When running @SSwarper, I am often getting errors with it, similar to this one I have pasted below. Oddly, it works for some of my subject data, but fails like this for others. I cannot attach my .afni.crashlog as it is not an image, but I have also pasted some of what it displays at the bottom of this.
Please let me know if you need more information.
Thanks!
+++ Command Echo:
3dQwarp -lite -base /Volumes/Research_Data/Rhoades_Projects/RestingStatefMRI/Masks_Templates/MNI152_2009_template_SSW.nii.gz[0] -source Sub_004_01_anat_warped/junk.SSwarper.WK3Ac5k8M1m_AffSS.nii -iniwarp Sub_004_01_anat_warped/junk.SSwarper.WK3Ac5k8M1m_QQ5_WARP.nii -warpscale 1 -pcl -inilev 6 -maxlev 7 -workhard:6:7 -wtgaus 4.5 -inedge -pblur -nodset -prefix Sub_004_01_anat_warped/junk.SSwarper.WK3Ac5k8M1m_QQ7.nii
++ 3dQwarp: AFNI version=AFNI_20.1.14 (Jun 10 2020) [64-bit]
++ Authored by: Zhark the (Hermite) Cubically Warped
++ Dataset zero-pad: xbot=15 xtop=14 ybot=13 ytop=22 zbot=15 ztop=9 voxels
++ Weightizing the base image: FWHM = 4.5 (vox)
++ +++++++++++ Begin warp optimization: base=/Volumes/Research_Data/Rhoades_Projects/RestingStatefMRI/Masks_Templates/MNI152_2009_template_SSW.nii.gz source=/Volumes/Research_Data/Rhoades_Projects/RestingStatefMRI/Raw_Data/Sub_004/Sub_004_01_anat_warped/junk.SSwarper.WK3Ac5k8M1m_AffSS.nii
Fatal Signal 11 (SIGSEGV) received
IW3D_setup_for_improvement
IW3D_warpomatic
IW3D_warp_s2bim
3dQwarp
Bottom of Debug Stack
** AFNI version = AFNI_20.1.14 Compile date = Jun 10 2020
** [[Precompiled binary macos_10.12_local: Jun 10 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/tlab/.afni.crashlog
++ SSW Step 6 ... piece 3a
Here is some of the .afni.crashlog (I was running a foreach loop so I have several errors that are similar, but they are not all the same either):
*********------ CRASH LOG ------------------------------***********
Fatal Signal 11 (SIGSEGV) received
.......... recent internal history .........................................
+++++++mri_free [7]: {ENTRY (file=mri_free.c line=49) from IW3D_cleanup_improvement {765040 ms}
-------mri_free [7]: EXIT} (file=mri_free.c line=50) to IW3D_cleanup_improvement {765040 ms}
+++++++mri_free [7]: {ENTRY (file=mri_free.c line=49) from IW3D_cleanup_improvement {765040 ms}
-------mri_free [7]: EXIT} (file=mri_free.c line=50) to IW3D_cleanup_improvement {765040 ms}
+++++++mri_free [7]: {ENTRY (file=mri_free.c line=49) from IW3D_cleanup_improvement {765040 ms}
-------mri_free [7]: EXIT} (file=mri_free.c line=50) to IW3D_cleanup_improvement {765040 ms}
+++++++IW3D_destroy [7]: {ENTRY (file=mri_nwarp.c line=935) from IW3D_cleanup_improvement {765040 ms}
-------IW3D_destroy [7]: EXIT} (file=mri_nwarp.c line=942) to IW3D_cleanup_improvement {765040 ms}
+++++++IW3D_destroy [7]: {ENTRY (file=mri_nwarp.c line=935) from IW3D_cleanup_improvement {765040 ms}
-------IW3D_destroy [7]: EXIT} (file=mri_nwarp.c line=942) to IW3D_cleanup_improvement {765040 ms}
+++++++IW3D_destroy [7]: {ENTRY (file=mri_nwarp.c line=935) from IW3D_cleanup_improvement {765040 ms}
-------IW3D_destroy [7]: EXIT} (file=mri_nwarp.c line=942) to IW3D_cleanup_improvement {765040 ms}
+++++++INCOR_destroy [7]: {ENTRY (file=thd_incorrelate.c line=1865) from IW3D_cleanup_improvement {765040 ms}
-------INCOR_destroy [7]: EXIT} (file=thd_incorrelate.c line=1867) to IW3D_cleanup_improvement {765040 ms}
------IW3D_cleanup_improvement [6]: EXIT} (file=mri_nwarp.c line=10220) to IW3D_setup_for_improvement {765040 ms}
++++++mri_to_float [6]: {ENTRY (file=mri_to_float.c line=19) from IW3D_setup_for_improvement {765040 ms}
+++++++mri_new_7D_generic [7]: {ENTRY (file=mri_new.c line=48) from mri_to_float {765040 ms}
-------mri_new_7D_generic [7]: EXIT} (file=mri_new.c line=143) to mri_to_float {765040 ms}
+++++++mri_add_name [7]: {ENTRY (file=mri_add_name.c line=19) from mri_to_float {765065 ms}
-------mri_add_name [7]: EXIT} (file=mri_add_name.c line=24) to mri_to_float {765065 ms}
------mri_to_float [6]: EXIT} (file=mri_to_float.c line=94) to IW3D_setup_for_improvement {765075 ms}
++++++mri_to_float [6]: {ENTRY (file=mri_to_float.c line=19) from IW3D_setup_for_improvement {765075 ms}
+++++++mri_new_7D_generic [7]: {ENTRY (file=mri_new.c line=48) from mri_to_float {765075 ms}
-------mri_new_7D_generic [7]: EXIT} (file=mri_new.c line=143) to mri_to_float {765075 ms}
+++++++mri_add_name [7]: {ENTRY (file=mri_add_name.c line=19) from mri_to_float {765100 ms}
-------mri_add_name [7]: EXIT} (file=mri_add_name.c line=24) to mri_to_float {765100 ms}
------mri_to_float [6]: EXIT} (file=mri_to_float.c line=94) to IW3D_setup_for_improvement {765110 ms}
++++++mri_maxabs [6]: {ENTRY (file=mri_max.c line=98) from IW3D_setup_for_improvement {765110 ms}
------mri_maxabs [6]: EXIT} (file=mri_max.c line=129) to IW3D_setup_for_improvement {765122 ms}
++++++mri_new_7D_generic [6]: {ENTRY (file=mri_new.c line=48) from IW3D_setup_for_improvement {765122 ms}
------mri_new_7D_generic [6]: EXIT} (file=mri_new.c line=143) to IW3D_setup_for_improvement {765122 ms}
............................................................................
IW3D_setup_for_improvement
IW3D_warpomatic
IW3D_warp_s2bim
3dQwarp
** AFNI compile date = Jun 10 2020
** [[Precompiled binary macos_10.12_local: Jun 10 2020]]
** Program Crash **
*********------ CRASH LOG ------------------------------***********
Fatal Signal 11 (SIGSEGV) received
.......... recent internal history .........................................
+++++++mri_free [7]: {ENTRY (file=mri_free.c line=49) from IW3D_cleanup_improvement {2290 ms}
-------mri_free [7]: EXIT} (file=mri_free.c line=50) to IW3D_cleanup_improvement {2290 ms}
+++++++mri_free [7]: {ENTRY (file=mri_free.c line=49) from IW3D_cleanup_improvement {2290 ms}
-------mri_free [7]: EXIT} (file=mri_free.c line=50) to IW3D_cleanup_improvement {2290 ms}
+++++++mri_free [7]: {ENTRY (file=mri_free.c line=49) from IW3D_cleanup_improvement {2290 ms}
-------mri_free [7]: EXIT} (file=mri_free.c line=50) to IW3D_cleanup_improvement {2290 ms}
+++++++IW3D_destroy [7]: {ENTRY (file=mri_nwarp.c line=935) from IW3D_cleanup_improvement {2290 ms}
-------IW3D_destroy [7]: EXIT} (file=mri_nwarp.c line=942) to IW3D_cleanup_improvement {2290 ms}
+++++++IW3D_destroy [7]: {ENTRY (file=mri_nwarp.c line=935) from IW3D_cleanup_improvement {2290 ms}
-------IW3D_destroy [7]: EXIT} (file=mri_nwarp.c line=942) to IW3D_cleanup_improvement {2290 ms}
+++++++IW3D_destroy [7]: {ENTRY (file=mri_nwarp.c line=935) from IW3D_cleanup_improvement {2290 ms}
-------IW3D_destroy [7]: EXIT} (file=mri_nwarp.c line=942) to IW3D_cleanup_improvement {2290 ms}
+++++++INCOR_destroy [7]: {ENTRY (file=thd_incorrelate.c line=1865) from IW3D_cleanup_improvement {2290 ms}
-------INCOR_destroy [7]: EXIT} (file=thd_incorrelate.c line=1867) to IW3D_cleanup_improvement {2291 ms}
------IW3D_cleanup_improvement [6]: EXIT} (file=mri_nwarp.c line=10220) to IW3D_setup_for_improvement {2291 ms}
++++++mri_to_float [6]: {ENTRY (file=mri_to_float.c line=19) from IW3D_setup_for_improvement {2291 ms}
+++++++mri_new_7D_generic [7]: {ENTRY (file=mri_new.c line=48) from mri_to_float {2291 ms}
-------mri_new_7D_generic [7]: EXIT} (file=mri_new.c line=143) to mri_to_float {2295 ms}
+++++++mri_add_name [7]: {ENTRY (file=mri_add_name.c line=19) from mri_to_float {2301 ms}
-------mri_add_name [7]: EXIT} (file=mri_add_name.c line=24) to mri_to_float {2301 ms}
------mri_to_float [6]: EXIT} (file=mri_to_float.c line=94) to IW3D_setup_for_improvement {2311 ms}
++++++mri_to_float [6]: {ENTRY (file=mri_to_float.c line=19) from IW3D_setup_for_improvement {2311 ms}
+++++++mri_new_7D_generic [7]: {ENTRY (file=mri_new.c line=48) from mri_to_float {2311 ms}
-------mri_new_7D_generic [7]: EXIT} (file=mri_new.c line=143) to mri_to_float {2315 ms}
+++++++mri_add_name [7]: {ENTRY (file=mri_add_name.c line=19) from mri_to_float {2325 ms}
-------mri_add_name [7]: EXIT} (file=mri_add_name.c line=24) to mri_to_float {2325 ms}
------mri_to_float [6]: EXIT} (file=mri_to_float.c line=94) to IW3D_setup_for_improvement {2334 ms}
++++++mri_maxabs [6]: {ENTRY (file=mri_max.c line=98) from IW3D_setup_for_improvement {2334 ms}
------mri_maxabs [6]: EXIT} (file=mri_max.c line=129) to IW3D_setup_for_improvement {2346 ms}
++++++mri_new_7D_generic [6]: {ENTRY (file=mri_new.c line=48) from IW3D_setup_for_improvement {2346 ms}
------mri_new_7D_generic [6]: EXIT} (file=mri_new.c line=143) to IW3D_setup_for_improvement {2351 ms}
............................................................................
IW3D_setup_for_improvement
IW3D_warpomatic
IW3D_warp_s2bim
3dQwarp
** AFNI compile date = Jun 10 2020
** [[Precompiled binary macos_10.12_local: Jun 10 2020]]
** Program Crash **
*********------ CRASH LOG ------------------------------***********
Fatal Signal 11 (SIGSEGV) received
.......... recent internal history .........................................
+++++++mri_free [7]: {ENTRY (file=mri_free.c line=49) from IW3D_cleanup_improvement {2575 ms}
-------mri_free [7]: EXIT} (file=mri_free.c line=50) to IW3D_cleanup_improvement {2575 ms}
+++++++mri_free [7]: {ENTRY (file=mri_free.c line=49) from IW3D_cleanup_improvement {2575 ms}
-------mri_free [7]: EXIT} (file=mri_free.c line=50) to IW3D_cleanup_improvement {2575 ms}
+++++++mri_free [7]: {ENTRY (file=mri_free.c line=49) from IW3D_cleanup_improvement {2575 ms}
-------mri_free [7]: EXIT} (file=mri_free.c line=50) to IW3D_cleanup_improvement {2575 ms}
+++++++IW3D_destroy [7]: {ENTRY (file=mri_nwarp.c line=935) from IW3D_cleanup_improvement {2575 ms}
-------IW3D_destroy [7]: EXIT} (file=mri_nwarp.c line=942) to IW3D_cleanup_improvement {2575 ms}
+++++++IW3D_destroy [7]: {ENTRY (file=mri_nwarp.c line=935) from IW3D_cleanup_improvement {2575 ms}
-------IW3D_destroy [7]: EXIT} (file=mri_nwarp.c line=942) to IW3D_cleanup_improvement {2575 ms}
+++++++IW3D_destroy [7]: {ENTRY (file=mri_nwarp.c line=935) from IW3D_cleanup_improvement {2575 ms}
-------IW3D_destroy [7]: EXIT} (file=mri_nwarp.c line=942) to IW3D_cleanup_improvement {2575 ms}
+++++++INCOR_destroy [7]: {ENTRY (file=thd_incorrelate.c line=1865) from IW3D_cleanup_improvement {2575 ms}
-------INCOR_destroy [7]: EXIT} (file=thd_incorrelate.c line=1867) to IW3D_cleanup_improvement {2575 ms}
------IW3D_cleanup_improvement [6]: EXIT} (file=mri_nwarp.c line=10220) to IW3D_setup_for_improvement {2575 ms}
++++++mri_to_float [6]: {ENTRY (file=mri_to_float.c line=19) from IW3D_setup_for_improvement {2575 ms}
+++++++mri_new_7D_generic [7]: {ENTRY (file=mri_new.c line=48) from mri_to_float {2575 ms}
-------mri_new_7D_generic [7]: EXIT} (file=mri_new.c line=143) to mri_to_float {2579 ms}
+++++++mri_add_name [7]: {ENTRY (file=mri_add_name.c line=19) from mri_to_float {2586 ms}
-------mri_add_name [7]: EXIT} (file=mri_add_name.c line=24) to mri_to_float {2586 ms}
------mri_to_float [6]: EXIT} (file=mri_to_float.c line=94) to IW3D_setup_for_improvement {2595 ms}
++++++mri_to_float [6]: {ENTRY (file=mri_to_float.c line=19) from IW3D_setup_for_improvement {2595 ms}
+++++++mri_new_7D_generic [7]: {ENTRY (file=mri_new.c line=48) from mri_to_float {2595 ms}
-------mri_new_7D_generic [7]: EXIT} (file=mri_new.c line=143) to mri_to_float {2599 ms}
+++++++mri_add_name [7]: {ENTRY (file=mri_add_name.c line=19) from mri_to_float {2610 ms}
-------mri_add_name [7]: EXIT} (file=mri_add_name.c line=24) to mri_to_float {2610 ms}
------mri_to_float [6]: EXIT} (file=mri_to_float.c line=94) to IW3D_setup_for_improvement {2619 ms}
++++++mri_maxabs [6]: {ENTRY (file=mri_max.c line=98) from IW3D_setup_for_improvement {2619 ms}
------mri_maxabs [6]: EXIT} (file=mri_max.c line=129) to IW3D_setup_for_improvement {2632 ms}
++++++mri_new_7D_generic [6]: {ENTRY (file=mri_new.c line=48) from IW3D_setup_for_improvement {2632 ms}
------mri_new_7D_generic [6]: EXIT} (file=mri_new.c line=143) to IW3D_setup_for_improvement {2636 ms}
............................................................................
IW3D_setup_for_improvement
IW3D_warpomatic
IW3D_warp_s2bim
3dQwarp
** AFNI compile date = Jun 10 2020
** [[Precompiled binary macos_10.12_local: Jun 10 2020]]
** Program Crash **
