Dear FS experts,
I have a problem with the command "recon-all".
In many cases when I use it on the same brain's MRI, on the CLUSTER COMPUTING
INFRASTRUCTURE, about 40% of my jobs finish without erros while the other are
killed at the command "nu_currect", as you can see from the file.log in
attachment.
Do you have any suggestions?
Thanks a lot for your help.
Best regardes,
Andrea
Thu May 23 13:58:52 CEST 2013
/lustre/home/tateo/Simulazione_FREESURF_GRID/Segmentazione/SUB_Or_test_16/001
/opt/exp_soft/mag/freesurfer/bin/recon-all
-debug -s 001 -autorecon-all
subjid 001
setenv SUBJECTS_DIR /lustre/home/tateo/Simulazione_FREESURF_GRID/Segmentazione/SUB_Or_test_16
FREESURFER_HOME /opt/exp_soft/mag/freesurfer
Actual FREESURFER_HOME /opt/exp_soft/mag/freesurfer
build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
Linux pccms114.ba.infn.it 2.6.18-348.1.1.el5 #1 SMP Thu Jan 24 13:25:42 CET 2013 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 32768
memorylocked 32 kbytes
maxproc 386293
total used free shared buffers cached
Mem: 49448428 46232160 3216268 0 900488 29561664
-/+ buffers/cache: 15770008 33678420
Swap: 16779884 613964 16165920
########################################
program versions used
$Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 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: 2013/05/23-11:58:53-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ User: tateo Machine: pccms114.ba.infn.it Platform: Linux PlatformVersion: 2.6.18-348.1.1.el5 CompilerName: GCC CompilerVersion: 30400
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: 2013/05/23-11:58:53-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: tateo Machine: pccms114.ba.infn.it Platform: Linux PlatformVersion: 2.6.18-348.1.1.el5 CompilerName: GCC CompilerVersion: 30400
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: 2013/05/23-11:58:53-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: tateo Machine: pccms114.ba.infn.it Platform: Linux PlatformVersion: 2.6.18-348.1.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-11:58:53-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize.c,v 1.73 2011/03/11 20:55:38 fischl Exp $ User: tateo Machine: pccms114.ba.infn.it Platform: Linux PlatformVersion: 2.6.18-348.1.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-11:58:53-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_watershed.cpp,v 1.96 2011/03/16 21:23:49 nicks Exp $ User: tateo Machine: pccms114.ba.infn.it Platform: Linux PlatformVersion: 2.6.18-348.1.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-11:58:54-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: tateo Machine: pccms114.ba.infn.it Platform: Linux PlatformVersion: 2.6.18-348.1.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-11:58:54-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: tateo Machine: pccms114.ba.infn.it Platform: Linux PlatformVersion: 2.6.18-348.1.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-11:58:54-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_label2label.c,v 1.40.2.1 2011/05/19 17:21:56 greve Exp $ User: tateo Machine: pccms114.ba.infn.it Platform: Linux PlatformVersion: 2.6.18-348.1.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-11:58:54-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_em_register.c,v 1.84 2011/03/16 21:23:48 nicks Exp $ User: tateo Machine: pccms114.ba.infn.it Platform: Linux PlatformVersion: 2.6.18-348.1.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-11:58:54-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_normalize.c,v 1.52 2011/03/02 00:04:14 nicks Exp $ User: tateo Machine: pccms114.ba.infn.it Platform: Linux PlatformVersion: 2.6.18-348.1.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-11:58:54-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_register.c,v 1.78 2011/03/02 14:27:40 fischl Exp $ User: tateo Machine: pccms114.ba.infn.it Platform: Linux PlatformVersion: 2.6.18-348.1.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-11:58:54-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_label.c,v 1.96 2011/03/02 00:04:13 nicks Exp $ User: tateo Machine: pccms114.ba.infn.it Platform: Linux PlatformVersion: 2.6.18-348.1.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-11:58:54-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: tateo Machine: pccms114.ba.infn.it Platform: Linux PlatformVersion: 2.6.18-348.1.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-11:58:55-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: tateo Machine: pccms114.ba.infn.it Platform: Linux PlatformVersion: 2.6.18-348.1.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-11:58:55-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: tateo Machine: pccms114.ba.infn.it Platform: Linux PlatformVersion: 2.6.18-348.1.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-11:58:55-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: tateo Machine: pccms114.ba.infn.it Platform: Linux PlatformVersion: 2.6.18-348.1.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-11:58:55-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: tateo Machine: pccms114.ba.infn.it Platform: Linux PlatformVersion: 2.6.18-348.1.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-11:58:55-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: tateo Machine: pccms114.ba.infn.it Platform: Linux PlatformVersion: 2.6.18-348.1.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-11:58:55-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: tateo Machine: pccms114.ba.infn.it Platform: Linux PlatformVersion: 2.6.18-348.1.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-11:58:55-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: tateo Machine: pccms114.ba.infn.it Platform: Linux PlatformVersion: 2.6.18-348.1.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-11:58:56-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: tateo Machine: pccms114.ba.infn.it Platform: Linux PlatformVersion: 2.6.18-348.1.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-11:58:56-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: tateo Machine: pccms114.ba.infn.it Platform: Linux PlatformVersion: 2.6.18-348.1.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-11:58:56-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: tateo Machine: pccms114.ba.infn.it Platform: Linux PlatformVersion: 2.6.18-348.1.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-11:58:56-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: tateo Machine: pccms114.ba.infn.it Platform: Linux PlatformVersion: 2.6.18-348.1.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-11:58:56-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_euler_number.c,v 1.8 2011/03/02 00:04:32 nicks Exp $ User: tateo Machine: pccms114.ba.infn.it Platform: Linux PlatformVersion: 2.6.18-348.1.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-11:58:57-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ User: tateo Machine: pccms114.ba.infn.it Platform: Linux PlatformVersion: 2.6.18-348.1.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-11:58:57-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: tateo Machine: pccms114.ba.infn.it Platform: Linux PlatformVersion: 2.6.18-348.1.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-11:58:57-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: tateo Machine: pccms114.ba.infn.it Platform: Linux PlatformVersion: 2.6.18-348.1.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-11:58:57-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: tateo Machine: pccms114.ba.infn.it Platform: Linux PlatformVersion: 2.6.18-348.1.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-11:58:58-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: tateo Machine: pccms114.ba.infn.it Platform: Linux PlatformVersion: 2.6.18-348.1.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-11:58:58-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: tateo Machine: pccms114.ba.infn.it Platform: Linux PlatformVersion: 2.6.18-348.1.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-11:58:58-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_calc.c,v 1.37.2.4 2011/04/04 00:53:08 nicks Exp $ User: tateo Machine: pccms114.ba.infn.it Platform: Linux PlatformVersion: 2.6.18-348.1.1.el5 CompilerName: GCC CompilerVersion: 30400
$Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $
ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-11:58:58-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ User: tateo Machine: pccms114.ba.infn.it Platform: Linux PlatformVersion: 2.6.18-348.1.1.el5 CompilerName: GCC CompilerVersion: 30400
$Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $
ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-11:58:59-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ User: tateo Machine: pccms114.ba.infn.it Platform: Linux PlatformVersion: 2.6.18-348.1.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-11:58:59-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: tateo Machine: pccms114.ba.infn.it Platform: Linux PlatformVersion: 2.6.18-348.1.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-11:58:59-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: tateo Machine: pccms114.ba.infn.it Platform: Linux PlatformVersion: 2.6.18-348.1.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-11:58:59-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: tateo Machine: pccms114.ba.infn.it Platform: Linux PlatformVersion: 2.6.18-348.1.1.el5 CompilerName: GCC CompilerVersion: 30400
ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/23-11:58:59-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ User: tateo Machine: pccms114.ba.infn.it Platform: Linux PlatformVersion: 2.6.18-348.1.1.el5 CompilerName: GCC CompilerVersion: 30400
#######################################
GCADIR /opt/exp_soft/mag/freesurfer/average
GCA RB_all_2008-03-26.gca
GCASkull RB_all_withskull_2008-03-26.gca
AvgCurvTif average.curvature.filled.buckner40.tif
GCSDIR /opt/exp_soft/mag/freesurfer/average
GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
#######################################
#--------------------------------------------
#@# MotionCor Thu May 23 13:59:00 CEST 2013
Found 1 runs
/lustre/home/tateo/Simulazione_FREESURF_GRID/Segmentazione/SUB_Or_test_16/001/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 /lustre/home/tateo/Simulazione_FREESURF_GRID/Segmentazione/SUB_Or_test_16/001/mri/orig/001.mgz /lustre/home/tateo/Simulazione_FREESURF_GRID/Segmentazione/SUB_Or_test_16/001/mri/rawavg.mgz
/lustre/home/tateo/Simulazione_FREESURF_GRID/Segmentazione/SUB_Or_test_16/001
mri_convert /lustre/home/tateo/Simulazione_FREESURF_GRID/Segmentazione/SUB_Or_test_16/001/mri/rawavg.mgz /lustre/home/tateo/Simulazione_FREESURF_GRID/Segmentazione/SUB_Or_test_16/001/mri/orig.mgz --conform
mri_convert /lustre/home/tateo/Simulazione_FREESURF_GRID/Segmentazione/SUB_Or_test_16/001/mri/rawavg.mgz /lustre/home/tateo/Simulazione_FREESURF_GRID/Segmentazione/SUB_Or_test_16/001/mri/orig.mgz --conform
$Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
reading from /lustre/home/tateo/Simulazione_FREESURF_GRID/Segmentazione/SUB_Or_test_16/001/mri/rawavg.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, -1, 0)
k_ras = (-0, -0, -1)
Original Data has (0.781, 2, 0.781) mm size and (256, 124, 256) 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 /lustre/home/tateo/Simulazione_FREESURF_GRID/Segmentazione/SUB_Or_test_16/001/mri/orig.mgz...
mri_add_xform_to_header -c /lustre/home/tateo/Simulazione_FREESURF_GRID/Segmentazione/SUB_Or_test_16/001/mri/transforms/talairach.xfm /lustre/home/tateo/Simulazione_FREESURF_GRID/Segmentazione/SUB_Or_test_16/001/mri/orig.mgz /lustre/home/tateo/Simulazione_FREESURF_GRID/Segmentazione/SUB_Or_test_16/001/mri/orig.mgz
INFO: extension is mgz
#--------------------------------------------
#@# Talairach Thu May 23 13:59:25 CEST 2013
/lustre/home/tateo/Simulazione_FREESURF_GRID/Segmentazione/SUB_Or_test_16/001/mri
talairach_avi --i orig.mgz --xfm transforms/talairach.auto.xfm
cp transforms/talairach.auto.xfm transforms/talairach.xfm
#--------------------------------------------
#@# Talairach Failure Detection Thu May 23 14:00:31 CEST 2013
/lustre/home/tateo/Simulazione_FREESURF_GRID/Segmentazione/SUB_Or_test_16/001/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7833, pval=0.8469 >= threshold=0.0050)
awk -f /opt/exp_soft/mag/freesurfer/bin/extract_talairach_avi_QA.awk /lustre/home/tateo/Simulazione_FREESURF_GRID/Segmentazione/SUB_Or_test_16/001/mri/transforms/talairach_avi.log
TalAviQA: 0.97411
z-score: 0
#--------------------------------------------
#@# Nu Intensity Correction Thu May 23 14:00:32 CEST 2013
mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2
/lustre/home/tateo/Simulazione_FREESURF_GRID/Segmentazione/SUB_Or_test_16/001/mri
/opt/exp_soft/mag/freesurfer/bin/mri_nu_correct.mni
--i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2
nIters 2
$Id: mri_nu_correct.mni,v 1.18 2011/03/02 20:16:39 nicks Exp $
Linux pccms114.ba.infn.it 2.6.18-348.1.1.el5 #1 SMP Thu Jan 24 13:25:42 CET 2013 x86_64 x86_64 x86_64 GNU/Linux
Thu May 23 14:00:32 CEST 2013
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
tmpdir is ./tmp.mri_nu_correct.mni.29808
/lustre/home/tateo/Simulazione_FREESURF_GRID/Segmentazione/SUB_Or_test_16/001/mri
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.29808/nu0.mnc -odt float
mri_convert orig.mgz ./tmp.mri_nu_correct.mni.29808/nu0.mnc -odt float
$Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
reading from orig.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0, -1)
k_ras = (0, 1, 0)
changing data type from uchar to float (noscale = 0)...
writing to ./tmp.mri_nu_correct.mni.29808/nu0.mnc...
--------------------------------------------------------
Iteration 1 Thu May 23 14:00:44 CEST 2013
nu_correct -clobber ./tmp.mri_nu_correct.mni.29808/nu0.mnc ./tmp.mri_nu_correct.mni.29808/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.29808/0/
[ta...@pccms114.ba.infn.it:/lustre/home/tateo/Simulazione_FREESURF_GRID/Segmentazione/SUB_Or_test_16/001/mri/] [2013-05-23 14:00:44] running:
/opt/exp_soft/mag/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.29808/0/ ./tmp.mri_nu_correct.mni.29808/nu0.mnc ./tmp.mri_nu_correct.mni.29808/nu1.imp
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Processing:.................................................................Done
Killed
ERROR: nu_correct
Linux pccms114.ba.infn.it 2.6.18-348.1.1.el5 #1 SMP Thu Jan 24 13:25:42 CET 2013 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 001 exited with ERRORS at Thu May 23 14:01:01 CEST 2013
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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