Hi all,
I am stuck with a license error in that freesurfer (after a simple
recon-all call for segmentation) continues to interrupt the process soon
after starting it, see complete copy of the error log file below.
I have freshly installed Freesurfer FROM SCRATCH and applied for a new
licence file which lies at the appropriate location.
What does "INVALID LICENSE FILE" actually indicate, how can the file be
invalid?
What can be done and why does the programm run absolutely smoothly on
another Linux-64-bit system??
vG Philipp
Sat Aug 30 17:17:48 CEST 2014
/net/PE1/raid1/enigma-mdd/data/WG_989
/net/PE1/raid1/enigma-mdd/freesurfer/bin/recon-all
-subjid WG_989 -all -hippo-subfields
subjid WG_989
setenv SUBJECTS_DIR /net/PE1/raid1/enigma-mdd/data
FREESURFER_HOME /net/PE1/raid1/enigma-mdd/freesurfer
Actual FREESURFER_HOME /net/PE1/raid1/enigma-mdd/freesurfer
build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
Linux PE3 3.11.6-4-desktop #1 SMP PREEMPT Wed Oct 30 18:04:56 UTC 2013
(e6d4a27) 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 2066987
maxlocks unlimited
maxsignal 2066987
maxmessage 819200
maxnice 0
maxrtprio 0
maxrttime unlimited
total used free shared buffers cached
Mem: 264665936 263134184 1531752 0 194912 255250340
-/+ buffers/cache: 7688932 256977004
Swap: 20972820 4929156 16043664
########################################
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: 2014/08/30-15:17:48-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: nmr Machine: PE3 Platform: Linux PlatformVersion:
3.11.6-4-desktop 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: 2014/08/30-15:17:49-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: nmr Machine: PE3 Platform: Linux
PlatformVersion: 3.11.6-4-desktop 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: 2014/08/30-15:17:49-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: nmr Machine: PE3 Platform: Linux PlatformVersion:
3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2014/08/30-15:17:49-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: nmr Machine: PE3 Platform: Linux PlatformVersion:
3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2014/08/30-15:17:49-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: nmr Machine: PE3 Platform: Linux
PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion:
40400
ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2014/08/30-15:17:49-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: nmr Machine: PE3 Platform: Linux PlatformVersion:
3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2014/08/30-15:17:49-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: nmr Machine: PE3 Platform: Linux PlatformVersion:
3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2014/08/30-15:17:49-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: nmr Machine: PE3 Platform: Linux
PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion:
40400
======= NUMBER OF OPENMP THREADS = 1 =======
ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2014/08/30-15:17:49-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: nmr Machine: PE3 Platform: Linux
PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion:
40400
ProgramName: mri_ca_normalize ProgramArguments: -all-info
ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:50-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: nmr Machine: PE3
Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC
CompilerVersion: 40400
ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2014/08/30-15:17:50-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: nmr Machine: PE3 Platform: Linux
PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion:
40400
ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2014/08/30-15:17:50-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: nmr Machine: PE3 Platform: Linux PlatformVersion:
3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2014/08/30-15:17:50-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: nmr Machine: PE3 Platform: Linux PlatformVersion:
3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2014/08/30-15:17:50-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: nmr Machine: PE3 Platform: Linux PlatformVersion:
3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2014/08/30-15:17:50-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: nmr Machine: PE3 Platform: Linux PlatformVersion:
3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_concatenate_lta ProgramArguments: -all-info
ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:50-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: nmr Machine: PE3 Platform:
Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC
CompilerVersion: 40400
ProgramName: mri_normalize_tp2 ProgramArguments: -all-info
ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:50-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: nmr Machine: PE3 Platform: Linux
PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion:
40400
ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2014/08/30-15:17:51-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: nmr Machine: PE3 Platform: Linux PlatformVersion:
3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2014/08/30-15:17:51-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: nmr Machine: PE3 Platform: Linux PlatformVersion:
3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2014/08/30-15:17:51-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: nmr Machine: PE3 Platform: Linux PlatformVersion:
3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2014/08/30-15:17:51-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: nmr Machine: PE3 Platform: Linux PlatformVersion:
3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_fix_topology ProgramArguments: -all-info
ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:51-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: nmr Machine: PE3 Platform: Linux
PlatformVersion: 3.11.6-4-desktop CompilerName: GCC CompilerVersion:
40400
ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2014/08/30-15:17:51-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: nmr Machine: PE3 Platform: Linux PlatformVersion:
3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2014/08/30-15:17:51-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: nmr Machine: PE3 Platform: Linux PlatformVersion:
3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_euler_number ProgramArguments: -all-info
ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:51-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: nmr Machine: PE3
Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC
CompilerVersion: 40400
ProgramName: mris_make_surfaces ProgramArguments: -all-info
ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:51-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: nmr Machine: PE3
Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC
CompilerVersion: 40400
ProgramName: mris_register ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2014/08/30-15:17:52-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: nmr Machine: PE3 Platform: Linux PlatformVersion:
3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2014/08/30-15:17:52-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: nmr Machine: PE3 Platform: Linux PlatformVersion:
3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_anatomical_stats ProgramArguments: -all-info
ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:52-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: nmr Machine: PE3 Platform:
Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC
CompilerVersion: 40400
ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2014/08/30-15:17:52-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: nmr Machine: PE3 Platform: Linux PlatformVersion:
3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400
ProgramName: mris_curvature_stats ProgramArguments: -all-info
ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:52-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: nmr Machine: PE3 Platform:
Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC
CompilerVersion: 40400
ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2014/08/30-15:17:52-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: nmr Machine: PE3 Platform: Linux PlatformVersion:
3.11.6-4-desktop 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: 2014/08/30-15:17:52-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: nmr Machine: PE3
Platform: Linux PlatformVersion: 3.11.6-4-desktop 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: 2014/08/30-15:17:52-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: nmr Machine: PE3
Platform: Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC
CompilerVersion: 40400
ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2014/08/30-15:17:52-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:
nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop
CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name:
stable5 $ TimeStamp: 2014/08/30-15:17:53-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:
nmr Machine: PE3 Platform: Linux PlatformVersion: 3.11.6-4-desktop
CompilerName: GCC CompilerVersion: 40400
ProgramName: mri_fuse_segmentations ProgramArguments: -all-info
ProgramVersion: $Name: stable5 $ TimeStamp: 2014/08/30-15:17:53-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: nmr Machine: PE3 Platform:
Linux PlatformVersion: 3.11.6-4-desktop CompilerName: GCC
CompilerVersion: 40400
ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion:
$Name: stable5 $ TimeStamp: 2014/08/30-15:17:53-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: nmr Machine: PE3 Platform: Linux PlatformVersion:
3.11.6-4-desktop CompilerName: GCC CompilerVersion: 40400
#######################################
GCADIR /net/PE1/raid1/enigma-mdd/freesurfer/average
GCA RB_all_2008-03-26.gca
GCASkull RB_all_withskull_2008-03-26.gca
AvgCurvTif average.curvature.filled.buckner40.tif
GCSDIR /net/PE1/raid1/enigma-mdd/freesurfer/average
GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs
#######################################
#--------------------------------------------
#@# MotionCor Sat Aug 30 17:17:53 CEST 2014
Found 1 runs
/net/PE1/raid1/enigma-mdd/data/WG_989/mri//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 /net/PE1/raid1/enigma-mdd/data/WG_989/mri//001.mgz
/net/PE1/raid1/enigma-mdd/data/WG_989/mri/rawavg.mgz
/net/PE1/raid1/enigma-mdd/data/WG_989
mri_convert /net/PE1/raid1/enigma-mdd/data/WG_989/mri/rawavg.mgz
/net/PE1/raid1/enigma-mdd/data/WG_989/mri/orig.mgz --conform
mri_convert /net/PE1/raid1/enigma-mdd/data/WG_989/mri/rawavg.mgz
/net/PE1/raid1/enigma-mdd/data/WG_989/mri/orig.mgz --conform
--------------------------------------------------------------------------
ERROR: Invalid FreeSurfer license key found in license file
/net/PE1/raid1/enigma-mdd/freesurfer/.license
If you are outside the NMR-Martinos Center,
go to http://surfer.nmr.mgh.harvard.edu to
get a valid license file (it's free).
If you are inside the NMR-Martinos Center,
make sure to source the standard environment.
--------------------------------------------------------------------------
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /net/PE1/raid1/enigma-mdd/data/WG_989/mri/rawavg.mgz...
Linux PE3 3.11.6-4-desktop #1 SMP PREEMPT Wed Oct 30 18:04:56 UTC 2013
(e6d4a27) x86_64 x86_64 x86_64 GNU/Linux
recon-all -s WG_989 exited with ERRORS at Sat Aug 30 17:17:57 CEST 2014
To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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