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Rebecca Lepping
March 10, 2020 01:48PM
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 **



Edited 1 time(s). Last edit at 03/10/2020 02:12PM by Rebecca Lepping.
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Subject Author Posted

@SSWarper Fatal Signal 11 (SIGSEGV) error

Rebecca Lepping March 10, 2020 01:48PM

Re: @SSWarper Fatal Signal 11 (SIGSEGV) error

rick reynolds March 10, 2020 04:48PM

Re: @SSWarper Fatal Signal 11 (SIGSEGV) error

Rebecca Lepping March 10, 2020 06:04PM