External Email - Use Caution        

Hello Freesurfer Developers

I am trying to create an average subject for 20 subjects using the function 
make_average_subject. But I keep running into a segmentation fault. I have 
attached the recon-all.log file.

I found a few other posts about the same problem which direct the users to the 
following patch:
https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/ 
(https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/)

But this patch does not have a readme file which can instruct the users about 
the steps that need to be followed to get rid of this bug. However, I have 
replaced the files in /usr/local/freesurfer/bin/ (i.e. the $FREESURFER_HOME) 
with the files given in this patch directory. But the problem still persists. 
Kindly provide the steps that need to be followed to make use of this patch 
properly.

Regards

Himanshu
Sun Sep 15 16:15:08 IST 2019
/home/leesa/Desktop/freesurfer_outputs/avgsubject
/home/leesa/freesurfer/bin/recon-all
-s avgsubject -cortribbon -aparc2aseg
subjid avgsubject
setenv SUBJECTS_DIR /home/leesa/Desktop/freesurfer_outputs
FREESURFER_HOME /home/leesa/freesurfer
Actual FREESURFER_HOME /home/leesa/freesurfer
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Linux sinha-Lenovo-Product 4.15.0-62-generic #69-Ubuntu SMP Wed Sep 4 20:55:53 
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      96050 
maxlocks     unlimited
maxsignal    96050 
maxmessage   819200 
maxnice      0 
maxrtprio    0 
maxrttime    unlimited

              total        used        free      shared  buff/cache   available
Mem:       24633364     3216096    13523204       84196     7894064    20933832
Swap:      18431996           0    18431996

########################################
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: 2019/09/15-10:45:08-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: leesa  Machine: sinha-Lenovo-Product  Platform: Linux  
PlatformVersion: 4.15.0-62-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: 2019/09/15-10:45:09-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: leesa  Machine: sinha-Lenovo-Product  Platform: Linux  
PlatformVersion: 4.15.0-62-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: 2019/09/15-10:45:09-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: leesa  Machine: sinha-Lenovo-Product  Platform: Linux  PlatformVersion: 
4.15.0-62-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name: 
 $  TimeStamp: 2019/09/15-10:45:09-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: 
leesa  Machine: sinha-Lenovo-Product  Platform: Linux  PlatformVersion: 
4.15.0-62-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: $Name: 
stable6 $  TimeStamp: 2019/09/15-10:45:09-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: leesa  Machine: sinha-Lenovo-Product  Platform: Linux  
PlatformVersion: 4.15.0-62-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_gcut  ProgramArguments: -all-info  ProgramVersion: $Name: 
stable6 $  TimeStamp: 2019/09/15-10:45:09-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: 
leesa  Machine: sinha-Lenovo-Product  Platform: Linux  PlatformVersion: 
4.15.0-62-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_segment  ProgramArguments: -all-info  ProgramVersion: $Name:  
$  TimeStamp: 2019/09/15-10:45:09-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: 
leesa  Machine: sinha-Lenovo-Product  Platform: Linux  PlatformVersion: 
4.15.0-62-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_label2label.bin  ProgramArguments: -all-info  ProgramVersion: 
$Name:  $  TimeStamp: 2019/09/15-10:45:09-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: leesa  Machine: sinha-Lenovo-Product  Platform: Linux  
PlatformVersion: 4.15.0-62-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_em_register  ProgramArguments: -all-info  ProgramVersion: 
$Name:  $  TimeStamp: 2019/09/15-10:45:10-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: leesa  Machine: sinha-Lenovo-Product  Platform: Linux  
PlatformVersion: 4.15.0-62-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_normalize  ProgramArguments: -all-info  ProgramVersion: 
$Name:  $  TimeStamp: 2019/09/15-10:45:10-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: leesa  Machine: sinha-Lenovo-Product  Platform: Linux  
PlatformVersion: 4.15.0-62-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_register  ProgramArguments: -all-info  ProgramVersion: 
$Name:  $  TimeStamp: 2019/09/15-10:45:10-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: leesa  Machine: sinha-Lenovo-Product  Platform: Linux  
PlatformVersion: 4.15.0-62-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_ca_label  ProgramArguments: -all-info  ProgramVersion: $Name:  
$  TimeStamp: 2019/09/15-10:45:10-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: 
leesa  Machine: sinha-Lenovo-Product  Platform: Linux  PlatformVersion: 
4.15.0-62-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_pretess  ProgramArguments: -all-info  ProgramVersion: $Name: 
stable6 $  TimeStamp: 2019/09/15-10:45:10-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: leesa  Machine: sinha-Lenovo-Product  Platform: Linux  PlatformVersion: 
4.15.0-62-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_fill  ProgramArguments: -all-info  ProgramVersion: $Name: 
stable6 $  TimeStamp: 2019/09/15-10:45:10-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: 
leesa  Machine: sinha-Lenovo-Product  Platform: Linux  PlatformVersion: 
4.15.0-62-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_tessellate  ProgramArguments: -all-info  ProgramVersion: 
$Name:  $  TimeStamp: 2019/09/15-10:45:10-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: leesa  Machine: sinha-Lenovo-Product  Platform: Linux  
PlatformVersion: 4.15.0-62-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_concatenate_lta.bin  ProgramArguments: -all-info  
ProgramVersion: $Name: stable6 $  TimeStamp: 2019/09/15-10:45:10-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: leesa  Machine: sinha-Lenovo-Product  
Platform: Linux  PlatformVersion: 4.15.0-62-generic  CompilerName: GCC  
CompilerVersion: 40400 
ProgramName: mri_normalize_tp2  ProgramArguments: -all-info  ProgramVersion: 
$Name: stable6 $  TimeStamp: 2019/09/15-10:45:10-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: leesa  Machine: sinha-Lenovo-Product  Platform: Linux  
PlatformVersion: 4.15.0-62-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_smooth  ProgramArguments: -all-info  ProgramVersion: $Name: 
stable6 $  TimeStamp: 2019/09/15-10:45:10-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: leesa  Machine: sinha-Lenovo-Product  Platform: Linux  PlatformVersion: 
4.15.0-62-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_inflate  ProgramArguments: -all-info  ProgramVersion: $Name: 
stable6 $  TimeStamp: 2019/09/15-10:45:10-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: leesa  Machine: sinha-Lenovo-Product  Platform: Linux  PlatformVersion: 
4.15.0-62-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_curvature  ProgramArguments: -all-info  ProgramVersion: 
$Name: stable6 $  TimeStamp: 2019/09/15-10:45:10-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: leesa  Machine: sinha-Lenovo-Product  Platform: Linux  
PlatformVersion: 4.15.0-62-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_sphere  ProgramArguments: -all-info  ProgramVersion: $Name: 
stable6 $  TimeStamp: 2019/09/15-10:45:11-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: 
leesa  Machine: sinha-Lenovo-Product  Platform: Linux  PlatformVersion: 
4.15.0-62-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_fix_topology  ProgramArguments: -all-info  ProgramVersion: 
$Name:  $  TimeStamp: 2019/09/15-10:45:11-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: leesa  Machine: sinha-Lenovo-Product  Platform: Linux  
PlatformVersion: 4.15.0-62-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_topo_fixer  ProgramArguments: -all-info  ProgramVersion: 
$Name: stable6 $  TimeStamp: 2019/09/15-10:45:11-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: leesa  Machine: sinha-Lenovo-Product  Platform: Linux  
PlatformVersion: 4.15.0-62-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_ca_label  ProgramArguments: -all-info  ProgramVersion: $Name: 
stable6 $  TimeStamp: 2019/09/15-10:45:11-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: leesa  Machine: sinha-Lenovo-Product  Platform: Linux  PlatformVersion: 
4.15.0-62-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_euler_number  ProgramArguments: -all-info  ProgramVersion: 
$Name: stable6 $  TimeStamp: 2019/09/15-10:45:11-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: leesa  Machine: sinha-Lenovo-Product  Platform: Linux  
PlatformVersion: 4.15.0-62-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_make_surfaces  ProgramArguments: -all-info  ProgramVersion: 
$Name:  $  TimeStamp: 2019/09/15-10:45:11-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: leesa  Machine: sinha-Lenovo-Product  Platform: Linux  
PlatformVersion: 4.15.0-62-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_register  ProgramArguments: -all-info  ProgramVersion: $Name: 
stable6 $  TimeStamp: 2019/09/15-10:45:11-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: leesa  Machine: sinha-Lenovo-Product  Platform: Linux  PlatformVersion: 
4.15.0-62-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_volmask  ProgramArguments: --all-info  ProgramVersion: $Name: 
 $  TimeStamp: 2019/09/15-10:45:11-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: 
leesa  Machine: sinha-Lenovo-Product  Platform: Linux  PlatformVersion: 
4.15.0-62-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_anatomical_stats  ProgramArguments: -all-info  
ProgramVersion: $Name: stable6 $  TimeStamp: 2019/09/15-10:45:11-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: leesa  Machine: sinha-Lenovo-Product  
Platform: Linux  PlatformVersion: 4.15.0-62-generic  CompilerName: GCC  
CompilerVersion: 40400 
ProgramName: mrisp_paint  ProgramArguments: -all-info  ProgramVersion: $Name: 
stable6 $  TimeStamp: 2019/09/15-10:45:11-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: leesa  Machine: sinha-Lenovo-Product  Platform: Linux  PlatformVersion: 
4.15.0-62-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_curvature_stats  ProgramArguments: -all-info  ProgramVersion: 
$Name: stable6 $  TimeStamp: 2019/09/15-10:45:11-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: leesa  Machine: sinha-Lenovo-Product  Platform: Linux  
PlatformVersion: 4.15.0-62-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mris_calc  ProgramArguments: -all-info  ProgramVersion: $Name: 
stable6 $  TimeStamp: 2019/09/15-10:45:11-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: leesa  Machine: sinha-Lenovo-Product  Platform: Linux  PlatformVersion: 
4.15.0-62-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: 2019/09/15-10:45:12-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: leesa  Machine: sinha-Lenovo-Product  
Platform: Linux  PlatformVersion: 4.15.0-62-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: 2019/09/15-10:45:12-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: leesa  Machine: sinha-Lenovo-Product  Platform: Linux  
PlatformVersion: 4.15.0-62-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_and  ProgramArguments: -all-info  ProgramVersion: $Name: 
stable6 $  TimeStamp: 2019/09/15-10:45:12-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: 
leesa  Machine: sinha-Lenovo-Product  Platform: Linux  PlatformVersion: 
4.15.0-62-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_or  ProgramArguments: -all-info  ProgramVersion: $Name: 
stable6 $  TimeStamp: 2019/09/15-10:45:12-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: 
leesa  Machine: sinha-Lenovo-Product  Platform: Linux  PlatformVersion: 
4.15.0-62-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_fuse_segmentations  ProgramArguments: -all-info  
ProgramVersion: $Name: stable6 $  TimeStamp: 2019/09/15-10:45:12-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: leesa  Machine: sinha-Lenovo-Product  
Platform: Linux  PlatformVersion: 4.15.0-62-generic  CompilerName: GCC  
CompilerVersion: 40400 
ProgramName: mri_segstats  ProgramArguments: -all-info  ProgramVersion: $Name: 
stable6 $  TimeStamp: 2019/09/15-10:45:12-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: leesa  Machine: sinha-Lenovo-Product  Platform: Linux  PlatformVersion: 
4.15.0-62-generic  CompilerName: GCC  CompilerVersion: 40400 
ProgramName: mri_relabel_hypointensities  ProgramArguments: -all-info  
ProgramVersion: $Name: stable6 $  TimeStamp: 2019/09/15-10:45:12-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: leesa  Machine: 
sinha-Lenovo-Product  Platform: Linux  PlatformVersion: 4.15.0-62-generic  
CompilerName: GCC  CompilerVersion: 40400 
#######################################
GCADIR /home/leesa/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 /home/leesa/freesurfer/average
GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
#######################################
#--------------------------------------------
#@# Cortical ribbon mask Sun Sep 15 16:15:12 IST 2019
/home/leesa/Desktop/freesurfer_outputs/avgsubject/mri

 mris_volmask --aseg_name aseg.presurf --label_left_white 2 --label_left_ribbon 
3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon avgsubject 

SUBJECTS_DIR is /home/leesa/Desktop/freesurfer_outputs
loading input data...
computing distance to left white surface 
computing distance to left pial surface 
computing distance to right white surface 
computing distance to right pial surface 
 hemi masks overlap voxels = 14
writing volume /home/leesa/Desktop/freesurfer_outputs/avgsubject/mri/ribbon.mgz
mris_volmask took 3.23 minutes
 writing ribbon files
#-----------------------------------------
#@# AParc-to-ASeg aparc Sun Sep 15 16:18:26 IST 2019
/home/leesa/Desktop/freesurfer_outputs/avgsubject

 mri_aparc2aseg --s avgsubject --volmask --aseg aseg.presurf.hypos --relabel 
mri/norm.mgz mri/transforms/talairach.m3z 
/home/leesa/freesurfer/average/RB_all_2016-05-10.vc700.gca 
mri/aseg.auto_noCCseg.label_intensities.txt 

relabeling unlikely voxels interior to white matter surface:
        norm: mri/norm.mgz
         XFORM: mri/transforms/talairach.m3z
        GCA: /home/leesa/freesurfer/average/RB_all_2016-05-10.vc700.gca
        label intensities: mri/aseg.auto_noCCseg.label_intensities.txt
SUBJECTS_DIR /home/leesa/Desktop/freesurfer_outputs
subject avgsubject
outvol /home/leesa/Desktop/freesurfer_outputs/avgsubject/mri/aparc+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0

Reading lh white surface 
 /home/leesa/Desktop/freesurfer_outputs/avgsubject/surf/lh.white

Reading lh pial surface 
 /home/leesa/Desktop/freesurfer_outputs/avgsubject/surf/lh.pial

Loading lh annotations from 
/home/leesa/Desktop/freesurfer_outputs/avgsubject/label/lh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally 
/home/leesa/Desktop/freesurfer_outputs/avgsubject/label/tmpdir.annot2std.14965/seg.1.cp_AARTI.ctab)

Reading rh white surface 
 /home/leesa/Desktop/freesurfer_outputs/avgsubject/surf/rh.white

Reading rh pial surface 
 /home/leesa/Desktop/freesurfer_outputs/avgsubject/surf/rh.pial

Loading rh annotations from 
/home/leesa/Desktop/freesurfer_outputs/avgsubject/label/rh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally 
/home/leesa/Desktop/freesurfer_outputs/avgsubject/label/tmpdir.annot2std.19273/seg.1.cp_AARTI.ctab)
Have color table for lh white annotation
Have color table for rh white annotation
Loading ribbon segmentation from 
/home/leesa/Desktop/freesurfer_outputs/avgsubject/mri/ribbon.mgz

Building hash of lh white

Building hash of lh pial

Building hash of rh white

Building hash of rh pial

Loading aseg from 
/home/leesa/Desktop/freesurfer_outputs/avgsubject/mri/aseg.presurf.hypos.mgz
ASeg Vox2RAS: -----------
-1.00000   0.00000   0.00000   128.00000;
 0.00000   0.00000   1.00000  -128.00000;
 0.00000  -1.00000   0.00000   128.00000;
 0.00000   0.00000   0.00000   1.00000;
mghRead(mri/norm.mgz, -1): could not open file
-------------------------

Labeling Slice
relabeling unlikely voxels in interior of white matter
Segmentation fault (core dumped)
Linux sinha-Lenovo-Product 4.15.0-62-generic #69-Ubuntu SMP Wed Sep 4 20:55:53 
UTC 2019 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s avgsubject exited with ERRORS at Sun Sep 15 16:18:44 IST 2019

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