Hello! I think I have read all of the threads on this topic but am still stumped as to what exactly is going on and how to resolve it. Generally it seems like when people have posted about this issue the solution has been to update the OS, update AFNI, or update the version of align_epi_anat.py. But I don't think those solutions would apply in this case.

Here is how I am calling aligh_epi_anat.py:

align_epi_anat.py
-epi deoblw_pb06.shellgame_26.r02.Cd3MP+orig
-anat shellgame_26.BrainExtractionBrain.nii.gz
-volreg on
-tshift off
-epi_base mean
-anat_has_skull no
-ginormous_move

And it gives me the error below. Oddly, if I use a different epi it works just fine. There is nothing I can find that is wrong with the EPI file. And this holds true for every subject.

#++ align_epi_anat version: 1.58
#++ turning on volume registration
#Script is running (command trimmed):
3dAttribute DELTA ./shellgame_26/shellgame_26.results/deoblw_pb06.shellgame_26.r02.Cd3MP+orig
#Script is running (command trimmed):
3dAttribute DELTA ./shellgame_26/shellgame_26.results/deoblw_pb06.shellgame_26.r02.Cd3MP+orig
#Script is running (command trimmed):
3dAttribute DELTA ./shellgame_26/shellgame_26.BrainExtractionBrain.nii.gz
#++ Multi-cost is lpc
#++ Removing all the temporary files
#Script is running:
\rm -f ./__tt_deoblw_pb06.shellgame_26.r02.Cd3MP*
#Script is running:
\rm -f ./__tt_shellgame_26.BrainExtractionBrain*
#Script is running (command trimmed):
3dcopy ./shellgame_26/shellgame_26.BrainExtractionBrain.nii.gz ./__tt_shellgame_26.BrainExtractionBrain+orig
++ 3dcopy: AFNI version=AFNI_18.3.05 (Nov 19 2018) [64-bit]
#Script is running (command trimmed):
3dinfo ./__tt_shellgame_26.BrainExtractionBrain+orig | \grep 'Data Axes Tilt:'|\grep 'Oblique'
#++ Dataset /net/rcss10/srv/export/ncf_mcl/share_root/02/shellgame/__tt_shellgame_26.BrainExtractionBrain+orig is not oblique
#Script is running (command trimmed):
3dinfo ./shellgame_26/shellgame_26.results/deoblw_pb06.shellgame_26.r02.Cd3MP+orig | \grep 'Data Axes Tilt:'|\grep 'Oblique'
#++ Dataset /net/rcss10/srv/export/ncf_mcl/share_root/02/shellgame/shellgame_26/shellgame_26.results/deoblw_pb06.shellgame_26.r02.Cd3MP+orig is not oblique
#Script is running (command trimmed):
3dAttribute DELTA ./__tt_shellgame_26.BrainExtractionBrain+orig
#++ Spacing for anat to oblique epi alignment is 1.000000
#Script is running (command trimmed):
3dcopy ./__tt_shellgame_26.BrainExtractionBrain+orig ./__tt_shellgame_26.BrainExtractionBrain_ob; @Align_Centers -base ./shellgame_26/shellgame_26.results/deoblw_pb06.shellgame_26.r02.Cd3MP+orig -dset ./__tt_shellgame_26.BrainExtractionBrain_ob+orig -no_cp
++ 3dcopy: AFNI version=AFNI_18.3.05 (Nov 19 2018) [64-bit]
++ 3drefit: AFNI version=AFNI_18.3.05 (Nov 19 2018) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset ./__tt_shellgame_26.BrainExtractionBrain_ob+orig
+ deoblique
++ 3drefit processed 1 datasets
#Script is running (command trimmed):
cat_matvec ./__tt_shellgame_26.BrainExtractionBrain_ob_shft.1D -I > ./__tt_shellgame_26.BrainExtractionBrain_shft_I.1D
#++ Volume registration for epi data
#Script is running (command trimmed):
3dTstat -mean -prefix ./shellgame_26/shellgame_26.results/__tt_deoblw_pb06.shellgame_26.r02.Cd3MP_vr_ts_tempalpha ./shellgame_26/shellgame_26.results/deoblw_pb06.shellgame_26.r02.Cd3MP+orig
++ 3dTstat: AFNI version=AFNI_18.3.05 (Nov 19 2018) [64-bit]
++ Authored by: KR Hammett & RW Cox
++ Output dataset ./shellgame_26/shellgame_26.results/__tt_deoblw_pb06.shellgame_26.r02.Cd3MP_vr_ts_tempalpha+orig.BRIK
#Script is running (command trimmed):
3dvolreg -prefix ./shellgame_26/shellgame_26.results/__tt_deoblw_pb06.shellgame_26.r02.Cd3MP_vr_vr_tempalpha -base ./shellgame_26/shellgame_26.results/__tt_deoblw_pb06.shellgame_26.r02.Cd3MP_vr_ts_tempalpha+orig'[0]' -cubic ./shellgame_26/shellgame_26.results/deoblw_pb06.shellgame_26.r02.Cd3MP+orig
++ 3dvolreg: AFNI version=AFNI_18.3.05 (Nov 19 2018) [64-bit]
++ Authored by: RW Cox
++ Max displacement in automask = 50.11 (mm) at sub-brick 156
++ Max delta displ in automask = 74.33 (mm) at sub-brick 136
#Script is running (command trimmed):
3dTstat -mean -prefix ./shellgame_26/shellgame_26.results/__tt_deoblw_pb06.shellgame_26.r02.Cd3MP_vr_vrt ./shellgame_26/shellgame_26.results/__tt_deoblw_pb06.shellgame_26.r02.Cd3MP_vr_vr_tempalpha+orig
++ 3dTstat: AFNI version=AFNI_18.3.05 (Nov 19 2018) [64-bit]
++ Authored by: KR Hammett & RW Cox
++ Output dataset ./shellgame_26/shellgame_26.results/__tt_deoblw_pb06.shellgame_26.r02.Cd3MP_vr_vrt+orig.BRIK
#Script is running (command trimmed):
3dvolreg -1Dfile ./deoblw_pb06.shellgame_26.r02.Cd3MP_vr_motion.1D -1Dmatrix_save ./__tt_deoblw_pb06.shellgame_26.r02.Cd3MP_vr_mat.aff12.1D -prefix ./__tt_deoblw_pb06.shellgame_26.r02.Cd3MP_vr -base ./shellgame_26/shellgame_26.results/__tt_deoblw_pb06.shellgame_26.r02.Cd3MP_vr_vrt+orig'[0]' -cubic ./shellgame_26/shellgame_26.results/deoblw_pb06.shellgame_26.r02.Cd3MP+orig
++ 3dvolreg: AFNI version=AFNI_18.3.05 (Nov 19 2018) [64-bit]
++ Authored by: RW Cox
++ Max displacement in automask = 40.35 (mm) at sub-brick 150
++ Max delta displ in automask = 64.66 (mm) at sub-brick 85
#++ Creating representative epi sub-brick
#Script is running (command trimmed):
3dTstat -mean -prefix ./__tt_deoblw_pb06.shellgame_26.r02.Cd3MP_vr_ts ./__tt_deoblw_pb06.shellgame_26.r02.Cd3MP_vr+orig
++ 3dTstat: AFNI version=AFNI_18.3.05 (Nov 19 2018) [64-bit]
++ Authored by: KR Hammett & RW Cox
++ Output dataset ./__tt_deoblw_pb06.shellgame_26.r02.Cd3MP_vr_ts+orig.BRIK
#++ removing skull or area outside brain
#Script is running (command trimmed):
3dSkullStrip -orig_vol -input ./__tt_deoblw_pb06.shellgame_26.r02.Cd3MP_vr_ts+orig -prefix ./__tt_deoblw_pb06.shellgame_26.r02.Cd3MP_vr_ts_ns

Fatal Signal 11 (SIGSEGV) received
SUMA_SurfGridIntersect
SUMA_FindVoxelsInSurface
3dSkullStrip
Bottom of Debug Stack
** AFNI version = AFNI_18.3.05 Compile date = Nov 19 2018
** [[Precompiled binary linux_openmp_64: Nov 19 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.
** Memory usage: chunks=247 bytes=62234026
** Crash log is appended to file /users/bernhard/.afni.crashlog
** ERROR: Could not strip skull

** ERROR - script failed