@SSWarper Fatal Signal 11 (SIGSEGV) error

I am trying to run @SSWarper, and for several of my datasets, I get this error. Temporary (junk) files are not written, so the script ultimately fails. I have changed my AFNI_NOMMAP to YES in an attempt to save memory for writing the temporary files, but no luck. See below for the error message and crash log. Any advice?

Command:

Align_Centers first because the original anat does not overlap with the template at all

@Align_Centers -no_cp -base MNI152_2009_template_SSW.nii.gz -dset $anat

@SSwarper
-input $anat
-base MNI152_2009_template_SSW.nii.gz
-subid {$subj}
-odir {$ssdir}
-unifize_off
-verb

Error:


Fatal Signal 11 (SIGSEGV) received
IW3D_setup_for_improvement
IW3D_warpomatic
IW3D_warp_s2bim
3dQwarp
Bottom of Debug Stack
** AFNI version = AFNI_20.0.18 Compile date = Feb 26 2020
** [[Precompiled binary macos_10.12_local: Feb 26 2020]]
** 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/rchambers/.afni.crashlog

------ CRASH LOG ------------------------------**
Fatal Signal 11 (SIGSEGV) received
… recent internal history …
+++++++mri_free [7]: {ENTRY (file=mri_free.c line=49) from IW3D_cleanup_improvement {7103 ms}
-------mri_free [7]: EXIT} (file=mri_free.c line=50) to IW3D_cleanup_improvement {7103 ms}
+++++++mri_free [7]: {ENTRY (file=mri_free.c line=49) from IW3D_cleanup_improvement {7103 ms}
-------mri_free [7]: EXIT} (file=mri_free.c line=50) to IW3D_cleanup_improvement {7103 ms}
+++++++mri_free [7]: {ENTRY (file=mri_free.c line=49) from IW3D_cleanup_improvement {7103 ms}
-------mri_free [7]: EXIT} (file=mri_free.c line=50) to IW3D_cleanup_improvement {7103 ms}
+++++++IW3D_destroy [7]: {ENTRY (file=mri_nwarp.c line=935) from IW3D_cleanup_improvement {7103 ms}
-------IW3D_destroy [7]: EXIT} (file=mri_nwarp.c line=942) to IW3D_cleanup_improvement {7103 ms}
+++++++IW3D_destroy [7]: {ENTRY (file=mri_nwarp.c line=935) from IW3D_cleanup_improvement {7103 ms}
-------IW3D_destroy [7]: EXIT} (file=mri_nwarp.c line=942) to IW3D_cleanup_improvement {7103 ms}
+++++++IW3D_destroy [7]: {ENTRY (file=mri_nwarp.c line=935) from IW3D_cleanup_improvement {7103 ms}
-------IW3D_destroy [7]: EXIT} (file=mri_nwarp.c line=942) to IW3D_cleanup_improvement {7103 ms}
+++++++INCOR_destroy [7]: {ENTRY (file=thd_incorrelate.c line=1865) from IW3D_cleanup_improvement {7103 ms}
-------INCOR_destroy [7]: EXIT} (file=thd_incorrelate.c line=1867) to IW3D_cleanup_improvement {7103 ms}
------IW3D_cleanup_improvement [6]: EXIT} (file=mri_nwarp.c line=10216) to IW3D_setup_for_improvement {7103 ms}
++++++mri_to_float [6]: {ENTRY (file=mri_to_float.c line=19) from IW3D_setup_for_improvement {7103 ms}
+++++++mri_new_7D_generic [7]: {ENTRY (file=mri_new.c line=48) from mri_to_float {7103 ms}
-------mri_new_7D_generic [7]: EXIT} (file=mri_new.c line=143) to mri_to_float {7110 ms}
+++++++mri_add_name [7]: {ENTRY (file=mri_add_name.c line=19) from mri_to_float {7121 ms}
-------mri_add_name [7]: EXIT} (file=mri_add_name.c line=24) to mri_to_float {7121 ms}
------mri_to_float [6]: EXIT} (file=mri_to_float.c line=94) to IW3D_setup_for_improvement {7137 ms}
++++++mri_to_float [6]: {ENTRY (file=mri_to_float.c line=19) from IW3D_setup_for_improvement {7137 ms}
+++++++mri_new_7D_generic [7]: {ENTRY (file=mri_new.c line=48) from mri_to_float {7137 ms}
-------mri_new_7D_generic [7]: EXIT} (file=mri_new.c line=143) to mri_to_float {7144 ms}
+++++++mri_add_name [7]: {ENTRY (file=mri_add_name.c line=19) from mri_to_float {7160 ms}
-------mri_add_name [7]: EXIT} (file=mri_add_name.c line=24) to mri_to_float {7160 ms}
------mri_to_float [6]: EXIT} (file=mri_to_float.c line=94) to IW3D_setup_for_improvement {7178 ms}
++++++mri_maxabs [6]: {ENTRY (file=mri_max.c line=98) from IW3D_setup_for_improvement {7178 ms}
------mri_maxabs [6]: EXIT} (file=mri_max.c line=129) to IW3D_setup_for_improvement {7191 ms}
++++++mri_new_7D_generic [6]: {ENTRY (file=mri_new.c line=48) from IW3D_setup_for_improvement {7191 ms}
------mri_new_7D_generic [6]: EXIT} (file=mri_new.c line=143) to IW3D_setup_for_improvement {7198 ms}

IW3D_setup_for_improvement
IW3D_warpomatic
IW3D_warp_s2bim
3dQwarp
** AFNI compile date = Feb 26 2020
** [[Precompiled binary macos_10.12_local: Feb 26 2020]]
** Program Crash **

Hi Rebecca,

Do you have the text output from that command saved in a file? If so, what is shown when grepping for warpomatic, as in:

grep "AFNI warpomatic" output.sswarper.txt

Thanks,

  • rick

grep “AFNI warpomatic” output.proc.ss.warper_newbatch4_20200306_4
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 21…200 26…238 21…195 [clock= 16m 58s 858ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 23s 668ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 24s 52ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 24s 756ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 24s 280ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 21…200 26…238 21…195 [clock= 17m 56s 313ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 21…200 26…238 21…195 [clock= 16m 42s 481ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 23s 276ms]
++ AFNI warpomatic: 224 x 264 x 219 volume ; autobbox = 22…201 26…238 22…196 [clock= 16m 32s 433ms]
++ AFNI warpomatic: 224 x 264 x 219 volume ; autobbox = 35…189 33…223 17…180 [clock= 26s 8ms]
++ AFNI warpomatic: 224 x 264 x 219 volume ; autobbox = 35…189 33…223 17…180 [clock= 24s 336ms]
++ AFNI warpomatic: 224 x 264 x 219 volume ; autobbox = 22…201 26…238 22…196 [clock= 16m 31s 532ms]
++ AFNI warpomatic: 224 x 264 x 219 volume ; autobbox = 35…189 33…223 17…180 [clock= 25s 333ms]
++ AFNI warpomatic: 224 x 264 x 219 volume ; autobbox = 35…189 33…223 17…180 [clock= 25s 937ms]
++ AFNI warpomatic: 224 x 264 x 219 volume ; autobbox = 35…189 33…223 17…180 [clock= 25s 720ms]
++ AFNI warpomatic: 224 x 264 x 219 volume ; autobbox = 35…189 33…223 17…180 [clock= 27s 203ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 21…200 26…238 21…195 [clock= 16m 28s 328ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 22s 895ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 21…200 26…238 21…195 [clock= 17m 10s 209ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 24s 755ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 25s 102ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 25s 77ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 25s 100ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 21…200 26…238 21…195 [clock= 16m 9s 117ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 25s 96ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 24s 447ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 24s 581ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 24s 496ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 21…200 26…238 21…195 [clock= 15m 35s 70ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 25s 300ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 25s 787ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 21…200 26…238 21…195 [clock= 17m 31s 409ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 26s 960ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 27s 496ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 30s 427ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 28s 905ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 21…200 26…238 21…195 [clock= 17m 42s 968ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 26s 188ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 24s 539ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 26s 257ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 27s 933ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 21…200 26…238 21…195 [clock= 17m 43s 837ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 26s 503ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 26s 889ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 26s 819ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 26s 752ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 21…200 26…238 21…195 [clock= 18m 9s 498ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 25s 696ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 26s 350ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 26s 515ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 26s 220ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 21…200 26…238 21…195 [clock= 18m 7s 283ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 26s 669ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 25s 884ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 27s 53ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 26s 823ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 21…200 26…238 21…195 [clock= 18m 4s 793ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 21…200 26…238 21…195 [clock= 15m 20s 59ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 30s 752ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 21…200 26…238 21…195 [clock= 18m 22s 148ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 26s 246ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 25s 610ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 21…200 26…238 21…195 [clock= 18m 28s 420ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 25s 871ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 26s 161ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 27s 104ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 26s 530ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 21…200 26…238 21…195 [clock= 18m 3s 921ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 26s 718ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 26s 899ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 27s 359ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 27s 485ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 21…200 26…238 21…195 [clock= 18m 6s 732ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 26s 147ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 21…200 26…238 21…195 [clock= 18m 18s 885ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 21…200 26…238 21…195 [clock= 18m 10s 211ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 21…200 26…238 21…195 [clock= 18m 19s 823ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 26s 599ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 26s 678ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 21…200 26…238 21…195 [clock= 18m 35s 725ms]
++ AFNI warpomatic: 226 x 264 x 221 volume ; autobbox = 23…202 26…238 23…197 [clock= 18m 26s 353ms]
++ AFNI warpomatic: 226 x 264 x 221 volume ; autobbox = 36…190 33…223 18…181 [clock= 27s 280ms]
++ AFNI warpomatic: 226 x 264 x 221 volume ; autobbox = 36…190 33…223 18…181 [clock= 27s 208ms]
++ AFNI warpomatic: 226 x 264 x 221 volume ; autobbox = 36…190 33…223 18…181 [clock= 27s 607ms]
++ AFNI warpomatic: 226 x 264 x 221 volume ; autobbox = 36…190 33…223 18…181 [clock= 27s 218ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 21…200 26…238 21…195 [clock= 18m 36s 137ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 26s 924ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 27s 391ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 27s 442ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 27s 835ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 21…200 26…238 21…195 [clock= 18m 47s 414ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 27s 890ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 29s 491ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 28s 536ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 27s 922ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 21…200 26…238 21…195 [clock= 14m 58s 459ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 26s 38ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 21…200 26…238 21…195 [clock= 20m 56s 995ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 26s 267ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 27s 703ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 26s 622ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 26s 173ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 21…200 26…238 21…195 [clock= 18m 14s 166ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 29s 765ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 30s 176ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 30s 20ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 32s 149ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 21…200 26…238 21…195 [clock= 18m 12s 503ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 30s 79ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 30s 637ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 30s 444ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 31s 709ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 21…200 26…238 21…195 [clock= 15m 16s 577ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 27s 718ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 21…200 26…238 21…195 [clock= 18m 0s 755ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 27s 148ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 27s 470ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 28s 51ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 27s 639ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 21…200 26…238 21…195 [clock= 17m 43s 577ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 26s 750ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 27s 70ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 27s 574ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 26s 33ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 21…200 26…238 21…195 [clock= 18m 33s 758ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 29s 132ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 21…200 26…238 21…195 [clock= 18m 8s 489ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 21…200 26…238 21…195 [clock= 17m 48s 541ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 27s 385ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 26s 422ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 25s 634ms]
++ AFNI warpomatic: 222 x 264 x 217 volume ; autobbox = 34…188 33…223 16…179 [clock= 26s 675ms]