects, a quick visual check and data inspection (i.e. 3dinfo) doesn't indicate anything out of the ordinary. The one thing that is different for these failing subjects is that their data was collected following a software update to our Siemens Prisma scanner (upgraded from syngo MR E11 to syngo MR XA30). Would this or some other issue be causing this error?

Thanks
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Subject Author Posted

Fatal Signal 11 (SIGSEGV) received

Dan September 18, 2022 02:27PM