When I run recon-all using freesurfer 5.2 latest beta it will segment
crash.
Linux mypc 3.7.4-204.fc18.x86_64 #1 SMP Wed Jan 23 16:44:29 UTC 2013
x86_64 x86_64 x86_64 GNU/Linux
/home/knutjbj/freesurfer/ernie
mri_convert /usr/local/freesurfer/subjects/sample-001.mgz
/home/knutjbj/freesurfer/ernie/mri/orig/001.mgz
mri_convert /usr/local/freesurfer/subjects/sample-001.mgz
/home/knutjbj/freesurfer/ernie/mri/orig/001.mgz
Segmentation fault
Linux super-knut 3.7.4-204.fc18.x86_64 #1 SMP Wed Jan 23 16:44:29 UTC
2013 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s ernie exited with ERRORS at ti. 29. jan. 19:25:15 +0100 2013
For more details, see the log file
/home/knutjbj/freesurfer/ernie/scripts/recon-all.log
To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Knut J
------------------------------
SUBJECT ernie
DATE ti. 29. jan. 19:28:17 +0100 2013
USER knutjbj
HOST mypc
PROCESSOR x86_64
OS Linux
Linux super-knut 3.7.4-204.fc18.x86_64 #1 SMP Wed Jan 23 16:44:29 UTC 2013
x86_64 x86_64 x86_64 GNU/Linux
$Id: recon-all,v 1.379.2.54 2013/01/15 22:31:19 nicks Exp $
/usr/local/freesurfer/bin/recon-all
PWD /home/knutjbj/freesurfer/ernie
CMD mri_convert /usr/local/freesurfer/subjects/sample-001.mgz
/home/knutjbj/freesurfer/ernie/mri/orig/001.mgz
ti. 29. jan. 19:28:13 +0100 2013
/home/knutjbj/freesurfer/ernie
/usr/local/freesurfer/bin/recon-all
-i /usr/local/freesurfer/subjects/sample-001.mgz -i /usr/local/freesurfer/subjects/sample-002.mgz -s ernie -debug
subjid ernie
setenv SUBJECTS_DIR /home/knutjbj/freesurfer
FREESURFER_HOME /usr/local/freesurfer
Actual FREESURFER_HOME /usr/local/freesurfer
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.2.0
Linux mypc 3.7.4-204.fc18.x86_64 #1 SMP Wed Jan 23 16:44:29 UTC 2013 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 1024
maxlocks unlimited
maxsignal 192659
maxmessage 819200
maxnice 0
maxrtprio 0
maxrttime unlimited
total used free shared buffers cached
Mem: 24683456 24399144 284312 0 654024 20092400
-/+ buffers/cache: 3652720 21030736
Swap: 49337340 3796 49333544
########################################
program versions used
$Id: recon-all,v 1.379.2.54 2013/01/15 22:31:19 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: 2013/01/29-18:28:13-GMT BuildTimeStamp: Jan 17 2013 00:19:38 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: knutjbj Machine: mypc Platform: Linux PlatformVersion: 3.7.4-204.fc18.x86_64 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: 2013/01/29-18:28:13-GMT BuildTimeStamp: Jan 17 2013 00:19:38 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: knutjbj Machine: mypc Platform: Linux PlatformVersion: 3.7.4-204.fc18.x86_64 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: 2013/01/29-18:28:13-GMT BuildTimeStamp: Jan 17 2013 00:19:38 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: knutjbj Machine: mypc Platform: Linux PlatformVersion: 3.7.4-204.fc18.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/29-18:28:13-GMT BuildTimeStamp: Jan 17 2013 00:19:38 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: knutjbj Machine: mypc Platform: Linux PlatformVersion: 3.7.4-204.fc18.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/29-18:28:13-GMT BuildTimeStamp: Jan 17 2013 00:19:38 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: knutjbj Machine: mypc Platform: Linux PlatformVersion: 3.7.4-204.fc18.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/29-18:28:13-GMT BuildTimeStamp: Jan 17 2013 00:19:38 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: knutjbj Machine: mypc Platform: Linux PlatformVersion: 3.7.4-204.fc18.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/29-18:28:13-GMT BuildTimeStamp: Jan 17 2013 00:19:38 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: knutjbj Machine: mypc Platform: Linux PlatformVersion: 3.7.4-204.fc18.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/29-18:28:13-GMT BuildTimeStamp: Jan 17 2013 00:19:38 CVS: $Id: mri_label2label.c,v 1.40.2.1 2011/05/19 17:21:56 greve Exp $ User: knutjbj Machine: mypc Platform: Linux PlatformVersion: 3.7.4-204.fc18.x86_64 CompilerName: GCC CompilerVersion: 40400
======= NUMBER OF OPENMP THREADS = 1 =======
ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/29-18:28:14-GMT BuildTimeStamp: Jan 17 2013 00:19:38 CVS: $Id: mri_em_register.c,v 1.84.2.2 2012/10/30 19:16:52 nicks Exp $ User: knutjbj Machine: mypc Platform: Linux PlatformVersion: 3.7.4-204.fc18.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/29-18:28:14-GMT BuildTimeStamp: Jan 17 2013 00:19:38 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: knutjbj Machine: mypc Platform: Linux PlatformVersion: 3.7.4-204.fc18.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/29-18:28:14-GMT BuildTimeStamp: Jan 17 2013 00:19:38 CVS: $Id: mri_ca_register.c,v 1.78.2.2 2012/11/14 22:03:02 nicks Exp $ User: knutjbj Machine: mypc Platform: Linux PlatformVersion: 3.7.4-204.fc18.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/29-18:28:14-GMT BuildTimeStamp: Jan 17 2013 00:19:38 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: knutjbj Machine: mypc Platform: Linux PlatformVersion: 3.7.4-204.fc18.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/29-18:28:14-GMT BuildTimeStamp: Jan 17 2013 00:19:38 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: knutjbj Machine: mypc Platform: Linux PlatformVersion: 3.7.4-204.fc18.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/29-18:28:14-GMT BuildTimeStamp: Jan 17 2013 00:19:38 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: knutjbj Machine: mypc Platform: Linux PlatformVersion: 3.7.4-204.fc18.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/29-18:28:14-GMT BuildTimeStamp: Jan 17 2013 00:19:38 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: knutjbj Machine: mypc Platform: Linux PlatformVersion: 3.7.4-204.fc18.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/29-18:28:14-GMT BuildTimeStamp: Jan 17 2013 00:19:38 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: knutjbj Machine: mypc Platform: Linux PlatformVersion: 3.7.4-204.fc18.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/29-18:28:14-GMT BuildTimeStamp: Jan 17 2013 00:19:38 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: knutjbj Machine: mypc Platform: Linux PlatformVersion: 3.7.4-204.fc18.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/29-18:28:14-GMT BuildTimeStamp: Jan 17 2013 00:19:38 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: knutjbj Machine: mypc Platform: Linux PlatformVersion: 3.7.4-204.fc18.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/29-18:28:14-GMT BuildTimeStamp: Jan 17 2013 00:19:38 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: knutjbj Machine: mypc Platform: Linux PlatformVersion: 3.7.4-204.fc18.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/29-18:28:14-GMT BuildTimeStamp: Jan 17 2013 00:19:38 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: knutjbj Machine: mypc Platform: Linux PlatformVersion: 3.7.4-204.fc18.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/29-18:28:14-GMT BuildTimeStamp: Jan 17 2013 00:19:38 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: knutjbj Machine: mypc Platform: Linux PlatformVersion: 3.7.4-204.fc18.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/29-18:28:14-GMT BuildTimeStamp: Jan 17 2013 00:19:38 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: knutjbj Machine: mypc Platform: Linux PlatformVersion: 3.7.4-204.fc18.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/29-18:28:15-GMT BuildTimeStamp: Jan 17 2013 00:19:38 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: knutjbj Machine: mypc Platform: Linux PlatformVersion: 3.7.4-204.fc18.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/29-18:28:15-GMT BuildTimeStamp: Jan 17 2013 00:19:38 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: knutjbj Machine: mypc Platform: Linux PlatformVersion: 3.7.4-204.fc18.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/29-18:28:15-GMT BuildTimeStamp: Jan 17 2013 00:19:38 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: knutjbj Machine: mypc Platform: Linux PlatformVersion: 3.7.4-204.fc18.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/29-18:28:15-GMT BuildTimeStamp: Jan 17 2013 00:19:38 CVS: $Id: mris_make_surfaces.c,v 1.127.2.3 2012/11/07 19:57:28 nicks Exp $ User: knutjbj Machine: mypc Platform: Linux PlatformVersion: 3.7.4-204.fc18.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/29-18:28:15-GMT BuildTimeStamp: Jan 17 2013 00:19:38 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: knutjbj Machine: mypc Platform: Linux PlatformVersion: 3.7.4-204.fc18.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/29-18:28:15-GMT BuildTimeStamp: Jan 17 2013 00:19:38 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: knutjbj Machine: mypc Platform: Linux PlatformVersion: 3.7.4-204.fc18.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/29-18:28:15-GMT BuildTimeStamp: Jan 17 2013 00:19:38 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: knutjbj Machine: mypc Platform: Linux PlatformVersion: 3.7.4-204.fc18.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/29-18:28:15-GMT BuildTimeStamp: Jan 17 2013 00:19:38 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: knutjbj Machine: mypc Platform: Linux PlatformVersion: 3.7.4-204.fc18.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/29-18:28:15-GMT BuildTimeStamp: Jan 17 2013 00:19:38 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: knutjbj Machine: mypc Platform: Linux PlatformVersion: 3.7.4-204.fc18.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/29-18:28:15-GMT BuildTimeStamp: Jan 17 2013 00:19:38 CVS: $Id: mris_calc.c,v 1.37.2.7 2012/08/15 21:47:25 mreuter Exp $ User: knutjbj Machine: mypc Platform: Linux PlatformVersion: 3.7.4-204.fc18.x86_64 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: 2013/01/29-18:28:15-GMT BuildTimeStamp: Jan 17 2013 00:19:38 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: knutjbj Machine: mypc Platform: Linux PlatformVersion: 3.7.4-204.fc18.x86_64 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: 2013/01/29-18:28:15-GMT BuildTimeStamp: Jan 17 2013 00:19:38 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: knutjbj Machine: mypc Platform: Linux PlatformVersion: 3.7.4-204.fc18.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/29-18:28:15-GMT BuildTimeStamp: Jan 17 2013 00:19:38 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: knutjbj Machine: mypc Platform: Linux PlatformVersion: 3.7.4-204.fc18.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/29-18:28:15-GMT BuildTimeStamp: Jan 17 2013 00:19:38 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: knutjbj Machine: mypc Platform: Linux PlatformVersion: 3.7.4-204.fc18.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/29-18:28:16-GMT BuildTimeStamp: Jan 17 2013 00:19:38 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: knutjbj Machine: mypc Platform: Linux PlatformVersion: 3.7.4-204.fc18.x86_64 CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/29-18:28:16-GMT BuildTimeStamp: Jan 17 2013 00:19:38 CVS: $Id: mri_segstats.c,v 1.75.2.8 2013/01/15 17:04:14 greve Exp $ User: knutjbj Machine: mypc Platform: Linux PlatformVersion: 3.7.4-204.fc18.x86_64 CompilerName: GCC CompilerVersion: 40400
#######################################
GCADIR /usr/local/freesurfer/average
GCA RB_all_2008-03-26.gca
GCASkull RB_all_withskull_2008-03-26.gca
AvgCurvTif average.curvature.filled.buckner40.tif
GCSDIR /usr/local/freesurfer/average
GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
#######################################
/home/knutjbj/freesurfer/ernie
mri_convert /usr/local/freesurfer/subjects/sample-001.mgz /home/knutjbj/freesurfer/ernie/mri/orig/001.mgz
mri_convert /usr/local/freesurfer/subjects/sample-001.mgz /home/knutjbj/freesurfer/ernie/mri/orig/001.mgz
Linux mypc 3.7.4-204.fc18.x86_64 #1 SMP Wed Jan 23 16:44:29 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s ernie exited with ERRORS at ti. 29. jan. 19:28:17 +0100 2013
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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