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September 13, 2018 06:45PM
Hi,

One of our users is getting a SIGSEGV when running 3dttest++ and using images as covariates. See usage and crashlog below. Let us know if see that we're doing something improper or if you would like data in order to reproduce it on your own.

Thanks!

Shane Kippenhan

*********------ CRASH LOG ------------------------------***********
Fatal Signal 11 (SIGSEGV) received
.......... recent internal history .........................................
-----THD_load_datablock [5]: EXIT} (file=thd_loaddblk.c line=150) to THD_extract_many_arrays
----THD_extract_many_arrays [4]: EXIT} (file=thd_dsetto1D.c line=638) to THD_dset_to_vectim
THD_dset_to_vectim -- setting parameters in vectim header
THD_dset_to_vectim -- VECTIM_scan()
---THD_dset_to_vectim [3]: EXIT} (file=thd_dset_to_vectim.c line=117) to 3dttest++ main
+++THD_dset_to_vectim [3]: {ENTRY (file=thd_dset_to_vectim.c line=26) from 3dttest++ main
++++THD_load_datablock [4]: {ENTRY (file=thd_loaddblk.c line=133) from THD_dset_to_vectim
+++++THD_load_nifti [5]: {ENTRY (file=thd_niftiread.c line=774) from THD_load_datablock
THD_load_nifti -- purging existing data bricks (if any)
++++++THD_purge_datablock [6]: {ENTRY (file=thd_purgedblk.c line=15) from THD_load_nifti
THD_purge_datablock -- MEM_MALLOC: clearing sub-bricks
+++++++mri_killpurge [7]: {ENTRY (file=mri_purger.c line=259) from THD_purge_datablock
mri_killpurge -- check if im==NULL ptr=0x2927fa8 OK
mri_killpurge -- can't killpurge NULL fname!
-------mri_killpurge [7]: EXIT} (file=mri_purger.c line=270) to THD_purge_datablock
------THD_purge_datablock [6]: EXIT} (file=thd_purgedblk.c line=39) to THD_load_nifti
THD_load_nifti -- calling nifti_image_read_bricks
THD_load_nifti -- copying brick pointers directly
THD_load_nifti -- doing floatscan
THD_load_nifti -- free-ing NBL
-----THD_load_nifti [5]: EXIT} (file=thd_niftiread.c line=945) to THD_load_datablock
----THD_load_datablock [4]: EXIT} (file=thd_loaddblk.c line=276) to THD_dset_to_vectim
THD_dset_to_vectim -- create index list
THD_dset_to_vectim -- ignore==0 --> extracting all at once
++++THD_extract_many_arrays [4]: {ENTRY (file=thd_dsetto1D.c line=551) from THD_dset_to_vectim
+++++THD_load_datablock [5]: {ENTRY (file=thd_loaddblk.c line=133) from THD_extract_many_arrays
-----THD_load_datablock [5]: EXIT} (file=thd_loaddblk.c line=150) to THD_extract_many_arrays
----THD_extract_many_arrays [4]: EXIT} (file=thd_dsetto1D.c line=638) to THD_dset_to_vectim
THD_dset_to_vectim -- setting parameters in vectim header
THD_dset_to_vectim -- VECTIM_scan()
---THD_dset_to_vectim [3]: EXIT} (file=thd_dset_to_vectim.c line=117) to 3dttest++ main
............................................................................
** Command line was:
3dttest++ -setA ALL SCAN_0001 VOL001.nii SCAN_0002 VOL002.nii SCAN_0003 VOL003.nii SCAN_0004 VOL004.nii -mask MASK.nii -covariates afni_dummy.cov -prefix RESULT_dummy
............................................................................
3dttest++ main
** Command line was:
3dttest++ -setA ALL SCAN_0001 VOL001.nii SCAN_0002 VOL002.nii SCAN_0003 VOL003.nii SCAN_0004 VOL004.nii -mask MASK.nii -covariates afni_dummy.cov -prefix RESULT_dummy
** AFNI compile date = Sep 12 2018
** [[Precompiled binary linux_ubuntu_16_64: Sep 12 2018]]
** Program Crash **

cat afni_dummy.cov

subject dsetcov ncov
SCAN_0001 VOL005.nii[0] 1
SCAN_0002 VOL006.nii[0] 2
SCAN_0003 VOL007.nii[0] 3
SCAN_0004 VOL008.nii[0] 4
Subject Author Posted

3dttest++ SEGV

shane.kippenhan September 13, 2018 06:45PM

Re: 3dttest++ SEGV

rick reynolds September 21, 2018 10:13AM



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