Dear Freesurfer Developers,
After updating my op to Ubunto from 14 to 16.04, and re-installing the
Freesurfer, when I run recon-all, it ended with an error message:
/media/yw/liu/Liu/freesurfer/subjects/A2090_1/mri
mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i
orig.mgz --o orig_nu.mgz
Linux yw-HP-Z240-Tower-Workstation 4.4.0-36-generic #55-Ubuntu SMP Thu Aug
11 18:01:55 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s A2090_1 exited with ERRORS at ke 7.9.2016 10.20.05 +0300
I have searched the list and could not find answer, need your help.
Best regards,
Yawu
1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
2) Platform: Ubuntu 16.04 LTS
3) recon-all.log: see attached
ke 7.9.2016 10.19.13 +0300
/media/yw/liu/Liu/freesurfer/subjects/A2090_1
/media/yw/liu/Liu/freesurfer/bin/recon-all
-s A2090_1 -i /media/yw/Files/Downloads/A2090_1.nii.gz
subjid A2090_1
setenv SUBJECTS_DIR /media/yw/liu/Liu/freesurfer/subjects
FREESURFER_HOME /media/yw/liu/Liu/freesurfer
Actual FREESURFER_HOME /media/yw/liu/Liu/freesurfer
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Linux yw-HP-Z240-Tower-Workstation 4.4.0-36-generic #55-Ubuntu SMP Thu Aug 11 18:01:55 UTC 2016 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 63697
maxlocks unlimited
maxsignal 63697
maxmessage 819200
maxnice 0
maxrtprio 0
maxrttime unlimited
total used free shared buff/cache available
Mem: 16351276 3354744 4574740 172548 8421792 12427864
Swap: 16694268 0 16694268
########################################
program versions used
$Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
$Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $
mri_convert -all-info
ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:13-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
FLIRT version 5.5
$Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $
mri_convert --version
stable5
ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:13-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:13-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:13-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:13-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:13-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:13-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:13-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
======= NUMBER OF OPENMP THREADS = 1 =======
ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:13-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:13-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:13-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
$Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $
ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:15-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
$Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $
ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:15-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:15-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:15-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:15-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:15-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
#######################################
GCADIR /media/yw/liu/Liu/freesurfer/average
GCA RB_all_2008-03-26.gca
GCASkull RB_all_withskull_2008-03-26.gca
AvgCurvTif average.curvature.filled.buckner40.tif
GCSDIR /media/yw/liu/Liu/freesurfer/average
GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
#######################################
/media/yw/liu/Liu/freesurfer/subjects/A2090_1
mri_convert /media/yw/Files/Downloads/A2090_1.nii.gz /media/yw/liu/Liu/freesurfer/subjects/A2090_1/mri/orig/001.mgz
mri_convert /media/yw/Files/Downloads/A2090_1.nii.gz /media/yw/liu/Liu/freesurfer/subjects/A2090_1/mri/orig/001.mgz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /media/yw/Files/Downloads/A2090_1.nii.gz...
TR=1900.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.988019, 0.152233, 0.0253719)
j_ras = (0.0617912, 0.239552, 0.968915)
k_ras = (-0.141423, -0.958874, 0.246088)
writing to /media/yw/liu/Liu/freesurfer/subjects/A2090_1/mri/orig/001.mgz...
#------------------------------------------
Started at ke 7.9.2016 10.19.13 +0300
Ended at ke 7.9.2016 10.19.26 +0300
#@#%# recon-all-run-time-hours 0,004
recon-all -s A2090_1 finished without error at ke 7.9.2016 10.19.26 +0300
New invocation of recon-all
ke 7.9.2016 10.19.48 +0300
/media/yw/liu/Liu/freesurfer/subjects/A2090_1
/media/yw/liu/Liu/freesurfer/bin/recon-all
-cw256 -subjid A2090_1 -all
subjid A2090_1
setenv SUBJECTS_DIR /media/yw/liu/Liu/freesurfer/subjects
FREESURFER_HOME /media/yw/liu/Liu/freesurfer
Actual FREESURFER_HOME /media/yw/liu/Liu/freesurfer
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Linux yw-HP-Z240-Tower-Workstation 4.4.0-36-generic #55-Ubuntu SMP Thu Aug 11 18:01:55 UTC 2016 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 63697
maxlocks unlimited
maxsignal 63697
maxmessage 819200
maxnice 0
maxrtprio 0
maxrttime unlimited
total used free shared buff/cache available
Mem: 16351276 3362268 4529864 172552 8459144 12420504
Swap: 16694268 0 16694268
########################################
program versions used
$Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
$Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $
mri_convert -all-info
ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
FLIRT version 5.5
$Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $
mri_convert --version
stable5
ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
======= NUMBER OF OPENMP THREADS = 1 =======
ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
$Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $
ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
$Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $
ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:19:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
#######################################
GCADIR /media/yw/liu/Liu/freesurfer/average
GCA RB_all_2008-03-26.gca
GCASkull RB_all_withskull_2008-03-26.gca
AvgCurvTif average.curvature.filled.buckner40.tif
GCSDIR /media/yw/liu/Liu/freesurfer/average
GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
#######################################
-cw256 option is now persistent (remove with -clean-cw256)
#--------------------------------------------
#@# MotionCor ke 7.9.2016 10.19.50 +0300
Found 1 runs
/media/yw/liu/Liu/freesurfer/subjects/A2090_1/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
WARNING: only one run found. This is OK, but motion
correction cannot be performed on one run, so I'll
copy the run to rawavg and continue.
cp /media/yw/liu/Liu/freesurfer/subjects/A2090_1/mri/orig/001.mgz /media/yw/liu/Liu/freesurfer/subjects/A2090_1/mri/rawavg.mgz
/media/yw/liu/Liu/freesurfer/subjects/A2090_1
mri_convert /media/yw/liu/Liu/freesurfer/subjects/A2090_1/mri/rawavg.mgz /media/yw/liu/Liu/freesurfer/subjects/A2090_1/mri/orig.mgz --conform --cw256
mri_convert /media/yw/liu/Liu/freesurfer/subjects/A2090_1/mri/rawavg.mgz /media/yw/liu/Liu/freesurfer/subjects/A2090_1/mri/orig.mgz --conform --cw256
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /media/yw/liu/Liu/freesurfer/subjects/A2090_1/mri/rawavg.mgz...
TR=1900.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.988019, 0.152233, 0.0253719)
j_ras = (0.0617912, 0.239552, 0.968915)
k_ras = (-0.141423, -0.958874, 0.246088)
Original Data has (0.488281, 0.488281, 1.5) mm size and (384, 512, 160) voxels.
Data is conformed to 1 mm size and 256 voxels for all directions
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram
Reslicing using trilinear interpolation
writing to /media/yw/liu/Liu/freesurfer/subjects/A2090_1/mri/orig.mgz...
mri_add_xform_to_header -c /media/yw/liu/Liu/freesurfer/subjects/A2090_1/mri/transforms/talairach.xfm /media/yw/liu/Liu/freesurfer/subjects/A2090_1/mri/orig.mgz /media/yw/liu/Liu/freesurfer/subjects/A2090_1/mri/orig.mgz
INFO: extension is mgz
#--------------------------------------------
#@# Talairach ke 7.9.2016 10.20.03 +0300
/media/yw/liu/Liu/freesurfer/subjects/A2090_1/mri
mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
Linux yw-HP-Z240-Tower-Workstation 4.4.0-36-generic #55-Ubuntu SMP Thu Aug 11 18:01:55 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s A2090_1 exited with ERRORS at ke 7.9.2016 10.20.05 +0300
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
New invocation of recon-all
ke 7.9.2016 10.28.20 +0300
/media/yw/liu/Liu/freesurfer/subjects/A2090_1
/media/yw/liu/Liu/freesurfer/bin/recon-all
-cw256 -subjid A2090_1 -all
subjid A2090_1
setenv SUBJECTS_DIR /media/yw/liu/Liu/freesurfer/subjects
FREESURFER_HOME /media/yw/liu/Liu/freesurfer
Actual FREESURFER_HOME /media/yw/liu/Liu/freesurfer
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Linux yw-HP-Z240-Tower-Workstation 4.4.0-36-generic #55-Ubuntu SMP Thu Aug 11 18:01:55 UTC 2016 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 63697
maxlocks unlimited
maxsignal 63697
maxmessage 819200
maxnice 0
maxrtprio 0
maxrttime unlimited
total used free shared buff/cache available
Mem: 16351276 3508568 4221720 176324 8620988 12269232
Swap: 16694268 0 16694268
########################################
program versions used
$Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $
$Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $
mri_convert -all-info
ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:28:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
FLIRT version 5.5
$Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $
mri_convert --version
stable5
ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:28:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37
ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:28:21-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:28:21-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:28:21-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:28:21-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:28:21-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:28:21-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
======= NUMBER OF OPENMP THREADS = 1 =======
ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:28:21-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:28:21-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:28:21-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:28:21-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:28:21-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:28:21-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:28:21-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:28:21-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:28:21-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:28:21-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:28:21-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:28:21-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:28:21-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:28:21-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:28:22-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:28:22-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:28:22-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:28:22-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:28:22-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:28:22-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:28:22-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:28:22-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:28:22-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:28:22-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
$Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $
ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:28:22-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
$Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $
ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:28:22-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:28:22-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:28:22-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:28:22-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/09/07-07:28:22-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: yw Machine: yw-HP-Z240-Tower-Workstation Platform: Linux PlatformVersion: 4.4.0-36-generic CompilerName: GCC CompilerVersion: 40400
#######################################
GCADIR /media/yw/liu/Liu/freesurfer/average
GCA RB_all_2008-03-26.gca
GCASkull RB_all_withskull_2008-03-26.gca
AvgCurvTif average.curvature.filled.buckner40.tif
GCSDIR /media/yw/liu/Liu/freesurfer/average
GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
#######################################
-cw256 option is now persistent (remove with -clean-cw256)
#--------------------------------------------
#@# MotionCor ke 7.9.2016 10.28.22 +0300
Found 1 runs
/media/yw/liu/Liu/freesurfer/subjects/A2090_1/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
WARNING: only one run found. This is OK, but motion
correction cannot be performed on one run, so I'll
copy the run to rawavg and continue.
cp /media/yw/liu/Liu/freesurfer/subjects/A2090_1/mri/orig/001.mgz /media/yw/liu/Liu/freesurfer/subjects/A2090_1/mri/rawavg.mgz
/media/yw/liu/Liu/freesurfer/subjects/A2090_1
mri_convert /media/yw/liu/Liu/freesurfer/subjects/A2090_1/mri/rawavg.mgz /media/yw/liu/Liu/freesurfer/subjects/A2090_1/mri/orig.mgz --conform --cw256
mri_convert /media/yw/liu/Liu/freesurfer/subjects/A2090_1/mri/rawavg.mgz /media/yw/liu/Liu/freesurfer/subjects/A2090_1/mri/orig.mgz --conform --cw256
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /media/yw/liu/Liu/freesurfer/subjects/A2090_1/mri/rawavg.mgz...
TR=1900.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.988019, 0.152233, 0.0253719)
j_ras = (0.0617912, 0.239552, 0.968915)
k_ras = (-0.141423, -0.958874, 0.246088)
Original Data has (0.488281, 0.488281, 1.5) mm size and (384, 512, 160) voxels.
Data is conformed to 1 mm size and 256 voxels for all directions
changing data type from float to uchar (noscale = 0)...
MRIchangeType: Building histogram
Reslicing using trilinear interpolation
writing to /media/yw/liu/Liu/freesurfer/subjects/A2090_1/mri/orig.mgz...
mri_add_xform_to_header -c /media/yw/liu/Liu/freesurfer/subjects/A2090_1/mri/transforms/talairach.xfm /media/yw/liu/Liu/freesurfer/subjects/A2090_1/mri/orig.mgz /media/yw/liu/Liu/freesurfer/subjects/A2090_1/mri/orig.mgz
INFO: extension is mgz
#--------------------------------------------
#@# Talairach ke 7.9.2016 10.28.36 +0300
/media/yw/liu/Liu/freesurfer/subjects/A2090_1/mri
mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
Linux yw-HP-Z240-Tower-Workstation 4.4.0-36-generic #55-Ubuntu SMP Thu Aug 11 18:01:55 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s A2090_1 exited with ERRORS at ke 7.9.2016 10.28.37 +0300
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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