Hi Martin, Thanks for your reply.
rawavg.mgz and orig.mgz does exist. When I run the command I get the following error: mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz /home/XYZ/Projects/tmp/fs_test/test/mri /home/XYZ/Toolboxes/freesurfer/bin/mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz nIters 1 $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ Linux comp_name 4.4.0-22-generic #39-Ubuntu SMP Thu May 5 16:53:32 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux Wed May 11 16:03:55 CEST 2016 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.3509 /home/XYZ/Projects/tmp/fs_test/test/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.3509/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.3509/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter 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.3509/nu0.mnc... -------------------------------------------------------- Iteration 1 Wed May 11 16:03:57 CEST 2016 nu_correct -clobber ./tmp.mri_nu_correct.mni.3509/nu0.mnc ./tmp.mri_nu_correct.mni.3509/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.3509/0/ -iterations 1000 -distance 50 Can't use 'defined(@array)' (Maybe you should just omit the defined()?) at /home/XYZ/Toolboxes/freesurfer/mni/bin/nu_estimate_np_and_em line 165. nu_correct: crashed while running nu_estimate_np_and_em (termination status=65280) ERROR: nu_correct best, mads On 05/11/2016 03:32 PM, Martin Reuter wrote: > Hi Mads, > > is the file being copied (does > /home/XYZ/Projects/tmp/fs_test/test/mri/rawavg.mgz and orig.mgz exist)? > If not, maybe some disk space / IO problem. > Also what happens when you run > > mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale > --i orig.mgz --o orig_nu.mgz > > directly? Maybe something is wrong with the MNI tools. > > Best, Martin > > On 05/11/2016 07:43 AM, Mads Jensen wrote: >> Dear FreeSurfer group, >> >> I get an error trying to run basic recon-all on a ubuntu 16.04 system. >> >> It finish with errors after a few minutes and I cannot find any help in >> the recon-all.log (pasted below). >> >> I have made the symbolic links from the installation notes. >> >> Any ideas or thoughts on what the problem might be or how to track it >> down would be very welcome. >> >> best regards, >> mads >> >> >> >> >> from bugr: >> FREESURFER_HOME: /home/XYZ/Toolboxes/freesurfer >> >> Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 >> >> Debian version: stretch/sid >> >> Kernel info: Linux 4.4.0-22-generic x86_64 >> >> >> recon-all.log: >> >> Mon May 9 11:12:07 CEST 2016 >> /home/XYZ/Projects/tmp/fs_test/test >> /home/XYZ/Toolboxes/freesurfer/bin/recon-all >> -all -subjid test -i T1.mgz >> subjid test >> setenv SUBJECTS_DIR /home/XYZ/Projects/tmp/fs_test >> FREESURFER_HOME /home/XYZ/Toolboxes/freesurfer >> Actual FREESURFER_HOME /home/XYZ/Toolboxes/freesurfer >> build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 >> Linux comp_name 4.4.0-22-generic #39-Ubuntu SMP Thu May 5 16:53:32 UTC >> 2016 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 62044 >> maxlocks unlimited >> maxsignal 62044 >> maxmessage 819200 >> maxnice 0 >> maxrtprio 0 >> maxrttime unlimited >> >> total used free shared buff/cache >> available >> Mem: 15924580 3455984 375968 323648 12092628 11975092 >> Swap: 16616956 254220 16362736 >> >> ######################################## >> 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: 2016/05/09-09:12:08-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: XYZ Machine: comp_name Platform: Linux >> PlatformVersion: 4.4.0-22-generic 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: 2016/05/09-09:12:08-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: XYZ Machine: comp_name >> Platform: Linux PlatformVersion: 4.4.0-22-generic 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: 2016/05/09-09:12:08-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: XYZ Machine: comp_name Platform: Linux >> PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 >> ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: >> $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-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: XYZ Machine: comp_name Platform: Linux >> PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 >> ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: >> $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-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: XYZ Machine: comp_name Platform: Linux >> PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 >> ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: >> $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-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: XYZ Machine: comp_name Platform: Linux >> PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 >> ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: >> $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-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: XYZ Machine: comp_name Platform: Linux >> PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 >> ProgramName: mri_label2label ProgramArguments: -all-info >> ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-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: XYZ Machine: comp_name >> Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC >> CompilerVersion: 40400 >> >> >> ======= NUMBER OF OPENMP THREADS = 1 ======= >> ProgramName: mri_em_register ProgramArguments: -all-info >> ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-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: XYZ Machine: comp_name >> Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC >> CompilerVersion: 40400 >> ProgramName: mri_ca_normalize ProgramArguments: -all-info >> ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:08-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: XYZ Machine: comp_name >> Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC >> CompilerVersion: 40400 >> ProgramName: mri_ca_register ProgramArguments: -all-info >> ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-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: XYZ Machine: comp_name >> Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC >> CompilerVersion: 40400 >> ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: >> $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-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: XYZ Machine: comp_name Platform: Linux >> PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 >> ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: >> $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-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: XYZ Machine: comp_name Platform: Linux >> PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 >> ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: >> $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-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: XYZ Machine: comp_name Platform: Linux >> PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 >> ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: >> $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-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: XYZ Machine: comp_name Platform: Linux >> PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 >> ProgramName: mri_concatenate_lta ProgramArguments: -all-info >> ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-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: XYZ Machine: comp_name >> Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC >> CompilerVersion: 40400 >> ProgramName: mri_normalize_tp2 ProgramArguments: -all-info >> ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-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: XYZ Machine: comp_name >> Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC >> CompilerVersion: 40400 >> ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: >> $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-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: XYZ Machine: comp_name Platform: Linux >> PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 >> ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: >> $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-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: XYZ Machine: comp_name Platform: Linux >> PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 >> ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: >> $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-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: XYZ Machine: comp_name Platform: Linux >> PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 >> ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: >> $Name: stable5 $ TimeStamp: 2016/05/09-09:12:09-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: XYZ Machine: comp_name Platform: Linux >> PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 >> ProgramName: mris_fix_topology ProgramArguments: -all-info >> ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-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: XYZ Machine: comp_name >> Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC >> CompilerVersion: 40400 >> ProgramName: mris_topo_fixer ProgramArguments: -all-info >> ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-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: XYZ Machine: comp_name >> Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC >> CompilerVersion: 40400 >> ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: >> $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-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: XYZ Machine: comp_name Platform: Linux >> PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 >> ProgramName: mris_euler_number ProgramArguments: -all-info >> ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-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: XYZ Machine: comp_name >> Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC >> CompilerVersion: 40400 >> ProgramName: mris_make_surfaces ProgramArguments: -all-info >> ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-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: XYZ Machine: comp_name >> Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC >> CompilerVersion: 40400 >> ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: >> $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-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: XYZ Machine: comp_name Platform: Linux >> PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 >> ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: >> $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-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: XYZ Machine: comp_name Platform: Linux >> PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 >> ProgramName: mris_anatomical_stats ProgramArguments: -all-info >> ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-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: >> XYZ Machine: comp_name Platform: Linux PlatformVersion: >> 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 >> ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: >> $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-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: XYZ Machine: comp_name Platform: Linux >> PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 >> ProgramName: mris_curvature_stats ProgramArguments: -all-info >> ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:10-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: XYZ Machine: comp_name >> Platform: Linux PlatformVersion: 4.4.0-22-generic CompilerName: GCC >> CompilerVersion: 40400 >> ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: >> $Name: stable5 $ TimeStamp: 2016/05/09-09:12:11-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: XYZ Machine: comp_name Platform: Linux >> PlatformVersion: 4.4.0-22-generic 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: 2016/05/09-09:12:11-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: >> 4.4.0-22-generic 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: 2016/05/09-09:12:11-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: >> 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 >> ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: >> $Name: stable5 $ TimeStamp: 2016/05/09-09:12:11-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: XYZ Machine: comp_name Platform: Linux >> PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 >> ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: >> stable5 $ TimeStamp: 2016/05/09-09:12:11-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: XYZ Machine: comp_name Platform: Linux PlatformVersion: >> 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 >> ProgramName: mri_fuse_segmentations ProgramArguments: -all-info >> ProgramVersion: $Name: stable5 $ TimeStamp: 2016/05/09-09:12:11-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: >> XYZ Machine: comp_name Platform: Linux PlatformVersion: >> 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 >> ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: >> $Name: stable5 $ TimeStamp: 2016/05/09-09:12:11-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: XYZ Machine: comp_name Platform: Linux >> PlatformVersion: 4.4.0-22-generic CompilerName: GCC CompilerVersion: 40400 >> ####################################### >> GCADIR /home/XYZ/Toolboxes/freesurfer/average >> GCA RB_all_2008-03-26.gca >> GCASkull RB_all_withskull_2008-03-26.gca >> AvgCurvTif average.curvature.filled.buckner40.tif >> GCSDIR /home/XYZ/Toolboxes/freesurfer/average >> GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs >> ####################################### >> /home/XYZ/Projects/tmp/fs_test/test >> >> mri_convert /home/XYZ/Projects/tmp/fs_test/T1.mgz >> /home/XYZ/Projects/tmp/fs_test/test/mri/orig/001.mgz >> >> mri_convert /home/XYZ/Projects/tmp/fs_test/T1.mgz >> /home/XYZ/Projects/tmp/fs_test/test/mri/orig/001.mgz >> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ >> reading from /home/XYZ/Projects/tmp/fs_test/T1.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) >> writing to /home/XYZ/Projects/tmp/fs_test/test/mri/orig/001.mgz... >> #-------------------------------------------- >> #@# MotionCor Mon May 9 11:12:13 CEST 2016 >> Found 1 runs >> /home/XYZ/Projects/tmp/fs_test/test/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 /home/XYZ/Projects/tmp/fs_test/test/mri/orig/001.mgz >> /home/XYZ/Projects/tmp/fs_test/test/mri/rawavg.mgz >> >> /home/XYZ/Projects/tmp/fs_test/test >> >> mri_convert /home/XYZ/Projects/tmp/fs_test/test/mri/rawavg.mgz >> /home/XYZ/Projects/tmp/fs_test/test/mri/orig.mgz --conform >> >> mri_convert /home/XYZ/Projects/tmp/fs_test/test/mri/rawavg.mgz >> /home/XYZ/Projects/tmp/fs_test/test/mri/orig.mgz --conform >> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ >> reading from /home/XYZ/Projects/tmp/fs_test/test/mri/rawavg.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) >> Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels. >> Data is conformed to 1 mm size and 256 voxels for all directions >> writing to /home/XYZ/Projects/tmp/fs_test/test/mri/orig.mgz... >> >> mri_add_xform_to_header -c >> /home/XYZ/Projects/tmp/fs_test/test/mri/transforms/talairach.xfm >> /home/XYZ/Projects/tmp/fs_test/test/mri/orig.mgz >> /home/XYZ/Projects/tmp/fs_test/test/mri/orig.mgz >> >> INFO: extension is mgz >> #-------------------------------------------- >> #@# Talairach Mon May 9 11:12:19 CEST 2016 >> /home/XYZ/Projects/tmp/fs_test/test/mri >> >> mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale >> --i orig.mgz --o orig_nu.mgz >> >> Linux comp_name 4.4.0-22-generic #39-Ubuntu SMP Thu May 5 16:53:32 UTC >> 2016 x86_64 x86_64 x86_64 GNU/Linux >> >> recon-all -s test exited with ERRORS at Mon May 9 11:12:21 CEST 2016 >> >> To report a problem, see >> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. 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