Hey,

I'm trying to run an analysis script resulting from an afni_proc invocation (see below) but cat_matvec is crashing. Any idea what could be causing this problem?
I'm happy to upload the offending files if it would help.

This is using afni version Precompiled binary linux_openmp_64: Apr 12 2017 (Version AFNI_17.1.01).

afni_proc.py -subj_id CMIT_01A						\
             -script ${preprocessingScript}					\
	     -out_dir ${outputDir}						\
	     -blocks despike tshift align tlrc volreg blur mask	regress		\
	     -copy_anat /data/jain/preApril/CMIT_01A/MPRAGE.nii	      					\
	     -dsets /data/jain/preApril/CMIT_01A/NT.nii  							\
	     -tcat_remove_first_trs 3						\
	     -tlrc_base MNI_caez_N27+tlrc					\
	     -volreg_align_to MIN_OUTLIER					\
	     -volreg_tlrc_warp  -tlrc_NL_warp \
             -tlrc_NL_warped_dsets /data/jain/preApril/CMIT_01A/afniGriefPreprocessed.NL/MPRAGE_al_keep+tlrc.HEAD \
                                   /data/jain/preApril/CMIT_01A/afniGriefPreprocessed.NL/anat.un.aff.Xat.1D \
                                   /data/jain/preApril/CMIT_01A/afniGriefPreprocessed.NL/anat.un.aff.qw_WARP.nii.gz				\
	     -blur_size 8							\
	     -blur_to_fwhm							\
	     -blur_opts_B2FW "-ACF -rate 0.2 -temper"				\
	     -mask_apply group							\
	     -mask_segment_anat yes						\
	     -mask_segment_erode yes						\
	     -regress_anaticor							\
	     -regress_bandpass 0.01 0.1						\
	     -regress_apply_mot_types demean deriv				\
	     -regress_ROI WMe							\
             -regress_censor_motion $motionThreshold              		\
	     -regress_censor_outliers $outlierThreshold                 	\
	     -regress_run_clustsim no						\
	     -regress_est_blur_errts

cat_matvec crashes as follows:

cat_matvec -ONELINE anat.un.aff.qw_WARP.nii.gz anat.un.aff.Xat.1D MPRAGE_al_keep_mat.aff12.1D

Fatal Signal 11 (SIGSEGV) received
    mri_read_double_ascii
   THD_read_dvecmat
  cat_matvec
 Bottom of Debug Stack
** AFNI version = AFNI_17.1.01  Compile date = Apr 12 2017
** [[Precompiled binary linux_openmp_64: Apr 12 2017]]
** 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 /home/colmconn/.afni.crashlog

I've tried running the cat_matvec from the command line with an uncompressed version of anat.un.aff.qw_WARP.nii.gz. With the same results. The crash log from the run of cat_matvec with the uncompressed anat file is as follows:

*********------ CRASH LOG ------------------------------***********
Fatal Signal 11 (SIGSEGV) received
.......... recent internal history .........................................
++cat_matvec [2]: {ENTRY (file=cat_matvec.c line=150) from Bottom of Debug Stack
+++AFNI_process_environ [3]: {ENTRY (file=afni_environ.c line=112) from cat_matvec
++++AFNI_suck_file [4]: {ENTRY (file=afni_environ.c line=25) from AFNI_process_environ
----AFNI_suck_file [4]: EXIT} (file=afni_environ.c line=30) to AFNI_process_environ
---AFNI_process_environ [3]: EXIT} (file=afni_environ.c line=132) to cat_matvec
+++AFNI_process_environ [3]: {ENTRY (file=afni_environ.c line=112) from cat_matvec
++++AFNI_suck_file [4]: {ENTRY (file=afni_environ.c line=25) from AFNI_process_environ
----AFNI_suck_file [4]: EXIT} (file=afni_environ.c line=30) to AFNI_process_environ
---AFNI_process_environ [3]: EXIT} (file=afni_environ.c line=132) to cat_matvec
+++AFNI_process_environ [3]: {ENTRY (file=afni_environ.c line=112) from cat_matvec
++++AFNI_suck_file [4]: {ENTRY (file=afni_environ.c line=25) from AFNI_process_environ
----AFNI_suck_file [4]: EXIT} (file=afni_environ.c line=30) to AFNI_process_environ
---AFNI_process_environ [3]: EXIT} (file=afni_environ.c line=132) to cat_matvec
+++THD_read_dvecmat [3]: {ENTRY (file=thd_read_vecmat.c line=16) from cat_matvec
++++mri_read_double_ascii [4]: {ENTRY (file=mri_read.c line=2663) from THD_read_dvecmat
+++++AFNI_process_environ [5]: {ENTRY (file=afni_environ.c line=112) from mri_read_double_ascii
++++++AFNI_suck_file [6]: {ENTRY (file=afni_environ.c line=25) from AFNI_process_environ
------AFNI_suck_file [6]: EXIT} (file=afni_environ.c line=30) to AFNI_process_environ
-----AFNI_process_environ [5]: EXIT} (file=afni_environ.c line=132) to mri_read_double_ascii
............................................................................
    mri_read_double_ascii
   THD_read_dvecmat
  cat_matvec
** AFNI compile date = Apr 12 2017
** [[Precompiled binary linux_openmp_64: Apr 12 2017]]
** Program Crash **

Edited 1 time(s). Last edit at 04/25/2017 02:19PM by Colm Connolly.