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.strapp...@weizmann.ac.il
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