External Email - Use Caution
Hi,
I have ran the lGI flag many times in the past. However, now that I am trying to run the flag on a new group of participants I get the below error. Will you please tell me how I can fix this?
Thanks so much,
Avi
New invocation of recon-all
Fri Aug 30 16:47:49 EDT 2019 /d/mjt/9/users/avideh/data/recon/MR160-114-0370_01 /usr/local/freesurfer/bin/recon-all -s MR160-114-0370_01 -localGI -openmp 2 subjid MR160-114-0370_01 setenv SUBJECTS_DIR /d/mjt/9/users/avideh/data/recon FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux apollo.sickkids.ca 4.15.0-50-generic #54-Ubuntu SMP Mon May 6 18:46:08 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 16384 kbytes maxproc 321903 maxlocks unlimited maxsignal 321903 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited
total used free shared buff/cache available Mem: 82473464 18994140 26581924 374636 36897400 62364472 Swap: 8388604 1922560 6466044
######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:49-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:49-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:49-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/08/30-20:47:49-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:49-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:49-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/08/30-20:47:49-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $
ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $
ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2019/08/30-20:47:50-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: avideh Machine: apollo.sickkids.ca Platform: Linux PlatformVersion: 4.15.0-50-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /usr/local/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /d/mjt/9/users/avideh/data/recon/MR160-114-0370_01/surf #-------------------------------------------- #@# Local Gyrification Index lh Fri Aug 30 16:47:51 EDT 2019
mris_compute_lgi --i lh.pial
================= rm -Rf /d/mjt/9/users/avideh/data/recon/MR160-114-0370_01/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mkdir -p /d/mjt/9/users/avideh/data/recon/MR160-114-0370_01/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mris_fill -c -r 1 lh.pial /d/mjt/9/users/avideh/data/recon/MR160-114-0370_01/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz ================= reading surface from lh.pial... writing filled volume to /d/mjt/9/users/avideh/data/recon/MR160-114-0370_01/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz... conforming output volume setting resolution for intermediate calculations to 1.0000 ================= make_outer_surface('/d/mjt/9/users/avideh/data/recon/MR160-114-0370_01/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/d/mjt/9/users/avideh/data/recon/MR160-114-0370_01/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'); exit =================
< M A T L A B (R) > Copyright 1984-2019 The MathWorks, Inc. R2019a Update 4 (9.6.0.1150989) 64-bit (glnxa64) June 26, 2019
For online documentation, see https://www.mathworks.com/support For product information, visit www.mathworks.com.
reading filled volume...
closing volume... { Undefined variable "matlab" or class "matlab.graphics.chart.internal.datachk".
Error in isosurface (line 76) data = matlab.graphics.chart.internal.datachk(data);
Error in make_outer_surface (line 49) [f,v] = isosurface(BW2,100); }
-------------------------------------------------------------------------------- std::terminate() detected at Fri Aug 30 16:48:20 2019 -0400 --------------------------------------------------------------------------------
Configuration: Crash Decoding : Disabled - No sandbox or build area path Crash Mode : continue (default) Default Encoding : US-ASCII Deployed : false Desktop Environment : MATE GNU C Library : 2.27 stable MATLAB Architecture : glnxa64 MATLAB Entitlement ID : 1261621 MATLAB Root : /usr/local/MATLAB/R2019a MATLAB Version : 9.6.0.1150989 (R2019a) Update 4 Operating System : Ubuntu 18.04.3 LTS Process ID : 2352 Processor ID : x86 Family 6 Model 44 Stepping 2, GenuineIntel Session Key : 75ad7f0e-24cf-4356-844c-9536f142fca0 Static TLS mitigation : Disabled: Unable to open display Window System : No active display
Fault Count: 1
Abnormal termination: std::terminate()
Register State (captured): RAX = 0000000000000000 RBX = 00007fee6ea82d98 RCX = 000000000000000a RDX = 00007fee6ea63e00 RSP = 00007fee4bff84a0 RBP = 00007fee4bff8860 RSI = 00007fee6ea2b3c6 RDI = 00007fee4bff84b0
R8 = 000000000000ffff R9 = 00007fee70e04740 R10 = 0000000000000000 R11 = 0000000000000005 R12 = 00007fee6ea72d08 R13 = 00007fee4bff8c20 R14 = 00007fee4bff9110 R15 = 00007fee4bff90e0
RIP = 00007fee6e97b1ae EFL = 00007fee6e8ab270
CS = 7480 FS = 71d8 GS = 7fee
Stack Trace (captured): [ 0] 0x00007fee6e972713 /usr/local/MATLAB/R2019a/bin/glnxa64/libmwfl.so+00829203 [ 1] 0x00007fee6e97290c /usr/local/MATLAB/R2019a/bin/glnxa64/libmwfl.so+00829708 _ZN10foundation4core4diag15stacktrace_base7captureEm+00000028 [ 2] 0x00007fee6e975052 /usr/local/MATLAB/R2019a/bin/glnxa64/libmwfl.so+00839762 [ 3] 0x00007fee64201553 /usr/local/MATLAB/R2019a/bin/glnxa64/libmwmcr.so+01213779 [ 4] 0x00007fee64204157 /usr/local/MATLAB/R2019a/bin/glnxa64/libmwmcr.so+01225047 [ 5] 0x00007fee6420438a /usr/local/MATLAB/R2019a/bin/glnxa64/libmwmcr.so+01225610 [ 6] 0x00007fee64204951 /usr/local/MATLAB/R2019a/bin/glnxa64/libmwmcr.so+01227089 [ 7] 0x00007fee642058d7 /usr/local/MATLAB/R2019a/bin/glnxa64/libmwmcr.so+01231063 [ 8] 0x00007fee70b1f3a6 /usr/local/MATLAB/R2019a/bin/glnxa64/../../sys/os/glnxa64/libstdc++.so.6+00582566 [ 9] 0x00007fee70b1e3d9 /usr/local/MATLAB/R2019a/bin/glnxa64/../../sys/os/glnxa64/libstdc++.so.6+00578521 [ 10] 0x00007fee70b1ed2d /usr/local/MATLAB/R2019a/bin/glnxa64/../../sys/os/glnxa64/libstdc++.so.6+00580909 __gxx_personality_v0+00000717 [ 11] 0x00007fee70889f03 /usr/local/MATLAB/R2019a/bin/glnxa64/../../sys/os/glnxa64/libgcc_s.so.1+00065283 [ 12] 0x00007fee7088a26b /usr/local/MATLAB/R2019a/bin/glnxa64/../../sys/os/glnxa64/libgcc_s.so.1+00066155 _Unwind_RaiseException+00000251 [ 13] 0x00007fee70b1f5fb /usr/local/MATLAB/R2019a/bin/glnxa64/../../sys/os/glnxa64/libstdc++.so.6+00583163 __cxa_throw+00000091 [ 14] 0x00007fee66376e22 /usr/local/MATLAB/R2019a/bin/glnxa64/matlab_startup_plugins/connector/openssl_initializer/../../../../../bin/glnxa64/libPocoFoundation.so.48+00900642 _ZN4Poco10MemoryPool7releaseEPv+00000162 [ 15] 0x00007fee66966e5f /usr/local/MATLAB/R2019a/bin/glnxa64/matlab_startup_plugins/connector/openssl_initializer/../../../../../bin/glnxa64/libPocoNet.so.48+00638559 _ZN4Poco3Net19HTTPHeaderStreamBufD2Ev+00000031 [ 16] 0x00007fee66967253 /usr/local/MATLAB/R2019a/bin/glnxa64/matlab_startup_plugins/connector/openssl_initializer/../../../../../bin/glnxa64/libPocoNet.so.48+00639571 _ZN4Poco3Net21HTTPHeaderInputStreamD1Ev+00000067 [ 17] 0x00007fee6695abc7 /usr/local/MATLAB/R2019a/bin/glnxa64/matlab_startup_plugins/connector/openssl_initializer/../../../../../bin/glnxa64/libPocoNet.so.48+00588743 _ZN4Poco3Net17HTTPClientSession15receiveResponseERNS0_12HTTPResponseE+00000199 [ 18] 0x00007fee58a7c827 /usr/local/MATLAB/R2019a/bin/glnxa64/ddux/ddux_impl/../../../../bin/glnxa64/libmwflhttpclient.so+00141351 [ 19] 0x00007fee58a76d38 /usr/local/MATLAB/R2019a/bin/glnxa64/ddux/ddux_impl/../../../../bin/glnxa64/libmwflhttpclient.so+00118072 [ 20] 0x00007fee58a7117d /usr/local/MATLAB/R2019a/bin/glnxa64/ddux/ddux_impl/../../../../bin/glnxa64/libmwflhttpclient.so+00094589 _ZNK10foundation10httpclient16WebServiceClient23doWebServiceTransactionERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKSt3mapIS8_S8_St4lessIS8_ESaISt4pairIS8_S8_EEES9_RNS1_18WebServiceResponseEiS9_+00000061 [ 21] 0x00007fee58a72409 /usr/local/MATLAB/R2019a/bin/glnxa64/ddux/ddux_impl/../../../../bin/glnxa64/libmwflhttpclient.so+00099337 _ZNK10foundation10httpclient16WebServiceClient25makeWebServiceTransactionERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKSt3mapIS8_S8_St4lessIS8_ESaISt4pairIS8_S8_EEES9_RNS1_18WebServiceResponseEiiS9_+00000121 [ 22] 0x00007fee58c02387 /usr/local/MATLAB/R2019a/bin/glnxa64/ddux/ddux_impl/mwddux_impl.so+00590727 [ 23] 0x00007fee58c0675b /usr/local/MATLAB/R2019a/bin/glnxa64/ddux/ddux_impl/mwddux_impl.so+00608091 [ 24] 0x00007fee58be9a68 /usr/local/MATLAB/R2019a/bin/glnxa64/ddux/ddux_impl/mwddux_impl.so+00490088 [ 25] 0x00007fee58c6beaa /usr/local/MATLAB/R2019a/bin/glnxa64/ddux/ddux_impl/mwddux_impl.so+01023658 [ 26] 0x00007fee58bf090a /usr/local/MATLAB/R2019a/bin/glnxa64/ddux/ddux_impl/mwddux_impl.so+00518410 [ 27] 0x00007fee6ef5f7ad /usr/local/MATLAB/R2019a/bin/glnxa64/libmwms.so+02697133 [ 28] 0x00007fee58bf0586 /usr/local/MATLAB/R2019a/bin/glnxa64/ddux/ddux_impl/mwddux_impl.so+00517510 [ 29] 0x00007fee6fe54bdd /usr/local/MATLAB/R2019a/bin/glnxa64/libmwboost_thread.so.1.65.1+00080861 [ 30] 0x00007fee70e196db /lib/x86_64-linux-gnu/libpthread.so.0+00030427 [ 31] 0x00007fee705aa88f /lib/x86_64-linux-gnu/libc.so.6+01185935 clone+00000063 [ 32] 0x0000000000000000 <unknown-module>+00000000
** This crash report has been saved to disk as /home/avideh/matlab_crash_dump.2352-1 **
MATLAB is exiting because of fatal error Killed
ERROR: make_outer_surface did not create output file '/d/mjt/9/users/avideh/data/recon/MR160-114-0370_01/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'! Linux apollo.sickkids.ca 4.15.0-50-generic #54-Ubuntu SMP Mon May 6 18:46:08 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s MR160-114-0370_01 exited with ERRORS at Fri Aug 30 16:48:21 EDT 2019
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting