Dear Experts,

I'm trying to average two monkey brains. I run this command line:

 make_average_subject --subjects MonkeyCelia MonkeyCassis --out AVGmonkeys

but it ended with errors.

I run the recon-all for both monkyes with the option -notal-check because I had problems with the Talairach registration. I don't know if this could be the cause.

Thanks a lot
Francesca

Tue Mar 13 20:04:06 CET 2018
/usr/local/freesurfer/subjects/AVGmonkeys
/usr/local/freesurfer/bin/recon-all
-s AVGmonkeys -cortribbon -aparc2aseg
subjid AVGmonkeys
setenv SUBJECTS_DIR /usr/local/freesurfer/subjects
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 shalimpc 4.4.0-116-generic #140-Ubuntu SMP Mon Feb 12 21:23:04 UTC 2018 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 64 kbytes
maxproc      63682
maxlocks     unlimited
maxsignal    63682
maxmessage   819200
maxnice      0
maxrtprio    0
maxrttime    unlimited

              total        used        free      shared  buff/cache   available
Mem:       16350220     4943572     7520800      278988     3885848    10739864
Swap:      19528700           0    19528700

########################################
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: 2018/03/13-19:04:06-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: francesca  Machine: shalimpc  Platform: Linux  PlatformVersion: 4.4.0-116-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: 2018/03/13-19:04:06-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: francesca  Machine: shalimpc  Platform: Linux  PlatformVersion: 4.4.0-116-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: 2018/03/13-19:04:06-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: francesca  Machine: shalimpc  Platform: Linux  PlatformVersion: 4.4.0-116-generic  CompilerName: GCC  CompilerVersion: 40400
ProgramName: mri_normalize  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2018/03/13-19:04:06-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: francesca  Machine: shalimpc  Platform: Linux  PlatformVersion: 4.4.0-116-generic  CompilerName: GCC  CompilerVersion: 40400
ProgramName: mri_watershed  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2018/03/13-19:04:06-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: francesca  Machine: shalimpc  Platform: Linux  PlatformVersion: 4.4.0-116-generic  CompilerName: GCC  CompilerVersion: 40400
ProgramName: mri_gcut  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2018/03/13-19:04:06-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: francesca  Machine: shalimpc  Platform: Linux  PlatformVersion: 4.4.0-116-generic  CompilerName: GCC  CompilerVersion: 40400
ProgramName: mri_segment  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2018/03/13-19:04:06-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: francesca  Machine: shalimpc  Platform: Linux  PlatformVersion: 4.4.0-116-generic  CompilerName: GCC  CompilerVersion: 40400
ProgramName: mri_label2label.bin  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2018/03/13-19:04:06-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: francesca  Machine: shalimpc  Platform: Linux  PlatformVersion: 4.4.0-116-generic  CompilerName: GCC  CompilerVersion: 40400
ProgramName: mri_em_register  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2018/03/13-19:04:06-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: francesca  Machine: shalimpc  Platform: Linux  PlatformVersion: 4.4.0-116-generic  CompilerName: GCC  CompilerVersion: 40400
ProgramName: mri_ca_normalize  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2018/03/13-19:04:06-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: francesca  Machine: shalimpc  Platform: Linux  PlatformVersion: 4.4.0-116-generic  CompilerName: GCC  CompilerVersion: 40400
ProgramName: mri_ca_register  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2018/03/13-19:04:06-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: francesca  Machine: shalimpc  Platform: Linux  PlatformVersion: 4.4.0-116-generic  CompilerName: GCC  CompilerVersion: 40400
ProgramName: mri_ca_label  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2018/03/13-19:04:06-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: francesca  Machine: shalimpc  Platform: Linux  PlatformVersion: 4.4.0-116-generic  CompilerName: GCC  CompilerVersion: 40400
ProgramName: mri_pretess  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2018/03/13-19:04:06-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: francesca  Machine: shalimpc  Platform: Linux  PlatformVersion: 4.4.0-116-generic  CompilerName: GCC  CompilerVersion: 40400
ProgramName: mri_fill  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2018/03/13-19:04:06-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: francesca  Machine: shalimpc  Platform: Linux  PlatformVersion: 4.4.0-116-generic  CompilerName: GCC  CompilerVersion: 40400
ProgramName: mri_tessellate  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2018/03/13-19:04:06-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: francesca  Machine: shalimpc  Platform: Linux  PlatformVersion: 4.4.0-116-generic  CompilerName: GCC  CompilerVersion: 40400
ProgramName: mri_concatenate_lta.bin  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2018/03/13-19:04:06-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: francesca  Machine: shalimpc  Platform: Linux  PlatformVersion: 4.4.0-116-generic  CompilerName: GCC  CompilerVersion: 40400
ProgramName: mri_normalize_tp2  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2018/03/13-19:04:06-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: francesca  Machine: shalimpc  Platform: Linux  PlatformVersion: 4.4.0-116-generic  CompilerName: GCC  CompilerVersion: 40400
ProgramName: mris_smooth  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2018/03/13-19:04:06-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: francesca  Machine: shalimpc  Platform: Linux  PlatformVersion: 4.4.0-116-generic  CompilerName: GCC  CompilerVersion: 40400
ProgramName: mris_inflate  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2018/03/13-19:04:06-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: francesca  Machine: shalimpc  Platform: Linux  PlatformVersion: 4.4.0-116-generic  CompilerName: GCC  CompilerVersion: 40400
ProgramName: mris_curvature  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2018/03/13-19:04:06-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: francesca  Machine: shalimpc  Platform: Linux  PlatformVersion: 4.4.0-116-generic  CompilerName: GCC  CompilerVersion: 40400
ProgramName: mris_sphere  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2018/03/13-19:04:06-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: francesca  Machine: shalimpc  Platform: Linux  PlatformVersion: 4.4.0-116-generic  CompilerName: GCC  CompilerVersion: 40400
ProgramName: mris_fix_topology  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2018/03/13-19:04:06-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: francesca  Machine: shalimpc  Platform: Linux  PlatformVersion: 4.4.0-116-generic  CompilerName: GCC  CompilerVersion: 40400
ProgramName: mris_topo_fixer  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2018/03/13-19:04:06-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: francesca  Machine: shalimpc  Platform: Linux  PlatformVersion: 4.4.0-116-generic  CompilerName: GCC  CompilerVersion: 40400
ProgramName: mris_ca_label  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2018/03/13-19:04:06-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: francesca  Machine: shalimpc  Platform: Linux  PlatformVersion: 4.4.0-116-generic  CompilerName: GCC  CompilerVersion: 40400
ProgramName: mris_euler_number  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2018/03/13-19:04:06-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: francesca  Machine: shalimpc  Platform: Linux  PlatformVersion: 4.4.0-116-generic  CompilerName: GCC  CompilerVersion: 40400
ProgramName: mris_make_surfaces  ProgramArguments: -all-info  ProgramVersion: $Name:  $  TimeStamp: 2018/03/13-19:04:06-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: francesca  Machine: shalimpc  Platform: Linux  PlatformVersion: 4.4.0-116-generic  CompilerName: GCC  CompilerVersion: 40400
ProgramName: mris_register  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2018/03/13-19:04:06-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: francesca  Machine: shalimpc  Platform: Linux  PlatformVersion: 4.4.0-116-generic  CompilerName: GCC  CompilerVersion: 40400
ProgramName: mris_volmask  ProgramArguments: --all-info  ProgramVersion: $Name:  $  TimeStamp: 2018/03/13-19:04:06-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: francesca  Machine: shalimpc  Platform: Linux  PlatformVersion: 4.4.0-116-generic  CompilerName: GCC  CompilerVersion: 40400
ProgramName: mris_anatomical_stats  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2018/03/13-19:04:06-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: francesca  Machine: shalimpc  Platform: Linux  PlatformVersion: 4.4.0-116-generic  CompilerName: GCC  CompilerVersion: 40400
ProgramName: mrisp_paint  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2018/03/13-19:04:06-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: francesca  Machine: shalimpc  Platform: Linux  PlatformVersion: 4.4.0-116-generic  CompilerName: GCC  CompilerVersion: 40400
ProgramName: mris_curvature_stats  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2018/03/13-19:04:06-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: francesca  Machine: shalimpc  Platform: Linux  PlatformVersion: 4.4.0-116-generic  CompilerName: GCC  CompilerVersion: 40400
ProgramName: mris_calc  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2018/03/13-19:04:06-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: francesca  Machine: shalimpc  Platform: Linux  PlatformVersion: 4.4.0-116-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: 2018/03/13-19:04:06-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: francesca  Machine: shalimpc  Platform: Linux  PlatformVersion: 4.4.0-116-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: 2018/03/13-19:04:06-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: francesca  Machine: shalimpc  Platform: Linux  PlatformVersion: 4.4.0-116-generic  CompilerName: GCC  CompilerVersion: 40400
ProgramName: mri_and  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2018/03/13-19:04:06-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: francesca  Machine: shalimpc  Platform: Linux  PlatformVersion: 4.4.0-116-generic  CompilerName: GCC  CompilerVersion: 40400
ProgramName: mri_or  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2018/03/13-19:04:06-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: francesca  Machine: shalimpc  Platform: Linux  PlatformVersion: 4.4.0-116-generic  CompilerName: GCC  CompilerVersion: 40400
ProgramName: mri_fuse_segmentations  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2018/03/13-19:04:06-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: francesca  Machine: shalimpc  Platform: Linux  PlatformVersion: 4.4.0-116-generic  CompilerName: GCC  CompilerVersion: 40400
ProgramName: mri_segstats  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2018/03/13-19:04:06-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: francesca  Machine: shalimpc  Platform: Linux  PlatformVersion: 4.4.0-116-generic  CompilerName: GCC  CompilerVersion: 40400
ProgramName: mri_relabel_hypointensities  ProgramArguments: -all-info  ProgramVersion: $Name: stable6 $  TimeStamp: 2018/03/13-19:04:06-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: francesca  Machine: shalimpc  Platform: Linux  PlatformVersion: 4.4.0-116-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
#######################################
#--------------------------------------------
#@# Cortical ribbon mask Tue Mar 13 20:04:06 CET 2018
/usr/local/freesurfer/subjects/AVGmonkeys/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 AVGmonkeys

SUBJECTS_DIR is /usr/local/freesurfer/subjects
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 = 34535
writing volume /usr/local/freesurfer/subjects/AVGmonkeys/mri/ribbon.mgz
ERROR: ribbon has non-zero value at location 0,0,0
Linux shalimpc 4.4.0-116-generic #140-Ubuntu SMP Mon Feb 12 21:23:04 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s AVGmonkeys exited with ERRORS at Tue Mar 13 20:26:58 CET 2018

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


--
Francesca Strappini, Ph.D.
Neurobiology Department
Weizmann Institute of Science
234 Herzl Street, Rehovot 7610001 Israel
Tel.: +972 58 444 2584
E-mail: francesca.strappini@weizmann.ac.il