Hi all,
the license file problem I have described earlier today could be solved by following earlier hints on a workaround, mainly in the following two contributions:
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg29404.html
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg29433.html
It turned out to be the same problem: by an update of the SuSe system (from an old system 11.x to 13.x), the libcrypt.so.1 tool could not be used any more. Copying an old version (of an old SuSe system) to the freesurfer/lib folder, linking it and adding the folder to the LD_LIBRARY_PATH worked out...
I think the problem should be pointed out in the installation instructions. The error message (I am not a sys admin...) that the license file is not valid was very misleading.
Best wishes, Philipp
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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