Thu Feb 20 04:07:52 EST 2014 /usr/local/freesurfer/subjects/GG /usr/local/freesurfer/bin/recon-all -s GG -i /home/fsuser/Downloads/GG2/IM_0184 subjid GG setenv SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos4-stable-pub-v5.2.0 Linux xubuntu-VirtualBox 3.2.0-59-generic #90-Ubuntu SMP Tue Jan 7 22:47:22 UTC 2014 i686 i686 i386 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 28137 maxlocks unlimited maxsignal 28137 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 3616244 740092 2876152 0 100848 412188 -/+ buffers/cache: 227056 3389188 Swap: 1944572 0 1944572 ######################################## program versions used $Id: recon-all,v 1.379.2.65 2013/02/19 22:34:56 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: 2014/02/20-09:07:52-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic 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: 2014/02/20-09:07:53-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@fishie (i686-pc-linux-gnu) on 2010-02-20 at 20:19:13 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:07:54-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:07:54-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:07:54-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:07:54-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:07:55-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:07:55-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_label2label.c,v 1.40.2.1 2011/05/19 17:21:56 greve Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:07:55-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:07:55-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:07:55-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:07:56-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:07:56-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:07:56-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:07:56-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:07:56-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:07:56-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:07:57-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:07:57-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:07:57-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:07:57-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:07:57-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:07:58-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:07:58-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:07:58-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2014/02/20-09:07:58-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mris_make_surfaces.c,v 1.127.2.3 2012/11/07 19:57:28 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:07:58-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:07:58-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:07:59-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:07:59-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:07:59-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:08:00-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 $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: 2014/02/20-09:08:00-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 $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: 2014/02/20-09:08:00-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:08:00-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:08:01-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:08:01-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:08:01-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /usr/local/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /usr/local/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /usr/local/freesurfer/subjects/GG mri_convert /home/fsuser/Downloads/GG2/IM_0184 /usr/local/freesurfer/subjects/GG/mri/orig/001.mgz mri_convert /home/fsuser/Downloads/GG2/IM_0184 /usr/local/freesurfer/subjects/GG/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/fsuser/Downloads/GG2/IM_0184... Starting DICOMRead2() dcmfile = /home/fsuser/Downloads/GG2/IM_0184 dcmdir = /home/fsuser/Downloads/GG2 Ref Series No = 101 Found 171 files, checking for dicoms Found 9 dicom files in series. First Sorting Computing Slice Direction Vs: 0 11 0 Vs: 0 1 0 Second Sorting Counting frames nframes = 1 nslices = 9 ndcmfiles = 9 PE Dir = COL (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- Loading pixel data TR=25.88, TE=4.37, TI=0.00, flip angle=45.00 warning: input volume axes are not orthogonal:i_dot_j = 0.000000, i_dot_k = 1.000000, j_dot_k = 0.000000 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (-0, -1, 0) warning: output volume axes are not orthogonal:i_dot_j = 0.000000, i_dot_k = 1.000000, j_dot_k = 0.000000 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (-0, -1, 0) writing to /usr/local/freesurfer/subjects/GG/mri/orig/001.mgz... #------------------------------------------ recon-all -s GG finished without error at Thu Feb 20 04:08:22 EST 2014 New invocation of recon-all Thu Feb 20 04:10:10 EST 2014 /usr/local/freesurfer/subjects/GG /usr/local/freesurfer/bin/recon-all -s GG -all subjid GG setenv SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos4-stable-pub-v5.2.0 Linux xubuntu-VirtualBox 3.2.0-59-generic #90-Ubuntu SMP Tue Jan 7 22:47:22 UTC 2014 i686 i686 i386 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 28137 maxlocks unlimited maxsignal 28137 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 3616244 964976 2651268 0 104216 627752 -/+ buffers/cache: 233008 3383236 Swap: 1944572 0 1944572 ######################################## program versions used $Id: recon-all,v 1.379.2.65 2013/02/19 22:34:56 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: 2014/02/20-09:10:10-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic 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: 2014/02/20-09:10:11-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@fishie (i686-pc-linux-gnu) on 2010-02-20 at 20:19:13 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:10:11-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:10:11-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:10:11-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:10:11-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:10:11-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:10:12-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_label2label.c,v 1.40.2.1 2011/05/19 17:21:56 greve Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:10:12-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:10:12-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:10:12-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:10:12-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:10:12-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:10:12-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:10:13-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:10:13-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:10:13-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:10:13-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:10:13-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:10:13-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:10:13-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:10:13-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:10:14-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:10:14-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:10:14-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2014/02/20-09:10:14-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mris_make_surfaces.c,v 1.127.2.3 2012/11/07 19:57:28 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:10:14-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:10:14-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:10:14-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:10:15-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:10:15-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:10:15-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 $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: 2014/02/20-09:10:15-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 $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: 2014/02/20-09:10:15-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:10:15-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:10:16-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:10:16-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:10:16-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /usr/local/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /usr/local/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #-------------------------------------------- #@# MotionCor Thu Feb 20 04:10:16 EST 2014 Found 1 runs /usr/local/freesurfer/subjects/GG/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 /usr/local/freesurfer/subjects/GG/mri/orig/001.mgz /usr/local/freesurfer/subjects/GG/mri/rawavg.mgz /usr/local/freesurfer/subjects/GG mri_convert /usr/local/freesurfer/subjects/GG/mri/rawavg.mgz /usr/local/freesurfer/subjects/GG/mri/orig.mgz --conform mri_convert /usr/local/freesurfer/subjects/GG/mri/rawavg.mgz /usr/local/freesurfer/subjects/GG/mri/orig.mgz --conform WARNING ==================++++++++++++++++++++++++======================================= The physical sizes are (300.00 mm, 300.00 mm, 99.00 mm), which cannot fit in 256^3 mm^3 volume. The resulting volume will have 300 slices. If you find problems, please let us know (freesurfer@nmr.mgh.harvard.edu). ==================================================++++++++++++++++++++++++=============== MRIresample(): source matrix has zero determinant; matrix is: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /usr/local/freesurfer/subjects/GG/mri/rawavg.mgz... TR=25.88, TE=4.37, TI=0.00, flip angle=45.00 warning: input volume axes are not orthogonal:i_dot_j = 0.000000, i_dot_k = 1.000000, j_dot_k = 0.000000 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (-0, -1, 0) Original Data has (0.9375, 0.9375, 11) mm size and (320, 320, 9) voxels. Data is conformed to 1 mm size and 300 voxels for all directions changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation -0.000 -0.000 -0.000 -6.900; -0.938 -0.000 -11.000 149.531; 0.000 -0.938 0.000 149.531; 0.000 0.000 0.000 1.000; Linux xubuntu-VirtualBox 3.2.0-59-generic #90-Ubuntu SMP Tue Jan 7 22:47:22 UTC 2014 i686 i686 i386 GNU/Linux recon-all -s GG exited with ERRORS at Thu Feb 20 04:10:21 EST 2014 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting New invocation of recon-all Thu Feb 20 04:12:13 EST 2014 /usr/local/freesurfer/subjects/GG /usr/local/freesurfer/bin/recon-all -s GG -all -notalairach subjid GG setenv SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos4-stable-pub-v5.2.0 Linux xubuntu-VirtualBox 3.2.0-59-generic #90-Ubuntu SMP Tue Jan 7 22:47:22 UTC 2014 i686 i686 i386 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 28137 maxlocks unlimited maxsignal 28137 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 3616244 1032704 2583540 0 105616 692588 -/+ buffers/cache: 234500 3381744 Swap: 1944572 0 1944572 ######################################## program versions used $Id: recon-all,v 1.379.2.65 2013/02/19 22:34:56 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: 2014/02/20-09:12:13-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic 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: 2014/02/20-09:12:13-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@fishie (i686-pc-linux-gnu) on 2010-02-20 at 20:19:13 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:12:14-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:12:14-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:12:14-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:12:14-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:12:14-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:12:14-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_label2label.c,v 1.40.2.1 2011/05/19 17:21:56 greve Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:12:14-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:12:15-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:12:15-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:12:15-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:12:15-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:12:15-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:12:15-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:12:15-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:12:16-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:12:16-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:12:16-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:12:16-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:12:16-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:12:16-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:12:16-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:12:17-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:12:17-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2014/02/20-09:12:17-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mris_make_surfaces.c,v 1.127.2.3 2012/11/07 19:57:28 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:12:17-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:12:17-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:12:17-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:12:17-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:12:18-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:12:18-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 $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: 2014/02/20-09:12:18-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 $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: 2014/02/20-09:12:18-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:12:18-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:12:18-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:12:18-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/20-09:12:19-GMT BuildTimeStamp: Feb 28 2013 15:02:59 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: fsuser Machine: xubuntu-VirtualBox Platform: Linux PlatformVersion: 3.2.0-59-generic CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /usr/local/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /usr/local/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #-------------------------------------------- #@# MotionCor Thu Feb 20 04:12:19 EST 2014 Found 1 runs /usr/local/freesurfer/subjects/GG/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 /usr/local/freesurfer/subjects/GG/mri/orig/001.mgz /usr/local/freesurfer/subjects/GG/mri/rawavg.mgz /usr/local/freesurfer/subjects/GG mri_convert /usr/local/freesurfer/subjects/GG/mri/rawavg.mgz /usr/local/freesurfer/subjects/GG/mri/orig.mgz --conform mri_convert /usr/local/freesurfer/subjects/GG/mri/rawavg.mgz /usr/local/freesurfer/subjects/GG/mri/orig.mgz --conform WARNING ==================++++++++++++++++++++++++======================================= The physical sizes are (300.00 mm, 300.00 mm, 99.00 mm), which cannot fit in 256^3 mm^3 volume. The resulting volume will have 300 slices. If you find problems, please let us know (freesurfer@nmr.mgh.harvard.edu). ==================================================++++++++++++++++++++++++=============== MRIresample(): source matrix has zero determinant; matrix is: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /usr/local/freesurfer/subjects/GG/mri/rawavg.mgz... TR=25.88, TE=4.37, TI=0.00, flip angle=45.00 warning: input volume axes are not orthogonal:i_dot_j = 0.000000, i_dot_k = 1.000000, j_dot_k = 0.000000 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (-0, -1, 0) Original Data has (0.9375, 0.9375, 11) mm size and (320, 320, 9) voxels. Data is conformed to 1 mm size and 300 voxels for all directions changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation -0.000 -0.000 -0.000 -6.900; -0.938 -0.000 -11.000 149.531; 0.000 -0.938 0.000 149.531; 0.000 0.000 0.000 1.000; Linux xubuntu-VirtualBox 3.2.0-59-generic #90-Ubuntu SMP Tue Jan 7 22:47:22 UTC 2014 i686 i686 i386 GNU/Linux recon-all -s GG exited with ERRORS at Thu Feb 20 04:12:23 EST 2014 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting