Problem with lGI - Freesurfer

3 Sep 2019


      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