Hi everyone,
I am trying to run the longitudinal stream on some images. I have 3
timepoints, and 2 of them finished the stream just fine, but a third quits
during autorecon1 during the 3rd and final longitudinal step. There is no
error message or anything, it just stops. The log file is attached--any
insight into what is going wrong will be appreciated.
Thanks,
Dana
Wed Oct 14 18:18:06 EDT 2009
/home/gfs06/dwm2003/FS/NC/NC2-CBIC.long.NC2-3T-base
/share/apps/freesurfer/bin/recon-all
-long NC2-CBIC NC2-3T-base -all
subjid NC2-CBIC.long.NC2-3T-base
setenv SUBJECTS_DIR /home/gfs06/dwm2003/FS/NC
FREESURFER_HOME /share/apps/freesurfer
Actual FREESURFER_HOME /share/apps/freesurfer
build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0
Linux compute-3-16.v4linux 2.6.18-53.el5 #1 SMP Wed Oct 10 16:34:19 EDT 2007 x86_64 x86_64 x86_64 GNU/Linux
cputime unlimited
filesize unlimited
datasize unlimited
stacksize 10240 kbytes
coredumpsize 0 kbytes
memoryuse unlimited
vmemoryuse unlimited
descriptors 1024
memorylocked 32 kbytes
maxproc 137216
total used free shared buffers cached
Mem: 16439348 1225236 15214112 0 107636 919464
-/+ buffers/cache: 198136 16241212
Swap: 8385920 0 8385920
########################################
program versions used
$Id: recon-all,v 1.133.2.57 2009/08/06 18:27:48 nicks Exp $
$Id: mri_motion_correct.fsl,v 1.7.2.1 2008/02/29 20:17:11 nicks Exp $
mri_convert -all-info
ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/14-22:18:07-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ User: dwm2003 Machine: compute-3-16.v4linux Platform: Linux PlatformVersion: 2.6.18-53.el5 CompilerName: GCC CompilerVersion: 30400
FLIRT version 5.5
$Id: talairach_avi,v 1.4.2.1 2009/07/30 19:22:07 nicks Exp $
mri_convert --version
stable4
ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/14-22:18:07-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: tkregister2.c,v 1.86.2.12 2009/03/19 22:04:20 greve Exp $ User: dwm2003 Machine: compute-3-16.v4linux Platform: Linux PlatformVersion: 2.6.18-53.el5 CompilerName: GCC CompilerVersion: 30400
Program nu_correct, built from:
Package MNI N3, version 1.10, compiled by ni...@minerva (x86_64-unknown-linux-gnu) on 2005-11-15 at 20:37:35
ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/14-22:18:07-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_normalize.c,v 1.52.2.2 2008/05/12 17:34:55 nicks Exp $ User: dwm2003 Machine: compute-3-16.v4linux Platform: Linux PlatformVersion: 2.6.18-53.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/14-22:18:07-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_watershed.cpp,v 1.67.2.5 2009/05/05 19:17:42 nicks Exp $ User: dwm2003 Machine: compute-3-16.v4linux Platform: Linux PlatformVersion: 2.6.18-53.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/14-22:18:07-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_segment.c,v 1.33.2.2 2007/11/21 04:38:38 nicks Exp $ User: dwm2003 Machine: compute-3-16.v4linux Platform: Linux PlatformVersion: 2.6.18-53.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/14-22:18:07-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_label2label.c,v 1.33 2007/08/10 18:23:46 greve Exp $ User: dwm2003 Machine: compute-3-16.v4linux Platform: Linux PlatformVersion: 2.6.18-53.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/14-22:18:07-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_em_register.c,v 1.57.2.2 2008/12/29 17:22:03 nicks Exp $ User: dwm2003 Machine: compute-3-16.v4linux Platform: Linux PlatformVersion: 2.6.18-53.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/14-22:18:07-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_ca_normalize.c,v 1.38.2.3 2009/08/02 15:00:46 nicks Exp $ User: dwm2003 Machine: compute-3-16.v4linux Platform: Linux PlatformVersion: 2.6.18-53.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/14-22:18:07-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_ca_register.c,v 1.63.2.3 2009/07/30 22:39:45 nicks Exp $ User: dwm2003 Machine: compute-3-16.v4linux Platform: Linux PlatformVersion: 2.6.18-53.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/14-22:18:07-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_ca_label.c,v 1.80.2.8 2009/07/30 23:22:53 nicks Exp $ User: dwm2003 Machine: compute-3-16.v4linux Platform: Linux PlatformVersion: 2.6.18-53.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/14-22:18:07-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_pretess.c,v 1.16 2007/01/18 20:23:47 nicks Exp $ User: dwm2003 Machine: compute-3-16.v4linux Platform: Linux PlatformVersion: 2.6.18-53.el5 CompilerName: GCC CompilerVersion: 30400
unknown option -ALL-INFO
ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/14-22:18:07-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_fill.c,v 1.111 2007/07/19 20:16:38 fischl Exp $ User: dwm2003 Machine: compute-3-16.v4linux Platform: Linux PlatformVersion: 2.6.18-53.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/14-22:18:07-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_tessellate.c,v 1.32 2007/04/26 21:44:21 fischl Exp $ User: dwm2003 Machine: compute-3-16.v4linux Platform: Linux PlatformVersion: 2.6.18-53.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/14-22:18:07-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_concatenate_lta.c,v 1.3.2.1 2009/05/06 23:40:38 nicks Exp $ User: dwm2003 Machine: compute-3-16.v4linux Platform: Linux PlatformVersion: 2.6.18-53.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/14-22:18:07-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_normalize_tp2.c,v 1.6 2007/01/08 18:10:12 nicks Exp $ User: dwm2003 Machine: compute-3-16.v4linux Platform: Linux PlatformVersion: 2.6.18-53.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/14-22:18:07-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mris_smooth.c,v 1.21 2007/01/01 18:16:19 fischl Exp $ User: dwm2003 Machine: compute-3-16.v4linux Platform: Linux PlatformVersion: 2.6.18-53.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/14-22:18:07-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mris_inflate.c,v 1.33.2.3 2008/04/22 19:47:47 nicks Exp $ User: dwm2003 Machine: compute-3-16.v4linux Platform: Linux PlatformVersion: 2.6.18-53.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/14-22:18:07-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mris_curvature.c,v 1.25 2007/07/20 16:42:32 fischl Exp $ User: dwm2003 Machine: compute-3-16.v4linux Platform: Linux PlatformVersion: 2.6.18-53.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/14-22:18:07-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mris_sphere.c,v 1.47 2007/03/08 18:36:08 greve Exp $ User: dwm2003 Machine: compute-3-16.v4linux Platform: Linux PlatformVersion: 2.6.18-53.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/14-22:18:07-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mris_fix_topology.c,v 1.43 2007/01/05 16:57:16 nicks Exp $ User: dwm2003 Machine: compute-3-16.v4linux Platform: Linux PlatformVersion: 2.6.18-53.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/14-22:18:07-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mris_topo_fixer.cpp,v 1.26.2.1 2007/11/18 03:06:20 nicks Exp $ User: dwm2003 Machine: compute-3-16.v4linux Platform: Linux PlatformVersion: 2.6.18-53.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/14-22:18:07-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mris_ca_label.c,v 1.23 2007/03/23 20:00:07 fischl Exp $ User: dwm2003 Machine: compute-3-16.v4linux Platform: Linux PlatformVersion: 2.6.18-53.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/14-22:18:07-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mris_euler_number.c,v 1.5 2006/12/29 02:09:10 nicks Exp $ User: dwm2003 Machine: compute-3-16.v4linux Platform: Linux PlatformVersion: 2.6.18-53.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/14-22:18:07-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mris_make_surfaces.c,v 1.99.2.5 2008/08/21 22:48:22 nicks Exp $ User: dwm2003 Machine: compute-3-16.v4linux Platform: Linux PlatformVersion: 2.6.18-53.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/14-22:18:07-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mris_register.c,v 1.48 2007/07/19 15:58:50 fischl Exp $ User: dwm2003 Machine: compute-3-16.v4linux Platform: Linux PlatformVersion: 2.6.18-53.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/14-22:18:07-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mris_anatomical_stats.c,v 1.54.2.7 2009/06/08 23:45:06 nicks Exp $ User: dwm2003 Machine: compute-3-16.v4linux Platform: Linux PlatformVersion: 2.6.18-53.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/14-22:18:07-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mrisp_paint.c,v 1.8 2007/02/13 16:57:23 fischl Exp $ User: dwm2003 Machine: compute-3-16.v4linux Platform: Linux PlatformVersion: 2.6.18-53.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/14-22:18:07-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mris_curvature_stats.c,v 1.28.2.5 2009/02/04 21:12:59 nicks Exp $ User: dwm2003 Machine: compute-3-16.v4linux Platform: Linux PlatformVersion: 2.6.18-53.el5 CompilerName: GCC CompilerVersion: 30400
$Id: mri_robust_register.cpp,v 1.22.2.1 2009/05/22 00:58:19 nicks Exp $
ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/14-22:18:07-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_robust_register.cpp,v 1.22.2.1 2009/05/22 00:58:19 nicks Exp $ User: dwm2003 Machine: compute-3-16.v4linux Platform: Linux PlatformVersion: 2.6.18-53.el5 CompilerName: GCC CompilerVersion: 30400
$Id: mri_robust_template.cpp,v 1.6.2.4 2009/08/05 16:30:00 nicks Exp $
ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/14-22:18:07-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_robust_template.cpp,v 1.6.2.4 2009/08/05 16:30:00 nicks Exp $ User: dwm2003 Machine: compute-3-16.v4linux Platform: Linux PlatformVersion: 2.6.18-53.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/14-22:18:07-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_and.c,v 1.2.2.1 2009/05/22 00:58:19 nicks Exp $ User: dwm2003 Machine: compute-3-16.v4linux Platform: Linux PlatformVersion: 2.6.18-53.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2009/10/14-22:18:07-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_or.c,v 1.1.2.1 2009/06/09 19:52:43 nicks Exp $ User: dwm2003 Machine: compute-3-16.v4linux Platform: Linux PlatformVersion: 2.6.18-53.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2009/10/14-22:18:07-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_fuse_segmentations.c,v 1.5.2.2 2009/06/10 19:42:00 nicks Exp $ User: dwm2003 Machine: compute-3-16.v4linux Platform: Linux PlatformVersion: 2.6.18-53.el5 CompilerName: GCC CompilerVersion: 30400
#######################################
GCA RB_all_2008-03-26.gca
GCASkull RB_all_withskull_2008-03-26.gca
AvgCurvTif average.curvature.filled.buckner40.tif
GCS curvature.buckner40.filled.desikan_killiany.2009-03-04.gcs
#######################################
#--------------------------------------------
#...@# MotionCor Wed Oct 14 18:18:07 EDT 2009
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