Hi Zeke, Thank you for clarifying this, it did help. You are right the perl version is 5.22
I will give the development version a try. best, mads On 05/11/2016 04:51 PM, Z K wrote: > Hello Mads, > > This is a recently discovered issue with the mni tools that ship with > freesurfer v5.3 and the latest version of perl (which probably comes > with Ubuntu 16). I know the issue exists with perl version 5.22 but I > dont know with what version the issue started. > > This has been fixed in the dev version of freesurfer and thus will be > fixed in the upcoming release of freesurfer version 6.0. Unfortunately, > you only have 2 options if you want to use freesurfer v5.3 on your > Ubuntu 16 machine: > > 1) Update to the newest Development Version of freesurfer: > > https://surfer.nmr.mgh.harvard.edu/fswiki/Download > > 2) Use the "sudo apt-get" tools to install a pre 5.22 version of perl on > your machine. > > Hope this helps. > > -Zeke > > > > > > On 05/11/2016 10:06 AM, Mads Jensen wrote: >> 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. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you > in error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
