Hi Philip, It seems that for a strange reason your ROIs are not getting saved. I never saw this one. I suppose that you are getting this error for all subjects? Do you have a way to transfer me one of your subject so that I can have a closer look?
Thanks, Marie On Aug 26, 2015, at 11:37 AM, Philip Deming <pdem...@wisc.edu<mailto:pdem...@wisc.edu>> wrote: Thanks for the quick response, Marie. Here's the full recon-all.log for this subject: FREESURFER_HOME /Volumes/apps/rhel6/freesurfer/freesurfer-latest Actual FREESURFER_HOME /Volumes/apps/rhel6/freesurfer/freesurfer_5.10_x86_64 build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Linux MRI-APP1.heri.psychiatry.wisc.edu<http://heri.psychiatry.wisc.edu> 2.6.32-431.11.2.el6.x86_64 #1 SMP Mon Mar 3 13:32:45 EST 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 1024 total used free shared buffers cached Mem: 99032816 98557552 475264 600 106540 92215824 -/+ buffers/cache: 6235188 92797628 Swap: 4194296 1154388 3039908 ######################################## program versions used $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 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: 2015/07/23-15:03:11-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ User: pdeming Machine: MRI-APP1.heri.psychiatry.wisc.edu<http://heri.psychiatry.wisc.edu> Platform: Linux PlatformVersion: 2.6.32-431.11.2.el6.x86_64 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: 2015/07/23-15:03:11-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: pdeming Machine: MRI-APP1.heri.psychiatry.wisc.edu<http://heri.psychiatry.wisc.edu> Platform: Linux PlatformVersion: 2.6.32-431.11.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 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: 2015/07/23-15:03:11-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: pdeming Machine: MRI-APP1.heri.psychiatry.wisc.edu<http://heri.psychiatry.wisc.edu> Platform: Linux PlatformVersion: 2.6.32-431.11.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/07/23-15:03:11-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize.c,v 1.73 2011/03/11 20:55:38 fischl Exp $ User: pdeming Machine: MRI-APP1.heri.psychiatry.wisc.edu<http://heri.psychiatry.wisc.edu> Platform: Linux PlatformVersion: 2.6.32-431.11.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/07/23-15:03:11-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_watershed.cpp,v 1.96 2011/03/16 21:23:49 nicks Exp $ User: pdeming Machine: MRI-APP1.heri.psychiatry.wisc.edu<http://heri.psychiatry.wisc.edu> Platform: Linux PlatformVersion: 2.6.32-431.11.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/07/23-15:03:11-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: pdeming Machine: MRI-APP1.heri.psychiatry.wisc.edu<http://heri.psychiatry.wisc.edu> Platform: Linux PlatformVersion: 2.6.32-431.11.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/07/23-15:03:12-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: pdeming Machine: MRI-APP1.heri.psychiatry.wisc.edu<http://heri.psychiatry.wisc.edu> Platform: Linux PlatformVersion: 2.6.32-431.11.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/07/23-15:03:12-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_label2label.c,v 1.40.2.1 2011/05/19 17:21:56 greve Exp $ User: pdeming Machine: MRI-APP1.heri.psychiatry.wisc.edu<http://heri.psychiatry.wisc.edu> Platform: Linux PlatformVersion: 2.6.32-431.11.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/07/23-15:03:12-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_em_register.c,v 1.84 2011/03/16 21:23:48 nicks Exp $ User: pdeming Machine: MRI-APP1.heri.psychiatry.wisc.edu<http://heri.psychiatry.wisc.edu> Platform: Linux PlatformVersion: 2.6.32-431.11.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/07/23-15:03:12-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_normalize.c,v 1.52 2011/03/02 00:04:14 nicks Exp $ User: pdeming Machine: MRI-APP1.heri.psychiatry.wisc.edu<http://heri.psychiatry.wisc.edu> Platform: Linux PlatformVersion: 2.6.32-431.11.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/07/23-15:03:12-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_register.c,v 1.78 2011/03/02 14:27:40 fischl Exp $ User: pdeming Machine: MRI-APP1.heri.psychiatry.wisc.edu<http://heri.psychiatry.wisc.edu> Platform: Linux PlatformVersion: 2.6.32-431.11.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/07/23-15:03:12-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_label.c,v 1.96 2011/03/02 00:04:13 nicks Exp $ User: pdeming Machine: MRI-APP1.heri.psychiatry.wisc.edu<http://heri.psychiatry.wisc.edu> Platform: Linux PlatformVersion: 2.6.32-431.11.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/07/23-15:03:12-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: pdeming Machine: MRI-APP1.heri.psychiatry.wisc.edu<http://heri.psychiatry.wisc.edu> Platform: Linux PlatformVersion: 2.6.32-431.11.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/07/23-15:03:12-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: pdeming Machine: MRI-APP1.heri.psychiatry.wisc.edu<http://heri.psychiatry.wisc.edu> Platform: Linux PlatformVersion: 2.6.32-431.11.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/07/23-15:03:12-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: pdeming Machine: MRI-APP1.heri.psychiatry.wisc.edu<http://heri.psychiatry.wisc.edu> Platform: Linux PlatformVersion: 2.6.32-431.11.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/07/23-15:03:13-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: pdeming Machine: MRI-APP1.heri.psychiatry.wisc.edu<http://heri.psychiatry.wisc.edu> Platform: Linux PlatformVersion: 2.6.32-431.11.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/07/23-15:03:13-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: pdeming Machine: MRI-APP1.heri.psychiatry.wisc.edu<http://heri.psychiatry.wisc.edu> Platform: Linux PlatformVersion: 2.6.32-431.11.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/07/23-15:03:13-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: pdeming Machine: MRI-APP1.heri.psychiatry.wisc.edu<http://heri.psychiatry.wisc.edu> Platform: Linux PlatformVersion: 2.6.32-431.11.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/07/23-15:03:13-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: pdeming Machine: MRI-APP1.heri.psychiatry.wisc.edu<http://heri.psychiatry.wisc.edu> Platform: Linux PlatformVersion: 2.6.32-431.11.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/07/23-15:03:13-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: pdeming Machine: MRI-APP1.heri.psychiatry.wisc.edu<http://heri.psychiatry.wisc.edu> Platform: Linux PlatformVersion: 2.6.32-431.11.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/07/23-15:03:13-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: pdeming Machine: MRI-APP1.heri.psychiatry.wisc.edu<http://heri.psychiatry.wisc.edu> Platform: Linux PlatformVersion: 2.6.32-431.11.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/07/23-15:03:13-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: pdeming Machine: MRI-APP1.heri.psychiatry.wisc.edu<http://heri.psychiatry.wisc.edu> Platform: Linux PlatformVersion: 2.6.32-431.11.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/07/23-15:03:13-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: pdeming Machine: MRI-APP1.heri.psychiatry.wisc.edu<http://heri.psychiatry.wisc.edu> Platform: Linux PlatformVersion: 2.6.32-431.11.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/07/23-15:03:13-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: pdeming Machine: MRI-APP1.heri.psychiatry.wisc.edu<http://heri.psychiatry.wisc.edu> Platform: Linux PlatformVersion: 2.6.32-431.11.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/07/23-15:03:14-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_euler_number.c,v 1.8 2011/03/02 00:04:32 nicks Exp $ User: pdeming Machine: MRI-APP1.heri.psychiatry.wisc.edu<http://heri.psychiatry.wisc.edu> Platform: Linux PlatformVersion: 2.6.32-431.11.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/07/23-15:03:14-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ User: pdeming Machine: MRI-APP1.heri.psychiatry.wisc.edu<http://heri.psychiatry.wisc.edu> Platform: Linux PlatformVersion: 2.6.32-431.11.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/07/23-15:03:14-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: pdeming Machine: MRI-APP1.heri.psychiatry.wisc.edu<http://heri.psychiatry.wisc.edu> Platform: Linux PlatformVersion: 2.6.32-431.11.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/07/23-15:03:14-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: pdeming Machine: MRI-APP1.heri.psychiatry.wisc.edu<http://heri.psychiatry.wisc.edu> Platform: Linux PlatformVersion: 2.6.32-431.11.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/07/23-15:03:14-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: pdeming Machine: MRI-APP1.heri.psychiatry.wisc.edu<http://heri.psychiatry.wisc.edu> Platform: Linux PlatformVersion: 2.6.32-431.11.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/07/23-15:03:14-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: pdeming Machine: MRI-APP1.heri.psychiatry.wisc.edu<http://heri.psychiatry.wisc.edu> Platform: Linux PlatformVersion: 2.6.32-431.11.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/07/23-15:03:14-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: pdeming Machine: MRI-APP1.heri.psychiatry.wisc.edu<http://heri.psychiatry.wisc.edu> Platform: Linux PlatformVersion: 2.6.32-431.11.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/07/23-15:03:14-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_calc.c,v 1.37.2.4 2011/04/04 00:53:08 nicks Exp $ User: pdeming Machine: MRI-APP1.heri.psychiatry.wisc.edu<http://heri.psychiatry.wisc.edu> Platform: Linux PlatformVersion: 2.6.32-431.11.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/07/23-15:03:14-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ User: pdeming Machine: MRI-APP1.heri.psychiatry.wisc.edu<http://heri.psychiatry.wisc.edu> Platform: Linux PlatformVersion: 2.6.32-431.11.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/07/23-15:03:14-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ User: pdeming Machine: MRI-APP1.heri.psychiatry.wisc.edu<http://heri.psychiatry.wisc.edu> Platform: Linux PlatformVersion: 2.6.32-431.11.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/07/23-15:03:14-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: pdeming Machine: MRI-APP1.heri.psychiatry.wisc.edu<http://heri.psychiatry.wisc.edu> Platform: Linux PlatformVersion: 2.6.32-431.11.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/07/23-15:03:15-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: pdeming Machine: MRI-APP1.heri.psychiatry.wisc.edu<http://heri.psychiatry.wisc.edu> Platform: Linux PlatformVersion: 2.6.32-431.11.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/07/23-15:03:15-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: pdeming Machine: MRI-APP1.heri.psychiatry.wisc.edu<http://heri.psychiatry.wisc.edu> Platform: Linux PlatformVersion: 2.6.32-431.11.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/07/23-15:03:15-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ User: pdeming Machine: MRI-APP1.heri.psychiatry.wisc.edu<http://heri.psychiatry.wisc.edu> Platform: Linux PlatformVersion: 2.6.32-431.11.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /Volumes/apps/rhel6/freesurfer/freesurfer-latest/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /Volumes/apps/rhel6/freesurfer/freesurfer-latest/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### INFO: current FREESURFER_HOME does not match that of previous processing. Current: /Volumes/apps/rhel6/freesurfer/freesurfer-latest Previous: /data2/grecc/freesurfer5.1.0 /Volumes/Vol3/Koenigs/WisPRIS_2013/UNM_PROC/FREESURFER/M87100094/surf #-------------------------------------------- #@# Local Gyrification Index lh Thu Jul 23 10:03:16 CDT 2015 mris_compute_lgi --i lh.pial ================= rm -Rf /Volumes/Vol3/Koenigs/WisPRIS_2013/UNM_PROC/FREESURFER/M87100094/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mkdir -p /Volumes/Vol3/Koenigs/WisPRIS_2013/UNM_PROC/FREESURFER/M87100094/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mris_fill -c -r 1 lh.pial /Volumes/Vol3/Koenigs/WisPRIS_2013/UNM_PROC/FREESURFER/M87100094/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz ================= reading surface from lh.pial... writing filled volume to /Volumes/Vol3/Koenigs/WisPRIS_2013/UNM_PROC/FREESURFER/M87100094/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz... conforming output volume setting resolution for intermediate calculations to 1.0000 ================= make_outer_surface('/Volumes/Vol3/Koenigs/WisPRIS_2013/UNM_PROC/FREESURFER/M87100094/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/Volumes/Vol3/Koenigs/WisPRIS_2013/UNM_PROC/FREESURFER/M87100094/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'); exit ================= < M A T L A B (R) > Copyright 1984-2014 The MathWorks, Inc. R2014a (8.3.0.532) 64-bit (glnxa64) February 11, 2014 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com<http://www.mathworks.com>. >> reading filled volume... closing volume... morphological closing done. writing outer surface... ================= mris_extract_main_component /Volumes/Vol3/Koenigs/WisPRIS_2013/UNM_PROC/FREESURFER/M87100094/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer /Volumes/Vol3/Koenigs/WisPRIS_2013/UNM_PROC/FREESURFER/M87100094/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-main ================= counting number of connected components... 64956 voxel in cpt #1: X=2 [v=64956,e=194862,f=129908] located at (-28.702967, -25.697208, 2.203984) For the whole surface: X=2 [v=64956,e=194862,f=129908] One single component has been found nothing to do done ================= mris_smooth -nw -n 30 /Volumes/Vol3/Koenigs/WisPRIS_2013/UNM_PROC/FREESURFER/M87100094/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-main ./lh.pial-outer-smoothed ================= smoothing for 30 iterations smoothing surface tessellation for 30 iterations... smoothing complete - recomputing first and second fundamental forms... ================= mris_euler_number ./lh.pial-outer-smoothed ================= euler # = v-e+f = 2g-2: 64956 - 194862 + 129908 = 2 --> 0 holes F =2V-4: 129908 = 129912-4 (0) 2E=3F: 389724 = 389724 (0) total defect index = 0 ================= mris_convert -n lh.pial-outer-smoothed /Volumes/Vol3/Koenigs/WisPRIS_2013/UNM_PROC/FREESURFER/M87100094/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-smoothed-normals.asc ================= ================= find_corresponding_center_FSformat('lh.pial','lh.pial-outer-smoothed',100,'/Volumes/Vol3/Koenigs/WisPRIS_2013/UNM_PROC/FREESURFER/M87100094/surf/tmp-mris_compute_lgi-lh.pial','/tmp/mrc_36149_.m'); exit ================= < M A T L A B (R) > Copyright 1984-2014 The MathWorks, Inc. R2014a (8.3.0.532) 64-bit (glnxa64) February 11, 2014 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com<http://www.mathworks.com>. >> FREESURFER_READ_SURF [v 1.2 ] ...reading surface file: lh.pial ...reading triangle file ...adding 1 to face indices for matlab compatibility. ...done ( 0.03 sec) FREESURFER_READ_SURF [v 1.2 ] ...reading surface file: lh.pial-outer-smoothed ...reading triangle file ...adding 1 to face indices for matlab compatibility. ...done ( 0.01 sec) deltaT = 14.7100 ================= make_roi_paths('lh.pial','lh.pial-outer-smoothed',25,100,'/Volumes/Vol3/Koenigs/WisPRIS_2013/UNM_PROC/FREESURFER/M87100094/surf/tmp-mris_compute_lgi-lh.pial','/tmp/mrp_36149_.m'); exit ================= < M A T L A B (R) > Copyright 1984-2014 The MathWorks, Inc. R2014a (8.3.0.532) 64-bit (glnxa64) February 11, 2014 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com<http://www.mathworks.com>. >> loading datas ... FREESURFER_READ_SURF [v 1.2 ] ...reading surface file: lh.pial ...reading triangle file ...adding 1 to face indices for matlab compatibility. ...done ( 0.03 sec) FREESURFER_READ_SURF [v 1.2 ] ...reading surface file: lh.pial-outer-smoothed ...reading triangle file ...adding 1 to face indices for matlab compatibility. ...done ( 0.01 sec) preparing outer mesh structure ... face 5000 / 129908 face 10000 / 129908 face 15000 / 129908 face 20000 / 129908 face 25000 / 129908 face 30000 / 129908 face 35000 / 129908 face 40000 / 129908 face 45000 / 129908 face 50000 / 129908 face 55000 / 129908 face 60000 / 129908 face 65000 / 129908 face 70000 / 129908 face 75000 / 129908 face 80000 / 129908 face 85000 / 129908 face 90000 / 129908 face 95000 / 129908 face 100000 / 129908 face 105000 / 129908 face 110000 / 129908 face 115000 / 129908 face 120000 / 129908 face 125000 / 129908 mesh_outer = vertices: [64956x3 double] faces: [129908x3 double] facesOfVertex: [64956x1 struct] preparing pial mesh structure ... ...searching for mesh edges...done (217.16 sec). ... creating path file for vertex 1 / 64956 area file for outer ROIs saved at 1 {Improper assignment with rectangular empty matrix. Error in dsearchn (line 79) [d(i),t(i)] = min(sum((x-yi).^2,2)); Error in mesh_vertex_nearest (line 29) nearestIndex = dsearchn(vertices,points); Error in reorganize_verticeslist (line 28) [nextindex,nextvalue]=mesh_vertex_nearest(mesh_total.vertices(remaininglist,:),mesh_total.vertices(verticeslist(start_vertex),:)); Error in make_roi_paths (line 93) reorglist = reorganize_verticeslist (mesh_total, A, mesh_outer, perim, verticeslist, step); } >> ERROR: make_roi_paths did not complete successfully! Linux MRI-APP1.heri.psychiatry.wisc.edu<http://heri.psychiatry.wisc.edu> 2.6.32-431.11.2.el6.x86_64 #1 SMP Mon Mar 3 13:32:45 EST 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s M87100094 exited with ERRORS at Thu Jul 23 10:08:31 CDT 2015 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting New invocation of recon-all Wed Aug 26 09:51:38 CDT 2015 /Volumes/Vol3/Koenigs/WisPRIS_2013/UNM_PROC/FREESURFER/M87100094 /usr/local/freesurfer/bin/recon-all -s M87100094/ -localGI subjid M87100094 setenv SUBJECTS_DIR /Volumes/Vol3/Koenigs/WisPRIS_2013/UNM_PROC/FREESURFER FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Linux KOENIGS-PC1 2.6.32-5-amd64 #1 SMP Wed Jun 17 16:09:06 UTC 2015 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 unlimited maxlocks unlimited maxsignal 16382 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 8180032 8053760 126272 0 408508 6972344 -/+ buffers/cache: 672908 7507124 Swap: 9912312 0 9912312 ######################################## program versions used $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 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: 2015/08/26-14:51:39-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ User: pdeming Machine: KOENIGS-PC1 Platform: Linux PlatformVersion: 2.6.32-5-amd64 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: 2015/08/26-14:51:39-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: pdeming Machine: KOENIGS-PC1 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 30400 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: 2015/08/26-14:51:39-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: pdeming Machine: KOENIGS-PC1 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/26-14:51:39-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize.c,v 1.73 2011/03/11 20:55:38 fischl Exp $ User: pdeming Machine: KOENIGS-PC1 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/26-14:51:40-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_watershed.cpp,v 1.96 2011/03/16 21:23:49 nicks Exp $ User: pdeming Machine: KOENIGS-PC1 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/26-14:51:40-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: pdeming Machine: KOENIGS-PC1 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/26-14:51:40-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: pdeming Machine: KOENIGS-PC1 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/26-14:51:40-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_label2label.c,v 1.40.2.1 2011/05/19 17:21:56 greve Exp $ User: pdeming Machine: KOENIGS-PC1 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/26-14:51:40-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_em_register.c,v 1.84 2011/03/16 21:23:48 nicks Exp $ User: pdeming Machine: KOENIGS-PC1 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/26-14:51:40-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_normalize.c,v 1.52 2011/03/02 00:04:14 nicks Exp $ User: pdeming Machine: KOENIGS-PC1 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/26-14:51:40-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_register.c,v 1.78 2011/03/02 14:27:40 fischl Exp $ User: pdeming Machine: KOENIGS-PC1 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/26-14:51:41-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_label.c,v 1.96 2011/03/02 00:04:13 nicks Exp $ User: pdeming Machine: KOENIGS-PC1 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/26-14:51:41-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: pdeming Machine: KOENIGS-PC1 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/26-14:51:41-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: pdeming Machine: KOENIGS-PC1 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/26-14:51:41-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: pdeming Machine: KOENIGS-PC1 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/26-14:51:41-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: pdeming Machine: KOENIGS-PC1 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/26-14:51:41-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: pdeming Machine: KOENIGS-PC1 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/26-14:51:41-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: pdeming Machine: KOENIGS-PC1 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/26-14:51:41-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: pdeming Machine: KOENIGS-PC1 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/26-14:51:41-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: pdeming Machine: KOENIGS-PC1 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/26-14:51:42-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: pdeming Machine: KOENIGS-PC1 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/26-14:51:42-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: pdeming Machine: KOENIGS-PC1 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/26-14:51:42-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: pdeming Machine: KOENIGS-PC1 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/26-14:51:42-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: pdeming Machine: KOENIGS-PC1 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/26-14:51:42-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_euler_number.c,v 1.8 2011/03/02 00:04:32 nicks Exp $ User: pdeming Machine: KOENIGS-PC1 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/26-14:51:42-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ User: pdeming Machine: KOENIGS-PC1 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/26-14:51:42-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: pdeming Machine: KOENIGS-PC1 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/26-14:51:42-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: pdeming Machine: KOENIGS-PC1 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/26-14:51:42-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: pdeming Machine: KOENIGS-PC1 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/26-14:51:43-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: pdeming Machine: KOENIGS-PC1 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/26-14:51:43-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: pdeming Machine: KOENIGS-PC1 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/26-14:51:43-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_calc.c,v 1.37.2.4 2011/04/04 00:53:08 nicks Exp $ User: pdeming Machine: KOENIGS-PC1 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/26-14:51:43-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ User: pdeming Machine: KOENIGS-PC1 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/26-14:51:43-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ User: pdeming Machine: KOENIGS-PC1 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/26-14:51:43-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: pdeming Machine: KOENIGS-PC1 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/26-14:51:43-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: pdeming Machine: KOENIGS-PC1 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/26-14:51:43-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: pdeming Machine: KOENIGS-PC1 Platform: Linux PlatformVersion: 2.6.32-5-amd64 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2015/08/26-14:51:44-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ User: pdeming Machine: KOENIGS-PC1 Platform: Linux PlatformVersion: 2.6.32-5-amd64 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 ####################################### INFO: current FREESURFER_HOME does not match that of previous processing. Current: /usr/local/freesurfer Previous: /data2/grecc/freesurfer5.1.0 /Volumes/Vol3/Koenigs/WisPRIS_2013/UNM_PROC/FREESURFER/M87100094/surf #-------------------------------------------- #@# Local Gyrification Index lh Wed Aug 26 09:51:45 CDT 2015 mris_compute_lgi --i lh.pial ================= rm -Rf /Volumes/Vol3/Koenigs/WisPRIS_2013/UNM_PROC/FREESURFER/M87100094/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mkdir -p /Volumes/Vol3/Koenigs/WisPRIS_2013/UNM_PROC/FREESURFER/M87100094/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mris_fill -c -r 1 lh.pial /Volumes/Vol3/Koenigs/WisPRIS_2013/UNM_PROC/FREESURFER/M87100094/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz ================= reading surface from lh.pial... writing filled volume to /Volumes/Vol3/Koenigs/WisPRIS_2013/UNM_PROC/FREESURFER/M87100094/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz... conforming output volume setting resolution for intermediate calculations to 1.0000 ================= make_outer_surface('/Volumes/Vol3/Koenigs/WisPRIS_2013/UNM_PROC/FREESURFER/M87100094/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/Volumes/Vol3/Koenigs/WisPRIS_2013/UNM_PROC/FREESURFER/M87100094/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'); exit ================= < M A T L A B (R) > Copyright 1984-2014 The MathWorks, Inc. R2014a (8.3.0.532) 64-bit (glnxa64) February 11, 2014 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com<http://www.mathworks.com>. >> reading filled volume... closing volume... morphological closing done. writing outer surface... ================= mris_extract_main_component /Volumes/Vol3/Koenigs/WisPRIS_2013/UNM_PROC/FREESURFER/M87100094/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer /Volumes/Vol3/Koenigs/WisPRIS_2013/UNM_PROC/FREESURFER/M87100094/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-main ================= counting number of connected components... 64956 voxel in cpt #1: X=2 [v=64956,e=194862,f=129908] located at (-28.702967, -25.697208, 2.203984) For the whole surface: X=2 [v=64956,e=194862,f=129908] One single component has been found nothing to do done ================= mris_smooth -nw -n 30 /Volumes/Vol3/Koenigs/WisPRIS_2013/UNM_PROC/FREESURFER/M87100094/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-main ./lh.pial-outer-smoothed ================= smoothing for 30 iterations smoothing surface tessellation for 30 iterations... smoothing complete - recomputing first and second fundamental forms... ================= mris_euler_number ./lh.pial-outer-smoothed ================= euler # = v-e+f = 2g-2: 64956 - 194862 + 129908 = 2 --> 0 holes F =2V-4: 129908 = 129912-4 (0) 2E=3F: 389724 = 389724 (0) total defect index = 0 ================= mris_convert -n lh.pial-outer-smoothed /Volumes/Vol3/Koenigs/WisPRIS_2013/UNM_PROC/FREESURFER/M87100094/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-smoothed-normals.asc ================= ================= find_corresponding_center_FSformat('lh.pial','lh.pial-outer-smoothed',100,'/Volumes/Vol3/Koenigs/WisPRIS_2013/UNM_PROC/FREESURFER/M87100094/surf/tmp-mris_compute_lgi-lh.pial','/tmp/mrc_28792_.m'); exit ================= < M A T L A B (R) > Copyright 1984-2014 The MathWorks, Inc. R2014a (8.3.0.532) 64-bit (glnxa64) February 11, 2014 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com<http://www.mathworks.com>. >> FREESURFER_READ_SURF [v 1.2 ] ...reading surface file: lh.pial ...reading triangle file ...adding 1 to face indices for matlab compatibility. ...done ( 0.03 sec) FREESURFER_READ_SURF [v 1.2 ] ...reading surface file: lh.pial-outer-smoothed ...reading triangle file ...adding 1 to face indices for matlab compatibility. ...done ( 0.01 sec) deltaT = 6.4500 ================= make_roi_paths('lh.pial','lh.pial-outer-smoothed',25,100,'/Volumes/Vol3/Koenigs/WisPRIS_2013/UNM_PROC/FREESURFER/M87100094/surf/tmp-mris_compute_lgi-lh.pial','/tmp/mrp_28792_.m'); exit ================= < M A T L A B (R) > Copyright 1984-2014 The MathWorks, Inc. R2014a (8.3.0.532) 64-bit (glnxa64) February 11, 2014 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com<http://www.mathworks.com>. >> loading datas ... FREESURFER_READ_SURF [v 1.2 ] ...reading surface file: lh.pial ...reading triangle file ...adding 1 to face indices for matlab compatibility. ...done ( 0.03 sec) FREESURFER_READ_SURF [v 1.2 ] ...reading surface file: lh.pial-outer-smoothed ...reading triangle file ...adding 1 to face indices for matlab compatibility. ...done ( 0.01 sec) preparing outer mesh structure ... face 5000 / 129908 face 10000 / 129908 face 15000 / 129908 face 20000 / 129908 face 25000 / 129908 face 30000 / 129908 face 35000 / 129908 face 40000 / 129908 face 45000 / 129908 face 50000 / 129908 face 55000 / 129908 face 60000 / 129908 face 65000 / 129908 face 70000 / 129908 face 75000 / 129908 face 80000 / 129908 face 85000 / 129908 face 90000 / 129908 face 95000 / 129908 face 100000 / 129908 face 105000 / 129908 face 110000 / 129908 face 115000 / 129908 face 120000 / 129908 face 125000 / 129908 mesh_outer = vertices: [64956x3 double] faces: [129908x3 double] facesOfVertex: [64956x1 struct] preparing pial mesh structure ... ...searching for mesh edges...done (175.16 sec). ... creating path file for vertex 1 / 64956 area file for outer ROIs saved at 1 {Improper assignment with rectangular empty matrix. Error in dsearchn (line 79) [d(i),t(i)] = min(sum((x-yi).^2,2)); Error in mesh_vertex_nearest (line 29) nearestIndex = dsearchn(vertices,points); Error in reorganize_verticeslist (line 28) [nextindex,nextvalue]=mesh_vertex_nearest(mesh_total.vertices(remaininglist,:),mesh_total.vertices(verticeslist(start_vertex),:)); Error in make_roi_paths (line 93) reorglist = reorganize_verticeslist (mesh_total, A, mesh_outer, perim, verticeslist, step); } >> ERROR: make_roi_paths did not complete successfully! Linux KOENIGS-PC1 2.6.32-5-amd64 #1 SMP Wed Jun 17 16:09:06 UTC 2015 x86_64 GNU/Linux recon-all -s M87100094 exited with ERRORS at Wed Aug 26 09:56:37 CDT 2015 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Marie Schaer <marie.sch...@unige.ch<mailto:marie.sch...@unige.ch>> Sent: Wednesday, August 26, 2015 10:24 AM To: Freesurfer support list Subject: Re: [Freesurfer] Error running recon-all -localGI Hi Philip, Can you send me the full recon-all.log for this subject so that I can see also matlab version and whether other vertices ran or if it crashed on the first one. Thanks, Marie On Aug 26, 2015, at 8:00 AM, Philip Deming <pdem...@wisc.edu<mailto:pdem...@wisc.edu>> wrote: Hi Freesurfer Support, I posted this question about a month ago, and I still haven't found a solution. Any help would be greatly appreciated. When running the recon-all -localGI command, I get the following errors, which result in the message: make_roi_paths did not complete successfully! Error in dsearchn (line 79) [d(i),t(i)] = min(sum((x-yi).^2,2)); Error in mesh_vertex_nearest (line 29) nearestIndex = dsearchn(vertices,points); Error in reorganize_verticeslist (line 28) [nextindex,nextvalue]=mesh_vertex_nearest(mesh_total.vertices(remaininglist,:),mesh_total.vertices(verticeslist(start_vertex),:)); Error in make_roi_paths (line 93) reorglist = reorganize_verticeslist (mesh_total, A, mesh_outer, perim, verticeslist, step); Thanks, Phil _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto: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<mailto: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 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.
