Fri Jul 5 14:08:23 EDT 2013 /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001 /usr/local/freesurfer/stable5_3_0/bin/recon-all -i /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/VNS_Mig001/structural/structural.nii -s VNS_Mig001 subjid VNS_Mig001 setenv SUBJECTS_DIR /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable5_3_0 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 Linux kyungmo2 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 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 4096 memorylocked 64 kbytes maxproc 4096 total used free shared buffers cached Mem: 3920436 3637424 283012 0 142320 3047952 -/+ buffers/cache: 447152 3473284 Swap: 12287992 0 12287992 ######################################## program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:24-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:24-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@kani (i686-pc-linux-gnu) on 2005-11-15 at 21:02:27 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:26-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:26-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:26-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:26-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:26-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:26-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:26-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:26-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:26-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:26-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:26-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:26-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:26-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:26-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:26-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:26-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:26-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:26-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:26-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:26-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:26-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:26-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:26-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:26-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:26-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:26-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:26-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:26-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:27-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:27-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:27-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:27-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:27-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:27-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:27-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:27-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer/stable5_3_0/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/stable5_3_0/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001 mri_convert /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/VNS_Mig001/structural/structural.nii /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri/orig/001.mgz mri_convert /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/VNS_Mig001/structural/structural.nii /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/VNS_Mig001/structural/structural.nii... TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.075335, -0.996781, -0.0274418) j_ras = (-0.032053, 0.0299265, -0.999038) k_ras = (-0.996643, 0.0743829, 0.0342044) writing to /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri/orig/001.mgz... #------------------------------------------ Started at Fri Jul 5 14:08:23 EDT 2013 Ended at Fri Jul 5 14:08:35 EDT 2013 #@#%# recon-all-run-time-hours 0.003 recon-all -s VNS_Mig001 finished without error at Fri Jul 5 14:08:35 EDT 2013 New invocation of recon-all Fri Jul 5 14:08:43 EDT 2013 /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001 /usr/local/freesurfer/stable5_3_0/bin/recon-all -autorecon1 -noskullstrip -s VNS_Mig001 -mail rllin subjid VNS_Mig001 setenv SUBJECTS_DIR /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable5_3_0 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 Linux kyungmo2 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 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 4096 memorylocked 64 kbytes maxproc 4096 total used free shared buffers cached Mem: 3920436 3657624 262812 0 142344 3066152 -/+ buffers/cache: 449128 3471308 Swap: 12287992 0 12287992 ######################################## program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:43-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:43-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@kani (i686-pc-linux-gnu) on 2005-11-15 at 21:02:27 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:43-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:43-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:43-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:43-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:43-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:43-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:43-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:43-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:43-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:43-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:43-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:43-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:43-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:43-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:43-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:43-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:43-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:43-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:43-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:43-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:43-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:43-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:43-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:43-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:44-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:44-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:44-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:44-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:44-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:44-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:44-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:44-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:44-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:44-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:44-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:08:44-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer/stable5_3_0/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/stable5_3_0/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #-------------------------------------------- #@# MotionCor Fri Jul 5 14:08:44 EDT 2013 Found 1 runs /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/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 /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri/orig/001.mgz /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri/rawavg.mgz /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001 mri_convert /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri/rawavg.mgz /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri/orig.mgz --conform mri_convert /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri/rawavg.mgz /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri/rawavg.mgz... TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.075335, -0.996781, -0.0274418) j_ras = (-0.032053, 0.0299265, -0.999038) k_ras = (-0.996643, 0.0743829, 0.0342044) Original Data has (1, 1, 1) mm size and (256, 256, 176) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri/orig.mgz... mri_add_xform_to_header -c /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri/transforms/talairach.xfm /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri/orig.mgz /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Fri Jul 5 14:09:15 EDT 2013 /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Fri Jul 5 14:14:40 EDT 2013 /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6944, pval=0.4932 >= threshold=0.0050) awk -f /usr/local/freesurfer/stable5_3_0/bin/extract_talairach_avi_QA.awk /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri/transforms/talairach_avi.log tal_QC_AZS /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri/transforms/talairach_avi.log TalAviQA: 0.97729 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Fri Jul 5 14:14:41 EDT 2013 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri /usr/local/freesurfer/stable5_3_0/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ Linux kyungmo2 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux Fri Jul 5 14:14:41 EDT 2013 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@kani (i686-pc-linux-gnu) on 2005-11-15 at 21:02:27 tmpdir is ./tmp.mri_nu_correct.mni.14857 /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.14857/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.14857/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig.mgz... TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -1.49012e-08, 8.56817e-08) j_ras = (-1.11759e-08, 9.31323e-10, -1) k_ras = (2.23517e-08, 1, 2.32831e-10) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.14857/nu0.mnc... -------------------------------------------------------- Iteration 1 Fri Jul 5 14:14:51 EDT 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.14857/nu0.mnc ./tmp.mri_nu_correct.mni.14857/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.14857/0/ [rllin@kyungmo2:/autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri/] [2013-07-05 14:14:51] running: /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.14857/0/ ./tmp.mri_nu_correct.mni.14857/nu0.mnc ./tmp.mri_nu_correct.mni.14857/nu1.imp Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Number of iterations: 42 CV of field change: 0.000974062 [rllin@kyungmo2:/autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri/] [2013-07-05 14:16:14] running: /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.14857/nu0.mnc ./tmp.mri_nu_correct.mni.14857/0//template.mnc Transforming slices:......................................................................................Done Not implemented yet in cache_volume_range_has_changed() Transforming slices:................................................................................................................................................................................................................................................................Done -------------------------------------------------------- Iteration 2 Fri Jul 5 14:16:27 EDT 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.14857/nu1.mnc ./tmp.mri_nu_correct.mni.14857/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.14857/1/ [rllin@kyungmo2:/autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri/] [2013-07-05 14:16:28] running: /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.14857/1/ ./tmp.mri_nu_correct.mni.14857/nu1.mnc ./tmp.mri_nu_correct.mni.14857/nu2.imp Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Processing:.................................................................Done Not implemented yet in cache_volume_range_has_changed() Number of iterations: 17 CV of field change: 0.000998914 [rllin@kyungmo2:/autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri/] [2013-07-05 14:17:03] running: /space/lyon/9/pubsw/Linux2/packages/mni/current/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.14857/nu1.mnc ./tmp.mri_nu_correct.mni.14857/1//template.mnc Transforming slices:......................................................................................Done Not implemented yet in cache_volume_range_has_changed() Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.14857/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.14857/ones.mgz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.14857/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.14857/ones.mgz sysname Linux hostname kyungmo2 machine x86_64 user rllin input ./tmp.mri_nu_correct.mni.14857/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.14857/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 Found 16777216 values in range Counting number of voxels Found 16777216 voxels in final mask mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.14857/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.14857/sum.junk --avgwf ./tmp.mri_nu_correct.mni.14857/input.mean.dat $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.14857/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.14857/sum.junk --avgwf ./tmp.mri_nu_correct.mni.14857/input.mean.dat sysname Linux hostname kyungmo2 machine x86_64 user rllin UseRobust 0 Loading ./tmp.mri_nu_correct.mni.14857/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 16777216.000 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.14857/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.14857/ones.mgz --i ./tmp.mri_nu_correct.mni.14857/nu2.mnc --sum ./tmp.mri_nu_correct.mni.14857/sum.junk --avgwf ./tmp.mri_nu_correct.mni.14857/output.mean.dat $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.14857/ones.mgz --i ./tmp.mri_nu_correct.mni.14857/nu2.mnc --sum ./tmp.mri_nu_correct.mni.14857/sum.junk --avgwf ./tmp.mri_nu_correct.mni.14857/output.mean.dat sysname Linux hostname kyungmo2 machine x86_64 user rllin UseRobust 0 Loading ./tmp.mri_nu_correct.mni.14857/ones.mgz Loading ./tmp.mri_nu_correct.mni.14857/nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 16777216.000 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.14857/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.14857/nu2.mnc ./tmp.mri_nu_correct.mni.14857/nu2.mnc mul .93613351809708358682 Saving result to './tmp.mri_nu_correct.mni.14857/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.14857/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.14857/nu2.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.14857/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -1.49012e-08, 8.56817e-08) j_ras = (-1.11759e-08, 9.31322e-10, -1) k_ras = (2.23517e-08, 1, 2.32831e-10) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 20 seconds. mapping (22, 178) to ( 3, 110) Fri Jul 5 14:19:26 EDT 2013 mri_nu_correct.mni done mri_add_xform_to_header -c /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Fri Jul 5 14:19:31 EDT 2013 /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.090 -0.096 -0.050 -1.165; 0.103 0.973 0.328 -32.526; 0.015 -0.275 1.092 -14.435; 0.000 0.000 0.000 1.000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 16 Starting OpenSpline(): npoints = 16 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 111 white matter peak found at 109 gm peak at 63 (63), valley at 35 (35) csf peak at 10, setting threshold to 45 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 61 (61), valley at 33 (33) csf peak at 30, setting threshold to 50 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 5 minutes and 24 seconds. #------------------------------------------ Started at Fri Jul 5 14:08:43 EDT 2013 Ended at Fri Jul 5 14:25:03 EDT 2013 #@#%# recon-all-run-time-hours 0.272 recon-all -s VNS_Mig001 finished without error at Fri Jul 5 14:25:03 EDT 2013 New invocation of recon-all Fri Jul 5 14:25:19 EDT 2013 /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001 /usr/local/freesurfer/stable5_3_0/bin/recon-all -autorecon2 -autorecon3 -subjid VNS_Mig001 -mail rllin subjid VNS_Mig001 setenv SUBJECTS_DIR /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable5_3_0 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 Linux kyungmo2 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 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 4096 memorylocked 64 kbytes maxproc 4096 total used free shared buffers cached Mem: 3920436 3118848 801588 0 109748 2569420 -/+ buffers/cache: 439680 3480756 Swap: 12287992 8 12287984 ######################################## program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:25:21-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:25:21-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@kani (i686-pc-linux-gnu) on 2005-11-15 at 21:02:27 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:25:27-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:25:27-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:25:27-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:25:27-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:25:28-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:25:28-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:25:29-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:25:29-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:25:30-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:25:30-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:25:30-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:25:30-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:25:30-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:25:30-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:25:30-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:25:30-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:25:31-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:25:31-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:25:31-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:25:31-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:25:31-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:25:31-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:25:32-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:25:32-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:25:33-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:25:33-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:25:33-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:25:33-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:25:33-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:25:33-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:25:33-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:25:33-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:25:34-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:25:34-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:25:34-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/07/05-18:25:34-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: rllin Machine: kyungmo2 Platform: Linux PlatformVersion: 2.6.32-279.22.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer/stable5_3_0/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/stable5_3_0/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #------------------------------------- #@# EM Registration Fri Jul 5 14:25:34 EDT 2013 /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /usr/local/freesurfer/stable5_3_0/average/RB_all_2008-03-26.gca transforms/talairach.lta ======= NUMBER OF OPENMP THREADS = 1 ======= aligning to atlas containing skull, setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/usr/local/freesurfer/stable5_3_0/average/RB_all_2008-03-26.gca'... average std = 6.9 using min determinant for regularization = 4.7 0 singular and 1812 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 14.9 or > 790.2 total sample mean = 84.4 (994 zeros) ************************************************ spacing=8, using 2772 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2772, passno 0, spacing 8 resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=17.0 skull bounding box = (65, 42, 37) --> (195, 176, 203) using (108, 87, 120) as brain centroid... mean wm in atlas = 107, using box (92,71,100) --> (123, 103,140) to find MRI wm before smoothing, mri peak at 108 after smoothing, mri peak at 108, scaling input intensities by 0.991 scaling channel 0 by 0.990741 initial log_p = -4.3 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.033662 @ (-9.091, 9.091, -9.091) max log p = -3.982907 @ (4.545, -4.545, -4.545) max log p = -3.936584 @ (2.273, 6.818, 2.273) max log p = -3.895652 @ (-1.136, 1.136, -3.409) max log p = -3.890436 @ (0.568, -1.705, 0.568) max log p = -3.890436 @ (0.000, 0.000, 0.000) Found translation: (-2.8, 10.8, -14.2): log p = -3.890 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.5, old_max_log_p =-3.9 (thresh=-3.9) 1.140 -0.034 0.126 -32.432; 0.000 1.194 0.320 -40.929; -0.150 -0.257 0.958 45.548; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.5, old_max_log_p =-3.5 (thresh=-3.5) 1.140 -0.034 0.126 -32.432; 0.000 1.194 0.320 -40.929; -0.150 -0.257 0.958 45.548; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.3, old_max_log_p =-3.5 (thresh=-3.5) 1.097 -0.038 0.125 -26.432; 0.004 1.170 0.319 -41.067; -0.150 -0.260 0.995 40.174; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3) 1.097 -0.038 0.125 -26.432; 0.005 1.192 0.325 -44.066; -0.150 -0.260 0.995 40.174; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3) 1.097 -0.038 0.125 -26.432; 0.005 1.192 0.325 -44.066; -0.150 -0.260 0.995 40.174; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3) 1.102 -0.074 0.099 -21.380; 0.045 1.194 0.295 -46.578; -0.132 -0.222 1.010 32.141; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3) 1.105 -0.074 0.099 -21.727; 0.045 1.190 0.293 -45.996; -0.132 -0.222 1.010 32.141; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.3, old_max_log_p =-3.3 (thresh=-3.3) 1.105 -0.074 0.099 -21.727; 0.045 1.187 0.293 -45.610; -0.132 -0.222 1.010 32.141; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2772 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.10495 -0.07395 0.09901 -21.72698; 0.04468 1.18677 0.29281 -45.61005; -0.13175 -0.22234 1.00957 32.14139; 0.00000 0.00000 0.00000 1.00000; nsamples 2772 Quasinewton: input matrix 1.10495 -0.07395 0.09901 -21.72698; 0.04468 1.18677 0.29281 -45.61005; -0.13175 -0.22234 1.00957 32.14139; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.105 -0.074 0.099 -21.727; 0.045 1.187 0.293 -45.610; -0.132 -0.222 1.010 32.141; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.3 (old=-4.3) transform before final EM align: 1.105 -0.074 0.099 -21.727; 0.045 1.187 0.293 -45.610; -0.132 -0.222 1.010 32.141; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 312841 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.10495 -0.07395 0.09901 -21.72698; 0.04468 1.18677 0.29281 -45.61005; -0.13175 -0.22234 1.00957 32.14139; 0.00000 0.00000 0.00000 1.00000; nsamples 312841 Quasinewton: input matrix 1.10495 -0.07395 0.09901 -21.72698; 0.04468 1.18677 0.29281 -45.61005; -0.13175 -0.22234 1.00957 32.14139; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 012: -log(p) = 3.8 tol 0.000000 final transform: 1.105 -0.074 0.099 -21.727; 0.045 1.187 0.293 -45.610; -0.132 -0.222 1.010 32.141; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach.lta... registration took 58 minutes and 52 seconds. #-------------------------------------- #@# CA Normalize Fri Jul 5 15:24:30 EDT 2013 /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /usr/local/freesurfer/stable5_3_0/average/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/usr/local/freesurfer/stable5_3_0/average/RB_all_2008-03-26.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=17.0 skull bounding box = (65, 42, 37) --> (195, 176, 203) using (108, 87, 120) as brain centroid... mean wm in atlas = 107, using box (92,71,100) --> (123, 103,140) to find MRI wm before smoothing, mri peak at 108 after smoothing, mri peak at 108, scaling input intensities by 0.991 scaling channel 0 by 0.990741 using 244171 sample points... INFO: compute sample coordinates transform 1.105 -0.074 0.099 -21.727; 0.045 1.187 0.293 -45.610; -0.132 -0.222 1.010 32.141; 0.000 0.000 0.000 1.000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (126, 50, 42) --> (192, 147, 198) Left_Cerebral_White_Matter: limiting intensities to 94.0 --> 131.0 1 of 598 (0.2%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (71, 52, 38) --> (133, 145, 196) Right_Cerebral_White_Matter: limiting intensities to 96.0 --> 131.0 0 of 800 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (136, 125, 69) --> (180, 161, 119) Left_Cerebellum_White_Matter: limiting intensities to 98.0 --> 131.0 0 of 11 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (94, 125, 63) --> (136, 163, 116) Right_Cerebellum_White_Matter: limiting intensities to 98.0 --> 131.0 0 of 27 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (117, 115, 99) --> (147, 173, 128) Brain_Stem: limiting intensities to 98.0 --> 131.0 0 of 35 (0.0%) samples deleted using 1471 total control points for intensity normalization... bias field = 1.018 +- 0.056 9 of 1470 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (126, 50, 42) --> (192, 147, 198) Left_Cerebral_White_Matter: limiting intensities to 95.0 --> 129.0 0 of 575 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (71, 52, 38) --> (133, 145, 196) Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 129.0 0 of 778 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (136, 125, 69) --> (180, 161, 119) Left_Cerebellum_White_Matter: limiting intensities to 87.0 --> 129.0 0 of 58 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (94, 125, 63) --> (136, 163, 116) Right_Cerebellum_White_Matter: limiting intensities to 89.0 --> 129.0 0 of 69 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (117, 115, 99) --> (147, 173, 128) Brain_Stem: limiting intensities to 85.0 --> 129.0 0 of 105 (0.0%) samples deleted using 1585 total control points for intensity normalization... bias field = 1.004 +- 0.053 4 of 1585 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (126, 50, 42) --> (192, 147, 198) Left_Cerebral_White_Matter: limiting intensities to 93.0 --> 128.0 0 of 579 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (71, 52, 38) --> (133, 145, 196) Right_Cerebral_White_Matter: limiting intensities to 96.0 --> 128.0 0 of 799 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (136, 125, 69) --> (180, 161, 119) Left_Cerebellum_White_Matter: limiting intensities to 84.0 --> 128.0 0 of 84 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (94, 125, 63) --> (136, 163, 116) Right_Cerebellum_White_Matter: limiting intensities to 84.0 --> 128.0 0 of 74 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (117, 115, 99) --> (147, 173, 128) Brain_Stem: limiting intensities to 78.0 --> 128.0 0 of 160 (0.0%) samples deleted using 1696 total control points for intensity normalization... bias field = 1.004 +- 0.039 5 of 1696 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 3 minutes and 31 seconds. #-------------------------------------- #@# CA Reg Fri Jul 5 15:28:16 EDT 2013 /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /usr/local/freesurfer/stable5_3_0/average/RB_all_2008-03-26.gca transforms/talairach.m3z not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log ======= NUMBER OF OPENMP THREADS = 1 ======= reading input volume 'norm.mgz'... reading GCA '/usr/local/freesurfer/stable5_3_0/average/RB_all_2008-03-26.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.42 (predicted orig area = 5.6) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.807, neg=0, invalid=96777 0001: dt=129.472000, rms=0.739 (8.521%), neg=0, invalid=96777 0002: dt=129.472000, rms=0.717 (2.868%), neg=0, invalid=96777 0003: dt=129.472000, rms=0.699 (2.570%), neg=0, invalid=96777 0004: dt=129.472000, rms=0.693 (0.819%), neg=0, invalid=96777 0005: dt=295.936000, rms=0.683 (1.495%), neg=0, invalid=96777 0006: dt=32.368000, rms=0.680 (0.417%), neg=0, invalid=96777 0007: dt=73.984000, rms=0.679 (0.212%), neg=0, invalid=96777 0008: dt=73.984000, rms=0.677 (0.203%), neg=0, invalid=96777 0009: dt=73.984000, rms=0.675 (0.357%), neg=0, invalid=96777 0010: dt=73.984000, rms=0.672 (0.460%), neg=0, invalid=96777 0011: dt=73.984000, rms=0.668 (0.497%), neg=0, invalid=96777 0012: dt=73.984000, rms=0.665 (0.495%), neg=0, invalid=96777 0013: dt=73.984000, rms=0.662 (0.441%), neg=0, invalid=96777 0014: dt=73.984000, rms=0.659 (0.393%), neg=0, invalid=96777 0015: dt=73.984000, rms=0.657 (0.317%), neg=0, invalid=96777 0016: dt=73.984000, rms=0.655 (0.289%), neg=0, invalid=96777 0017: dt=73.984000, rms=0.654 (0.294%), neg=0, invalid=96777 0018: dt=73.984000, rms=0.652 (0.316%), neg=0, invalid=96777 0019: dt=73.984000, rms=0.650 (0.281%), neg=0, invalid=96777 0020: dt=73.984000, rms=0.648 (0.214%), neg=0, invalid=96777 0021: dt=73.984000, rms=0.647 (0.203%), neg=0, invalid=96777 0022: dt=73.984000, rms=0.646 (0.216%), neg=0, invalid=96777 0023: dt=73.984000, rms=0.644 (0.231%), neg=0, invalid=96777 0024: dt=73.984000, rms=0.643 (0.203%), neg=0, invalid=96777 0025: dt=73.984000, rms=0.642 (0.183%), neg=0, invalid=96777 0026: dt=73.984000, rms=0.640 (0.178%), neg=0, invalid=96777 0027: dt=73.984000, rms=0.639 (0.176%), neg=0, invalid=96777 0028: dt=73.984000, rms=0.638 (0.193%), neg=0, invalid=96777 0029: dt=73.984000, rms=0.637 (0.171%), neg=0, invalid=96777 0030: dt=73.984000, rms=0.636 (0.135%), neg=0, invalid=96777 0031: dt=73.984000, rms=0.635 (0.105%), neg=0, invalid=96777 0032: dt=73.984000, rms=0.635 (0.100%), neg=0, invalid=96777 0033: dt=129.472000, rms=0.634 (0.086%), neg=0, invalid=96777 0034: dt=129.472000, rms=0.634 (-0.044%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.634, neg=0, invalid=96777 0035: dt=92.480000, rms=0.634 (0.047%), neg=0, invalid=96777 0036: dt=517.888000, rms=0.633 (0.211%), neg=0, invalid=96777 0037: dt=129.472000, rms=0.632 (0.103%), neg=0, invalid=96777 0038: dt=129.472000, rms=0.632 (0.042%), neg=0, invalid=96777 0039: dt=129.472000, rms=0.632 (-0.004%), neg=0, invalid=96777 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.636, neg=0, invalid=96777 0040: dt=145.152000, rms=0.626 (1.598%), neg=0, invalid=96777 0041: dt=145.152000, rms=0.615 (1.708%), neg=0, invalid=96777 0042: dt=20.736000, rms=0.613 (0.429%), neg=0, invalid=96777 0043: dt=124.416000, rms=0.609 (0.580%), neg=0, invalid=96777 0044: dt=62.208000, rms=0.606 (0.499%), neg=0, invalid=96777 0045: dt=36.288000, rms=0.604 (0.286%), neg=0, invalid=96777 0046: dt=248.832000, rms=0.600 (0.733%), neg=0, invalid=96777 0047: dt=31.104000, rms=0.597 (0.557%), neg=0, invalid=96777 0048: dt=82.944000, rms=0.596 (0.161%), neg=0, invalid=96777 0049: dt=82.944000, rms=0.594 (0.261%), neg=0, invalid=96777 0050: dt=82.944000, rms=0.593 (0.122%), neg=0, invalid=96777 0051: dt=82.944000, rms=0.588 (0.879%), neg=0, invalid=96777 0052: dt=82.944000, rms=0.584 (0.678%), neg=0, invalid=96777 0053: dt=82.944000, rms=0.582 (0.433%), neg=0, invalid=96777 0054: dt=82.944000, rms=0.578 (0.638%), neg=0, invalid=96777 0055: dt=82.944000, rms=0.575 (0.533%), neg=0, invalid=96777 0056: dt=82.944000, rms=0.572 (0.439%), neg=0, invalid=96777 0057: dt=82.944000, rms=0.570 (0.371%), neg=0, invalid=96777 0058: dt=82.944000, rms=0.568 (0.350%), neg=0, invalid=96777 0059: dt=82.944000, rms=0.567 (0.288%), neg=0, invalid=96777 0060: dt=82.944000, rms=0.565 (0.246%), neg=0, invalid=96777 0061: dt=82.944000, rms=0.564 (0.280%), neg=0, invalid=96777 0062: dt=82.944000, rms=0.563 (0.068%), neg=0, invalid=96777 0063: dt=82.944000, rms=0.562 (0.213%), neg=0, invalid=96777 0064: dt=82.944000, rms=0.561 (0.218%), neg=0, invalid=96777 0065: dt=82.944000, rms=0.560 (0.117%), neg=0, invalid=96777 0066: dt=82.944000, rms=0.560 (0.006%), neg=0, invalid=96777 0067: dt=36.288000, rms=0.559 (0.145%), neg=0, invalid=96777 0068: dt=5.184000, rms=0.559 (0.001%), neg=0, invalid=96777 0069: dt=5.184000, rms=0.559 (0.000%), neg=0, invalid=96777 0070: dt=5.184000, rms=0.559 (-0.002%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.559, neg=0, invalid=96777 0071: dt=82.944000, rms=0.558 (0.162%), neg=0, invalid=96777 0072: dt=36.288000, rms=0.558 (0.070%), neg=0, invalid=96777 0073: dt=36.288000, rms=0.558 (0.056%), neg=0, invalid=96777 0074: dt=36.288000, rms=0.557 (0.057%), neg=0, invalid=96777 0075: dt=36.288000, rms=0.557 (0.003%), neg=0, invalid=96777 0076: dt=36.288000, rms=0.557 (0.006%), neg=0, invalid=96777 0077: dt=36.288000, rms=0.557 (0.035%), neg=0, invalid=96777 0078: dt=36.288000, rms=0.557 (0.085%), neg=0, invalid=96777 0079: dt=36.288000, rms=0.556 (0.020%), neg=0, invalid=96777 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.578, neg=0, invalid=96777 0080: dt=0.000000, rms=0.578 (0.001%), neg=0, invalid=96777 0081: dt=0.000000, rms=0.578 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.578, neg=0, invalid=96777 0082: dt=0.000000, rms=0.578 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.645, neg=0, invalid=96777 0083: dt=4.248544, rms=0.627 (2.784%), neg=0, invalid=96777 0084: dt=1.008000, rms=0.627 (0.050%), neg=0, invalid=96777 0085: dt=1.008000, rms=0.627 (-0.003%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.627, neg=0, invalid=96777 0086: dt=0.015750, rms=0.627 (0.000%), neg=0, invalid=96777 0087: dt=0.000000, rms=0.627 (0.000%), neg=0, invalid=96777 0088: dt=0.000000, rms=0.627 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.696, neg=0, invalid=96777 0089: dt=1.449477, rms=0.687 (1.342%), neg=0, invalid=96777 0090: dt=1.313901, rms=0.684 (0.437%), neg=0, invalid=96777 0091: dt=0.468750, rms=0.684 (0.065%), neg=0, invalid=96777 0092: dt=0.468750, rms=0.684 (0.008%), neg=0, invalid=96777 0093: dt=0.468750, rms=0.684 (-0.046%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.684, neg=0, invalid=96777 0094: dt=0.801887, rms=0.683 (0.073%), neg=0, invalid=96777 0095: dt=0.000000, rms=0.683 (-0.001%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.629, neg=0, invalid=96777 0096: dt=0.384000, rms=0.614 (2.414%), neg=0, invalid=96777 0097: dt=0.000000, rms=0.614 (0.001%), neg=0, invalid=96777 0098: dt=0.050000, rms=0.614 (-0.357%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.614, neg=0, invalid=96777 0099: dt=0.000000, rms=0.614 (0.000%), neg=0, invalid=96777 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11725 (24) mri peak = 0.16739 (20) Left_Lateral_Ventricle (4): linear fit = 0.69 x + 0.0 (997 voxels, overlap=0.004) Left_Lateral_Ventricle (4): linear fit = 0.69 x + 0.0 (997 voxels, peak = 17), gca=16.7 gca peak = 0.14022 (22) mri peak = 0.11926 (18) Right_Lateral_Ventricle (43): linear fit = 0.76 x + 0.0 (864 voxels, overlap=0.346) Right_Lateral_Ventricle (43): linear fit = 0.76 x + 0.0 (864 voxels, peak = 17), gca=16.8 gca peak = 0.24234 (100) mri peak = 0.13183 (101) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (313 voxels, overlap=1.004) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (313 voxels, peak = 102), gca=101.5 gca peak = 0.19192 (97) mri peak = 0.08550 (103) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (265 voxels, overlap=1.006) Left_Pallidum (13): linear fit = 1.01 x + 0.0 (265 voxels, peak = 98), gca=98.5 gca peak = 0.24007 (63) mri peak = 0.04825 (103) Right_Hippocampus (53): linear fit = 1.62 x + 0.0 (484 voxels, overlap=0.016) Right_Hippocampus (53): linear fit = 1.62 x + 0.0 (484 voxels, peak = 102), gca=102.4 gca peak = 0.29892 (64) mri peak = 0.09732 (74) Left_Hippocampus (17): linear fit = 1.12 x + 0.0 (500 voxels, overlap=0.672) Left_Hippocampus (17): linear fit = 1.12 x + 0.0 (500 voxels, peak = 71), gca=71.4 gca peak = 0.12541 (104) mri peak = 0.11744 (107) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (57849 voxels, overlap=0.696) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (57849 voxels, peak = 107), gca=106.6 gca peak = 0.13686 (104) mri peak = 0.10532 (107) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (59581 voxels, overlap=0.713) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (59581 voxels, peak = 107), gca=106.6 gca peak = 0.11691 (63) mri peak = 0.04079 (68) Left_Cerebral_Cortex (3): linear fit = 1.05 x + 0.0 (18860 voxels, overlap=0.881) Left_Cerebral_Cortex (3): linear fit = 1.05 x + 0.0 (18860 voxels, peak = 66), gca=66.5 gca peak = 0.13270 (63) mri peak = 0.03901 (68) Right_Cerebral_Cortex (42): linear fit = 1.09 x + 0.0 (19460 voxels, overlap=0.730) Right_Cerebral_Cortex (42): linear fit = 1.09 x + 0.0 (19460 voxels, peak = 68), gca=68.4 gca peak = 0.15182 (70) mri peak = 0.12045 (79) Right_Caudate (50): linear fit = 1.12 x + 0.0 (245 voxels, overlap=0.320) Right_Caudate (50): linear fit = 1.12 x + 0.0 (245 voxels, peak = 78), gca=78.1 gca peak = 0.14251 (76) mri peak = 0.08851 (86) Left_Caudate (11): linear fit = 1.09 x + 0.0 (664 voxels, overlap=0.551) Left_Caudate (11): linear fit = 1.09 x + 0.0 (664 voxels, peak = 82), gca=82.5 gca peak = 0.12116 (60) mri peak = 0.04847 (68) Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (15988 voxels, overlap=0.606) Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (15988 voxels, peak = 68), gca=67.5 gca peak = 0.12723 (61) mri peak = 0.04623 (68) Right_Cerebellum_Cortex (47): linear fit = 1.11 x + 0.0 (21490 voxels, overlap=0.632) Right_Cerebellum_Cortex (47): linear fit = 1.11 x + 0.0 (21490 voxels, peak = 67), gca=67.4 gca peak = 0.22684 (88) mri peak = 0.09000 (93) Left_Cerebellum_White_Matter (7): linear fit = 1.04 x + 0.0 (7434 voxels, overlap=0.582) Left_Cerebellum_White_Matter (7): linear fit = 1.04 x + 0.0 (7434 voxels, peak = 92), gca=92.0 gca peak = 0.21067 (87) mri peak = 0.09553 (93) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (6877 voxels, overlap=0.807) Right_Cerebellum_White_Matter (46): linear fit = 1.05 x + 0.0 (6877 voxels, peak = 92), gca=91.8 gca peak = 0.25455 (62) mri peak = 0.10381 (69) Left_Amygdala (18): linear fit = 1.11 x + 0.0 (280 voxels, overlap=0.428) Left_Amygdala (18): linear fit = 1.11 x + 0.0 (280 voxels, peak = 69), gca=68.5 gca peak = 0.39668 (62) mri peak = 0.06733 (75) Right_Amygdala (54): linear fit = 1.11 x + 0.0 (248 voxels, overlap=0.797) Right_Amygdala (54): linear fit = 1.11 x + 0.0 (248 voxels, peak = 69), gca=68.5 gca peak = 0.10129 (93) mri peak = 0.08070 (104) Left_Thalamus_Proper (10): linear fit = 1.12 x + 0.0 (4619 voxels, overlap=0.248) Left_Thalamus_Proper (10): linear fit = 1.12 x + 0.0 (4619 voxels, peak = 104), gca=103.7 gca peak = 0.12071 (89) mri peak = 0.08018 (101) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (3257 voxels, overlap=0.478) Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (3257 voxels, peak = 100), gca=100.1 gca peak = 0.13716 (82) mri peak = 0.05989 (88) Left_Putamen (12): linear fit = 1.07 x + 0.0 (2041 voxels, overlap=0.784) Left_Putamen (12): linear fit = 1.07 x + 0.0 (2041 voxels, peak = 87), gca=87.3 gca peak = 0.15214 (84) mri peak = 0.06348 (84) Right_Putamen (51): linear fit = 1.04 x + 0.0 (1985 voxels, overlap=0.918) Right_Putamen (51): linear fit = 1.04 x + 0.0 (1985 voxels, peak = 88), gca=87.8 gca peak = 0.08983 (85) mri peak = 0.08287 (93) Brain_Stem (16): linear fit = 1.11 x + 0.0 (9565 voxels, overlap=0.532) Brain_Stem (16): linear fit = 1.11 x + 0.0 (9565 voxels, peak = 94), gca=93.9 gca peak = 0.11809 (92) mri peak = 0.11675 (102) Right_VentralDC (60): linear fit = 1.08 x + 0.0 (783 voxels, overlap=0.188) Right_VentralDC (60): linear fit = 1.08 x + 0.0 (783 voxels, peak = 99), gca=98.9 gca peak = 0.12914 (94) mri peak = 0.10247 (100) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (941 voxels, overlap=0.329) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (941 voxels, peak = 101), gca=101.1 gca peak = 0.21100 (36) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.13542 (27) mri peak = 0.18035 (20) Fourth_Ventricle (15): linear fit = 0.71 x + 0.0 (191 voxels, overlap=0.023) Fourth_Ventricle (15): linear fit = 0.71 x + 0.0 (191 voxels, peak = 19), gca=19.3 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.21802 (40) gca peak Third_Ventricle = 0.21100 (36) gca peak CSF = 0.17123 (45) gca peak Left_Accumbens_area = 0.25875 (69) gca peak Left_undetermined = 0.96240 (36) gca peak Left_vessel = 0.33262 (65) gca peak Left_choroid_plexus = 0.09846 (46) gca peak Right_Inf_Lat_Vent = 0.28113 (34) gca peak Right_Hippocampus = 0.24007 (63) gca peak Right_Accumbens_area = 0.27120 (72) gca peak Right_vessel = 0.61915 (60) gca peak Right_choroid_plexus = 0.12775 (51) gca peak Fifth_Ventricle = 0.45329 (44) gca peak WM_hypointensities = 0.11729 (81) gca peak non_WM_hypointensities = 0.10912 (56) gca peak Optic_Chiasm = 0.33287 (75) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means setting label Right_Hippocampus based on Left_Hippocampus = 1.12 x + 0: 71 estimating mean gm scale to be 1.10 x + 0.0 estimating mean wm scale to be 1.02 x + 0.0 estimating mean csf scale to be 0.72 x + 0.0 saving intensity scales to talairach.label_intensities.txt **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.624, neg=0, invalid=96777 0100: dt=92.480000, rms=0.619 (0.834%), neg=0, invalid=96777 0101: dt=129.472000, rms=0.617 (0.372%), neg=0, invalid=96777 0102: dt=443.904000, rms=0.613 (0.574%), neg=0, invalid=96777 0103: dt=92.480000, rms=0.612 (0.214%), neg=0, invalid=96777 0104: dt=295.936000, rms=0.609 (0.405%), neg=0, invalid=96777 0105: dt=32.368000, rms=0.609 (0.110%), neg=0, invalid=96777 0106: dt=55.488000, rms=0.608 (0.050%), neg=0, invalid=96777 0107: dt=221.952000, rms=0.608 (0.088%), neg=0, invalid=96777 0108: dt=129.472000, rms=0.607 (0.194%), neg=0, invalid=96777 0109: dt=129.472000, rms=0.606 (0.065%), neg=0, invalid=96777 0110: dt=369.920000, rms=0.605 (0.209%), neg=0, invalid=96777 0111: dt=55.488000, rms=0.604 (0.112%), neg=0, invalid=96777 0112: dt=73.984000, rms=0.604 (0.020%), neg=0, invalid=96777 0113: dt=73.984000, rms=0.604 (0.037%), neg=0, invalid=96777 0114: dt=73.984000, rms=0.604 (0.070%), neg=0, invalid=96777 0115: dt=73.984000, rms=0.603 (0.124%), neg=0, invalid=96777 0116: dt=73.984000, rms=0.602 (0.119%), neg=0, invalid=96777 0117: dt=73.984000, rms=0.601 (0.122%), neg=0, invalid=96777 0118: dt=73.984000, rms=0.601 (0.148%), neg=0, invalid=96777 0119: dt=73.984000, rms=0.600 (0.157%), neg=0, invalid=96777 0120: dt=73.984000, rms=0.599 (0.159%), neg=0, invalid=96777 0121: dt=73.984000, rms=0.598 (0.175%), neg=0, invalid=96777 0122: dt=73.984000, rms=0.597 (0.164%), neg=0, invalid=96777 0123: dt=73.984000, rms=0.596 (0.138%), neg=0, invalid=96777 0124: dt=73.984000, rms=0.595 (0.126%), neg=0, invalid=96777 0125: dt=73.984000, rms=0.594 (0.133%), neg=0, invalid=96777 0126: dt=73.984000, rms=0.593 (0.132%), neg=0, invalid=96777 0127: dt=73.984000, rms=0.593 (0.118%), neg=0, invalid=96777 0128: dt=73.984000, rms=0.592 (0.112%), neg=0, invalid=96777 0129: dt=73.984000, rms=0.591 (0.118%), neg=0, invalid=96777 0130: dt=73.984000, rms=0.591 (0.106%), neg=0, invalid=96777 0131: dt=73.984000, rms=0.590 (0.102%), neg=0, invalid=96777 0132: dt=73.984000, rms=0.590 (0.106%), neg=0, invalid=96777 0133: dt=73.984000, rms=0.589 (0.130%), neg=0, invalid=96777 0134: dt=73.984000, rms=0.588 (0.105%), neg=0, invalid=96777 0135: dt=73.984000, rms=0.587 (0.111%), neg=0, invalid=96777 0136: dt=73.984000, rms=0.587 (0.097%), neg=0, invalid=96777 0137: dt=73.984000, rms=0.586 (0.084%), neg=0, invalid=96777 0138: dt=73.984000, rms=0.586 (0.075%), neg=0, invalid=96777 0139: dt=73.984000, rms=0.585 (0.096%), neg=0, invalid=96777 0140: dt=73.984000, rms=0.585 (0.088%), neg=0, invalid=96777 0141: dt=73.984000, rms=0.585 (0.066%), neg=0, invalid=96777 0142: dt=73.984000, rms=0.584 (0.080%), neg=0, invalid=96777 0143: dt=73.984000, rms=0.584 (0.072%), neg=0, invalid=96777 0144: dt=73.984000, rms=0.583 (0.051%), neg=0, invalid=96777 0145: dt=73.984000, rms=0.583 (0.040%), neg=0, invalid=96777 0146: dt=73.984000, rms=0.583 (0.071%), neg=0, invalid=96777 0147: dt=73.984000, rms=0.582 (0.092%), neg=0, invalid=96777 0148: dt=73.984000, rms=0.582 (0.078%), neg=0, invalid=96777 0149: dt=73.984000, rms=0.581 (0.062%), neg=0, invalid=96777 0150: dt=73.984000, rms=0.581 (0.055%), neg=0, invalid=96777 0151: dt=73.984000, rms=0.581 (0.061%), neg=0, invalid=96777 0152: dt=73.984000, rms=0.580 (0.051%), neg=0, invalid=96777 0153: dt=73.984000, rms=0.580 (0.051%), neg=0, invalid=96777 0154: dt=73.984000, rms=0.580 (0.039%), neg=0, invalid=96777 0155: dt=73.984000, rms=0.580 (0.030%), neg=0, invalid=96777 0156: dt=73.984000, rms=0.579 (0.031%), neg=0, invalid=96777 0157: dt=73.984000, rms=0.579 (0.033%), neg=0, invalid=96777 0158: dt=73.984000, rms=0.579 (0.039%), neg=0, invalid=96777 0159: dt=73.984000, rms=0.579 (0.045%), neg=0, invalid=96777 0160: dt=73.984000, rms=0.579 (0.047%), neg=0, invalid=96777 0161: dt=73.984000, rms=0.578 (0.041%), neg=0, invalid=96777 0162: dt=73.984000, rms=0.578 (0.034%), neg=0, invalid=96777 0163: dt=73.984000, rms=0.578 (0.008%), neg=0, invalid=96777 0164: dt=73.984000, rms=0.578 (0.001%), neg=0, invalid=96777 0165: dt=221.952000, rms=0.578 (0.041%), neg=0, invalid=96777 0166: dt=3.468000, rms=0.578 (-0.001%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.578, neg=0, invalid=96777 0167: dt=110.976000, rms=0.577 (0.103%), neg=0, invalid=96777 0168: dt=129.472000, rms=0.576 (0.170%), neg=0, invalid=96777 0169: dt=32.368000, rms=0.576 (0.001%), neg=0, invalid=96777 0170: dt=32.368000, rms=0.576 (-0.002%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.577, neg=0, invalid=96777 0171: dt=145.152000, rms=0.574 (0.596%), neg=0, invalid=96777 0172: dt=62.208000, rms=0.568 (0.976%), neg=0, invalid=96777 0173: dt=36.288000, rms=0.566 (0.271%), neg=0, invalid=96777 0174: dt=82.944000, rms=0.564 (0.510%), neg=0, invalid=96777 0175: dt=25.920000, rms=0.562 (0.238%), neg=0, invalid=96777 0176: dt=145.152000, rms=0.559 (0.586%), neg=0, invalid=96777 0177: dt=25.920000, rms=0.558 (0.249%), neg=0, invalid=96777 0178: dt=248.832000, rms=0.553 (0.761%), neg=0, invalid=96777 0179: dt=25.920000, rms=0.552 (0.306%), neg=0, invalid=96777 0180: dt=145.152000, rms=0.549 (0.443%), neg=0, invalid=96777 0181: dt=36.288000, rms=0.548 (0.122%), neg=0, invalid=96777 0182: dt=124.416000, rms=0.547 (0.283%), neg=0, invalid=96777 0183: dt=25.920000, rms=0.546 (0.133%), neg=0, invalid=96777 0184: dt=248.832000, rms=0.544 (0.452%), neg=0, invalid=96777 0185: dt=25.920000, rms=0.543 (0.150%), neg=0, invalid=96777 0186: dt=82.944000, rms=0.542 (0.173%), neg=0, invalid=96777 0187: dt=36.288000, rms=0.542 (0.082%), neg=0, invalid=96777 0188: dt=62.208000, rms=0.541 (0.123%), neg=0, invalid=96777 0189: dt=25.920000, rms=0.541 (0.058%), neg=0, invalid=96777 0190: dt=145.152000, rms=0.539 (0.202%), neg=0, invalid=96777 0191: dt=20.736000, rms=0.539 (0.049%), neg=0, invalid=96777 0192: dt=20.736000, rms=0.539 (0.059%), neg=0, invalid=96777 0193: dt=20.736000, rms=0.539 (0.070%), neg=0, invalid=96777 0194: dt=20.736000, rms=0.538 (0.091%), neg=0, invalid=96777 0195: dt=20.736000, rms=0.537 (0.104%), neg=0, invalid=96777 0196: dt=20.736000, rms=0.537 (0.124%), neg=0, invalid=96777 0197: dt=20.736000, rms=0.536 (0.139%), neg=0, invalid=96777 0198: dt=20.736000, rms=0.535 (0.153%), neg=0, invalid=96777 0199: dt=20.736000, rms=0.534 (0.150%), neg=0, invalid=96777 0200: dt=20.736000, rms=0.534 (0.165%), neg=0, invalid=96777 0201: dt=20.736000, rms=0.533 (0.156%), neg=0, invalid=96777 0202: dt=20.736000, rms=0.532 (0.163%), neg=0, invalid=96777 0203: dt=20.736000, rms=0.531 (0.153%), neg=0, invalid=96777 0204: dt=20.736000, rms=0.530 (0.162%), neg=0, invalid=96777 0205: dt=20.736000, rms=0.529 (0.158%), neg=0, invalid=96777 0206: dt=20.736000, rms=0.529 (0.134%), neg=0, invalid=96777 0207: dt=20.736000, rms=0.528 (0.144%), neg=0, invalid=96777 0208: dt=20.736000, rms=0.527 (0.145%), neg=0, invalid=96777 0209: dt=20.736000, rms=0.526 (0.128%), neg=0, invalid=96777 0210: dt=20.736000, rms=0.526 (0.122%), neg=0, invalid=96777 0211: dt=20.736000, rms=0.525 (0.104%), neg=0, invalid=96777 0212: dt=20.736000, rms=0.525 (0.112%), neg=0, invalid=96777 0213: dt=20.736000, rms=0.524 (0.114%), neg=0, invalid=96777 0214: dt=20.736000, rms=0.523 (0.111%), neg=0, invalid=96777 0215: dt=20.736000, rms=0.523 (0.103%), neg=0, invalid=96777 0216: dt=20.736000, rms=0.522 (0.097%), neg=0, invalid=96777 0217: dt=20.736000, rms=0.522 (0.081%), neg=0, invalid=96777 0218: dt=20.736000, rms=0.522 (0.082%), neg=0, invalid=96777 0219: dt=20.736000, rms=0.521 (0.084%), neg=0, invalid=96777 0220: dt=20.736000, rms=0.521 (0.089%), neg=0, invalid=96777 0221: dt=20.736000, rms=0.521 (0.004%), neg=0, invalid=96777 0222: dt=20.736000, rms=0.521 (0.003%), neg=0, invalid=96777 0223: dt=31.104000, rms=0.520 (0.029%), neg=0, invalid=96777 0224: dt=36.288000, rms=0.520 (0.008%), neg=0, invalid=96777 0225: dt=18.144000, rms=0.520 (0.008%), neg=0, invalid=96777 0226: dt=18.144000, rms=0.520 (0.021%), neg=0, invalid=96777 0227: dt=18.144000, rms=0.520 (0.012%), neg=0, invalid=96777 0228: dt=18.144000, rms=0.520 (0.019%), neg=0, invalid=96777 0229: dt=18.144000, rms=0.520 (0.021%), neg=0, invalid=96777 0230: dt=9.072000, rms=0.520 (0.005%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.520, neg=0, invalid=96777 0231: dt=9.072000, rms=0.520 (0.047%), neg=0, invalid=96777 0232: dt=145.152000, rms=0.518 (0.376%), neg=0, invalid=96777 0233: dt=9.072000, rms=0.518 (0.042%), neg=0, invalid=96777 0234: dt=9.072000, rms=0.517 (0.029%), neg=0, invalid=96777 0235: dt=0.567000, rms=0.517 (0.003%), neg=0, invalid=96777 0236: dt=0.283500, rms=0.517 (0.001%), neg=0, invalid=96777 0237: dt=0.121500, rms=0.517 (0.000%), neg=0, invalid=96777 0238: dt=0.001898, rms=0.517 (0.000%), neg=0, invalid=96777 0239: dt=0.000949, rms=0.517 (0.000%), neg=0, invalid=96777 0240: dt=0.000475, rms=0.517 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.523, neg=0, invalid=96777 0241: dt=44.800000, rms=0.516 (1.364%), neg=0, invalid=96777 0242: dt=38.400000, rms=0.510 (1.134%), neg=0, invalid=96777 0243: dt=10.415842, rms=0.508 (0.474%), neg=0, invalid=96777 0244: dt=44.800000, rms=0.504 (0.754%), neg=0, invalid=96777 0245: dt=8.970874, rms=0.502 (0.348%), neg=0, invalid=96777 0246: dt=44.800000, rms=0.499 (0.617%), neg=0, invalid=96777 0247: dt=8.490566, rms=0.498 (0.278%), neg=0, invalid=96777 0248: dt=102.400000, rms=0.494 (0.667%), neg=0, invalid=96777 0249: dt=8.571429, rms=0.492 (0.523%), neg=0, invalid=96777 0250: dt=25.600000, rms=0.490 (0.385%), neg=0, invalid=96777 0251: dt=9.600000, rms=0.489 (0.121%), neg=0, invalid=96777 0252: dt=44.800000, rms=0.488 (0.256%), neg=0, invalid=96777 0253: dt=8.000000, rms=0.487 (0.118%), neg=0, invalid=96777 0254: dt=44.800000, rms=0.486 (0.248%), neg=0, invalid=96777 0255: dt=11.200000, rms=0.485 (0.141%), neg=0, invalid=96777 0256: dt=179.200000, rms=0.482 (0.631%), neg=0, invalid=96777 0257: dt=9.955556, rms=0.481 (0.287%), neg=0, invalid=96777 0258: dt=25.600000, rms=0.480 (0.164%), neg=0, invalid=96777 0259: dt=6.400000, rms=0.480 (0.046%), neg=0, invalid=96777 0260: dt=6.400000, rms=0.480 (0.035%), neg=0, invalid=96777 0261: dt=6.400000, rms=0.480 (0.036%), neg=0, invalid=96777 0262: dt=6.400000, rms=0.479 (0.057%), neg=0, invalid=96777 0263: dt=6.400000, rms=0.479 (0.075%), neg=0, invalid=96777 0264: dt=6.400000, rms=0.479 (0.075%), neg=0, invalid=96777 0265: dt=6.400000, rms=0.478 (0.081%), neg=0, invalid=96777 0266: dt=6.400000, rms=0.478 (0.100%), neg=0, invalid=96777 0267: dt=6.400000, rms=0.477 (0.116%), neg=0, invalid=96777 0268: dt=6.400000, rms=0.477 (0.125%), neg=0, invalid=96777 0269: dt=6.400000, rms=0.476 (0.115%), neg=0, invalid=96777 0270: dt=6.400000, rms=0.476 (0.115%), neg=0, invalid=96777 0271: dt=6.400000, rms=0.475 (0.109%), neg=0, invalid=96777 0272: dt=6.400000, rms=0.474 (0.116%), neg=0, invalid=96777 0273: dt=6.400000, rms=0.474 (0.119%), neg=0, invalid=96777 0274: dt=6.400000, rms=0.473 (0.112%), neg=0, invalid=96777 0275: dt=6.400000, rms=0.473 (0.105%), neg=0, invalid=96777 0276: dt=6.400000, rms=0.472 (0.103%), neg=0, invalid=96777 0277: dt=6.400000, rms=0.472 (0.095%), neg=0, invalid=96777 0278: dt=6.400000, rms=0.471 (0.105%), neg=0, invalid=96777 0279: dt=6.400000, rms=0.471 (0.103%), neg=0, invalid=96777 0280: dt=6.400000, rms=0.471 (0.089%), neg=0, invalid=96777 0281: dt=6.400000, rms=0.470 (0.086%), neg=0, invalid=96777 0282: dt=6.400000, rms=0.470 (0.085%), neg=0, invalid=96777 0283: dt=6.400000, rms=0.469 (0.076%), neg=0, invalid=96777 0284: dt=6.400000, rms=0.469 (0.066%), neg=0, invalid=96777 0285: dt=6.400000, rms=0.469 (0.046%), neg=0, invalid=96777 0286: dt=6.400000, rms=0.469 (0.064%), neg=0, invalid=96777 0287: dt=6.400000, rms=0.468 (0.074%), neg=0, invalid=96777 0288: dt=6.400000, rms=0.468 (0.065%), neg=0, invalid=96777 0289: dt=6.400000, rms=0.468 (0.060%), neg=0, invalid=96777 0290: dt=6.400000, rms=0.467 (0.064%), neg=0, invalid=96777 0291: dt=6.400000, rms=0.467 (0.044%), neg=0, invalid=96777 0292: dt=6.400000, rms=0.467 (0.042%), neg=0, invalid=96777 0293: dt=6.400000, rms=0.467 (0.049%), neg=0, invalid=96777 0294: dt=6.400000, rms=0.467 (0.044%), neg=0, invalid=96777 0295: dt=6.400000, rms=0.466 (0.035%), neg=0, invalid=96777 0296: dt=6.400000, rms=0.466 (0.038%), neg=0, invalid=96777 0297: dt=6.400000, rms=0.466 (0.037%), neg=0, invalid=96777 0298: dt=6.400000, rms=0.466 (0.045%), neg=0, invalid=96777 0299: dt=6.400000, rms=0.466 (0.037%), neg=0, invalid=96777 0300: dt=6.400000, rms=0.465 (0.044%), neg=0, invalid=96777 0301: dt=6.400000, rms=0.465 (0.046%), neg=0, invalid=96777 0302: dt=6.400000, rms=0.465 (0.041%), neg=0, invalid=96777 0303: dt=6.400000, rms=0.465 (0.034%), neg=0, invalid=96777 0304: dt=6.400000, rms=0.465 (0.031%), neg=0, invalid=96777 0305: dt=6.400000, rms=0.465 (0.033%), neg=0, invalid=96777 0306: dt=6.400000, rms=0.464 (0.014%), neg=0, invalid=96777 0307: dt=6.400000, rms=0.464 (-0.008%), neg=0, invalid=96777 0308: dt=2.000000, rms=0.464 (0.000%), neg=0, invalid=96777 0309: dt=25.600000, rms=0.464 (0.020%), neg=0, invalid=96777 0310: dt=2.800000, rms=0.464 (0.004%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.464, neg=0, invalid=96777 0311: dt=32.000000, rms=0.463 (0.237%), neg=0, invalid=96777 0312: dt=11.200000, rms=0.463 (0.159%), neg=0, invalid=96777 0313: dt=11.200000, rms=0.462 (0.041%), neg=0, invalid=96777 0314: dt=11.200000, rms=0.462 (0.042%), neg=0, invalid=96777 0315: dt=11.200000, rms=0.462 (0.044%), neg=0, invalid=96777 0316: dt=11.200000, rms=0.462 (0.043%), neg=0, invalid=96777 0317: dt=11.200000, rms=0.462 (0.033%), neg=0, invalid=96777 0318: dt=11.200000, rms=0.462 (0.022%), neg=0, invalid=96777 0319: dt=11.200000, rms=0.462 (0.001%), neg=0, invalid=96777 0320: dt=11.200000, rms=0.461 (0.010%), neg=0, invalid=96777 0321: dt=11.200000, rms=0.461 (0.020%), neg=0, invalid=96777 0322: dt=44.800000, rms=0.461 (0.030%), neg=0, invalid=96777 0323: dt=2.800000, rms=0.461 (0.006%), neg=0, invalid=96777 0324: dt=2.800000, rms=0.461 (0.008%), neg=0, invalid=96777 0325: dt=2.800000, rms=0.461 (0.004%), neg=0, invalid=96777 0326: dt=2.800000, rms=0.461 (0.002%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.479, neg=0, invalid=96777 0327: dt=0.000000, rms=0.479 (0.002%), neg=0, invalid=96777 0328: dt=0.000000, rms=0.479 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.479, neg=0, invalid=96777 0329: dt=0.000000, rms=0.479 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.514, neg=0, invalid=96777 0330: dt=1.355191, rms=0.510 (0.754%), neg=0, invalid=96777 0331: dt=0.320000, rms=0.510 (0.015%), neg=0, invalid=96777 0332: dt=0.320000, rms=0.510 (-0.012%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.510, neg=0, invalid=96777 0333: dt=0.477273, rms=0.510 (0.060%), neg=0, invalid=96777 0334: dt=0.256000, rms=0.510 (0.009%), neg=0, invalid=96777 0335: dt=0.256000, rms=0.510 (-0.007%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.471, neg=0, invalid=96777 0336: dt=0.448000, rms=0.457 (3.061%), neg=0, invalid=96777 0337: dt=0.320000, rms=0.455 (0.384%), neg=0, invalid=96777 0338: dt=0.007000, rms=0.455 (0.007%), neg=0, invalid=96777 0339: dt=0.007000, rms=0.455 (0.005%), neg=0, invalid=96777 0340: dt=0.007000, rms=0.455 (0.014%), neg=0, invalid=96777 0341: dt=0.007000, rms=0.455 (0.018%), neg=0, invalid=96777 0342: dt=0.007000, rms=0.455 (0.021%), neg=0, invalid=96777 0343: dt=0.007000, rms=0.455 (0.025%), neg=0, invalid=96777 0344: dt=0.007000, rms=0.455 (0.030%), neg=0, invalid=96777 0345: dt=0.007000, rms=0.455 (0.032%), neg=0, invalid=96777 0346: dt=0.007000, rms=0.454 (0.031%), neg=0, invalid=96777 0347: dt=0.007000, rms=0.454 (0.039%), neg=0, invalid=96777 0348: dt=0.007000, rms=0.454 (0.039%), neg=0, invalid=96777 0349: dt=0.007000, rms=0.454 (0.038%), neg=0, invalid=96777 0350: dt=0.007000, rms=0.454 (0.038%), neg=0, invalid=96777 0351: dt=0.007000, rms=0.454 (0.040%), neg=0, invalid=96777 0352: dt=0.007000, rms=0.453 (0.040%), neg=0, invalid=96777 0353: dt=0.007000, rms=0.453 (0.042%), neg=0, invalid=96777 0354: dt=0.007000, rms=0.453 (0.040%), neg=0, invalid=96777 0355: dt=0.007000, rms=0.453 (0.038%), neg=0, invalid=96777 0356: dt=0.007000, rms=0.453 (0.037%), neg=0, invalid=96777 0357: dt=0.007000, rms=0.452 (0.039%), neg=0, invalid=96777 0358: dt=0.007000, rms=0.452 (0.036%), neg=0, invalid=96777 0359: dt=0.007000, rms=0.452 (0.037%), neg=0, invalid=96777 0360: dt=0.007000, rms=0.452 (0.036%), neg=0, invalid=96777 0361: dt=0.007000, rms=0.452 (0.032%), neg=0, invalid=96777 0362: dt=0.007000, rms=0.452 (0.033%), neg=0, invalid=96777 0363: dt=0.007000, rms=0.452 (0.033%), neg=0, invalid=96777 0364: dt=0.007000, rms=0.451 (0.031%), neg=0, invalid=96777 0365: dt=0.007000, rms=0.451 (0.029%), neg=0, invalid=96777 0366: dt=0.007000, rms=0.451 (0.029%), neg=0, invalid=96777 0367: dt=0.007000, rms=0.451 (0.028%), neg=0, invalid=96777 0368: dt=0.007000, rms=0.451 (0.024%), neg=0, invalid=96777 0369: dt=0.007000, rms=0.451 (0.027%), neg=0, invalid=96777 0370: dt=0.007000, rms=0.451 (0.024%), neg=0, invalid=96777 0371: dt=0.007000, rms=0.451 (0.022%), neg=0, invalid=96777 0372: dt=0.384000, rms=0.450 (0.058%), neg=0, invalid=96777 0373: dt=0.028000, rms=0.450 (0.002%), neg=0, invalid=96777 0374: dt=0.028000, rms=0.450 (0.007%), neg=0, invalid=96777 0375: dt=0.028000, rms=0.450 (0.009%), neg=0, invalid=96777 0376: dt=0.028000, rms=0.450 (0.011%), neg=0, invalid=96777 0377: dt=0.028000, rms=0.450 (0.015%), neg=0, invalid=96777 0378: dt=0.028000, rms=0.450 (0.017%), neg=0, invalid=96777 0379: dt=0.028000, rms=0.450 (0.019%), neg=0, invalid=96777 0380: dt=0.014000, rms=0.450 (-0.001%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.450, neg=0, invalid=96777 0381: dt=0.020000, rms=0.450 (0.040%), neg=0, invalid=96777 0382: dt=0.028000, rms=0.450 (0.056%), neg=0, invalid=96777 0383: dt=0.028000, rms=0.449 (0.051%), neg=0, invalid=96777 0384: dt=0.007000, rms=0.449 (0.013%), neg=0, invalid=96777 0385: dt=0.007000, rms=0.449 (0.013%), neg=0, invalid=96777 0386: dt=0.007000, rms=0.449 (0.021%), neg=0, invalid=96777 0387: dt=0.007000, rms=0.449 (0.033%), neg=0, invalid=96777 0388: dt=0.007000, rms=0.449 (0.039%), neg=0, invalid=96777 0389: dt=0.007000, rms=0.449 (0.046%), neg=0, invalid=96777 0390: dt=0.007000, rms=0.448 (0.049%), neg=0, invalid=96777 0391: dt=0.007000, rms=0.448 (0.055%), neg=0, invalid=96777 0392: dt=0.007000, rms=0.448 (0.054%), neg=0, invalid=96777 0393: dt=0.007000, rms=0.448 (0.057%), neg=0, invalid=96777 0394: dt=0.007000, rms=0.447 (0.061%), neg=0, invalid=96777 0395: dt=0.007000, rms=0.447 (0.059%), neg=0, invalid=96777 0396: dt=0.007000, rms=0.447 (0.055%), neg=0, invalid=96777 0397: dt=0.007000, rms=0.447 (0.054%), neg=0, invalid=96777 0398: dt=0.007000, rms=0.446 (0.052%), neg=0, invalid=96777 0399: dt=0.007000, rms=0.446 (0.045%), neg=0, invalid=96777 0400: dt=0.007000, rms=0.446 (0.044%), neg=0, invalid=96777 0401: dt=0.007000, rms=0.446 (0.039%), neg=0, invalid=96777 0402: dt=0.007000, rms=0.446 (0.038%), neg=0, invalid=96777 0403: dt=0.007000, rms=0.445 (0.034%), neg=0, invalid=96777 0404: dt=0.007000, rms=0.445 (0.028%), neg=0, invalid=96777 0405: dt=0.007000, rms=0.445 (0.026%), neg=0, invalid=96777 0406: dt=0.007000, rms=0.445 (0.022%), neg=0, invalid=96777 0407: dt=0.007000, rms=0.445 (0.016%), neg=0, invalid=96777 0408: dt=0.000000, rms=0.445 (-0.000%), neg=0, invalid=96777 label assignment complete, 0 changed (0.00%) ********************************************************************************************* ********************************************************************************************* ********************************************************************************************* ********************* ALLOWING NEGATIVE NODES IN DEFORMATION ******************************** ********************************************************************************************* ********************************************************************************************* ********************************************************************************************* **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.443, neg=0, invalid=96777 0409: dt=0.000000, rms=0.443 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.443, neg=0, invalid=96777 0410: dt=295.936000, rms=0.443 (0.138%), neg=0, invalid=96777 0411: dt=27.744000, rms=0.443 (0.002%), neg=0, invalid=96777 0412: dt=27.744000, rms=0.443 (0.003%), neg=0, invalid=96777 0413: dt=27.744000, rms=0.443 (-0.008%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.443, neg=0, invalid=96777 0414: dt=20.736000, rms=0.443 (0.026%), neg=0, invalid=96777 0415: dt=20.736000, rms=0.443 (0.014%), neg=0, invalid=96777 0416: dt=20.736000, rms=0.442 (0.014%), neg=0, invalid=96777 0417: dt=20.736000, rms=0.442 (0.004%), neg=0, invalid=96777 0418: dt=20.736000, rms=0.442 (-0.009%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.442, neg=0, invalid=96777 0419: dt=124.416000, rms=0.440 (0.542%), neg=0, invalid=96777 0420: dt=25.920000, rms=0.440 (0.090%), neg=0, invalid=96777 0421: dt=25.920000, rms=0.439 (0.056%), neg=0, invalid=96777 0422: dt=25.920000, rms=0.439 (0.028%), neg=0, invalid=96777 0423: dt=25.920000, rms=0.439 (0.019%), neg=0, invalid=96777 0424: dt=124.416000, rms=0.439 (0.123%), neg=0, invalid=96777 0425: dt=25.920000, rms=0.438 (0.088%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.438, neg=0, invalid=96777 iter 0, gcam->neg = 5 after 0 iterations, nbhd size=0, neg = 0 0426: dt=32.000000, rms=0.436 (0.447%), neg=0, invalid=96777 0427: dt=11.200000, rms=0.435 (0.373%), neg=0, invalid=96777 0428: dt=11.200000, rms=0.434 (0.191%), neg=0, invalid=96777 0429: dt=11.200000, rms=0.433 (0.166%), neg=0, invalid=96777 0430: dt=11.200000, rms=0.432 (0.215%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0431: dt=11.200000, rms=0.431 (0.265%), neg=0, invalid=96777 0432: dt=11.200000, rms=0.430 (0.241%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0433: dt=11.200000, rms=0.429 (0.233%), neg=0, invalid=96777 0434: dt=11.200000, rms=0.428 (0.171%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0435: dt=11.200000, rms=0.428 (0.158%), neg=0, invalid=96777 0436: dt=11.200000, rms=0.427 (0.155%), neg=0, invalid=96777 0437: dt=11.200000, rms=0.426 (0.163%), neg=0, invalid=96777 0438: dt=11.200000, rms=0.426 (0.179%), neg=0, invalid=96777 0439: dt=11.200000, rms=0.425 (0.171%), neg=0, invalid=96777 0440: dt=11.200000, rms=0.424 (0.154%), neg=0, invalid=96777 0441: dt=11.200000, rms=0.424 (0.148%), neg=0, invalid=96777 0442: dt=11.200000, rms=0.423 (0.153%), neg=0, invalid=96777 0443: dt=11.200000, rms=0.422 (0.127%), neg=0, invalid=96777 0444: dt=11.200000, rms=0.422 (0.108%), neg=0, invalid=96777 0445: dt=11.200000, rms=0.422 (0.093%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0446: dt=19.200000, rms=0.421 (0.028%), neg=0, invalid=96777 0447: dt=19.200000, rms=0.421 (-0.010%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.421, neg=0, invalid=96777 0448: dt=32.000000, rms=0.420 (0.382%), neg=0, invalid=96777 0449: dt=11.200000, rms=0.419 (0.172%), neg=0, invalid=96777 0450: dt=11.200000, rms=0.419 (0.093%), neg=0, invalid=96777 0451: dt=11.200000, rms=0.418 (0.168%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 6 iterations, nbhd size=1, neg = 0 0452: dt=11.200000, rms=0.417 (0.178%), neg=0, invalid=96777 iter 0, gcam->neg = 21 after 11 iterations, nbhd size=1, neg = 0 0453: dt=11.200000, rms=0.417 (0.144%), neg=0, invalid=96777 0454: dt=11.200000, rms=0.416 (0.100%), neg=0, invalid=96777 0455: dt=11.200000, rms=0.416 (0.015%), neg=0, invalid=96777 0456: dt=8.000000, rms=0.416 (0.067%), neg=0, invalid=96777 0457: dt=19.200000, rms=0.416 (0.045%), neg=0, invalid=96777 0458: dt=19.200000, rms=0.416 (-0.039%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.420, neg=0, invalid=96777 0459: dt=3.666667, rms=0.420 (0.075%), neg=0, invalid=96777 0460: dt=2.304000, rms=0.420 (0.023%), neg=0, invalid=96777 0461: dt=2.304000, rms=0.420 (0.000%), neg=0, invalid=96777 iter 0, gcam->neg = 5 after 7 iterations, nbhd size=1, neg = 0 0462: dt=2.304000, rms=0.420 (-0.030%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.420, neg=0, invalid=96777 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0463: dt=4.800000, rms=0.420 (0.100%), neg=0, invalid=96777 0464: dt=2.880000, rms=0.420 (0.012%), neg=0, invalid=96777 0465: dt=2.880000, rms=0.419 (0.054%), neg=0, invalid=96777 0466: dt=2.880000, rms=0.419 (0.074%), neg=0, invalid=96777 iter 0, gcam->neg = 17 after 8 iterations, nbhd size=1, neg = 0 0467: dt=2.880000, rms=0.419 (0.021%), neg=0, invalid=96777 0468: dt=2.880000, rms=0.419 (-0.036%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.423, neg=0, invalid=96777 0469: dt=0.000000, rms=0.423 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.423, neg=0, invalid=96777 0470: dt=0.000000, rms=0.423 (0.000%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.416, neg=0, invalid=96777 iter 0, gcam->neg = 516 after 32 iterations, nbhd size=3, neg = 0 0471: dt=1.683112, rms=0.386 (7.302%), neg=0, invalid=96777 0472: dt=0.000109, rms=0.386 (0.007%), neg=0, invalid=96777 0473: dt=0.000109, rms=0.386 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.386, neg=0, invalid=96777 0474: dt=0.000109, rms=0.386 (0.000%), neg=0, invalid=96777 0475: dt=0.000000, rms=0.386 (0.000%), neg=0, invalid=96777 label assignment complete, 0 changed (0.00%) label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.375, neg=0, invalid=96777 0476: dt=0.000000, rms=0.376 (-0.197%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.376, neg=0, invalid=96777 0477: dt=73.984000, rms=0.376 (0.008%), neg=0, invalid=96777 0478: dt=110.976000, rms=0.376 (0.003%), neg=0, invalid=96777 0479: dt=110.976000, rms=0.376 (0.000%), neg=0, invalid=96777 0480: dt=110.976000, rms=0.376 (-0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.376, neg=0, invalid=96777 0481: dt=0.000000, rms=0.376 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.376, neg=0, invalid=96777 iter 0, gcam->neg = 1 after 14 iterations, nbhd size=2, neg = 0 0482: dt=36.288000, rms=0.376 (0.016%), neg=0, invalid=96777 0483: dt=0.060750, rms=0.376 (0.000%), neg=0, invalid=96777 0484: dt=0.060750, rms=0.376 (0.000%), neg=0, invalid=96777 0485: dt=0.060750, rms=0.376 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.376, neg=0, invalid=96777 0486: dt=2.800000, rms=0.376 (0.011%), neg=0, invalid=96777 0487: dt=11.200000, rms=0.376 (0.061%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 12 iterations, nbhd size=2, neg = 0 0488: dt=9.600000, rms=0.376 (0.026%), neg=0, invalid=96777 0489: dt=9.600000, rms=0.376 (-0.086%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.376, neg=0, invalid=96777 0490: dt=6.400000, rms=0.376 (0.030%), neg=0, invalid=96777 iter 0, gcam->neg = 21 after 200 iterations, nbhd size=3, neg = 5 starting rms=0.007, neg=5, removing folds in lattice.... iter 1, dt=0.000031: new neg 0, old_neg 5, delta 5, rms=0.002 (67.702%) 0491: dt=38.400000, rms=0.375 (0.382%), neg=0, invalid=96777 iter 0, gcam->neg = 6 after 9 iterations, nbhd size=1, neg = 0 0492: dt=44.800000, rms=0.374 (0.125%), neg=0, invalid=96777 iter 0, gcam->neg = 49 after 200 iterations, nbhd size=3, neg = 11 starting rms=0.012, neg=11, removing folds in lattice.... iter 1, dt=0.000023: new neg 3, old_neg 11, delta 8, rms=0.003 (75.233%) iter 2, dt=0.000036: new neg 0, old_neg 3, delta 3, rms=0.002 (24.361%) 0493: dt=44.800000, rms=0.374 (-0.192%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.376, neg=0, invalid=96777 iter 0, gcam->neg = 3 after 15 iterations, nbhd size=2, neg = 0 0494: dt=1.008000, rms=0.376 (0.033%), neg=0, invalid=96777 iter 0, gcam->neg = 14 after 17 iterations, nbhd size=2, neg = 0 0495: dt=2.304000, rms=0.375 (0.109%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0496: dt=0.694444, rms=0.375 (0.021%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0497: dt=0.694444, rms=0.375 (0.034%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 7 iterations, nbhd size=1, neg = 0 0498: dt=0.694444, rms=0.375 (0.053%), neg=0, invalid=96777 iter 0, gcam->neg = 5 after 15 iterations, nbhd size=2, neg = 0 0499: dt=0.694444, rms=0.375 (0.071%), neg=0, invalid=96777 iter 0, gcam->neg = 12 after 15 iterations, nbhd size=2, neg = 0 0500: dt=0.694444, rms=0.374 (0.080%), neg=0, invalid=96777 iter 0, gcam->neg = 14 after 17 iterations, nbhd size=2, neg = 0 0501: dt=0.694444, rms=0.374 (0.076%), neg=0, invalid=96777 iter 0, gcam->neg = 29 after 17 iterations, nbhd size=2, neg = 0 0502: dt=0.694444, rms=0.374 (0.056%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.374, neg=0, invalid=96777 iter 0, gcam->neg = 16 after 10 iterations, nbhd size=1, neg = 0 0503: dt=3.529412, rms=0.373 (0.115%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0504: dt=0.144000, rms=0.373 (0.004%), neg=0, invalid=96777 0505: dt=0.144000, rms=0.373 (0.007%), neg=0, invalid=96777 0506: dt=0.144000, rms=0.373 (0.013%), neg=0, invalid=96777 0507: dt=0.144000, rms=0.373 (0.018%), neg=0, invalid=96777 0508: dt=0.144000, rms=0.373 (0.023%), neg=0, invalid=96777 0509: dt=0.144000, rms=0.373 (0.025%), neg=0, invalid=96777 0510: dt=0.144000, rms=0.373 (0.028%), neg=0, invalid=96777 0511: dt=0.144000, rms=0.373 (0.030%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 19 iterations, nbhd size=3, neg = 0 0512: dt=0.144000, rms=0.373 (0.029%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0513: dt=0.144000, rms=0.373 (0.033%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0514: dt=0.144000, rms=0.372 (0.034%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 15 iterations, nbhd size=2, neg = 0 0515: dt=0.144000, rms=0.372 (0.029%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.376, neg=0, invalid=96777 0516: dt=0.000000, rms=0.376 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.376, neg=0, invalid=96777 0517: dt=0.000000, rms=0.376 (0.000%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.370, neg=0, invalid=96777 iter 0, gcam->neg = 398 after 35 iterations, nbhd size=4, neg = 0 0518: dt=0.755435, rms=0.360 (2.691%), neg=0, invalid=96777 0519: dt=0.000078, rms=0.360 (0.002%), neg=0, invalid=96777 0520: dt=0.000078, rms=0.360 (0.000%), neg=0, invalid=96777 0521: dt=0.000078, rms=0.360 (0.000%), neg=0, invalid=96777 0522: dt=0.000078, rms=0.360 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.360, neg=0, invalid=96777 0523: dt=0.000438, rms=0.360 (0.000%), neg=0, invalid=96777 0524: dt=0.000047, rms=0.360 (0.000%), neg=0, invalid=96777 0525: dt=0.000047, rms=0.360 (-0.000%), neg=0, invalid=96777 writing output transformation to transforms/talairach.m3z... GCAMwrite registration took 9 hours, 27 minutes and 28 seconds. #-------------------------------------- #@# CA Reg Inv Sat Jul 6 00:56:00 EDT 2013 /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z Inverting GCAM Saving inverse #-------------------------------------- #@# Remove Neck Sat Jul 6 00:58:32 EDT 2013 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /usr/local/freesurfer/stable5_3_0/average/RB_all_2008-03-26.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/usr/local/freesurfer/stable5_3_0/average/RB_all_2008-03-26.gca'... reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... removing structures at least 25 mm from brain... 11611305 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 2 minutes and 48 seconds. #-------------------------------------- #@# SkullLTA Sat Jul 6 01:01:35 EDT 2013 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /usr/local/freesurfer/stable5_3_0/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull_2.lta ======= NUMBER OF OPENMP THREADS = 1 ======= aligning to atlas containing skull, setting unknown_nbr_spacing = 5 using previously computed transform transforms/talairach.lta reading 1 input volumes... logging results to talairach_with_skull_2.log reading '/usr/local/freesurfer/stable5_3_0/average/RB_all_withskull_2008-03-26.gca'... average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu_noneck.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=9.0 skull bounding box = (49, 27, 23) --> (209, 205, 221) using (102, 86, 122) as brain centroid... mean wm in atlas = 126, using box (82,64,98) --> (121, 107,146) to find MRI wm before smoothing, mri peak at 107 after smoothing, mri peak at 107, scaling input intensities by 1.178 scaling channel 0 by 1.17757 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-3.9 (thresh=-3.9) 1.105 -0.074 0.099 -21.727; 0.045 1.187 0.293 -45.610; -0.132 -0.222 1.010 32.141; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 1 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-4.0 (thresh=-4.0) 1.085 -0.035 0.108 -24.312; 0.004 1.203 0.328 -47.975; -0.131 -0.256 0.981 37.043; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.085 -0.035 0.108 -24.312; 0.004 1.203 0.328 -47.975; -0.131 -0.256 0.981 37.043; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 3 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.085 -0.037 0.116 -24.111; 0.002 1.203 0.345 -49.220; -0.140 -0.275 0.973 41.141; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.086 -0.037 0.116 -24.286; 0.002 1.203 0.345 -49.220; -0.140 -0.275 0.973 41.141; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3481 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.08634 -0.03704 0.11607 -24.28583; 0.00218 1.20269 0.34536 -49.22022; -0.13969 -0.27506 0.97315 41.14121; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.08634 -0.03704 0.11607 -24.28583; 0.00218 1.20269 0.34536 -49.22022; -0.13969 -0.27506 0.97315 41.14121; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 006: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.086 -0.037 0.116 -24.286; 0.002 1.203 0.345 -49.220; -0.140 -0.275 0.973 41.141; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.9 (old=-3.9) transform before final EM align: 1.086 -0.037 0.116 -24.286; 0.002 1.203 0.345 -49.220; -0.140 -0.275 0.973 41.141; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 382743 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.08634 -0.03704 0.11607 -24.28583; 0.00218 1.20269 0.34536 -49.22022; -0.13969 -0.27506 0.97315 41.14121; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.08634 -0.03704 0.11607 -24.28583; 0.00218 1.20269 0.34536 -49.22022; -0.13969 -0.27506 0.97315 41.14121; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 008: -log(p) = 4.3 tol 0.000000 final transform: 1.086 -0.037 0.116 -24.286; 0.002 1.203 0.345 -49.220; -0.140 -0.275 0.973 41.141; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull_2.lta... registration took 48 minutes and 40 seconds. #-------------------------------------- #@# SubCort Seg Sat Jul 6 01:50:29 EDT 2013 mri_ca_label -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/stable5_3_0/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz sysname Linux hostname kyungmo2 machine x86_64 setenv SUBJECTS_DIR /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer cd /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri mri_ca_label -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/stable5_3_0/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 reading 1 input volumes... reading classifier array from /usr/local/freesurfer/stable5_3_0/average/RB_all_2008-03-26.gca... reading input volume from norm.mgz... average std[0] = 6.9 reading transform from transforms/talairach.m3z... Atlas used for the 3D morph was /usr/local/freesurfer/stable5_3_0/average/RB_all_2008-03-26.gca average std = 6.9 using min determinant for regularization = 4.7 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15151 (27) mri peak = 0.16091 (18) Left_Lateral_Ventricle (4): linear fit = 0.67 x + 0.0 (2586 voxels, overlap=0.030) Left_Lateral_Ventricle (4): linear fit = 0.67 x + 0.0 (2586 voxels, peak = 18), gca=18.0 gca peak = 0.14982 (20) mri peak = 0.14135 (18) Right_Lateral_Ventricle (43): linear fit = 0.81 x + 0.0 (2080 voxels, overlap=0.527) Right_Lateral_Ventricle (43): linear fit = 0.81 x + 0.0 (2080 voxels, peak = 16), gca=16.3 gca peak = 0.28003 (97) mri peak = 0.19094 (102) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (207 voxels, overlap=1.013) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (207 voxels, peak = 99), gca=99.4 gca peak = 0.18160 (96) mri peak = 0.18664 (103) Left_Pallidum (13): linear fit = 1.04 x + 0.0 (245 voxels, overlap=0.747) Left_Pallidum (13): linear fit = 1.04 x + 0.0 (245 voxels, peak = 100), gca=100.3 gca peak = 0.27536 (62) mri peak = 0.10565 (73) Right_Hippocampus (53): linear fit = 1.15 x + 0.0 (574 voxels, overlap=0.082) Right_Hippocampus (53): linear fit = 1.15 x + 0.0 (574 voxels, peak = 72), gca=71.6 gca peak = 0.32745 (63) mri peak = 0.10728 (74) Left_Hippocampus (17): linear fit = 1.13 x + 0.0 (645 voxels, overlap=0.426) Left_Hippocampus (17): linear fit = 1.13 x + 0.0 (645 voxels, peak = 72), gca=71.5 gca peak = 0.08597 (105) mri peak = 0.13119 (107) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (31375 voxels, overlap=0.653) Right_Cerebral_White_Matter (41): linear fit = 1.01 x + 0.0 (31375 voxels, peak = 107), gca=106.6 gca peak = 0.09209 (106) mri peak = 0.10991 (107) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (32931 voxels, overlap=0.613) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (32931 voxels, peak = 108), gca=107.6 gca peak = 0.07826 (63) mri peak = 0.04181 (72) Left_Cerebral_Cortex (3): linear fit = 1.08 x + 0.0 (16172 voxels, overlap=0.893) Left_Cerebral_Cortex (3): linear fit = 1.08 x + 0.0 (16172 voxels, peak = 68), gca=67.7 gca peak = 0.08598 (64) mri peak = 0.04451 (65) Right_Cerebral_Cortex (42): linear fit = 1.05 x + 0.0 (16107 voxels, overlap=0.843) Right_Cerebral_Cortex (42): linear fit = 1.05 x + 0.0 (16107 voxels, peak = 68), gca=67.5 gca peak = 0.24164 (71) mri peak = 0.11167 (81) Right_Caudate (50): linear fit = 1.12 x + 0.0 (600 voxels, overlap=0.016) Right_Caudate (50): linear fit = 1.12 x + 0.0 (600 voxels, peak = 79), gca=79.2 gca peak = 0.18227 (75) mri peak = 0.11139 (86) Left_Caudate (11): linear fit = 1.08 x + 0.0 (600 voxels, overlap=0.576) Left_Caudate (11): linear fit = 1.08 x + 0.0 (600 voxels, peak = 81), gca=80.6 gca peak = 0.10629 (62) mri peak = 0.06001 (68) Left_Cerebellum_Cortex (8): linear fit = 1.13 x + 0.0 (15527 voxels, overlap=0.633) Left_Cerebellum_Cortex (8): linear fit = 1.13 x + 0.0 (15527 voxels, peak = 70), gca=70.4 gca peak = 0.11668 (59) mri peak = 0.06002 (68) Right_Cerebellum_Cortex (47): linear fit = 1.13 x + 0.0 (16511 voxels, overlap=0.541) Right_Cerebellum_Cortex (47): linear fit = 1.13 x + 0.0 (16511 voxels, peak = 67), gca=67.0 gca peak = 0.17849 (88) mri peak = 0.14044 (93) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (4969 voxels, overlap=0.603) Left_Cerebellum_White_Matter (7): linear fit = 1.05 x + 0.0 (4969 voxels, peak = 93), gca=92.8 gca peak = 0.16819 (86) mri peak = 0.15482 (93) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (5284 voxels, overlap=0.423) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (5284 voxels, peak = 92), gca=91.6 gca peak = 0.41688 (64) mri peak = 0.10277 (69) Left_Amygdala (18): linear fit = 1.11 x + 0.0 (253 voxels, overlap=0.571) Left_Amygdala (18): linear fit = 1.11 x + 0.0 (253 voxels, peak = 71), gca=70.7 gca peak = 0.42394 (62) mri peak = 0.18182 (72) Right_Amygdala (54): linear fit = 1.13 x + 0.0 (182 voxels, overlap=0.050) Right_Amygdala (54): linear fit = 1.13 x + 0.0 (182 voxels, peak = 70), gca=70.4 gca peak = 0.10041 (96) mri peak = 0.10661 (101) Left_Thalamus_Proper (10): linear fit = 1.08 x + 0.0 (3364 voxels, overlap=0.452) Left_Thalamus_Proper (10): linear fit = 1.08 x + 0.0 (3364 voxels, peak = 103), gca=103.2 gca peak = 0.13978 (88) mri peak = 0.10492 (101) Right_Thalamus_Proper (49): linear fit = 1.13 x + 0.0 (3209 voxels, overlap=0.327) Right_Thalamus_Proper (49): linear fit = 1.13 x + 0.0 (3209 voxels, peak = 100), gca=99.9 gca peak = 0.08514 (81) mri peak = 0.07211 (90) Left_Putamen (12): linear fit = 1.07 x + 0.0 (1633 voxels, overlap=0.742) Left_Putamen (12): linear fit = 1.07 x + 0.0 (1633 voxels, peak = 86), gca=86.3 gca peak = 0.09624 (82) mri peak = 0.07147 (87) Right_Putamen (51): linear fit = 1.09 x + 0.0 (1539 voxels, overlap=0.747) Right_Putamen (51): linear fit = 1.09 x + 0.0 (1539 voxels, peak = 89), gca=89.0 gca peak = 0.07543 (88) mri peak = 0.07723 (93) Brain_Stem (16): linear fit = 1.09 x + 0.0 (9251 voxels, overlap=0.600) Brain_Stem (16): linear fit = 1.09 x + 0.0 (9251 voxels, peak = 95), gca=95.5 gca peak = 0.12757 (95) mri peak = 0.10419 (105) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (795 voxels, overlap=0.279) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (795 voxels, peak = 104), gca=104.0 gca peak = 0.17004 (92) mri peak = 0.08696 (101) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (886 voxels, overlap=0.336) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (886 voxels, peak = 100), gca=99.8 gca peak = 0.21361 (36) mri peak = 0.18758 (21) gca peak = 0.26069 (23) mri peak = 0.31821 (20) Fourth_Ventricle (15): linear fit = 0.81 x + 0.0 (60 voxels, overlap=0.427) Fourth_Ventricle (15): linear fit = 0.81 x + 0.0 (60 voxels, peak = 19), gca=18.7 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.31795 (35) gca peak Third_Ventricle = 0.21361 (36) gca peak CSF = 0.14367 (38) gca peak Left_Accumbens_area = 0.57033 (70) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.65201 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.31129 (32) gca peak Right_Accumbens_area = 0.30219 (72) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.72939 (42) gca peak WM_hypointensities = 0.14821 (82) gca peak non_WM_hypointensities = 0.10354 (53) gca peak Optic_Chiasm = 0.34849 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.11 x + 0.0 estimating mean wm scale to be 1.01 x + 0.0 estimating mean csf scale to be 0.77 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.19758 (18) mri peak = 0.16091 (18) Left_Lateral_Ventricle (4): linear fit = 0.98 x + 0.0 (2586 voxels, overlap=0.908) Left_Lateral_Ventricle (4): linear fit = 0.98 x + 0.0 (2586 voxels, peak = 18), gca=17.6 gca peak = 0.17421 (17) mri peak = 0.14135 (18) Right_Lateral_Ventricle (43): linear fit = 0.93 x + 0.0 (2080 voxels, overlap=0.831) Right_Lateral_Ventricle (43): linear fit = 0.93 x + 0.0 (2080 voxels, peak = 16), gca=15.7 gca peak = 0.30211 (100) mri peak = 0.19094 (102) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (207 voxels, overlap=1.003) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (207 voxels, peak = 100), gca=100.5 gca peak = 0.18298 (100) mri peak = 0.18664 (103) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (245 voxels, overlap=0.883) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (245 voxels, peak = 100), gca=100.0 gca peak = 0.25883 (72) mri peak = 0.10565 (73) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (574 voxels, overlap=1.000) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (574 voxels, peak = 72), gca=72.0 gca peak = 0.22787 (71) mri peak = 0.10728 (74) Left_Hippocampus (17): linear fit = 0.98 x + 0.0 (645 voxels, overlap=1.000) Left_Hippocampus (17): linear fit = 0.98 x + 0.0 (645 voxels, peak = 69), gca=69.2 gca peak = 0.08542 (107) mri peak = 0.13119 (107) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (31375 voxels, overlap=0.699) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (31375 voxels, peak = 107), gca=107.0 gca peak = 0.08744 (107) mri peak = 0.10991 (107) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (32931 voxels, overlap=0.670) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (32931 voxels, peak = 108), gca=107.5 gca peak = 0.07166 (68) mri peak = 0.04181 (72) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (16172 voxels, overlap=0.910) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (16172 voxels, peak = 67), gca=67.0 gca peak = 0.08489 (67) mri peak = 0.04451 (65) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (16107 voxels, overlap=0.954) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (16107 voxels, peak = 67), gca=67.0 gca peak = 0.24944 (82) mri peak = 0.11167 (81) Right_Caudate (50): linear fit = 1.01 x + 0.0 (600 voxels, overlap=1.004) Right_Caudate (50): linear fit = 1.01 x + 0.0 (600 voxels, peak = 83), gca=83.2 gca peak = 0.16079 (80) mri peak = 0.11139 (86) Left_Caudate (11): linear fit = 1.01 x + 0.0 (600 voxels, overlap=0.971) Left_Caudate (11): linear fit = 1.01 x + 0.0 (600 voxels, peak = 81), gca=81.2 gca peak = 0.09373 (69) mri peak = 0.06001 (68) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (15527 voxels, overlap=0.988) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (15527 voxels, peak = 69), gca=69.0 gca peak = 0.10851 (68) mri peak = 0.06002 (68) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (16511 voxels, overlap=0.989) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (16511 voxels, peak = 68), gca=68.0 gca peak = 0.17166 (92) mri peak = 0.14044 (93) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (4969 voxels, overlap=0.949) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (4969 voxels, peak = 92), gca=91.5 gca peak = 0.16064 (92) mri peak = 0.15482 (93) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5284 voxels, overlap=0.950) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5284 voxels, peak = 92), gca=91.5 gca peak = 0.30766 (70) mri peak = 0.10277 (69) Left_Amygdala (18): linear fit = 1.03 x + 0.0 (253 voxels, overlap=1.027) Left_Amygdala (18): linear fit = 1.03 x + 0.0 (253 voxels, peak = 72), gca=72.4 gca peak = 0.34037 (71) mri peak = 0.18182 (72) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (182 voxels, overlap=1.008) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (182 voxels, peak = 71), gca=71.0 gca peak = 0.10535 (103) mri peak = 0.10661 (101) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3364 voxels, overlap=0.839) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3364 voxels, peak = 102), gca=102.5 gca peak = 0.11210 (100) mri peak = 0.10492 (101) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3209 voxels, overlap=0.843) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3209 voxels, peak = 100), gca=100.0 gca peak = 0.07944 (86) mri peak = 0.07211 (90) Left_Putamen (12): linear fit = 0.99 x + 0.0 (1633 voxels, overlap=0.951) Left_Putamen (12): linear fit = 0.99 x + 0.0 (1633 voxels, peak = 85), gca=84.7 gca peak = 0.10053 (82) mri peak = 0.07147 (87) Right_Putamen (51): linear fit = 0.98 x + 0.0 (1539 voxels, overlap=0.912) Right_Putamen (51): linear fit = 0.98 x + 0.0 (1539 voxels, peak = 80), gca=80.0 gca peak = 0.07345 (96) mri peak = 0.07723 (93) Brain_Stem (16): linear fit = 1.00 x + 0.0 (9251 voxels, overlap=0.815) Brain_Stem (16): linear fit = 1.00 x + 0.0 (9251 voxels, peak = 96), gca=96.5 gca peak = 0.12557 (100) mri peak = 0.10419 (105) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (795 voxels, overlap=0.802) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (795 voxels, peak = 100), gca=100.5 gca peak = 0.16614 (100) mri peak = 0.08696 (101) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (886 voxels, overlap=0.872) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (886 voxels, peak = 100), gca=100.5 gca peak = 0.23315 (29) mri peak = 0.18758 (21) gca peak = 0.24321 (19) mri peak = 0.31821 (20) Fourth_Ventricle (15): linear fit = 0.98 x + 0.0 (60 voxels, overlap=0.808) Fourth_Ventricle (15): linear fit = 0.98 x + 0.0 (60 voxels, peak = 19), gca=18.5 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.26487 (40) gca peak Third_Ventricle = 0.23315 (29) gca peak CSF = 0.22625 (35) gca peak Left_Accumbens_area = 0.57145 (75) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.65148 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.23903 (37) gca peak Right_Accumbens_area = 0.35741 (80) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.45329 (33) gca peak WM_hypointensities = 0.17549 (83) gca peak non_WM_hypointensities = 0.10249 (54) gca peak Optic_Chiasm = 0.34565 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.00 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 0.96 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 19207 gm and wm labels changed (%20 to gray, %80 to white out of all changed labels) 235 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 64238 changed. image ll: -2.115, PF=1.000 pass 2: 8760 changed. pass 3: 2742 changed. writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 42 minutes and 11 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri/transforms/cc_up.lta VNS_Mig001 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri/transforms/cc_up.lta reading aseg from /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri/aseg.auto_noCCseg.mgz reading norm from /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri/norm.mgz 68126 voxels in left wm, 52069 in right wm, xrange [123, 138] searching rotation angles z=[-4 10], y=[-2 12] searching scale 1 Z rot -4.2 searching scale 1 Z rot -4.0 searching scale 1 Z rot -3.7 searching scale 1 Z rot -3.5 searching scale 1 Z rot -3.2 searching scale 1 Z rot -3.0 searching scale 1 Z rot -2.7 searching scale 1 Z rot -2.5 searching scale 1 Z rot -2.2 searching scale 1 Z rot -2.0 searching scale 1 Z rot -1.7 searching scale 1 Z rot -1.5 searching scale 1 Z rot -1.2 searching scale 1 Z rot -1.0 searching scale 1 Z rot -0.7 searching scale 1 Z rot -0.5 searching scale 1 Z rot -0.2 searching scale 1 Z rot 0.0 searching scale 1 Z rot 0.3 searching scale 1 Z rot 0.5 searching scale 1 Z rot 0.8 searching scale 1 Z rot 1.0 searching scale 1 Z rot 1.3 searching scale 1 Z rot 1.5 searching scale 1 Z rot 1.8 searching scale 1 Z rot 2.0 searching scale 1 Z rot 2.3 searching scale 1 Z rot 2.5 searching scale 1 Z rot 2.8 searching scale 1 Z rot 3.0 searching scale 1 Z rot 3.3 searching scale 1 Z rot 3.5 searching scale 1 Z rot 3.8 searching scale 1 Z rot 4.0 searching scale 1 Z rot 4.3 searching scale 1 Z rot 4.5 searching scale 1 Z rot 4.8 searching scale 1 Z rot 5.0 searching scale 1 Z rot 5.3 searching scale 1 Z rot 5.5 searching scale 1 Z rot 5.8 searching scale 1 Z rot 6.0 searching scale 1 Z rot 6.3 searching scale 1 Z rot 6.5 searching scale 1 Z rot 6.8 searching scale 1 Z rot 7.0 searching scale 1 Z rot 7.3 searching scale 1 Z rot 7.5 searching scale 1 Z rot 7.8 searching scale 1 Z rot 8.0 searching scale 1 Z rot 8.3 searching scale 1 Z rot 8.5 searching scale 1 Z rot 8.8 searching scale 1 Z rot 9.0 searching scale 1 Z rot 9.3 searching scale 1 Z rot 9.5 global minimum found at slice 130.2, rotations (4.91, 2.79) final transformation (x=130.2, yr=4.907, zr=2.788): 0.995 -0.049 0.085 -5.740; 0.048 0.999 0.004 25.373; -0.086 0.000 0.996 35.515; 0.000 0.000 0.000 1.000; updating x range to be [126, 131] in xformed coordinates best xformed slice 128 cc center is found at 128 144 122 eigenvectors: -0.001 0.004 1.000; -0.135 -0.991 0.004; 0.991 -0.135 0.002; error in mid anterior detected - correcting... error in mid anterior detected - correcting... writing aseg with callosum to /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri/aseg.auto.mgz... corpus callosum matter segmentation took 2.5 minutes #-------------------------------------- #@# Merge ASeg Sat Jul 6 02:35:36 EDT 2013 cp aseg.auto.mgz aseg.mgz #-------------------------------------------- #@# Intensity Normalization2 Sat Jul 6 02:35:36 EDT 2013 /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading from norm.mgz... Reading aseg aseg.mgz normalizing image... processing with aseg removing outliers in the aseg WM... 2403 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 74 (74), valley at 32 (32) csf peak at 19, setting threshold to 55 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 74 (74), valley at 32 (32) csf peak at 19, setting threshold to 55 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 8 minutes and 57 seconds. #-------------------------------------------- #@# Mask BFS Sat Jul 6 02:44:55 EDT 2013 /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1356368 voxels in mask (pct= 11.76) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Sat Jul 6 02:45:14 EDT 2013 mri_segment brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (104.0): 103.3 +- 7.0 [80.0 --> 125.0] GM (75.0) : 73.4 +- 10.0 [30.0 --> 96.0] setting bottom of white matter range to 83.4 setting top of gray matter range to 93.4 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels... reclassifying voxels using Gaussian border classifier... removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 4127 sparsely connected voxels removed... thickening thin strands.... 20 segments, 3653 filled 0 bright non-wm voxels segmented. 2806 diagonally connected voxels added... white matter segmentation took 3.6 minutes writing output to wm.seg.mgz... mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 1.57 minutes reading wm segmentation from wm.seg.mgz... 79 voxels added to wm to prevent paths from MTL structures to cortex 2006 additional wm voxels added 0 additional wm voxels added SEG EDIT: 48145 voxels turned on, 44433 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 0 new 0 115,126,128 old 0 new 0 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 21 found - 21 modified | TOTAL: 21 pass 2 (xy+): 0 found - 21 modified | TOTAL: 21 pass 1 (xy-): 17 found - 17 modified | TOTAL: 38 pass 2 (xy-): 0 found - 17 modified | TOTAL: 38 pass 1 (yz+): 27 found - 27 modified | TOTAL: 65 pass 2 (yz+): 0 found - 27 modified | TOTAL: 65 pass 1 (yz-): 17 found - 17 modified | TOTAL: 82 pass 2 (yz-): 0 found - 17 modified | TOTAL: 82 pass 1 (xz+): 28 found - 28 modified | TOTAL: 110 pass 2 (xz+): 0 found - 28 modified | TOTAL: 110 pass 1 (xz-): 12 found - 12 modified | TOTAL: 122 pass 2 (xz-): 0 found - 12 modified | TOTAL: 122 Iteration Number : 1 pass 1 (+++): 8 found - 8 modified | TOTAL: 8 pass 2 (+++): 0 found - 8 modified | TOTAL: 8 pass 1 (+++): 7 found - 7 modified | TOTAL: 15 pass 2 (+++): 0 found - 7 modified | TOTAL: 15 pass 1 (+++): 12 found - 12 modified | TOTAL: 27 pass 2 (+++): 0 found - 12 modified | TOTAL: 27 pass 1 (+++): 8 found - 8 modified | TOTAL: 35 pass 2 (+++): 0 found - 8 modified | TOTAL: 35 Iteration Number : 1 pass 1 (++): 60 found - 60 modified | TOTAL: 60 pass 2 (++): 0 found - 60 modified | TOTAL: 60 pass 1 (+-): 64 found - 64 modified | TOTAL: 124 pass 2 (+-): 0 found - 64 modified | TOTAL: 124 pass 1 (--): 49 found - 49 modified | TOTAL: 173 pass 2 (--): 0 found - 49 modified | TOTAL: 173 pass 1 (-+): 55 found - 55 modified | TOTAL: 228 pass 2 (-+): 0 found - 55 modified | TOTAL: 228 Iteration Number : 2 pass 1 (xy+): 3 found - 3 modified | TOTAL: 3 pass 2 (xy+): 0 found - 3 modified | TOTAL: 3 pass 1 (xy-): 1 found - 1 modified | TOTAL: 4 pass 2 (xy-): 0 found - 1 modified | TOTAL: 4 pass 1 (yz+): 4 found - 4 modified | TOTAL: 8 pass 2 (yz+): 0 found - 4 modified | TOTAL: 8 pass 1 (yz-): 1 found - 1 modified | TOTAL: 9 pass 2 (yz-): 0 found - 1 modified | TOTAL: 9 pass 1 (xz+): 1 found - 1 modified | TOTAL: 10 pass 2 (xz+): 0 found - 1 modified | TOTAL: 10 pass 1 (xz-): 2 found - 2 modified | TOTAL: 12 pass 2 (xz-): 0 found - 2 modified | TOTAL: 12 Iteration Number : 2 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 pass 1 (+++): 2 found - 2 modified | TOTAL: 4 pass 2 (+++): 0 found - 2 modified | TOTAL: 4 Iteration Number : 2 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 1 found - 1 modified | TOTAL: 2 pass 2 (+-): 0 found - 1 modified | TOTAL: 2 pass 1 (--): 1 found - 1 modified | TOTAL: 3 pass 2 (--): 0 found - 1 modified | TOTAL: 3 pass 1 (-+): 2 found - 2 modified | TOTAL: 5 pass 2 (-+): 0 found - 2 modified | TOTAL: 5 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 1 found - 1 modified | TOTAL: 1 pass 2 (xz+): 0 found - 1 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 1 found - 1 modified | TOTAL: 1 pass 2 (--): 0 found - 1 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 408 (out of 525086: 0.077702) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Sat Jul 6 02:50:58 EDT 2013 /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.auto_noCCseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.105 -0.074 0.099 -21.727; 0.045 1.187 0.293 -45.610; -0.132 -0.222 1.010 32.141; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 1.105 -0.074 0.099 -21.727; 0.045 1.187 0.293 -45.610; -0.132 -0.222 1.010 32.141; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 2984 (min = 350, max = 1400), aspect = 1.31 (min = 0.10, max = 0.75) need search nearby using seed (127, 119, 154), TAL = (1.0, 26.0, 9.0) talairach voxel to voxel transform 0.892 0.037 -0.098 24.229; -0.059 0.797 -0.225 42.297; 0.103 0.180 0.928 -19.360; 0.000 0.000 0.000 1.000; segmentation indicates cc at (127, 119, 154) --> (1.0, 26.0, 9.0) done. writing output to filled.mgz... filling took 1.8 minutes talairach cc position changed to (1.00, 26.00, 9.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(19.00, 26.00, 9.00) SRC: (110.73, 95.97, 156.29) search lh wm seed point around talairach space (-17.00, 26.00, 9.00), SRC: (142.83, 93.85, 160.01) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram to separate WM into two hemispheres ... Find the largest connected component for each hemisphere ... #-------------------------------------------- #@# Tessellate lh Sat Jul 6 02:52:56 EDT 2013 /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 0 found - 0 modified | TOTAL: 1 pass 1 (yz-): 1 found - 1 modified | TOTAL: 2 pass 2 (yz-): 0 found - 1 modified | TOTAL: 2 pass 1 (xz+): 0 found - 0 modified | TOTAL: 2 pass 1 (xz-): 0 found - 0 modified | TOTAL: 2 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 0 found - 0 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 3 (out of 251471: 0.001193) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ slice 40: 99 vertices, 115 faces slice 50: 3044 vertices, 3209 faces slice 60: 9833 vertices, 10147 faces slice 70: 19480 vertices, 19827 faces slice 80: 29512 vertices, 29835 faces slice 90: 39862 vertices, 40188 faces slice 100: 50045 vertices, 50408 faces slice 110: 60839 vertices, 61228 faces slice 120: 70879 vertices, 71248 faces slice 130: 80480 vertices, 80825 faces slice 140: 89969 vertices, 90344 faces slice 150: 98782 vertices, 99094 faces slice 160: 106625 vertices, 106926 faces slice 170: 113979 vertices, 114218 faces slice 180: 119942 vertices, 120179 faces slice 190: 124738 vertices, 124934 faces slice 200: 127116 vertices, 127159 faces slice 210: 127130 vertices, 127166 faces slice 220: 127130 vertices, 127166 faces slice 230: 127130 vertices, 127166 faces slice 240: 127130 vertices, 127166 faces slice 250: 127130 vertices, 127166 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 127130 voxel in cpt #1: X=-36 [v=127130,e=381498,f=254332] located at (-27.344812, -14.106505, 28.894855) For the whole surface: X=-36 [v=127130,e=381498,f=254332] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Sat Jul 6 02:53:32 EDT 2013 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 lh Sat Jul 6 02:53:50 EDT 2013 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/scripts avg radius = 46.5 mm, total surface area = 66901 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 1.4 minutes Not saving sulc step 000: RMS=0.100 (target=0.015) step 005: RMS=0.073 (target=0.015) step 010: RMS=0.054 (target=0.015) step 015: RMS=0.047 (target=0.015) step 020: RMS=0.041 (target=0.015) step 025: RMS=0.036 (target=0.015) step 030: RMS=0.032 (target=0.015) step 035: RMS=0.030 (target=0.015) step 040: RMS=0.029 (target=0.015) step 045: RMS=0.027 (target=0.015) step 050: RMS=0.027 (target=0.015) step 055: RMS=0.027 (target=0.015) step 060: RMS=0.026 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh Sat Jul 6 02:55:28 EDT 2013 /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 1.02 +- 0.60 (0.00-->6.68) (max @ vno 57212 --> 57218) face area 0.03 +- 0.03 (-0.07-->0.93) scaling brain by 0.325... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.391, avgs=0 005/300: dt: 0.9000, rms radial error=176.130, avgs=0 010/300: dt: 0.9000, rms radial error=175.571, avgs=0 015/300: dt: 0.9000, rms radial error=174.837, avgs=0 020/300: dt: 0.9000, rms radial error=173.999, avgs=0 025/300: dt: 0.9000, rms radial error=173.102, avgs=0 030/300: dt: 0.9000, rms radial error=172.171, avgs=0 035/300: dt: 0.9000, rms radial error=171.223, avgs=0 040/300: dt: 0.9000, rms radial error=170.266, avgs=0 045/300: dt: 0.9000, rms radial error=169.312, avgs=0 050/300: dt: 0.9000, rms radial error=168.367, avgs=0 055/300: dt: 0.9000, rms radial error=167.425, avgs=0 060/300: dt: 0.9000, rms radial error=166.486, avgs=0 065/300: dt: 0.9000, rms radial error=165.551, avgs=0 070/300: dt: 0.9000, rms radial error=164.620, avgs=0 075/300: dt: 0.9000, rms radial error=163.694, avgs=0 080/300: dt: 0.9000, rms radial error=162.773, avgs=0 085/300: dt: 0.9000, rms radial error=161.856, avgs=0 090/300: dt: 0.9000, rms radial error=160.947, avgs=0 095/300: dt: 0.9000, rms radial error=160.046, avgs=0 100/300: dt: 0.9000, rms radial error=159.148, avgs=0 105/300: dt: 0.9000, rms radial error=158.256, avgs=0 110/300: dt: 0.9000, rms radial error=157.368, avgs=0 115/300: dt: 0.9000, rms radial error=156.486, avgs=0 120/300: dt: 0.9000, rms radial error=155.608, avgs=0 125/300: dt: 0.9000, rms radial error=154.734, avgs=0 130/300: dt: 0.9000, rms radial error=153.866, avgs=0 135/300: dt: 0.9000, rms radial error=153.002, avgs=0 140/300: dt: 0.9000, rms radial error=152.142, avgs=0 145/300: dt: 0.9000, rms radial error=151.287, avgs=0 150/300: dt: 0.9000, rms radial error=150.437, avgs=0 155/300: dt: 0.9000, rms radial error=149.591, avgs=0 160/300: dt: 0.9000, rms radial error=148.750, avgs=0 165/300: dt: 0.9000, rms radial error=147.913, avgs=0 170/300: dt: 0.9000, rms radial error=147.081, avgs=0 175/300: dt: 0.9000, rms radial error=146.254, avgs=0 180/300: dt: 0.9000, rms radial error=145.431, avgs=0 185/300: dt: 0.9000, rms radial error=144.612, avgs=0 190/300: dt: 0.9000, rms radial error=143.798, avgs=0 195/300: dt: 0.9000, rms radial error=142.989, avgs=0 200/300: dt: 0.9000, rms radial error=142.184, avgs=0 205/300: dt: 0.9000, rms radial error=141.384, avgs=0 210/300: dt: 0.9000, rms radial error=140.588, avgs=0 215/300: dt: 0.9000, rms radial error=139.796, avgs=0 220/300: dt: 0.9000, rms radial error=139.009, avgs=0 225/300: dt: 0.9000, rms radial error=138.226, avgs=0 230/300: dt: 0.9000, rms radial error=137.447, avgs=0 235/300: dt: 0.9000, rms radial error=136.673, avgs=0 240/300: dt: 0.9000, rms radial error=135.903, avgs=0 245/300: dt: 0.9000, rms radial error=135.137, avgs=0 250/300: dt: 0.9000, rms radial error=134.376, avgs=0 255/300: dt: 0.9000, rms radial error=133.619, avgs=0 260/300: dt: 0.9000, rms radial error=132.866, avgs=0 265/300: dt: 0.9000, rms radial error=132.117, avgs=0 270/300: dt: 0.9000, rms radial error=131.373, avgs=0 275/300: dt: 0.9000, rms radial error=130.632, avgs=0 280/300: dt: 0.9000, rms radial error=129.896, avgs=0 285/300: dt: 0.9000, rms radial error=129.164, avgs=0 290/300: dt: 0.9000, rms radial error=128.436, avgs=0 295/300: dt: 0.9000, rms radial error=127.712, avgs=0 300/300: dt: 0.9000, rms radial error=126.991, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 14681.63 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00017 epoch 2 (K=40.0), pass 1, starting sse = 2414.15 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00015 epoch 3 (K=160.0), pass 1, starting sse = 247.77 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.11/11 = 0.00990 epoch 4 (K=640.0), pass 1, starting sse = 14.17 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.21/19 = 0.01120 final writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.19 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology lh Sat Jul 6 03:07:16 EDT 2013 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 VNS_Mig001 lh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ before topology correction, eno=-36 (nv=127130, nf=254332, ne=381498, g=19) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 9 iterations marking ambiguous vertices... 3563 ambiguous faces found in tessellation segmenting defects... 23 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 23 defects to be corrected 0 vertices coincident reading input surface /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.3015 (-4.6507) -vertex loglikelihood: -6.0883 (-3.0442) -normal dot loglikelihood: -3.6118 (-3.6118) -quad curv loglikelihood: -6.3319 (-3.1659) Total Loglikelihood : -25.3335 CORRECTING DEFECT 0 (vertices=384, convex hull=183) After retessellation of defect 0, euler #=-20 (125076,374584,249488) : difference with theory (-20) = 0 CORRECTING DEFECT 1 (vertices=13, convex hull=31) After retessellation of defect 1, euler #=-19 (125077,374597,249501) : difference with theory (-19) = 0 CORRECTING DEFECT 2 (vertices=25, convex hull=52) After retessellation of defect 2, euler #=-18 (125086,374644,249540) : difference with theory (-18) = 0 CORRECTING DEFECT 3 (vertices=155, convex hull=132) After retessellation of defect 3, euler #=-17 (125163,374943,249763) : difference with theory (-17) = 0 CORRECTING DEFECT 4 (vertices=7, convex hull=21) After retessellation of defect 4, euler #=-16 (125166,374958,249776) : difference with theory (-16) = 0 CORRECTING DEFECT 5 (vertices=29, convex hull=53) After retessellation of defect 5, euler #=-15 (125183,375028,249830) : difference with theory (-15) = 0 CORRECTING DEFECT 6 (vertices=219, convex hull=213) After retessellation of defect 6, euler #=-14 (125287,375451,250150) : difference with theory (-14) = 0 CORRECTING DEFECT 7 (vertices=513, convex hull=317) After retessellation of defect 7, euler #=-13 (125407,375978,250558) : difference with theory (-13) = 0 CORRECTING DEFECT 8 (vertices=13, convex hull=19) After retessellation of defect 8, euler #=-12 (125408,375987,250567) : difference with theory (-12) = 0 CORRECTING DEFECT 9 (vertices=6, convex hull=28) After retessellation of defect 9, euler #=-11 (125411,376007,250585) : difference with theory (-11) = 0 CORRECTING DEFECT 10 (vertices=26, convex hull=56) After retessellation of defect 10, euler #=-10 (125422,376066,250634) : difference with theory (-10) = 0 CORRECTING DEFECT 11 (vertices=35, convex hull=21) After retessellation of defect 11, euler #=-9 (125425,376080,250646) : difference with theory (-9) = 0 CORRECTING DEFECT 12 (vertices=10, convex hull=15) After retessellation of defect 12, euler #=-8 (125428,376091,250655) : difference with theory (-8) = 0 CORRECTING DEFECT 13 (vertices=74, convex hull=40) After retessellation of defect 13, euler #=-7 (125432,376119,250680) : difference with theory (-7) = 0 CORRECTING DEFECT 14 (vertices=65, convex hull=37) After retessellation of defect 14, euler #=-6 (125442,376163,250715) : difference with theory (-6) = 0 CORRECTING DEFECT 15 (vertices=11, convex hull=20) After retessellation of defect 15, euler #=-5 (125442,376167,250720) : difference with theory (-5) = 0 CORRECTING DEFECT 16 (vertices=319, convex hull=85) After retessellation of defect 16, euler #=-4 (125451,376230,250775) : difference with theory (-4) = 0 CORRECTING DEFECT 17 (vertices=57, convex hull=44) After retessellation of defect 17, euler #=-3 (125469,376297,250825) : difference with theory (-3) = 0 CORRECTING DEFECT 18 (vertices=27, convex hull=28) After retessellation of defect 18, euler #=-2 (125474,376322,250846) : difference with theory (-2) = 0 CORRECTING DEFECT 19 (vertices=43, convex hull=96) After retessellation of defect 19, euler #=-1 (125497,376433,250935) : difference with theory (-1) = 0 CORRECTING DEFECT 20 (vertices=19, convex hull=25) After retessellation of defect 20, euler #=0 (125498,376447,250949) : difference with theory (0) = 0 CORRECTING DEFECT 21 (vertices=40, convex hull=29) After retessellation of defect 21, euler #=1 (125503,376470,250968) : difference with theory (1) = 0 CORRECTING DEFECT 22 (vertices=46, convex hull=76) After retessellation of defect 22, euler #=2 (125512,376530,251020) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.22 (0.11-->10.79) (max @ vno 80969 --> 86475) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.22 (0.11-->10.79) (max @ vno 80969 --> 86475) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 81 mutations (38.4%), 130 crossovers (61.6%), 105 vertices were eliminated building final representation... 1618 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=125512, nf=251020, ne=376530, g=0) writing corrected surface to /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 29.9 minutes 0 defective edges removing intersecting faces 000: 231 intersecting mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 125512 - 376530 + 251020 = 2 --> 0 holes F =2V-4: 251020 = 251024-4 (0) 2E=3F: 753060 = 753060 (0) total defect index = 0 /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 29 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Sat Jul 6 03:37:57 EDT 2013 /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs VNS_Mig001 lh only generating white matter surface not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri/filled.mgz... reading volume /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri/brain.finalsurfs.mgz... reading volume /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri/wm.mgz... 14576 bright wm thresholded. 0 bright non-wm voxels segmented. reading original surface position from /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/lh.orig... computing class statistics... border white: 245868 voxels (1.47%) border gray 259178 voxels (1.54%) WM (96.0): 97.3 +- 7.4 [70.0 --> 110.0] GM (85.0) : 83.1 +- 11.3 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 62.7 (was 70) setting MAX_BORDER_WHITE to 112.4 (was 105) setting MIN_BORDER_WHITE to 74.0 (was 85) setting MAX_CSF to 51.5 (was 40) setting MAX_GRAY to 97.6 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 68.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 40.2 (was 40) repositioning cortical surface to gray/white boundary reading volume /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.04-->3.76) (max @ vno 73635 --> 79186) face area 0.28 +- 0.12 (0.00-->2.22) mean absolute distance = 0.87 +- 1.13 3585 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105, GM=74 mean inside = 96.3, mean outside = 79.4 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group mean border=83.1, 70 (70) missing vertices, mean dist 0.2 [0.9 (%33.1)->0.8 (%66.9))] %50 local maxima, %45 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=kyung, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.91 +- 0.26 (0.10-->3.99) (max @ vno 52404 --> 125108) face area 0.28 +- 0.13 (0.00-->2.32) mean absolute distance = 0.41 +- 0.70 2793 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4613777.5, rms=9.98 001: dt: 0.5000, sse=5174067.5, rms=7.159 (0.000%) 002: dt: 0.5000, sse=5429407.5, rms=5.328 (0.000%) 003: dt: 0.5000, sse=5729790.0, rms=4.151 (0.000%) 004: dt: 0.5000, sse=5913457.5, rms=3.454 (0.000%) 005: dt: 0.5000, sse=6064759.0, rms=3.107 (0.000%) 006: dt: 0.5000, sse=6117530.0, rms=2.933 (0.000%) 007: dt: 0.5000, sse=6166821.0, rms=2.856 (0.000%) 008: dt: 0.5000, sse=6167088.0, rms=2.799 (0.000%) rms = 2.78, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=6172334.5, rms=2.776 (0.000%) 010: dt: 0.2500, sse=3759896.0, rms=1.900 (0.000%) 011: dt: 0.2500, sse=3498310.2, rms=1.711 (0.000%) rms = 1.68, time step reduction 2 of 3 to 0.125... 012: dt: 0.2500, sse=3375650.0, rms=1.677 (0.000%) rms = 1.64, time step reduction 3 of 3 to 0.062... 013: dt: 0.1250, sse=3318057.8, rms=1.644 (0.000%) positioning took 2.9 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group mean border=86.1, 60 (28) missing vertices, mean dist -0.3 [0.5 (%70.7)->0.3 (%29.3))] %67 local maxima, %28 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=kyung, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.25 (0.07-->4.00) (max @ vno 52404 --> 125108) face area 0.35 +- 0.16 (0.00-->3.02) mean absolute distance = 0.28 +- 0.40 2522 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3853801.0, rms=4.49 014: dt: 0.5000, sse=4133331.8, rms=2.741 (0.000%) 015: dt: 0.5000, sse=4583565.5, rms=2.548 (0.000%) 016: dt: 0.5000, sse=4925570.5, rms=2.399 (0.000%) rms = 2.65, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=4024504.8, rms=1.760 (0.000%) 018: dt: 0.2500, sse=3734128.2, rms=1.483 (0.000%) 019: dt: 0.2500, sse=3616954.0, rms=1.422 (0.000%) rms = 1.42, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=3567108.8, rms=1.419 (0.000%) rms = 1.40, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=3540498.0, rms=1.396 (0.000%) positioning took 1.9 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 1 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group mean border=88.9, 72 (25) missing vertices, mean dist -0.2 [0.3 (%75.7)->0.2 (%24.3))] %84 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=kyung, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.25 (0.08-->4.17) (max @ vno 52404 --> 125108) face area 0.34 +- 0.16 (0.00-->2.92) mean absolute distance = 0.21 +- 0.30 2748 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3792771.2, rms=3.66 022: dt: 0.5000, sse=3995595.0, rms=2.304 (0.000%) rms = 2.45, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=3770268.2, rms=1.692 (0.000%) 024: dt: 0.2500, sse=3698510.2, rms=1.355 (0.000%) 025: dt: 0.2500, sse=3674989.8, rms=1.279 (0.000%) rms = 1.28, time step reduction 2 of 3 to 0.125... rms = 1.27, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=3655509.2, rms=1.266 (0.000%) positioning took 1.4 minutes inhibiting deformation at non-cortical midline structures... removing 1 vertex label from ripped group removing 2 vertex label from ripped group mean border=89.8, 78 (21) missing vertices, mean dist -0.1 [0.2 (%59.2)->0.2 (%40.8))] %88 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=kyung, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=3674121.0, rms=1.69 027: dt: 0.5000, sse=4559343.0, rms=1.555 (0.000%) rms = 2.08, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=4106637.8, rms=1.136 (0.000%) 029: dt: 0.2500, sse=3944793.2, rms=1.062 (0.000%) rms = 1.02, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=4028758.5, rms=1.016 (0.000%) rms = 1.00, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=4019025.0, rms=1.004 (0.000%) positioning took 1.2 minutes inhibiting deformation at non-cortical midline structures... generating cortex label... 10 non-cortical segments detected only using segment with 2293 vertices erasing segment 1 (vno[0] = 48372) erasing segment 2 (vno[0] = 75430) erasing segment 3 (vno[0] = 79914) erasing segment 4 (vno[0] = 91019) erasing segment 5 (vno[0] = 91091) erasing segment 6 (vno[0] = 91951) erasing segment 7 (vno[0] = 93617) erasing segment 8 (vno[0] = 96123) erasing segment 9 (vno[0] = 125454) writing cortex label to /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/label/lh.cortex.label... writing curvature file /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/lh.curv writing smoothed area to lh.area writing curvature file /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/lh.area vertex spacing 0.89 +- 0.25 (0.02-->4.12) (max @ vno 52404 --> 125108) face area 0.33 +- 0.16 (0.00-->2.88) refinement took 11.7 minutes #-------------------------------------------- #@# Smooth2 lh Sat Jul 6 03:49:50 EDT 2013 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/scripts smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 lh Sat Jul 6 03:50:00 EDT 2013 /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 46.7 mm, total surface area = 75667 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.114 (target=0.015) step 005: RMS=0.078 (target=0.015) step 010: RMS=0.057 (target=0.015) step 015: RMS=0.047 (target=0.015) step 020: RMS=0.039 (target=0.015) step 025: RMS=0.032 (target=0.015) step 030: RMS=0.027 (target=0.015) step 035: RMS=0.023 (target=0.015) step 040: RMS=0.020 (target=0.015) step 045: RMS=0.018 (target=0.015) step 050: RMS=0.017 (target=0.015) step 055: RMS=0.016 (target=0.015) inflation complete. inflation took 1.3 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 108 vertices thresholded to be in k1 ~ [-0.22 0.60], k2 ~ [-0.11 0.06] total integrated curvature = 0.656*4pi (8.240) --> 0 handles ICI = 1.5, FI = 9.6, variation=162.606 98 vertices thresholded to be in [-0.02 0.02] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 115 vertices thresholded to be in [-0.14 0.24] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.017, std = 0.024 done. #----------------------------------------- #@# Curvature Stats lh Sat Jul 6 03:54:22 EDT 2013 /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm VNS_Mig001 lh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/lh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ VNS_Mig001/lh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 227 ] Gb_filter = 0 WARN: S lookup min: -0.445859 WARN: S explicit min: 0.000000 vertex = 35 WARN: C lookup max: 108.799789 WARN: C explicit max: 59.977024 vertex = 81729 #-------------------------------------------- #@# Sphere lh Sat Jul 6 03:54:41 EDT 2013 /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/scripts mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... scaling brain by 0.304... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=kyung, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %19.50 pass 1: epoch 2 of 3 starting distance error %19.50 unfolding complete - removing small folds... starting distance error %19.47 removing remaining folds... final distance error %19.49 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/lh.sphere spherical transformation took 1.42 hours #-------------------------------------------- #@# Surf Reg lh Sat Jul 6 05:20:02 EDT 2013 /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/scripts mris_register -curv ../surf/lh.sphere /usr/local/freesurfer/stable5_3_0/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading surface from ../surf/lh.sphere... reading template parameterization from /usr/local/freesurfer/stable5_3_0/average/lh.average.curvature.filled.buckner40.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=kyung, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 0 randomSeed 0 tol=5.0e-01, sigma=0.0, host=kyung, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading lh.sulc curvature mean = -0.000, std = 0.577 curvature mean = 0.028, std = 0.934 curvature mean = 0.023, std = 0.870 Starting MRISrigidBodyAlignGlobal() d=32.00 min @ (0.00, -8.00, -8.00) sse = 191673.2, tmin=4.8357 d=16.00 min @ (0.00, 0.00, 4.00) sse = 173535.2, tmin=7.2548 d=8.00 min @ (2.00, 2.00, 0.00) sse = 170082.4, tmin=9.6741 d=4.00 min @ (-1.00, 0.00, -1.00) sse = 165973.0, tmin=12.1147 d=1.00 min @ (-0.25, -0.25, 0.00) sse = 165821.2, tmin=17.0389 d=0.50 min @ (0.12, 0.00, 0.00) sse = 165818.7, tmin=19.5065 tol=1.0e+00, sigma=0.5, host=kyung, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 19.51 min curvature mean = 0.014, std = 0.963 curvature mean = 0.010, std = 0.946 curvature mean = 0.013, std = 0.976 curvature mean = 0.004, std = 0.976 curvature mean = 0.011, std = 0.979 curvature mean = 0.001, std = 0.990 2 Reading smoothwm curvature mean = -0.024, std = 0.280 curvature mean = 0.003, std = 0.068 curvature mean = 0.062, std = 0.365 curvature mean = 0.003, std = 0.080 curvature mean = 0.022, std = 0.571 curvature mean = 0.004, std = 0.086 curvature mean = 0.012, std = 0.713 curvature mean = 0.004, std = 0.089 curvature mean = 0.004, std = 0.821 MRISregister() return, current seed 0 writing registered surface to ../surf/lh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white lh Sat Jul 6 06:21:55 EDT 2013 mris_jacobian ../surf/lh.white ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white... writing curvature file ../surf/lh.jacobian_white #-------------------------------------------- #@# AvgCurv lh Sat Jul 6 06:22:01 EDT 2013 /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/scripts mrisp_paint -a 5 /usr/local/freesurfer/stable5_3_0/average/lh.average.curvature.filled.buckner40.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /usr/local/freesurfer/stable5_3_0/average/lh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/lh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Sat Jul 6 06:22:05 EDT 2013 /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 VNS_Mig001 lh ../surf/lh.sphere.reg /usr/local/freesurfer/stable5_3_0/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /usr/local/freesurfer/stable5_3_0/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs... reading color table from GCSA file.... average std = 1.0 using min determinant for regularization = 0.011 0 singular and 384 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 991 labels changed using aseg relabeling using gibbs priors... 000: 2867 changed, 125512 examined... 001: 697 changed, 12191 examined... 002: 158 changed, 3764 examined... 003: 57 changed, 965 examined... 004: 29 changed, 343 examined... 005: 9 changed, 163 examined... 006: 7 changed, 56 examined... 007: 2 changed, 38 examined... 008: 3 changed, 13 examined... 009: 0 changed, 11 examined... 240 labels changed using aseg 000: 108 total segments, 53 labels (170 vertices) changed 001: 55 total segments, 4 labels (4 vertices) changed 002: 51 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 27 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1299 vertices marked for relabeling... 1299 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 1 minutes and 27 seconds. #-------------------------------------------- #@# Make Pial Surf lh Sat Jul 6 06:23:34 EDT 2013 /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs VNS_Mig001 lh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri/filled.mgz... reading volume /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri/brain.finalsurfs.mgz... reading volume /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri/wm.mgz... 14576 bright wm thresholded. 0 bright non-wm voxels segmented. reading original surface position from /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/lh.orig... computing class statistics... border white: 245868 voxels (1.47%) border gray 259178 voxels (1.54%) WM (96.0): 97.3 +- 7.4 [70.0 --> 110.0] GM (85.0) : 83.1 +- 11.3 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 62.7 (was 70) setting MAX_BORDER_WHITE to 112.4 (was 105) setting MIN_BORDER_WHITE to 74.0 (was 85) setting MAX_CSF to 51.5 (was 40) setting MAX_GRAY to 97.6 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 68.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 40.2 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105, GM=74 mean inside = 96.3, mean outside = 79.4 smoothing surface for 5 iterations... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.04-->3.76) (max @ vno 73635 --> 79186) face area 0.28 +- 0.12 (0.00-->2.22) mean absolute distance = 0.87 +- 1.13 3624 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 1 with 325 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 6 with 2 points - only 0.00% unknown mean border=83.1, 70 (70) missing vertices, mean dist 0.2 [0.9 (%33.2)->0.8 (%66.8))] %50 local maxima, %45 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=kyung, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.91 +- 0.26 (0.10-->3.99) (max @ vno 52404 --> 125108) face area 0.28 +- 0.13 (0.00-->2.32) mean absolute distance = 0.41 +- 0.70 2810 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4622673.5, rms=9.97 001: dt: 0.5000, sse=5191339.0, rms=7.155 (0.000%) 002: dt: 0.5000, sse=5446380.5, rms=5.327 (0.000%) 003: dt: 0.5000, sse=5749673.0, rms=4.151 (0.000%) 004: dt: 0.5000, sse=5931621.0, rms=3.456 (0.000%) 005: dt: 0.5000, sse=6086431.5, rms=3.109 (0.000%) 006: dt: 0.5000, sse=6136453.5, rms=2.935 (0.000%) 007: dt: 0.5000, sse=6189692.5, rms=2.858 (0.000%) 008: dt: 0.5000, sse=6185902.0, rms=2.802 (0.000%) rms = 2.78, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=6194851.5, rms=2.777 (0.000%) 010: dt: 0.2500, sse=3774581.5, rms=1.904 (0.000%) 011: dt: 0.2500, sse=3511597.8, rms=1.716 (0.000%) rms = 1.68, time step reduction 2 of 3 to 0.125... 012: dt: 0.2500, sse=3388952.0, rms=1.682 (0.000%) rms = 1.65, time step reduction 3 of 3 to 0.062... 013: dt: 0.1250, sse=3331205.5, rms=1.649 (0.000%) positioning took 2.9 minutes inhibiting deformation at non-cortical midline structures... deleting segment 3 with 204 points - only 0.00% unknown deleting segment 5 with 25 points - only 0.00% unknown deleting segment 6 with 36 points - only 0.00% unknown removing 3 vertex label from ripped group mean border=86.0, 60 (28) missing vertices, mean dist -0.3 [0.5 (%70.6)->0.3 (%29.4))] %67 local maxima, %28 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=kyung, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.25 (0.07-->4.00) (max @ vno 52404 --> 125108) face area 0.35 +- 0.16 (0.00-->3.02) mean absolute distance = 0.28 +- 0.40 2532 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3869440.8, rms=4.49 014: dt: 0.5000, sse=4152941.8, rms=2.740 (0.000%) 015: dt: 0.5000, sse=4605293.5, rms=2.548 (0.000%) 016: dt: 0.5000, sse=4949343.0, rms=2.399 (0.000%) rms = 2.65, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=4045344.0, rms=1.761 (0.000%) 018: dt: 0.2500, sse=3754145.5, rms=1.486 (0.000%) 019: dt: 0.2500, sse=3636869.5, rms=1.425 (0.000%) rms = 1.42, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=3586330.8, rms=1.422 (0.000%) rms = 1.40, time step reduction 3 of 3 to 0.062... 021: dt: 0.1250, sse=3559618.2, rms=1.399 (0.000%) positioning took 1.9 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 228 points - only 0.00% unknown deleting segment 4 with 24 points - only 0.00% unknown removing 2 vertex label from ripped group removing 3 vertex label from ripped group deleting segment 6 with 3 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 7 with 3 points - only 0.00% unknown mean border=88.9, 72 (25) missing vertices, mean dist -0.2 [0.3 (%75.7)->0.2 (%24.3))] %84 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=kyung, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.25 (0.08-->4.17) (max @ vno 52404 --> 125108) face area 0.34 +- 0.16 (0.00-->2.92) mean absolute distance = 0.21 +- 0.30 2784 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3813083.8, rms=3.66 022: dt: 0.5000, sse=4020458.8, rms=2.302 (0.000%) rms = 2.45, time step reduction 1 of 3 to 0.250... 023: dt: 0.2500, sse=3793960.8, rms=1.693 (0.000%) 024: dt: 0.2500, sse=3721763.2, rms=1.358 (0.000%) 025: dt: 0.2500, sse=3696850.5, rms=1.281 (0.000%) rms = 1.29, time step reduction 2 of 3 to 0.125... rms = 1.27, time step reduction 3 of 3 to 0.062... 026: dt: 0.1250, sse=3677350.0, rms=1.269 (0.000%) positioning took 1.4 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 237 points - only 0.00% unknown deleting segment 1 with 34 points - only 0.00% unknown deleting segment 2 with 12 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 4 with 25 points - only 0.00% unknown mean border=89.8, 78 (21) missing vertices, mean dist -0.1 [0.2 (%59.2)->0.2 (%40.8))] %89 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=kyung, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=3696801.0, rms=1.69 027: dt: 0.5000, sse=4589601.5, rms=1.554 (0.000%) rms = 2.08, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=4134483.8, rms=1.137 (0.000%) 029: dt: 0.2500, sse=3971208.5, rms=1.064 (0.000%) rms = 1.02, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=4055981.5, rms=1.018 (0.000%) rms = 1.01, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=4046280.2, rms=1.007 (0.000%) positioning took 1.2 minutes inhibiting deformation at non-cortical midline structures... smoothing surface for 5 iterations... mean border=62.7, 80 (80) missing vertices, mean dist 1.9 [2.1 (%0.0)->2.3 (%100.0))] %31 local maxima, %46 large gradients and %19 min vals, 1012 gradients ignored tol=1.0e-04, sigma=2.0, host=kyung, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=20621458.0, rms=27.57 001: dt: 0.5000, sse=16193754.0, rms=23.990 (0.000%) 002: dt: 0.5000, sse=12825002.0, rms=20.883 (0.000%) 003: dt: 0.5000, sse=10406990.0, rms=18.261 (0.000%) 004: dt: 0.5000, sse=8861039.0, rms=16.057 (0.000%) 005: dt: 0.5000, sse=7809087.0, rms=14.213 (0.000%) 006: dt: 0.5000, sse=7076192.5, rms=12.660 (0.000%) 007: dt: 0.5000, sse=6551040.0, rms=11.218 (0.000%) 008: dt: 0.5000, sse=6150697.5, rms=9.809 (0.000%) 009: dt: 0.5000, sse=5843409.5, rms=8.390 (0.000%) 010: dt: 0.5000, sse=5661732.5, rms=7.038 (0.000%) 011: dt: 0.5000, sse=5575568.0, rms=5.875 (0.000%) 012: dt: 0.5000, sse=5673383.5, rms=5.074 (0.000%) 013: dt: 0.5000, sse=5786051.0, rms=4.596 (0.000%) 014: dt: 0.5000, sse=5856850.5, rms=4.343 (0.000%) 015: dt: 0.5000, sse=5933061.0, rms=4.179 (0.000%) 016: dt: 0.5000, sse=5943790.5, rms=4.083 (0.000%) 017: dt: 0.5000, sse=5987968.5, rms=4.001 (0.000%) rms = 3.97, time step reduction 1 of 3 to 0.250... 018: dt: 0.5000, sse=5985981.5, rms=3.970 (0.000%) 019: dt: 0.2500, sse=3874113.0, rms=2.938 (0.000%) 020: dt: 0.2500, sse=3653021.5, rms=2.636 (0.000%) 021: dt: 0.2500, sse=3537839.0, rms=2.579 (0.000%) rms = 2.56, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=3512790.5, rms=2.556 (0.000%) 023: dt: 0.1250, sse=3324475.5, rms=2.351 (0.000%) rms = 2.32, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=3296673.0, rms=2.322 (0.000%) positioning took 5.0 minutes mean border=58.9, 526 (8) missing vertices, mean dist 0.2 [0.2 (%36.5)->0.5 (%63.5))] %50 local maxima, %32 large gradients and %13 min vals, 336 gradients ignored tol=1.0e-04, sigma=1.0, host=kyung, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=4172637.8, rms=5.83 025: dt: 0.5000, sse=4231701.5, rms=4.152 (0.000%) 026: dt: 0.5000, sse=5335829.5, rms=4.099 (0.000%) rms = 4.21, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=4296684.5, rms=3.028 (0.000%) 028: dt: 0.2500, sse=3936386.0, rms=2.618 (0.000%) 029: dt: 0.2500, sse=3878234.5, rms=2.536 (0.000%) rms = 2.49, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=3850076.5, rms=2.494 (0.000%) 031: dt: 0.1250, sse=3663654.8, rms=2.240 (0.000%) rms = 2.20, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=3639597.5, rms=2.200 (0.000%) positioning took 1.8 minutes mean border=56.8, 674 (5) missing vertices, mean dist 0.1 [0.2 (%33.3)->0.3 (%66.7))] %62 local maxima, %20 large gradients and %13 min vals, 342 gradients ignored tol=1.0e-04, sigma=0.5, host=kyung, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=3841145.0, rms=3.57 rms = 3.99, time step reduction 1 of 3 to 0.250... 033: dt: 0.2500, sse=3653995.8, rms=2.785 (0.000%) 034: dt: 0.2500, sse=3628428.2, rms=2.370 (0.000%) 035: dt: 0.2500, sse=3745037.2, rms=2.312 (0.000%) rms = 2.33, time step reduction 2 of 3 to 0.125... 036: dt: 0.1250, sse=3691074.8, rms=2.228 (0.000%) 037: dt: 0.1250, sse=3632062.2, rms=2.108 (0.000%) rms = 2.09, time step reduction 3 of 3 to 0.062... 038: dt: 0.1250, sse=3612211.5, rms=2.090 (0.000%) positioning took 1.5 minutes mean border=55.9, 1401 (4) missing vertices, mean dist 0.0 [0.2 (%42.0)->0.2 (%58.0))] %66 local maxima, %16 large gradients and %13 min vals, 276 gradients ignored tol=1.0e-04, sigma=0.2, host=kyung, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing pial surface to /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=3639868.0, rms=2.41 rms = 3.34, time step reduction 1 of 3 to 0.250... 039: dt: 0.2500, sse=3566275.0, rms=2.130 (0.000%) rms = 2.10, time step reduction 2 of 3 to 0.125... 040: dt: 0.2500, sse=3690445.8, rms=2.095 (0.000%) 041: dt: 0.1250, sse=3614466.5, rms=2.002 (0.000%) rms = 1.97, time step reduction 3 of 3 to 0.062... 042: dt: 0.1250, sse=3629383.0, rms=1.974 (0.000%) positioning took 1.0 minutes writing curvature file /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/lh.area.pial vertex spacing 0.98 +- 0.40 (0.06-->5.74) (max @ vno 84498 --> 83557) face area 0.39 +- 0.28 (0.00-->5.56) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 125512 vertices processed 25000 of 125512 vertices processed 50000 of 125512 vertices processed 75000 of 125512 vertices processed 100000 of 125512 vertices processed 125000 of 125512 vertices processed 0 of 125512 vertices processed 25000 of 125512 vertices processed 50000 of 125512 vertices processed 75000 of 125512 vertices processed 100000 of 125512 vertices processed 125000 of 125512 vertices processed thickness calculation complete, 235:302 truncations. 32442 vertices at 0 distance 90333 vertices at 1 distance 77114 vertices at 2 distance 28294 vertices at 3 distance 7951 vertices at 4 distance 2477 vertices at 5 distance 864 vertices at 6 distance 315 vertices at 7 distance 104 vertices at 8 distance 41 vertices at 9 distance 27 vertices at 10 distance 21 vertices at 11 distance 8 vertices at 12 distance 9 vertices at 13 distance 5 vertices at 14 distance 3 vertices at 15 distance 3 vertices at 16 distance 3 vertices at 17 distance 3 vertices at 18 distance 4 vertices at 19 distance 9 vertices at 20 distance writing curvature file /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/lh.thickness positioning took 22.9 minutes #-------------------------------------------- #@# Surf Volume lh Sat Jul 6 06:46:27 EDT 2013 /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.volume lh.area.mid mul lh.thickness Saving result to 'lh.volume' (type = MRI_CURV_FILE) [ ok ] #----------------------------------------- #@# WM/GM Contrast lh Sat Jul 6 06:46:28 EDT 2013 /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/scripts pctsurfcon --s VNS_Mig001 --lh-only Log file is /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/scripts/pctsurfcon.log Sat Jul 6 06:46:28 EDT 2013 setenv SUBJECTS_DIR /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer cd /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/scripts /usr/local/freesurfer/stable5_3_0/bin/pctsurfcon $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $ Linux kyungmo2 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 mri_vol2surf --mov /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/tmp.pctsurfcon.1525/lh.wm.mgh --regheader VNS_Mig001 --cortex srcvol = /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri/orig.mgz as target reference. Loading label /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/label/lh.cortex.label Reading surface /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/lh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 -1 -1 -1 using old Done mapping volume to surface Number of source voxels hit = 69086 Masking with /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/label/lh.cortex.label Writing to /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/tmp.pctsurfcon.1525/lh.wm.mgh Dim: 125512 1 1 mri_vol2surf --mov /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/tmp.pctsurfcon.1525/lh.gm.mgh --projfrac 0.3 --regheader VNS_Mig001 --cortex srcvol = /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri/orig.mgz as target reference. Loading label /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/label/lh.cortex.label Reading surface /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/lh.white Done reading source surface Reading thickness /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 81930 Masking with /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/label/lh.cortex.label Writing to /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/tmp.pctsurfcon.1525/lh.gm.mgh Dim: 125512 1 1 mri_concat /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/tmp.pctsurfcon.1525/lh.wm.mgh /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/tmp.pctsurfcon.1525/lh.gm.mgh --paired-diff-norm --mul 100 --o /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/lh.w-g.pct.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing Combining pairs nframes = 1 Multiplying by 100.000000 Writing to /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/lh.w-g.pct.mgh mri_segstats --in /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/lh.w-g.pct.mgh --annot VNS_Mig001 lh aparc --sum /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/stats/lh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --in /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/lh.w-g.pct.mgh --annot VNS_Mig001 lh aparc --sum /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/stats/lh.w-g.pct.stats --snr sysname Linux hostname kyungmo2 machine x86_64 user rllin UseRobust 0 Constructing seg from annotation Reading annotation reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Seg base 1000 Loading /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/lh.w-g.pct.mgh Vertex Area is 0.658074 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 1000 unknown 0 0.000 1 1001 bankssts 1588 1099.790 2 1002 caudalanteriorcingulate 929 600.688 3 1003 caudalmiddlefrontal 3594 2420.370 4 1004 corpuscallosum 0 0.000 5 1005 cuneus 2047 1230.185 6 1006 entorhinal 524 368.527 7 1007 fusiform 4306 2853.693 8 1008 inferiorparietal 7452 5001.189 9 1009 inferiortemporal 3953 2684.810 10 1010 isthmuscingulate 1637 1042.900 11 1011 lateraloccipital 6611 4078.526 12 1012 lateralorbitofrontal 3630 2473.086 13 1013 lingual 4274 2706.854 14 1014 medialorbitofrontal 2670 1785.363 15 1015 middletemporal 3864 2608.445 16 1016 parahippocampal 1012 659.522 17 1017 paracentral 1934 1211.146 18 1018 parsopercularis 2111 1442.142 19 1019 parsorbitalis 900 586.090 20 1020 parstriangularis 1699 1137.770 21 1021 pericalcarine 1935 1230.306 22 1022 postcentral 6136 3892.980 23 1023 posteriorcingulate 1575 1025.141 24 1024 precentral 7250 4619.906 25 1025 precuneus 5179 3451.778 26 1026 rostralanteriorcingulate 1271 833.853 27 1027 rostralmiddlefrontal 7114 4794.724 28 1028 superiorfrontal 10164 6976.690 29 1029 superiorparietal 6915 4433.917 30 1030 superiortemporal 4862 3257.405 31 1031 supramarginal 5398 3536.345 32 1032 frontalpole 303 205.103 33 1033 temporalpole 668 478.878 34 1034 transversetemporal 597 365.758 35 1035 insula 3284 2152.277 Reporting on 34 segmentations mri_segstats done Cleaning up #----------------------------------------- #@# Parcellation Stats lh Sat Jul 6 06:46:49 EDT 2013 /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/scripts mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab VNS_Mig001 lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri/wm.mgz... reading input surface /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/lh.white... reading input pial surface /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/lh.pial... reading input white surface /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/lh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1588 1100 2502 2.414 0.336 0.132 0.036 18 2.3 bankssts 929 601 1636 2.716 0.557 0.185 0.081 31 3.4 caudalanteriorcingulate 3594 2420 6345 2.435 0.465 0.141 0.057 87 9.3 caudalmiddlefrontal 2047 1230 2392 1.800 0.455 0.160 0.066 43 5.8 cuneus 524 369 1600 3.469 0.597 0.133 0.037 5 0.7 entorhinal 4306 2854 8762 2.775 0.631 0.148 0.051 74 8.8 fusiform 7452 5001 13296 2.410 0.499 0.144 0.046 108 13.8 inferiorparietal 3953 2685 8309 2.727 0.606 0.158 0.069 150 12.1 inferiortemporal 1637 1043 2933 2.479 0.701 0.159 0.064 36 4.1 isthmuscingulate 6611 4079 9511 2.143 0.606 0.154 0.059 115 15.9 lateraloccipital 3630 2473 6652 2.538 0.604 0.148 0.051 57 7.5 lateralorbitofrontal 4274 2707 5859 1.989 0.550 0.149 0.054 82 9.9 lingual 2670 1785 4798 2.422 0.660 0.153 0.065 57 6.9 medialorbitofrontal 3864 2608 9019 2.768 0.650 0.146 0.060 91 7.7 middletemporal 1012 660 2010 2.560 0.651 0.110 0.032 10 1.2 parahippocampal 1934 1211 3220 2.408 0.503 0.116 0.039 19 3.1 paracentral 2111 1442 3775 2.347 0.420 0.151 0.052 36 4.5 parsopercularis 900 586 2067 2.844 0.536 0.159 0.062 18 2.1 parsorbitalis 1699 1138 2878 2.296 0.420 0.137 0.040 22 2.9 parstriangularis 1935 1230 1822 1.607 0.424 0.150 0.069 70 6.1 pericalcarine 6136 3893 9668 2.178 0.561 0.133 0.047 87 12.3 postcentral 1575 1025 2863 2.578 0.531 0.167 0.067 37 4.0 posteriorcingulate 7250 4620 12741 2.553 0.524 0.128 0.050 92 15.9 precentral 5179 3452 8466 2.350 0.527 0.143 0.047 77 10.2 precuneus 1271 834 2467 2.711 0.608 0.155 0.064 36 3.3 rostralanteriorcingulate 7114 4795 12027 2.216 0.468 0.159 0.063 136 16.1 rostralmiddlefrontal 10164 6977 20461 2.536 0.542 0.154 0.065 199 26.6 superiorfrontal 6915 4434 10361 2.141 0.448 0.135 0.055 133 15.2 superiorparietal 4862 3257 9838 2.669 0.555 0.131 0.046 59 9.9 superiortemporal 5398 3536 9635 2.528 0.493 0.146 0.059 270 14.7 supramarginal 303 205 599 2.317 0.361 0.183 0.107 9 1.5 frontalpole 668 479 2331 3.670 0.475 0.157 0.059 12 1.7 temporalpole 597 366 1037 2.519 0.282 0.136 0.043 7 1.1 transversetemporal 3284 2152 6245 2.950 0.804 0.130 0.056 47 7.5 insula #----------------------------------------- #@# Cortical Parc 2 lh Sat Jul 6 06:47:59 EDT 2013 /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 VNS_Mig001 lh ../surf/lh.sphere.reg /usr/local/freesurfer/stable5_3_0/average/lh.destrieux.simple.2009-07-29.gcs ../label/lh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /usr/local/freesurfer/stable5_3_0/average/lh.destrieux.simple.2009-07-29.gcs... reading color table from GCSA file.... average std = 3.9 0.2 using min determinant for regularization = 0.000 0 singular and 1066 ill-conditioned covariance matrices regularized input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 59 labels changed using aseg relabeling using gibbs priors... 000: 8427 changed, 125512 examined... 001: 2044 changed, 32472 examined... 002: 596 changed, 10538 examined... 003: 275 changed, 3395 examined... 004: 123 changed, 1522 examined... 005: 68 changed, 704 examined... 006: 36 changed, 364 examined... 007: 18 changed, 200 examined... 008: 11 changed, 90 examined... 009: 8 changed, 65 examined... 010: 6 changed, 57 examined... 011: 0 changed, 22 examined... 22 labels changed using aseg 000: 256 total segments, 174 labels (1503 vertices) changed 001: 89 total segments, 8 labels (28 vertices) changed 002: 81 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 108 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 543 vertices marked for relabeling... 543 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 1 minutes and 40 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Sat Jul 6 06:49:39 EDT 2013 /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/scripts mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.a2009s.stats -b -a ../label/lh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab VNS_Mig001 lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri/wm.mgz... reading input surface /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/lh.white... reading input pial surface /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/lh.pial... reading input white surface /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/lh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1075 768 1793 2.097 0.463 0.143 0.076 17 1.6 G_and_S_frontomargin 1121 739 1857 2.401 0.544 0.159 0.057 16 2.6 G_and_S_occipital_inf 1526 874 2489 2.372 0.502 0.127 0.050 23 2.8 G_and_S_paracentral 1474 997 3076 2.584 0.486 0.145 0.044 22 2.7 G_and_S_subcentral 760 490 1492 2.409 0.362 0.184 0.093 20 2.8 G_and_S_transv_frontopol 2356 1584 4217 2.525 0.544 0.144 0.049 37 4.7 G_and_S_cingul-Ant 1175 816 2050 2.519 0.575 0.155 0.063 26 3.4 G_and_S_cingul-Mid-Ant 1238 839 2226 2.466 0.486 0.144 0.050 20 2.6 G_and_S_cingul-Mid-Post 635 408 1433 2.808 0.415 0.175 0.066 14 1.6 G_cingul-Post-dorsal 291 169 529 2.459 0.884 0.137 0.066 4 0.6 G_cingul-Post-ventral 1845 1075 2167 1.735 0.458 0.167 0.116 91 9.0 G_cuneus 1324 883 2666 2.461 0.413 0.169 0.066 30 3.6 G_front_inf-Opercular 400 235 907 2.866 0.353 0.153 0.055 7 1.0 G_front_inf-Orbital 1011 669 1964 2.331 0.376 0.152 0.049 19 2.0 G_front_inf-Triangul 3949 2652 8423 2.521 0.450 0.174 0.078 126 13.3 G_front_middle 6900 4677 15307 2.638 0.551 0.166 0.078 170 21.9 G_front_sup 503 316 1057 3.250 0.593 0.163 0.101 13 2.0 G_Ins_lg_and_S_cent_ins 781 486 2188 3.680 0.742 0.147 0.073 18 2.4 G_insular_short 2366 1481 4841 2.689 0.490 0.167 0.074 55 6.7 G_occipital_middle 1403 866 1865 1.907 0.411 0.142 0.048 19 2.7 G_occipital_sup 1711 1095 3677 2.700 0.453 0.150 0.055 33 3.8 G_oc-temp_lat-fusifor 2822 1711 3943 1.952 0.561 0.162 0.067 69 8.0 G_oc-temp_med-Lingual 1353 880 3339 3.007 0.769 0.133 0.045 18 2.2 G_oc-temp_med-Parahip 2291 1539 5270 2.776 0.544 0.164 0.068 52 6.0 G_orbital 2520 1690 5465 2.598 0.434 0.157 0.053 45 5.3 G_pariet_inf-Angular 2850 1876 6165 2.723 0.447 0.162 0.077 246 10.8 G_pariet_inf-Supramar 2431 1525 4560 2.322 0.455 0.143 0.051 37 5.0 G_parietal_sup 2429 1446 4263 2.336 0.516 0.140 0.057 44 6.1 G_postcentral 2755 1612 5911 2.806 0.391 0.131 0.055 37 6.4 G_precentral 2660 1747 5199 2.497 0.520 0.162 0.060 55 6.5 G_precuneus 962 655 2203 2.539 0.462 0.188 0.073 28 2.9 G_rectus 420 269 688 2.522 0.865 0.143 0.108 24 2.0 G_subcallosal 490 283 949 2.615 0.286 0.143 0.051 8 1.1 G_temp_sup-G_T_transv 2023 1328 4847 2.805 0.477 0.155 0.068 38 5.9 G_temp_sup-Lateral 421 294 1129 3.428 0.540 0.088 0.021 2 0.4 G_temp_sup-Plan_polar 889 597 1567 2.463 0.422 0.101 0.026 5 0.9 G_temp_sup-Plan_tempo 2303 1526 5686 2.843 0.536 0.178 0.096 137 9.8 G_temporal_inf 2629 1741 6919 2.929 0.583 0.158 0.072 80 5.7 G_temporal_middle 286 193 405 2.345 0.332 0.123 0.030 2 0.3 Lat_Fis-ant-Horizont 163 123 249 2.128 0.416 0.118 0.023 1 0.1 Lat_Fis-ant-Vertical 1113 738 1362 2.240 0.453 0.130 0.038 9 1.8 Lat_Fis-post 2130 1207 2402 1.833 0.517 0.152 0.062 40 5.1 Pole_occipital 1705 1173 5129 3.378 0.645 0.160 0.062 30 4.5 Pole_temporal 2425 1570 2686 1.834 0.670 0.145 0.063 76 6.6 S_calcarine 3436 2286 4323 2.106 0.608 0.120 0.045 39 7.6 S_central 883 621 1269 2.174 0.466 0.100 0.024 5 0.9 S_cingul-Marginalis 431 306 743 2.865 0.372 0.105 0.023 2 0.4 S_circular_insula_ant 1307 894 2101 2.632 0.623 0.101 0.028 8 1.6 S_circular_insula_inf 1743 1193 2467 2.380 0.446 0.105 0.025 9 1.9 S_circular_insula_sup 1006 706 1763 2.919 0.778 0.142 0.038 16 1.7 S_collat_transv_ant 433 295 507 2.123 0.344 0.144 0.046 4 0.8 S_collat_transv_post 1842 1270 2573 2.038 0.404 0.140 0.039 23 3.2 S_front_inf 1274 859 1686 2.010 0.464 0.152 0.052 21 2.7 S_front_middle 3057 2059 4730 2.343 0.406 0.128 0.038 31 4.8 S_front_sup 466 315 569 1.959 0.346 0.114 0.031 3 0.6 S_interm_prim-Jensen 2994 1982 3860 2.074 0.416 0.119 0.033 27 4.2 S_intrapariet_and_P_trans 842 584 999 1.857 0.455 0.139 0.037 8 1.4 S_oc_middle_and_Lunatus 1230 804 1578 2.129 0.385 0.121 0.032 9 1.6 S_oc_sup_and_transversal 527 363 775 2.391 0.499 0.153 0.038 6 0.9 S_occipital_ant 674 461 1095 2.483 0.504 0.128 0.038 6 1.0 S_oc-temp_lat 1925 1339 2893 2.371 0.457 0.125 0.031 18 2.4 S_oc-temp_med_and_Lingual 429 297 551 1.921 0.405 0.101 0.018 2 0.4 S_orbital_lateral 701 491 951 2.116 0.656 0.125 0.034 6 1.0 S_orbital_med-olfact 1261 870 2012 2.385 0.628 0.148 0.048 18 2.4 S_orbital-H_Shaped 1883 1234 2339 2.067 0.561 0.123 0.033 17 2.6 S_parieto_occipital 1178 692 1255 2.334 0.683 0.166 0.067 35 3.2 S_pericallosal 2518 1665 3516 2.255 0.509 0.141 0.043 30 4.5 S_postcentral 1721 1167 2540 2.346 0.441 0.136 0.047 20 3.2 S_precentral-inf-part 1084 759 1462 2.113 0.398 0.110 0.028 6 1.3 S_precentral-sup-part 654 445 1081 2.537 0.822 0.150 0.078 12 1.7 S_suborbital 1105 738 1596 2.279 0.373 0.142 0.046 14 2.1 S_subparietal 987 673 1392 2.313 0.554 0.126 0.037 9 1.8 S_temporal_inf 5566 3818 8520 2.316 0.452 0.130 0.036 61 8.3 S_temporal_sup 315 216 415 2.367 0.443 0.133 0.046 3 0.7 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 lh Sat Jul 6 06:50:54 EDT 2013 /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 VNS_Mig001 lh ../surf/lh.sphere.reg /usr/local/freesurfer/stable5_3_0/average/lh.DKTatlas40.gcs ../label/lh.aparc.DKTatlas40.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /usr/local/freesurfer/stable5_3_0/average/lh.DKTatlas40.gcs... reading color table from GCSA file.... average std = 0.9 using min determinant for regularization = 0.007 0 singular and 293 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 916 labels changed using aseg relabeling using gibbs priors... 000: 2582 changed, 125512 examined... 001: 587 changed, 10999 examined... 002: 174 changed, 3333 examined... 003: 77 changed, 973 examined... 004: 37 changed, 432 examined... 005: 13 changed, 206 examined... 006: 9 changed, 71 examined... 007: 4 changed, 48 examined... 008: 5 changed, 30 examined... 009: 6 changed, 27 examined... 010: 6 changed, 30 examined... 011: 5 changed, 34 examined... 012: 9 changed, 31 examined... 013: 5 changed, 41 examined... 014: 4 changed, 20 examined... 015: 1 changed, 20 examined... 016: 0 changed, 7 examined... 210 labels changed using aseg 000: 59 total segments, 26 labels (235 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 58 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 460 vertices marked for relabeling... 460 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas40.annot... classification took 1 minutes and 26 seconds. #----------------------------------------- #@# Parcellation Stats 3 lh Sat Jul 6 06:52:21 EDT 2013 /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/scripts mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas40.stats -b -a ../label/lh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab VNS_Mig001 lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot. reading volume /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri/wm.mgz... reading input surface /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/lh.white... reading input pial surface /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/lh.pial... reading input white surface /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/lh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 36 entries read (originally /Applications/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.DKTatlas40.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1410 932 2468 2.645 0.608 0.172 0.071 39 4.3 caudalanteriorcingulate 3713 2508 6630 2.442 0.465 0.141 0.057 88 9.5 caudalmiddlefrontal 2812 1724 3363 1.836 0.451 0.153 0.087 98 10.3 cuneus 505 356 1505 3.435 0.599 0.133 0.036 5 0.6 entorhinal 3903 2587 7500 2.687 0.588 0.147 0.049 66 7.6 fusiform 7082 4758 12701 2.410 0.505 0.143 0.045 100 13.1 inferiorparietal 4033 2726 8838 2.820 0.665 0.158 0.071 150 12.6 inferiortemporal 1604 1023 2867 2.472 0.701 0.159 0.065 35 4.0 isthmuscingulate 6733 4159 9641 2.130 0.605 0.154 0.059 118 16.1 lateraloccipital 3840 2602 6968 2.473 0.639 0.155 0.068 71 8.7 lateralorbitofrontal 4262 2698 5832 1.986 0.550 0.149 0.055 82 9.8 lingual 2253 1516 4207 2.400 0.629 0.152 0.058 45 5.3 medialorbitofrontal 5303 3584 11526 2.690 0.624 0.146 0.057 113 10.4 middletemporal 1014 663 2015 2.562 0.647 0.109 0.031 10 1.3 parahippocampal 2115 1349 3626 2.419 0.505 0.118 0.038 20 3.4 paracentral 1947 1329 3406 2.347 0.406 0.154 0.054 34 4.2 parsopercularis 1116 720 2431 2.804 0.438 0.149 0.053 18 2.4 parsorbitalis 1962 1330 3228 2.193 0.395 0.136 0.040 26 3.3 parstriangularis 1962 1245 1840 1.602 0.426 0.151 0.069 72 6.2 pericalcarine 6664 4248 10420 2.179 0.560 0.134 0.049 95 13.6 postcentral 1680 1098 3006 2.570 0.523 0.164 0.066 38 4.2 posteriorcingulate 7220 4579 12566 2.549 0.527 0.128 0.050 93 15.9 precentral 5081 3374 8474 2.360 0.532 0.144 0.048 77 10.2 precuneus 1757 1160 3206 2.667 0.644 0.162 0.075 52 5.1 rostralanteriorcingulate 4631 3108 8016 2.271 0.523 0.155 0.055 83 10.2 rostralmiddlefrontal 11589 7927 22889 2.479 0.525 0.156 0.066 233 31.2 superiorfrontal 5479 3503 8465 2.196 0.426 0.132 0.041 67 9.2 superiorparietal 6912 4682 14288 2.710 0.602 0.134 0.046 87 13.6 superiortemporal 5305 3489 9434 2.532 0.498 0.148 0.060 269 14.7 supramarginal 567 347 996 2.529 0.273 0.136 0.044 7 1.0 transversetemporal 2932 1925 5773 3.004 0.801 0.127 0.052 41 6.3 insula #-------------------------------------------- #@# Tessellate rh Sat Jul 6 06:53:31 EDT 2013 /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 pass 2 (xy+): 0 found - 2 modified | TOTAL: 2 pass 1 (xy-): 0 found - 0 modified | TOTAL: 2 pass 1 (yz+): 2 found - 2 modified | TOTAL: 4 pass 2 (yz+): 0 found - 2 modified | TOTAL: 4 pass 1 (yz-): 0 found - 0 modified | TOTAL: 4 pass 1 (xz+): 0 found - 0 modified | TOTAL: 4 pass 1 (xz-): 0 found - 0 modified | TOTAL: 4 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 1 found - 1 modified | TOTAL: 1 pass 2 (-+): 0 found - 1 modified | TOTAL: 1 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 5 (out of 257555: 0.001941) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ slice 40: 422 vertices, 480 faces slice 50: 5349 vertices, 5599 faces slice 60: 14116 vertices, 14440 faces slice 70: 24606 vertices, 25035 faces slice 80: 36087 vertices, 36443 faces slice 90: 46724 vertices, 47089 faces slice 100: 57869 vertices, 58223 faces slice 110: 68167 vertices, 68509 faces slice 120: 77870 vertices, 78215 faces slice 130: 87445 vertices, 87809 faces slice 140: 96088 vertices, 96437 faces slice 150: 104016 vertices, 104306 faces slice 160: 111653 vertices, 111945 faces slice 170: 118157 vertices, 118425 faces slice 180: 123299 vertices, 123513 faces slice 190: 127463 vertices, 127615 faces slice 200: 128986 vertices, 129022 faces slice 210: 128986 vertices, 129022 faces slice 220: 128986 vertices, 129022 faces slice 230: 128986 vertices, 129022 faces slice 240: 128986 vertices, 129022 faces slice 250: 128986 vertices, 129022 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 128986 voxel in cpt #1: X=-36 [v=128986,e=387066,f=258044] located at (24.200758, -19.223816, 27.183323) For the whole surface: X=-36 [v=128986,e=387066,f=258044] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 rh Sat Jul 6 06:55:14 EDT 2013 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 rh Sat Jul 6 06:55:24 EDT 2013 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/scripts avg radius = 47.2 mm, total surface area = 68314 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 1.4 minutes Not saving sulc step 000: RMS=0.099 (target=0.015) step 005: RMS=0.072 (target=0.015) step 010: RMS=0.054 (target=0.015) step 015: RMS=0.045 (target=0.015) step 020: RMS=0.040 (target=0.015) step 025: RMS=0.035 (target=0.015) step 030: RMS=0.032 (target=0.015) step 035: RMS=0.028 (target=0.015) step 040: RMS=0.028 (target=0.015) step 045: RMS=0.027 (target=0.015) step 050: RMS=0.025 (target=0.015) step 055: RMS=0.025 (target=0.015) step 060: RMS=0.025 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere rh Sat Jul 6 06:56:50 EDT 2013 /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 1.02 +- 0.60 (0.00-->6.88) (max @ vno 97619 --> 97643) face area 0.03 +- 0.03 (-0.18-->0.67) scaling brain by 0.322... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.157, avgs=0 005/300: dt: 0.9000, rms radial error=175.900, avgs=0 010/300: dt: 0.9000, rms radial error=175.348, avgs=0 015/300: dt: 0.9000, rms radial error=174.623, avgs=0 020/300: dt: 0.9000, rms radial error=173.792, avgs=0 025/300: dt: 0.9000, rms radial error=172.895, avgs=0 030/300: dt: 0.9000, rms radial error=171.964, avgs=0 035/300: dt: 0.9000, rms radial error=171.015, avgs=0 040/300: dt: 0.9000, rms radial error=170.058, avgs=0 045/300: dt: 0.9000, rms radial error=169.097, avgs=0 050/300: dt: 0.9000, rms radial error=168.154, avgs=0 055/300: dt: 0.9000, rms radial error=167.218, avgs=0 060/300: dt: 0.9000, rms radial error=166.285, avgs=0 065/300: dt: 0.9000, rms radial error=165.356, avgs=0 070/300: dt: 0.9000, rms radial error=164.431, avgs=0 075/300: dt: 0.9000, rms radial error=163.511, avgs=0 080/300: dt: 0.9000, rms radial error=162.595, avgs=0 085/300: dt: 0.9000, rms radial error=161.684, avgs=0 090/300: dt: 0.9000, rms radial error=160.777, avgs=0 095/300: dt: 0.9000, rms radial error=159.876, avgs=0 100/300: dt: 0.9000, rms radial error=158.979, avgs=0 105/300: dt: 0.9000, rms radial error=158.087, avgs=0 110/300: dt: 0.9000, rms radial error=157.200, avgs=0 115/300: dt: 0.9000, rms radial error=156.317, avgs=0 120/300: dt: 0.9000, rms radial error=155.439, avgs=0 125/300: dt: 0.9000, rms radial error=154.565, avgs=0 130/300: dt: 0.9000, rms radial error=153.696, avgs=0 135/300: dt: 0.9000, rms radial error=152.832, avgs=0 140/300: dt: 0.9000, rms radial error=151.973, avgs=0 145/300: dt: 0.9000, rms radial error=151.118, avgs=0 150/300: dt: 0.9000, rms radial error=150.269, avgs=0 155/300: dt: 0.9000, rms radial error=149.424, avgs=0 160/300: dt: 0.9000, rms radial error=148.584, avgs=0 165/300: dt: 0.9000, rms radial error=147.749, avgs=0 170/300: dt: 0.9000, rms radial error=146.918, avgs=0 175/300: dt: 0.9000, rms radial error=146.091, avgs=0 180/300: dt: 0.9000, rms radial error=145.269, avgs=0 185/300: dt: 0.9000, rms radial error=144.451, avgs=0 190/300: dt: 0.9000, rms radial error=143.637, avgs=0 195/300: dt: 0.9000, rms radial error=142.828, avgs=0 200/300: dt: 0.9000, rms radial error=142.024, avgs=0 205/300: dt: 0.9000, rms radial error=141.224, avgs=0 210/300: dt: 0.9000, rms radial error=140.428, avgs=0 215/300: dt: 0.9000, rms radial error=139.637, avgs=0 220/300: dt: 0.9000, rms radial error=138.850, avgs=0 225/300: dt: 0.9000, rms radial error=138.068, avgs=0 230/300: dt: 0.9000, rms radial error=137.290, avgs=0 235/300: dt: 0.9000, rms radial error=136.516, avgs=0 240/300: dt: 0.9000, rms radial error=135.746, avgs=0 245/300: dt: 0.9000, rms radial error=134.981, avgs=0 250/300: dt: 0.9000, rms radial error=134.220, avgs=0 255/300: dt: 0.9000, rms radial error=133.463, avgs=0 260/300: dt: 0.9000, rms radial error=132.711, avgs=0 265/300: dt: 0.9000, rms radial error=131.963, avgs=0 270/300: dt: 0.9000, rms radial error=131.219, avgs=0 275/300: dt: 0.9000, rms radial error=130.480, avgs=0 280/300: dt: 0.9000, rms radial error=129.744, avgs=0 285/300: dt: 0.9000, rms radial error=129.013, avgs=0 290/300: dt: 0.9000, rms radial error=128.286, avgs=0 295/300: dt: 0.9000, rms radial error=127.563, avgs=0 300/300: dt: 0.9000, rms radial error=126.844, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 14931.70 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00017 epoch 2 (K=40.0), pass 1, starting sse = 2470.27 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00010 epoch 3 (K=160.0), pass 1, starting sse = 253.60 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.08/11 = 0.00707 epoch 4 (K=640.0), pass 1, starting sse = 15.44 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.14/15 = 0.00905 final writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.19 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology rh Sat Jul 6 07:08:07 EDT 2013 cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 VNS_Mig001 rh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ before topology correction, eno=-36 (nv=128986, nf=258044, ne=387066, g=19) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 8 iterations marking ambiguous vertices... 3230 ambiguous faces found in tessellation segmenting defects... 25 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 7 into 3 -merging segment 11 into 10 -merging segment 14 into 10 22 defects to be corrected 0 vertices coincident reading input surface /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.2692 (-4.6346) -vertex loglikelihood: -6.0908 (-3.0454) -normal dot loglikelihood: -3.6039 (-3.6039) -quad curv loglikelihood: -6.4599 (-3.2299) Total Loglikelihood : -25.4237 CORRECTING DEFECT 0 (vertices=32, convex hull=67) After retessellation of defect 0, euler #=-21 (127055,380508,253432) : difference with theory (-19) = 2 CORRECTING DEFECT 1 (vertices=6, convex hull=17) After retessellation of defect 1, euler #=-20 (127055,380513,253438) : difference with theory (-18) = 2 CORRECTING DEFECT 2 (vertices=23, convex hull=40) After retessellation of defect 2, euler #=-19 (127064,380556,253473) : difference with theory (-17) = 2 CORRECTING DEFECT 3 (vertices=152, convex hull=204) After retessellation of defect 3, euler #=-17 (127079,380697,253601) : difference with theory (-16) = 1 CORRECTING DEFECT 4 (vertices=9, convex hull=19) After retessellation of defect 4, euler #=-16 (127081,380708,253611) : difference with theory (-15) = 1 CORRECTING DEFECT 5 (vertices=162, convex hull=135) After retessellation of defect 5, euler #=-15 (127142,380953,253796) : difference with theory (-14) = 1 CORRECTING DEFECT 6 (vertices=24, convex hull=47) After retessellation of defect 6, euler #=-14 (127151,380995,253830) : difference with theory (-13) = 1 CORRECTING DEFECT 7 (vertices=13, convex hull=24) After retessellation of defect 7, euler #=-13 (127155,381013,253845) : difference with theory (-12) = 1 CORRECTING DEFECT 8 (vertices=16, convex hull=27) After retessellation of defect 8, euler #=-13 (127158,381033,253862) : difference with theory (-11) = 2 CORRECTING DEFECT 9 (vertices=762, convex hull=484) After retessellation of defect 9, euler #=-10 (127342,381825,254473) : difference with theory (-10) = 0 CORRECTING DEFECT 10 (vertices=8, convex hull=19) After retessellation of defect 10, euler #=-9 (127343,381832,254480) : difference with theory (-9) = 0 CORRECTING DEFECT 11 (vertices=18, convex hull=48) After retessellation of defect 11, euler #=-8 (127352,381874,254514) : difference with theory (-8) = 0 CORRECTING DEFECT 12 (vertices=54, convex hull=23) After retessellation of defect 12, euler #=-7 (127355,381888,254526) : difference with theory (-7) = 0 CORRECTING DEFECT 13 (vertices=81, convex hull=65) After retessellation of defect 13, euler #=-6 (127378,381986,254602) : difference with theory (-6) = 0 CORRECTING DEFECT 14 (vertices=40, convex hull=47) After retessellation of defect 14, euler #=-5 (127389,382036,254642) : difference with theory (-5) = 0 CORRECTING DEFECT 15 (vertices=186, convex hull=60) After retessellation of defect 15, euler #=-4 (127400,382095,254691) : difference with theory (-4) = 0 CORRECTING DEFECT 16 (vertices=187, convex hull=46) After retessellation of defect 16, euler #=-3 (127410,382144,254731) : difference with theory (-3) = 0 CORRECTING DEFECT 17 (vertices=19, convex hull=31) After retessellation of defect 17, euler #=-2 (127414,382165,254749) : difference with theory (-2) = 0 CORRECTING DEFECT 18 (vertices=33, convex hull=29) After retessellation of defect 18, euler #=-1 (127416,382181,254764) : difference with theory (-1) = 0 CORRECTING DEFECT 19 (vertices=21, convex hull=54) After retessellation of defect 19, euler #=0 (127424,382226,254802) : difference with theory (0) = 0 CORRECTING DEFECT 20 (vertices=49, convex hull=35) After retessellation of defect 20, euler #=1 (127433,382262,254830) : difference with theory (1) = 0 CORRECTING DEFECT 21 (vertices=54, convex hull=80) After retessellation of defect 21, euler #=2 (127456,382362,254908) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.22 (0.04-->9.04) (max @ vno 83631 --> 128056) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.22 (0.04-->9.04) (max @ vno 83631 --> 128056) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 111 mutations (38.5%), 177 crossovers (61.5%), 210 vertices were eliminated building final representation... 1530 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=127456, nf=254908, ne=382362, g=0) writing corrected surface to /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 43.6 minutes 0 defective edges removing intersecting faces 000: 136 intersecting mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 127456 - 382362 + 254908 = 2 --> 0 holes F =2V-4: 254908 = 254912-4 (0) 2E=3F: 764724 = 764724 (0) total defect index = 0 /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 14 intersecting 001: 7 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf rh Sat Jul 6 07:51:59 EDT 2013 /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs VNS_Mig001 rh only generating white matter surface not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri/filled.mgz... reading volume /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri/brain.finalsurfs.mgz... reading volume /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri/wm.mgz... 14110 bright wm thresholded. 0 bright non-wm voxels segmented. reading original surface position from /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/rh.orig... computing class statistics... border white: 245868 voxels (1.47%) border gray 259178 voxels (1.54%) WM (96.0): 97.3 +- 7.5 [70.0 --> 110.0] GM (85.0) : 83.1 +- 11.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 63.9 (was 70) setting MAX_BORDER_WHITE to 112.5 (was 105) setting MIN_BORDER_WHITE to 75.0 (was 85) setting MAX_CSF to 52.9 (was 40) setting MAX_GRAY to 97.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 69.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 41.8 (was 40) repositioning cortical surface to gray/white boundary reading volume /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.02-->5.46) (max @ vno 83631 --> 127291) face area 0.28 +- 0.12 (0.00-->3.74) mean absolute distance = 0.87 +- 1.13 3614 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105, GM=75 mean inside = 96.4, mean outside = 79.8 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... mean border=83.9, 79 (79) missing vertices, mean dist 0.2 [1.0 (%34.1)->0.8 (%65.9))] %47 local maxima, %48 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=kyung, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.91 +- 0.25 (0.07-->5.81) (max @ vno 83631 --> 127291) face area 0.28 +- 0.13 (0.00-->3.39) mean absolute distance = 0.42 +- 0.72 2943 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4513288.0, rms=9.63 001: dt: 0.5000, sse=5054164.0, rms=6.803 (0.000%) 002: dt: 0.5000, sse=5284627.5, rms=5.012 (0.000%) 003: dt: 0.5000, sse=5532080.0, rms=3.885 (0.000%) 004: dt: 0.5000, sse=5695448.5, rms=3.236 (0.000%) 005: dt: 0.5000, sse=5801039.0, rms=2.914 (0.000%) 006: dt: 0.5000, sse=5852382.5, rms=2.762 (0.000%) 007: dt: 0.5000, sse=5858594.0, rms=2.695 (0.000%) rms = 2.65, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=5879757.5, rms=2.652 (0.000%) 009: dt: 0.2500, sse=3564663.0, rms=1.796 (0.000%) 010: dt: 0.2500, sse=3311136.0, rms=1.613 (0.000%) rms = 1.58, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=3210354.5, rms=1.578 (0.000%) rms = 1.55, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=3163326.0, rms=1.549 (0.000%) positioning took 2.7 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group mean border=86.9, 67 (21) missing vertices, mean dist -0.3 [0.5 (%70.5)->0.2 (%29.5))] %66 local maxima, %29 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=kyung, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.89 +- 0.25 (0.05-->5.85) (max @ vno 79054 --> 127213) face area 0.34 +- 0.16 (0.00-->4.22) mean absolute distance = 0.28 +- 0.38 3030 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3709731.8, rms=4.53 013: dt: 0.5000, sse=3947228.8, rms=2.781 (0.000%) 014: dt: 0.5000, sse=4373666.5, rms=2.461 (0.000%) 015: dt: 0.5000, sse=4704071.0, rms=2.313 (0.000%) rms = 2.51, time step reduction 1 of 3 to 0.250... 016: dt: 0.2500, sse=3841165.0, rms=1.690 (0.000%) 017: dt: 0.2500, sse=3550283.2, rms=1.407 (0.000%) 018: dt: 0.2500, sse=3447918.8, rms=1.349 (0.000%) rms = 1.34, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=3400385.0, rms=1.343 (0.000%) rms = 1.32, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=3367978.8, rms=1.322 (0.000%) positioning took 1.9 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 1 vertex label from ripped group removing 2 vertex label from ripped group mean border=89.8, 64 (17) missing vertices, mean dist -0.2 [0.3 (%76.3)->0.2 (%23.7))] %84 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=kyung, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.25 (0.07-->5.95) (max @ vno 79054 --> 127213) face area 0.33 +- 0.16 (0.00-->4.12) mean absolute distance = 0.20 +- 0.29 2420 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3640963.5, rms=3.73 021: dt: 0.5000, sse=3810658.2, rms=2.264 (0.000%) rms = 2.34, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=3601407.2, rms=1.675 (0.000%) 023: dt: 0.2500, sse=3537722.0, rms=1.306 (0.000%) 024: dt: 0.2500, sse=3516609.2, rms=1.216 (0.000%) rms = 1.22, time step reduction 2 of 3 to 0.125... rms = 1.20, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=3496814.8, rms=1.205 (0.000%) positioning took 1.4 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 1 vertex label from ripped group removing 2 vertex label from ripped group mean border=90.7, 63 (11) missing vertices, mean dist -0.1 [0.2 (%59.3)->0.2 (%40.7))] %88 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=kyung, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing white matter surface to /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=3516502.8, rms=1.63 026: dt: 0.5000, sse=4319006.5, rms=1.481 (0.000%) rms = 1.97, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=3911341.5, rms=1.087 (0.000%) 028: dt: 0.2500, sse=3767888.0, rms=1.010 (0.000%) rms = 0.98, time step reduction 2 of 3 to 0.125... 029: dt: 0.2500, sse=3840209.5, rms=0.976 (0.000%) rms = 0.96, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=3837905.2, rms=0.963 (0.000%) positioning took 1.2 minutes inhibiting deformation at non-cortical midline structures... generating cortex label... 10 non-cortical segments detected only using segment with 1866 vertices erasing segment 1 (vno[0] = 56370) erasing segment 2 (vno[0] = 72418) erasing segment 3 (vno[0] = 91838) erasing segment 4 (vno[0] = 95276) erasing segment 5 (vno[0] = 100860) erasing segment 6 (vno[0] = 100903) erasing segment 7 (vno[0] = 102226) erasing segment 8 (vno[0] = 102927) erasing segment 9 (vno[0] = 102938) writing cortex label to /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/label/rh.cortex.label... writing curvature file /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/rh.curv writing smoothed area to rh.area writing curvature file /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/rh.area vertex spacing 0.88 +- 0.25 (0.06-->6.02) (max @ vno 79054 --> 127213) face area 0.33 +- 0.16 (0.00-->3.95) refinement took 11.7 minutes #-------------------------------------------- #@# Smooth2 rh Sat Jul 6 08:03:39 EDT 2013 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/scripts smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 rh Sat Jul 6 08:03:49 EDT 2013 /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated avg radius = 47.5 mm, total surface area = 76550 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.112 (target=0.015) step 005: RMS=0.077 (target=0.015) step 010: RMS=0.055 (target=0.015) step 015: RMS=0.045 (target=0.015) step 020: RMS=0.038 (target=0.015) step 025: RMS=0.031 (target=0.015) step 030: RMS=0.026 (target=0.015) step 035: RMS=0.022 (target=0.015) step 040: RMS=0.020 (target=0.015) step 045: RMS=0.017 (target=0.015) step 050: RMS=0.015 (target=0.015) inflation complete. inflation took 1.3 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/rh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 121 vertices thresholded to be in k1 ~ [-0.28 0.30], k2 ~ [-0.12 0.06] total integrated curvature = 0.599*4pi (7.525) --> 0 handles ICI = 1.5, FI = 10.7, variation=177.635 100 vertices thresholded to be in [-0.01 0.01] writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 120 vertices thresholded to be in [-0.13 0.15] done. writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.017, std = 0.024 done. #----------------------------------------- #@# Curvature Stats rh Sat Jul 6 08:07:53 EDT 2013 /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm VNS_Mig001 rh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/rh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ VNS_Mig001/rh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 206 ] Gb_filter = 0 WARN: S lookup min: -0.334831 WARN: S explicit min: 0.000000 vertex = 1008 #-------------------------------------------- #@# Sphere rh Sat Jul 6 08:08:03 EDT 2013 /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/scripts mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... scaling brain by 0.304... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=kyung, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %19.87 pass 1: epoch 2 of 3 starting distance error %19.80 unfolding complete - removing small folds... starting distance error %19.73 removing remaining folds... final distance error %19.75 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/rh.sphere spherical transformation took 1.53 hours #-------------------------------------------- #@# Surf Reg rh Sat Jul 6 09:39:50 EDT 2013 /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/scripts mris_register -curv ../surf/rh.sphere /usr/local/freesurfer/stable5_3_0/average/rh.average.curvature.filled.buckner40.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading surface from ../surf/rh.sphere... reading template parameterization from /usr/local/freesurfer/stable5_3_0/average/rh.average.curvature.filled.buckner40.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=kyung, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 1 randomSeed 0 tol=5.0e-01, sigma=0.0, host=kyung, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading rh.sulc curvature mean = 0.000, std = 0.572 curvature mean = 0.011, std = 0.937 curvature mean = 0.026, std = 0.860 Starting MRISrigidBodyAlignGlobal() d=16.00 min @ (0.00, -4.00, 0.00) sse = 211224.0, tmin=7.2646 d=2.00 min @ (0.00, 0.50, 0.00) sse = 210650.9, tmin=14.6559 d=1.00 min @ (0.25, 0.00, 0.00) sse = 210525.5, tmin=17.0872 tol=1.0e+00, sigma=0.5, host=kyung, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 19.51 min curvature mean = 0.005, std = 0.949 curvature mean = 0.011, std = 0.943 curvature mean = 0.001, std = 0.958 curvature mean = 0.005, std = 0.975 curvature mean = 0.000, std = 0.959 curvature mean = 0.001, std = 0.990 2 Reading smoothwm curvature mean = -0.025, std = 0.297 curvature mean = 0.005, std = 0.070 curvature mean = 0.057, std = 0.347 curvature mean = 0.005, std = 0.084 curvature mean = 0.019, std = 0.540 curvature mean = 0.006, std = 0.090 curvature mean = 0.009, std = 0.675 curvature mean = 0.006, std = 0.093 curvature mean = 0.003, std = 0.772 MRISregister() return, current seed 0 writing registered surface to ../surf/rh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white rh Sat Jul 6 10:40:21 EDT 2013 mris_jacobian ../surf/rh.white ../surf/rh.sphere.reg ../surf/rh.jacobian_white reading surface from ../surf/rh.white... writing curvature file ../surf/rh.jacobian_white #-------------------------------------------- #@# AvgCurv rh Sat Jul 6 10:40:27 EDT 2013 /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/scripts mrisp_paint -a 5 /usr/local/freesurfer/stable5_3_0/average/rh.average.curvature.filled.buckner40.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/rh.sphere.reg... reading template parameterization from /usr/local/freesurfer/stable5_3_0/average/rh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc rh Sat Jul 6 10:40:31 EDT 2013 /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 VNS_Mig001 rh ../surf/rh.sphere.reg /usr/local/freesurfer/stable5_3_0/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/rh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /usr/local/freesurfer/stable5_3_0/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs... reading color table from GCSA file.... average std = 0.7 using min determinant for regularization = 0.006 0 singular and 311 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1096 labels changed using aseg relabeling using gibbs priors... 000: 2705 changed, 127456 examined... 001: 624 changed, 11623 examined... 002: 157 changed, 3483 examined... 003: 58 changed, 922 examined... 004: 26 changed, 351 examined... 005: 8 changed, 152 examined... 006: 0 changed, 47 examined... 154 labels changed using aseg 000: 93 total segments, 54 labels (247 vertices) changed 001: 40 total segments, 2 labels (8 vertices) changed 002: 38 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 42 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1446 vertices marked for relabeling... 1446 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 1 minutes and 31 seconds. #-------------------------------------------- #@# Make Pial Surf rh Sat Jul 6 10:42:04 EDT 2013 /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs VNS_Mig001 rh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri/filled.mgz... reading volume /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri/brain.finalsurfs.mgz... reading volume /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri/wm.mgz... 14110 bright wm thresholded. 0 bright non-wm voxels segmented. reading original surface position from /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/rh.orig... computing class statistics... border white: 245868 voxels (1.47%) border gray 259178 voxels (1.54%) WM (96.0): 97.3 +- 7.5 [70.0 --> 110.0] GM (85.0) : 83.1 +- 11.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 63.9 (was 70) setting MAX_BORDER_WHITE to 112.5 (was 105) setting MIN_BORDER_WHITE to 75.0 (was 85) setting MAX_CSF to 52.9 (was 40) setting MAX_GRAY to 97.5 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 69.5 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 41.8 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=105, GM=75 mean inside = 96.4, mean outside = 79.8 smoothing surface for 5 iterations... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.02-->5.46) (max @ vno 83631 --> 127291) face area 0.28 +- 0.12 (0.00-->3.74) mean absolute distance = 0.87 +- 1.13 3634 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 2 with 121 points - only 0.00% unknown mean border=83.9, 79 (79) missing vertices, mean dist 0.2 [1.0 (%34.1)->0.8 (%65.9))] %47 local maxima, %48 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=kyung, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.91 +- 0.25 (0.07-->5.81) (max @ vno 83631 --> 127291) face area 0.28 +- 0.13 (0.00-->3.39) mean absolute distance = 0.42 +- 0.72 2821 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=4516639.0, rms=9.62 001: dt: 0.5000, sse=5061298.0, rms=6.801 (0.000%) 002: dt: 0.5000, sse=5292445.0, rms=5.011 (0.000%) 003: dt: 0.5000, sse=5540856.0, rms=3.884 (0.000%) 004: dt: 0.5000, sse=5702256.5, rms=3.236 (0.000%) 005: dt: 0.5000, sse=5809759.5, rms=2.914 (0.000%) 006: dt: 0.5000, sse=5858898.0, rms=2.761 (0.000%) 007: dt: 0.5000, sse=5867815.5, rms=2.694 (0.000%) rms = 2.65, time step reduction 1 of 3 to 0.250... 008: dt: 0.5000, sse=5887430.5, rms=2.652 (0.000%) 009: dt: 0.2500, sse=3569020.8, rms=1.796 (0.000%) 010: dt: 0.2500, sse=3315456.0, rms=1.613 (0.000%) rms = 1.58, time step reduction 2 of 3 to 0.125... 011: dt: 0.2500, sse=3214620.2, rms=1.579 (0.000%) rms = 1.55, time step reduction 3 of 3 to 0.062... 012: dt: 0.1250, sse=3167492.8, rms=1.549 (0.000%) positioning took 2.7 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 3 with 40 points - only 0.00% unknown deleting segment 4 with 38 points - only 0.00% unknown deleting segment 5 with 48 points - only 27.08% unknown mean border=86.9, 73 (21) missing vertices, mean dist -0.3 [0.5 (%70.5)->0.2 (%29.5))] %66 local maxima, %30 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=kyung, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.89 +- 0.25 (0.05-->5.85) (max @ vno 79054 --> 127213) face area 0.34 +- 0.16 (0.00-->4.23) mean absolute distance = 0.28 +- 0.38 3050 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3719131.8, rms=4.53 013: dt: 0.5000, sse=3958547.5, rms=2.780 (0.000%) 014: dt: 0.5000, sse=4385072.5, rms=2.460 (0.000%) 015: dt: 0.5000, sse=4713034.0, rms=2.312 (0.000%) rms = 2.51, time step reduction 1 of 3 to 0.250... 016: dt: 0.2500, sse=3850472.0, rms=1.690 (0.000%) 017: dt: 0.2500, sse=3559319.2, rms=1.408 (0.000%) 018: dt: 0.2500, sse=3457164.8, rms=1.349 (0.000%) rms = 1.34, time step reduction 2 of 3 to 0.125... 019: dt: 0.2500, sse=3410034.8, rms=1.344 (0.000%) rms = 1.32, time step reduction 3 of 3 to 0.062... 020: dt: 0.1250, sse=3378113.2, rms=1.323 (0.000%) positioning took 1.9 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 1 with 13 points - only 0.00% unknown deleting segment 2 with 107 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 4 with 1 points - only 0.00% unknown deleting segment 5 with 48 points - only 27.08% unknown removing 2 vertex label from ripped group deleting segment 6 with 2 points - only 0.00% unknown mean border=89.8, 64 (17) missing vertices, mean dist -0.2 [0.3 (%76.3)->0.2 (%23.7))] %84 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=kyung, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.89 +- 0.25 (0.07-->5.95) (max @ vno 79054 --> 127213) face area 0.33 +- 0.16 (0.00-->4.12) mean absolute distance = 0.20 +- 0.29 2446 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3651469.0, rms=3.73 021: dt: 0.5000, sse=3820091.5, rms=2.265 (0.000%) rms = 2.34, time step reduction 1 of 3 to 0.250... 022: dt: 0.2500, sse=3610513.8, rms=1.676 (0.000%) 023: dt: 0.2500, sse=3547033.2, rms=1.307 (0.000%) 024: dt: 0.2500, sse=3525719.2, rms=1.217 (0.000%) rms = 1.22, time step reduction 2 of 3 to 0.125... rms = 1.21, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=3505876.2, rms=1.206 (0.000%) positioning took 1.4 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group deleting segment 1 with 145 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 2 with 1 points - only 0.00% unknown deleting segment 3 with 48 points - only 27.08% unknown removing 2 vertex label from ripped group deleting segment 4 with 2 points - only 0.00% unknown mean border=90.7, 63 (11) missing vertices, mean dist -0.1 [0.2 (%59.3)->0.2 (%40.7))] %88 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=kyung, nav=0, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=3525698.2, rms=1.63 026: dt: 0.5000, sse=4328708.0, rms=1.481 (0.000%) rms = 1.97, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=3921128.0, rms=1.087 (0.000%) 028: dt: 0.2500, sse=3778520.8, rms=1.010 (0.000%) rms = 0.98, time step reduction 2 of 3 to 0.125... 029: dt: 0.2500, sse=3850156.8, rms=0.977 (0.000%) rms = 0.96, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=3848170.2, rms=0.964 (0.000%) positioning took 1.2 minutes inhibiting deformation at non-cortical midline structures... smoothing surface for 5 iterations... mean border=63.6, 89 (89) missing vertices, mean dist 1.8 [0.1 (%0.0)->2.3 (%100.0))] %34 local maxima, %44 large gradients and %18 min vals, 772 gradients ignored tol=1.0e-04, sigma=2.0, host=kyung, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 1.000 averaging target values for 5 iterations... 000: dt: 0.0000, sse=20897400.0, rms=27.54 001: dt: 0.5000, sse=16454347.0, rms=24.008 (0.000%) 002: dt: 0.5000, sse=13086542.0, rms=20.960 (0.000%) 003: dt: 0.5000, sse=10679603.0, rms=18.398 (0.000%) 004: dt: 0.5000, sse=9099615.0, rms=16.248 (0.000%) 005: dt: 0.5000, sse=8057873.5, rms=14.467 (0.000%) 006: dt: 0.5000, sse=7323040.5, rms=12.946 (0.000%) 007: dt: 0.5000, sse=6781496.5, rms=11.500 (0.000%) 008: dt: 0.5000, sse=6328016.0, rms=10.044 (0.000%) 009: dt: 0.5000, sse=5987421.0, rms=8.545 (0.000%) 010: dt: 0.5000, sse=5729922.0, rms=7.113 (0.000%) 011: dt: 0.5000, sse=5698016.0, rms=5.934 (0.000%) 012: dt: 0.5000, sse=5749260.5, rms=5.107 (0.000%) 013: dt: 0.5000, sse=5909659.0, rms=4.656 (0.000%) 014: dt: 0.5000, sse=5965204.0, rms=4.392 (0.000%) 015: dt: 0.5000, sse=6046592.5, rms=4.254 (0.000%) 016: dt: 0.5000, sse=6044437.0, rms=4.161 (0.000%) 017: dt: 0.5000, sse=6085725.0, rms=4.101 (0.000%) rms = 4.05, time step reduction 1 of 3 to 0.250... 018: dt: 0.5000, sse=6075330.0, rms=4.052 (0.000%) 019: dt: 0.2500, sse=3907561.2, rms=2.976 (0.000%) 020: dt: 0.2500, sse=3694222.8, rms=2.655 (0.000%) rms = 2.61, time step reduction 2 of 3 to 0.125... 021: dt: 0.2500, sse=3553850.5, rms=2.607 (0.000%) 022: dt: 0.1250, sse=3327012.2, rms=2.341 (0.000%) rms = 2.30, time step reduction 3 of 3 to 0.062... 023: dt: 0.1250, sse=3290295.5, rms=2.301 (0.000%) positioning took 4.9 minutes mean border=59.8, 578 (6) missing vertices, mean dist 0.2 [0.2 (%34.5)->0.4 (%65.5))] %51 local maxima, %31 large gradients and %13 min vals, 221 gradients ignored tol=1.0e-04, sigma=1.0, host=kyung, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 averaging target values for 5 iterations... 000: dt: 0.0000, sse=4228448.0, rms=5.98 024: dt: 0.5000, sse=4242860.5, rms=4.226 (0.000%) rms = 4.22, time step reduction 1 of 3 to 0.250... 025: dt: 0.5000, sse=5327718.5, rms=4.221 (0.000%) 026: dt: 0.2500, sse=3921731.2, rms=2.882 (0.000%) 027: dt: 0.2500, sse=3973908.2, rms=2.573 (0.000%) rms = 2.53, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=3849880.8, rms=2.533 (0.000%) 029: dt: 0.1250, sse=3634950.5, rms=2.178 (0.000%) 030: dt: 0.1250, sse=3609800.2, rms=2.114 (0.000%) rms = 2.11, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=3594719.0, rms=2.110 (0.000%) positioning took 1.7 minutes mean border=57.5, 700 (2) missing vertices, mean dist 0.1 [0.2 (%31.5)->0.3 (%68.5))] %63 local maxima, %20 large gradients and %13 min vals, 233 gradients ignored tol=1.0e-04, sigma=0.5, host=kyung, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 averaging target values for 5 iterations... 000: dt: 0.0000, sse=3812967.0, rms=3.60 rms = 4.13, time step reduction 1 of 3 to 0.250... 032: dt: 0.2500, sse=3623734.5, rms=2.793 (0.000%) 033: dt: 0.2500, sse=3587313.0, rms=2.374 (0.000%) 034: dt: 0.2500, sse=3719976.5, rms=2.295 (0.000%) rms = 2.32, time step reduction 2 of 3 to 0.125... 035: dt: 0.1250, sse=3661979.0, rms=2.206 (0.000%) 036: dt: 0.1250, sse=3601971.8, rms=2.078 (0.000%) rms = 2.05, time step reduction 3 of 3 to 0.062... 037: dt: 0.1250, sse=3588091.5, rms=2.054 (0.000%) positioning took 1.5 minutes mean border=56.6, 1601 (1) missing vertices, mean dist 0.0 [0.2 (%41.2)->0.2 (%58.8))] %67 local maxima, %15 large gradients and %13 min vals, 174 gradients ignored tol=1.0e-04, sigma=0.2, host=kyung, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 writing pial surface to /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=3619043.2, rms=2.40 rms = 3.38, time step reduction 1 of 3 to 0.250... 038: dt: 0.2500, sse=3538150.5, rms=2.112 (0.000%) rms = 2.07, time step reduction 2 of 3 to 0.125... 039: dt: 0.2500, sse=3639742.8, rms=2.074 (0.000%) 040: dt: 0.1250, sse=3563688.0, rms=1.982 (0.000%) rms = 1.96, time step reduction 3 of 3 to 0.062... 041: dt: 0.1250, sse=3573922.8, rms=1.956 (0.000%) positioning took 1.0 minutes writing curvature file /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/rh.area.pial vertex spacing 0.98 +- 0.40 (0.10-->7.80) (max @ vno 79054 --> 127213) face area 0.38 +- 0.28 (0.00-->9.11) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 127456 vertices processed 25000 of 127456 vertices processed 50000 of 127456 vertices processed 75000 of 127456 vertices processed 100000 of 127456 vertices processed 125000 of 127456 vertices processed 0 of 127456 vertices processed 25000 of 127456 vertices processed 50000 of 127456 vertices processed 75000 of 127456 vertices processed 100000 of 127456 vertices processed 125000 of 127456 vertices processed thickness calculation complete, 247:365 truncations. 36495 vertices at 0 distance 93510 vertices at 1 distance 76134 vertices at 2 distance 27241 vertices at 3 distance 7682 vertices at 4 distance 2296 vertices at 5 distance 719 vertices at 6 distance 260 vertices at 7 distance 75 vertices at 8 distance 34 vertices at 9 distance 23 vertices at 10 distance 17 vertices at 11 distance 16 vertices at 12 distance 8 vertices at 13 distance 9 vertices at 14 distance 8 vertices at 15 distance 2 vertices at 16 distance 6 vertices at 17 distance 5 vertices at 18 distance 9 vertices at 19 distance 1 vertices at 20 distance writing curvature file /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/rh.thickness positioning took 22.7 minutes #-------------------------------------------- #@# Surf Volume rh Sat Jul 6 11:04:48 EDT 2013 /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.volume rh.area.mid mul rh.thickness Saving result to 'rh.volume' (type = MRI_CURV_FILE) [ ok ] #----------------------------------------- #@# WM/GM Contrast rh Sat Jul 6 11:04:50 EDT 2013 /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/scripts pctsurfcon --s VNS_Mig001 --rh-only Log file is /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/scripts/pctsurfcon.log Sat Jul 6 11:04:50 EDT 2013 setenv SUBJECTS_DIR /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer cd /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/scripts /usr/local/freesurfer/stable5_3_0/bin/pctsurfcon $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $ Linux kyungmo2 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 mri_vol2surf --mov /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/tmp.pctsurfcon.3717/rh.wm.mgh --regheader VNS_Mig001 --cortex srcvol = /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri/orig.mgz as target reference. Loading label /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/label/rh.cortex.label Reading surface /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/rh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 -1 -1 -1 using old Done mapping volume to surface Number of source voxels hit = 69900 Masking with /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/label/rh.cortex.label Writing to /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/tmp.pctsurfcon.3717/rh.wm.mgh Dim: 127456 1 1 mri_vol2surf --mov /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/tmp.pctsurfcon.3717/rh.gm.mgh --projfrac 0.3 --regheader VNS_Mig001 --cortex srcvol = /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri/orig.mgz as target reference. Loading label /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/label/rh.cortex.label Reading surface /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/rh.white Done reading source surface Reading thickness /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 83064 Masking with /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/label/rh.cortex.label Writing to /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/tmp.pctsurfcon.3717/rh.gm.mgh Dim: 127456 1 1 mri_concat /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/tmp.pctsurfcon.3717/rh.wm.mgh /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/tmp.pctsurfcon.3717/rh.gm.mgh --paired-diff-norm --mul 100 --o /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/rh.w-g.pct.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing Combining pairs nframes = 1 Multiplying by 100.000000 Writing to /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/rh.w-g.pct.mgh mri_segstats --in /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/rh.w-g.pct.mgh --annot VNS_Mig001 rh aparc --sum /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/stats/rh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --in /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/rh.w-g.pct.mgh --annot VNS_Mig001 rh aparc --sum /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/stats/rh.w-g.pct.stats --snr sysname Linux hostname kyungmo2 machine x86_64 user rllin UseRobust 0 Constructing seg from annotation Reading annotation reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Seg base 2000 Loading /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/rh.w-g.pct.mgh Vertex Area is 0.65325 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 2000 unknown 0 0.000 1 2001 bankssts 1230 844.408 2 2002 caudalanteriorcingulate 1082 695.014 3 2003 caudalmiddlefrontal 2773 1851.793 4 2004 corpuscallosum 0 0.000 5 2005 cuneus 2202 1304.602 6 2006 entorhinal 542 385.265 7 2007 fusiform 4814 3119.085 8 2008 inferiorparietal 8351 5535.243 9 2009 inferiortemporal 4313 2765.416 10 2010 isthmuscingulate 1407 887.802 11 2011 lateraloccipital 6700 4130.032 12 2012 lateralorbitofrontal 3526 2420.013 13 2013 lingual 3885 2433.359 14 2014 medialorbitofrontal 2735 1837.845 15 2015 middletemporal 4210 2869.541 16 2016 parahippocampal 937 621.607 17 2017 paracentral 1985 1270.277 18 2018 parsopercularis 1598 1046.649 19 2019 parsorbitalis 1224 807.530 20 2020 parstriangularis 2432 1643.504 21 2021 pericalcarine 2331 1402.247 22 2022 postcentral 5847 3574.387 23 2023 posteriorcingulate 1646 1065.715 24 2024 precentral 7289 4557.298 25 2025 precuneus 5369 3471.621 26 2026 rostralanteriorcingulate 799 552.606 27 2027 rostralmiddlefrontal 8134 5504.856 28 2028 superiorfrontal 10090 6906.956 29 2029 superiorparietal 7094 4474.326 30 2030 superiortemporal 5324 3555.271 31 2031 supramarginal 5154 3403.375 32 2032 frontalpole 279 186.532 33 2033 temporalpole 522 364.686 34 2034 transversetemporal 621 371.411 35 2035 insula 3399 2272.737 Reporting on 34 segmentations mri_segstats done Cleaning up #----------------------------------------- #@# Parcellation Stats rh Sat Jul 6 11:05:13 EDT 2013 /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/scripts mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab VNS_Mig001 rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri/wm.mgz... reading input surface /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/rh.white... reading input pial surface /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/rh.pial... reading input white surface /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/rh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1230 844 1908 2.403 0.421 0.121 0.032 12 1.4 bankssts 1082 695 1918 2.446 0.678 0.150 0.050 21 2.2 caudalanteriorcingulate 2773 1852 5069 2.537 0.388 0.130 0.046 32 5.2 caudalmiddlefrontal 2202 1305 2572 1.805 0.464 0.141 0.053 45 4.6 cuneus 542 385 1762 3.641 0.630 0.140 0.053 8 1.1 entorhinal 4814 3119 9747 2.790 0.603 0.139 0.067 117 9.9 fusiform 8351 5535 14564 2.438 0.495 0.145 0.050 131 17.6 inferiorparietal 4313 2765 8909 2.825 0.610 0.140 0.064 105 10.6 inferiortemporal 1407 888 2578 2.649 0.764 0.160 0.056 26 3.0 isthmuscingulate 6700 4130 9634 2.092 0.533 0.149 0.092 149 14.0 lateraloccipital 3526 2420 6486 2.489 0.655 0.154 0.059 73 8.6 lateralorbitofrontal 3885 2433 5132 1.975 0.569 0.153 0.072 104 9.5 lingual 2735 1838 4626 2.247 0.626 0.149 0.055 55 6.1 medialorbitofrontal 4210 2870 9787 2.842 0.614 0.145 0.052 69 9.0 middletemporal 937 622 1943 2.746 0.725 0.126 0.039 11 1.5 parahippocampal 1985 1270 3362 2.441 0.546 0.119 0.034 17 3.0 paracentral 1598 1047 3013 2.549 0.413 0.124 0.049 18 3.5 parsopercularis 1224 808 2558 2.605 0.578 0.158 0.057 22 2.7 parsorbitalis 2432 1644 4381 2.354 0.465 0.126 0.034 26 3.5 parstriangularis 2331 1402 2297 1.677 0.450 0.144 0.206 65 7.9 pericalcarine 5847 3574 8649 2.161 0.520 0.125 0.054 132 13.2 postcentral 1646 1066 2844 2.483 0.714 0.157 0.057 32 3.8 posteriorcingulate 7289 4557 12713 2.592 0.479 0.118 0.040 82 12.1 precentral 5369 3472 8360 2.251 0.528 0.142 0.076 95 11.9 precuneus 799 553 1720 2.857 0.553 0.148 0.062 18 1.9 rostralanteriorcingulate 8134 5505 13586 2.180 0.424 0.149 0.057 261 19.6 rostralmiddlefrontal 10090 6907 19430 2.506 0.463 0.146 0.058 204 24.1 superiorfrontal 7094 4474 10761 2.171 0.477 0.133 0.047 99 12.8 superiorparietal 5324 3555 10985 2.785 0.463 0.123 0.036 63 8.3 superiortemporal 5154 3403 9389 2.528 0.506 0.147 0.048 80 9.9 supramarginal 279 187 573 2.270 0.383 0.183 0.058 7 0.6 frontalpole 522 365 2017 3.749 0.583 0.180 0.091 18 1.9 temporalpole 621 371 1094 2.642 0.371 0.133 0.048 8 1.0 transversetemporal 3399 2273 6563 2.895 0.852 0.134 0.050 58 6.9 insula #----------------------------------------- #@# Cortical Parc 2 rh Sat Jul 6 11:06:24 EDT 2013 /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 VNS_Mig001 rh ../surf/rh.sphere.reg /usr/local/freesurfer/stable5_3_0/average/rh.destrieux.simple.2009-07-29.gcs ../label/rh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /usr/local/freesurfer/stable5_3_0/average/rh.destrieux.simple.2009-07-29.gcs... reading color table from GCSA file.... average std = 1.9 0.2 using min determinant for regularization = 0.000 0 singular and 851 ill-conditioned covariance matrices regularized input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 6 labels changed using aseg relabeling using gibbs priors... 000: 9138 changed, 127456 examined... 001: 2150 changed, 35214 examined... 002: 657 changed, 11023 examined... 003: 288 changed, 3690 examined... 004: 146 changed, 1645 examined... 005: 70 changed, 826 examined... 006: 34 changed, 372 examined... 007: 18 changed, 204 examined... 008: 8 changed, 84 examined... 009: 6 changed, 49 examined... 010: 4 changed, 33 examined... 011: 3 changed, 21 examined... 012: 0 changed, 17 examined... 7 labels changed using aseg 000: 261 total segments, 176 labels (1564 vertices) changed 001: 94 total segments, 9 labels (20 vertices) changed 002: 85 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 109 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 810 vertices marked for relabeling... 810 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 1 minutes and 47 seconds. #----------------------------------------- #@# Parcellation Stats 2 rh Sat Jul 6 11:08:17 EDT 2013 /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/scripts mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab VNS_Mig001 rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri/wm.mgz... reading input surface /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/rh.white... reading input pial surface /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/rh.pial... reading input white surface /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/rh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 915 637 1448 2.060 0.397 0.162 0.055 17 2.1 G_and_S_frontomargin 1095 714 2000 2.503 0.477 0.141 0.042 15 1.9 G_and_S_occipital_inf 1397 793 2234 2.331 0.501 0.119 0.081 66 2.5 G_and_S_paracentral 1362 893 2650 2.657 0.426 0.152 0.047 22 2.7 G_and_S_subcentral 984 658 1843 2.257 0.422 0.183 0.071 25 2.7 G_and_S_transv_frontopol 2473 1676 4422 2.489 0.580 0.147 0.061 43 6.0 G_and_S_cingul-Ant 1314 898 2596 2.626 0.492 0.144 0.048 21 2.5 G_and_S_cingul-Mid-Ant 1290 868 2446 2.704 0.588 0.138 0.043 17 2.2 G_and_S_cingul-Mid-Post 614 389 1285 2.627 0.530 0.171 0.064 14 1.6 G_cingul-Post-dorsal 345 197 864 3.187 0.563 0.143 0.044 5 0.6 G_cingul-Post-ventral 2113 1190 2449 1.782 0.456 0.153 0.225 77 6.9 G_cuneus 953 603 2296 2.844 0.323 0.143 0.065 16 2.7 G_front_inf-Opercular 281 184 638 2.827 0.502 0.165 0.046 6 0.5 G_front_inf-Orbital 1234 819 2707 2.530 0.377 0.149 0.051 20 2.6 G_front_inf-Triangul 3680 2473 7652 2.440 0.402 0.173 0.071 90 10.5 G_front_middle 7009 4742 14724 2.576 0.478 0.162 0.070 183 20.5 G_front_sup 532 349 1238 3.294 0.542 0.151 0.057 11 1.1 G_Ins_lg_and_S_cent_ins 635 396 1891 3.611 0.706 0.161 0.080 17 2.2 G_insular_short 2398 1517 4939 2.602 0.411 0.164 0.062 52 5.4 G_occipital_middle 1756 979 2539 2.123 0.434 0.135 0.045 30 3.4 G_occipital_sup 1972 1210 4099 2.736 0.465 0.145 0.061 39 4.5 G_oc-temp_lat-fusifor 2698 1582 3694 1.960 0.570 0.160 0.087 91 7.6 G_oc-temp_med-Lingual 1553 1039 3910 3.146 0.872 0.144 0.056 33 3.7 G_oc-temp_med-Parahip 2404 1638 5765 2.747 0.563 0.176 0.077 72 7.6 G_orbital 2766 1791 5981 2.700 0.473 0.169 0.077 66 8.9 G_pariet_inf-Angular 2675 1727 5505 2.643 0.491 0.158 0.055 51 5.6 G_pariet_inf-Supramar 2028 1304 3946 2.413 0.472 0.148 0.059 33 4.1 G_parietal_sup 2172 1174 3415 2.243 0.474 0.127 0.066 45 8.0 G_postcentral 2764 1535 5740 2.842 0.363 0.121 0.052 46 5.9 G_precentral 2566 1590 4760 2.331 0.579 0.164 0.124 72 8.4 G_precuneus 744 496 1574 2.408 0.441 0.152 0.044 16 1.4 G_rectus 385 256 620 2.387 0.888 0.107 0.039 7 0.4 G_subcallosal 525 318 1015 2.754 0.389 0.151 0.047 8 1.0 G_temp_sup-G_T_transv 1933 1248 5003 2.971 0.410 0.150 0.054 37 4.4 G_temp_sup-Lateral 614 419 1509 3.241 0.453 0.105 0.029 4 0.6 G_temp_sup-Plan_polar 801 538 1479 2.513 0.477 0.115 0.030 8 0.9 G_temp_sup-Plan_tempo 2622 1627 6249 2.995 0.552 0.161 0.089 93 9.0 G_temporal_inf 2645 1764 6885 2.983 0.540 0.159 0.064 55 6.7 G_temporal_middle 582 381 927 2.371 0.446 0.104 0.024 4 0.6 Lat_Fis-ant-Horizont 188 134 243 2.109 0.410 0.109 0.024 1 0.2 Lat_Fis-ant-Vertical 1424 964 1862 2.279 0.410 0.125 0.034 11 1.8 Lat_Fis-post 2859 1657 3379 1.809 0.483 0.145 0.152 90 6.4 Pole_occipital 1630 1106 5369 3.467 0.740 0.169 0.070 38 4.7 Pole_temporal 2410 1566 2731 1.907 0.631 0.144 0.055 38 6.0 S_calcarine 3029 2068 3855 2.053 0.568 0.112 0.030 20 3.9 S_central 1108 750 1499 2.165 0.342 0.107 0.028 7 1.3 S_cingul-Marginalis 627 421 1016 2.807 0.401 0.104 0.027 3 0.7 S_circular_insula_ant 1448 967 2399 2.817 0.561 0.098 0.027 9 1.8 S_circular_insula_inf 1397 966 2131 2.514 0.412 0.113 0.027 9 1.6 S_circular_insula_sup 1192 809 1975 2.670 0.504 0.108 0.023 8 1.1 S_collat_transv_ant 589 387 648 1.863 0.507 0.149 0.050 7 1.3 S_collat_transv_post 2095 1425 3042 2.152 0.425 0.107 0.026 14 2.3 S_front_inf 2031 1375 2737 2.034 0.369 0.125 0.056 136 5.8 S_front_middle 2391 1665 3861 2.347 0.396 0.110 0.028 20 2.6 S_front_sup 356 237 630 2.512 0.566 0.157 0.047 5 0.9 S_interm_prim-Jensen 3133 2029 3913 2.037 0.414 0.122 0.034 30 4.4 S_intrapariet_and_P_trans 1166 773 1376 1.876 0.456 0.146 0.044 14 2.2 S_oc_middle_and_Lunatus 1300 872 1621 2.013 0.429 0.113 0.027 9 1.4 S_oc_sup_and_transversal 751 498 992 2.241 0.309 0.132 0.038 8 1.2 S_occipital_ant 919 633 1298 2.484 0.427 0.120 0.030 8 1.1 S_oc-temp_lat 1507 1054 2287 2.449 0.534 0.129 0.091 60 2.7 S_oc-temp_med_and_Lingual 460 314 546 1.918 0.391 0.123 0.032 3 0.6 S_orbital_lateral 921 639 1061 1.742 0.706 0.104 0.024 6 1.0 S_orbital_med-olfact 1424 967 2161 2.253 0.558 0.157 0.052 21 3.0 S_orbital-H_Shaped 1760 1161 2158 2.102 0.454 0.125 0.035 17 2.6 S_parieto_occipital 1529 937 1567 2.130 0.732 0.146 0.051 30 2.8 S_pericallosal 2217 1501 2975 2.150 0.431 0.114 0.029 16 2.7 S_postcentral 1081 720 1635 2.461 0.394 0.099 0.024 6 1.0 S_precentral-inf-part 1600 1076 2319 2.395 0.410 0.114 0.036 12 2.6 S_precentral-sup-part 279 194 415 2.423 0.561 0.151 0.032 4 0.4 S_suborbital 1338 901 2065 2.275 0.488 0.141 0.042 15 2.3 S_subparietal 775 535 1016 2.278 0.460 0.126 0.026 6 1.1 S_temporal_inf 5827 4037 8813 2.369 0.448 0.115 0.029 48 7.1 S_temporal_sup 254 181 397 2.739 0.390 0.129 0.031 3 0.3 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 rh Sat Jul 6 11:09:32 EDT 2013 /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 VNS_Mig001 rh ../surf/rh.sphere.reg /usr/local/freesurfer/stable5_3_0/average/rh.DKTatlas40.gcs ../label/rh.aparc.DKTatlas40.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /usr/local/freesurfer/stable5_3_0/average/rh.DKTatlas40.gcs... reading color table from GCSA file.... average std = 0.9 using min determinant for regularization = 0.008 0 singular and 237 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 951 labels changed using aseg relabeling using gibbs priors... 000: 2589 changed, 127456 examined... 001: 618 changed, 11115 examined... 002: 149 changed, 3385 examined... 003: 62 changed, 934 examined... 004: 19 changed, 345 examined... 005: 9 changed, 108 examined... 006: 3 changed, 54 examined... 007: 0 changed, 14 examined... 123 labels changed using aseg 000: 65 total segments, 32 labels (94 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 42 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 788 vertices marked for relabeling... 788 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas40.annot... classification took 1 minutes and 30 seconds. #----------------------------------------- #@# Parcellation Stats 3 rh Sat Jul 6 11:11:06 EDT 2013 /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/scripts mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas40.stats -b -a ../label/rh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab VNS_Mig001 rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas40.annot. reading volume /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri/wm.mgz... reading input surface /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/rh.white... reading input pial surface /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/rh.pial... reading input white surface /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/surf/rh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 36 entries read (originally /Applications/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.DKTatlas40.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1072 688 1905 2.448 0.678 0.151 0.051 21 2.2 caudalanteriorcingulate 2942 1972 5270 2.517 0.403 0.130 0.045 34 5.4 caudalmiddlefrontal 2684 1580 3162 1.835 0.450 0.139 0.055 54 6.0 cuneus 543 388 1729 3.627 0.622 0.132 0.042 7 0.9 entorhinal 4215 2727 8022 2.702 0.500 0.138 0.070 109 8.7 fusiform 7810 5166 13562 2.426 0.507 0.146 0.052 124 16.8 inferiorparietal 4781 3081 10407 2.899 0.678 0.141 0.062 111 11.5 inferiortemporal 1453 917 2659 2.641 0.759 0.159 0.056 26 3.1 isthmuscingulate 7108 4376 10250 2.097 0.537 0.148 0.088 154 14.6 lateraloccipital 3997 2768 7321 2.383 0.674 0.161 0.062 97 10.3 lateralorbitofrontal 3894 2437 5166 1.982 0.569 0.153 0.072 103 9.6 lingual 2338 1577 4133 2.251 0.662 0.145 0.050 48 4.9 medialorbitofrontal 5160 3520 11285 2.763 0.597 0.141 0.047 80 10.2 middletemporal 899 598 1881 2.762 0.725 0.125 0.038 11 1.4 parahippocampal 2030 1298 3461 2.452 0.548 0.118 0.034 17 3.1 paracentral 1679 1100 3117 2.542 0.425 0.124 0.048 20 3.6 parsopercularis 1317 854 2561 2.620 0.556 0.142 0.050 19 2.6 parsorbitalis 2583 1741 4611 2.324 0.481 0.125 0.034 28 3.8 parstriangularis 2326 1396 2294 1.678 0.451 0.144 0.207 65 7.9 pericalcarine 6378 3937 9443 2.164 0.509 0.126 0.053 138 14.2 postcentral 1779 1152 3106 2.494 0.702 0.158 0.057 36 4.1 posteriorcingulate 6843 4257 12068 2.605 0.478 0.117 0.041 78 11.4 precentral 5392 3482 8515 2.255 0.531 0.144 0.078 98 12.3 precuneus 887 611 1825 2.836 0.558 0.146 0.059 16 1.9 rostralanteriorcingulate 5201 3527 8990 2.246 0.420 0.147 0.055 201 12.9 rostralmiddlefrontal 13208 8998 24218 2.406 0.489 0.148 0.059 269 31.7 superiorfrontal 6039 3839 9264 2.191 0.473 0.131 0.045 79 10.2 superiorparietal 6940 4631 14839 2.844 0.561 0.130 0.043 97 12.3 superiortemporal 4921 3259 9009 2.547 0.505 0.146 0.048 76 9.2 supramarginal 532 321 952 2.595 0.342 0.135 0.052 7 0.9 transversetemporal 2893 1936 5906 3.009 0.743 0.130 0.047 41 5.5 insula #-------------------------------------------- #@# Cortical ribbon mask Sat Jul 6 11:12:09 EDT 2013 /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon VNS_Mig001 SUBJECTS_DIR is /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer loading input data... computing distance to left white surface computing distance to left pial surface computing distance to right white surface computing distance to right pial surface hemi masks overlap voxels = 54 writing volume /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001/mri/ribbon.mgz writing ribbon files #-------------------------------------------- #@# ASeg Stats Sat Jul 6 11:37:41 EDT 2013 /autofs/space/kyungmo2_003/users/rllin/MIGRAV/data/freesurfer/VNS_Mig001 mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /usr/local/freesurfer/stable5_3_0/ASegStatsLUT.txt --subject VNS_Mig001 $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /usr/local/freesurfer/stable5_3_0/ASegStatsLUT.txt --subject VNS_Mig001 sysname Linux hostname kyungmo2 machine x86_64 user rllin UseRobust 0 atlas_icv (eTIV) = 1535415 mm^3 (det: 1.268781 ) Segmentation fault (core dumped) Linux kyungmo2 2.6.32-279.22.1.el6.x86_64 #1 SMP Wed Feb 6 03:10:46 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s VNS_Mig001 exited with ERRORS at Sat Jul 6 11:38:22 EDT 2013 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting