Tue Apr 24 14:49:24 EDT 2012 /prod3/allegra/barcs_fs/SUBJECTS_MPRAGE/S8861CSO1 /opt/freesurfer/bin/recon-all -i /prod3/allegra/barcs_fs/structurals/S8861CSO1/1/fs40S8861CSO1.nii.gz -subjid S8861CSO1 subjid S8861CSO1 setenv SUBJECTS_DIR /prod3/allegra/barcs_fs/SUBJECTS_MPRAGE FREESURFER_HOME /opt/freesurfer Actual FREESURFER_HOME /opt/freesurfer-5.1.0 build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Linux hhlxnrcas23 2.6.18-128.el5 #1 SMP Wed Jan 21 10:41:14 EST 2009 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize unlimited memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 32 kbytes maxproc 137216 total used free shared buffers cached Mem: 16439228 4198352 12240876 0 121332 3591052 -/+ buffers/cache: 485968 15953260 Swap: 16410388 289800 16120588 ######################################## program versions used $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/24-18:49:24-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ User: Skhadka Machine: hhlxnrcas23 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/24-18:49:25-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: Skhadka Machine: hhlxnrcas23 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/24-18:49:25-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: Skhadka Machine: hhlxnrcas23 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/24-18:49:25-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize.c,v 1.73 2011/03/11 20:55:38 fischl Exp $ User: Skhadka Machine: hhlxnrcas23 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/24-18:49:25-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_watershed.cpp,v 1.96 2011/03/16 21:23:49 nicks Exp $ User: Skhadka Machine: hhlxnrcas23 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/24-18:49:25-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: Skhadka Machine: hhlxnrcas23 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/24-18:49:25-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: Skhadka Machine: hhlxnrcas23 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/24-18:49:25-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_label2label.c,v 1.40.2.1 2011/05/19 17:21:56 greve Exp $ User: Skhadka Machine: hhlxnrcas23 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/24-18:49:26-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_em_register.c,v 1.84 2011/03/16 21:23:48 nicks Exp $ User: Skhadka Machine: hhlxnrcas23 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/24-18:49:26-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_normalize.c,v 1.52 2011/03/02 00:04:14 nicks Exp $ User: Skhadka Machine: hhlxnrcas23 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/24-18:49:26-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_register.c,v 1.78 2011/03/02 14:27:40 fischl Exp $ User: Skhadka Machine: hhlxnrcas23 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/24-18:49:26-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_label.c,v 1.96 2011/03/02 00:04:13 nicks Exp $ User: Skhadka Machine: hhlxnrcas23 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/24-18:49:26-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: Skhadka Machine: hhlxnrcas23 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/24-18:49:26-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: Skhadka Machine: hhlxnrcas23 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/24-18:49:26-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: Skhadka Machine: hhlxnrcas23 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/24-18:49:26-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: Skhadka Machine: hhlxnrcas23 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/24-18:49:27-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: Skhadka Machine: hhlxnrcas23 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/24-18:49:27-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: Skhadka Machine: hhlxnrcas23 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/24-18:49:27-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: Skhadka Machine: hhlxnrcas23 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/24-18:49:27-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: Skhadka Machine: hhlxnrcas23 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/24-18:49:27-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: Skhadka Machine: hhlxnrcas23 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/24-18:49:27-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: Skhadka Machine: hhlxnrcas23 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/24-18:49:27-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: Skhadka Machine: hhlxnrcas23 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/24-18:49:28-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: Skhadka Machine: hhlxnrcas23 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/24-18:49:28-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_euler_number.c,v 1.8 2011/03/02 00:04:32 nicks Exp $ User: Skhadka Machine: hhlxnrcas23 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/24-18:49:28-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ User: Skhadka Machine: hhlxnrcas23 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/24-18:49:28-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: Skhadka Machine: hhlxnrcas23 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/24-18:49:28-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: Skhadka Machine: hhlxnrcas23 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/24-18:49:28-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: Skhadka Machine: hhlxnrcas23 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/24-18:49:28-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: Skhadka Machine: hhlxnrcas23 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/24-18:49:28-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: Skhadka Machine: hhlxnrcas23 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/24-18:49:29-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_calc.c,v 1.37.2.4 2011/04/04 00:53:08 nicks Exp $ User: Skhadka Machine: hhlxnrcas23 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/24-18:49:29-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ User: Skhadka Machine: hhlxnrcas23 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/24-18:49:29-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ User: Skhadka Machine: hhlxnrcas23 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/24-18:49:29-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: Skhadka Machine: hhlxnrcas23 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/24-18:49:29-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: Skhadka Machine: hhlxnrcas23 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/24-18:49:29-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: Skhadka Machine: hhlxnrcas23 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/24-18:49:29-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ User: Skhadka Machine: hhlxnrcas23 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /opt/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /opt/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /prod3/allegra/barcs_fs/SUBJECTS_MPRAGE/S8861CSO1 mri_convert /prod3/allegra/barcs_fs/structurals/S8861CSO1/1/fs40S8861CSO1.nii.gz /prod3/allegra/barcs_fs/SUBJECTS_MPRAGE/S8861CSO1/mri/orig/001.mgz mri_convert /prod3/allegra/barcs_fs/structurals/S8861CSO1/1/fs40S8861CSO1.nii.gz /prod3/allegra/barcs_fs/SUBJECTS_MPRAGE/S8861CSO1/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /prod3/allegra/barcs_fs/structurals/S8861CSO1/1/fs40S8861CSO1.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to /prod3/allegra/barcs_fs/SUBJECTS_MPRAGE/S8861CSO1/mri/orig/001.mgz... #------------------------------------------ recon-all -s S8861CSO1 finished without error at Tue Apr 24 14:49:38 EDT 2012 New invocation of recon-all Wed Apr 25 15:14:14 EDT 2012 /tmp/Skhadka/S8861CSO1 /opt/freesurfer/bin/recon-all -no-isrunning -mprage -autorecon1 -autorecon2 -hippo-subfields -subjid S8861CSO1 subjid S8861CSO1 setenv SUBJECTS_DIR /tmp/Skhadka FREESURFER_HOME /opt/freesurfer Actual FREESURFER_HOME /opt/freesurfer-5.1.0 build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Linux hhlxnrcas09 2.6.18-128.el5 #1 SMP Wed Jan 21 10:41:14 EST 2009 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize unlimited memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 32 kbytes maxproc 137216 total used free shared buffers cached Mem: 16308156 9712524 6595632 0 170668 8154144 -/+ buffers/cache: 1387712 14920444 Swap: 18481144 152780 18328364 ######################################## program versions used $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/25-19:14:14-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ User: Skhadka Machine: hhlxnrcas09 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/25-19:14:14-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: Skhadka Machine: hhlxnrcas09 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/25-19:14:14-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: Skhadka Machine: hhlxnrcas09 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/25-19:14:14-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize.c,v 1.73 2011/03/11 20:55:38 fischl Exp $ User: Skhadka Machine: hhlxnrcas09 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/25-19:14:14-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_watershed.cpp,v 1.96 2011/03/16 21:23:49 nicks Exp $ User: Skhadka Machine: hhlxnrcas09 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/25-19:14:15-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: Skhadka Machine: hhlxnrcas09 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/25-19:14:15-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: Skhadka Machine: hhlxnrcas09 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/25-19:14:15-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_label2label.c,v 1.40.2.1 2011/05/19 17:21:56 greve Exp $ User: Skhadka Machine: hhlxnrcas09 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/25-19:14:15-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_em_register.c,v 1.84 2011/03/16 21:23:48 nicks Exp $ User: Skhadka Machine: hhlxnrcas09 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/25-19:14:15-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_normalize.c,v 1.52 2011/03/02 00:04:14 nicks Exp $ User: Skhadka Machine: hhlxnrcas09 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/25-19:14:15-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_register.c,v 1.78 2011/03/02 14:27:40 fischl Exp $ User: Skhadka Machine: hhlxnrcas09 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/25-19:14:15-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_label.c,v 1.96 2011/03/02 00:04:13 nicks Exp $ User: Skhadka Machine: hhlxnrcas09 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/25-19:14:15-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: Skhadka Machine: hhlxnrcas09 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/25-19:14:15-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: Skhadka Machine: hhlxnrcas09 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/25-19:14:15-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: Skhadka Machine: hhlxnrcas09 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/25-19:14:16-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: Skhadka Machine: hhlxnrcas09 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/25-19:14:16-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: Skhadka Machine: hhlxnrcas09 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/25-19:14:16-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: Skhadka Machine: hhlxnrcas09 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/25-19:14:16-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: Skhadka Machine: hhlxnrcas09 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/25-19:14:16-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: Skhadka Machine: hhlxnrcas09 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/25-19:14:16-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: Skhadka Machine: hhlxnrcas09 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/25-19:14:16-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: Skhadka Machine: hhlxnrcas09 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/25-19:14:16-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: Skhadka Machine: hhlxnrcas09 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/25-19:14:16-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: Skhadka Machine: hhlxnrcas09 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/25-19:14:16-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_euler_number.c,v 1.8 2011/03/02 00:04:32 nicks Exp $ User: Skhadka Machine: hhlxnrcas09 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/25-19:14:17-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ User: Skhadka Machine: hhlxnrcas09 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/25-19:14:17-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: Skhadka Machine: hhlxnrcas09 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/25-19:14:17-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: Skhadka Machine: hhlxnrcas09 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/25-19:14:17-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: Skhadka Machine: hhlxnrcas09 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/25-19:14:17-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: Skhadka Machine: hhlxnrcas09 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/25-19:14:17-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: Skhadka Machine: hhlxnrcas09 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/25-19:14:17-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_calc.c,v 1.37.2.4 2011/04/04 00:53:08 nicks Exp $ User: Skhadka Machine: hhlxnrcas09 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/25-19:14:17-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ User: Skhadka Machine: hhlxnrcas09 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/25-19:14:17-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ User: Skhadka Machine: hhlxnrcas09 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/25-19:14:18-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: Skhadka Machine: hhlxnrcas09 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/25-19:14:18-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: Skhadka Machine: hhlxnrcas09 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/25-19:14:18-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: Skhadka Machine: hhlxnrcas09 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/04/25-19:14:18-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ User: Skhadka Machine: hhlxnrcas09 Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /opt/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /opt/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #-------------------------------------------- #@# MotionCor Wed Apr 25 15:14:18 EDT 2012 Found 1 runs /tmp/Skhadka/S8861CSO1/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 /tmp/Skhadka/S8861CSO1/mri/orig/001.mgz /tmp/Skhadka/S8861CSO1/mri/rawavg.mgz /tmp/Skhadka/S8861CSO1 mri_convert /tmp/Skhadka/S8861CSO1/mri/rawavg.mgz /tmp/Skhadka/S8861CSO1/mri/orig.mgz --conform mri_convert /tmp/Skhadka/S8861CSO1/mri/rawavg.mgz /tmp/Skhadka/S8861CSO1/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /tmp/Skhadka/S8861CSO1/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) Original Data has (1, 1, 1) mm size and (208, 256, 176) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /tmp/Skhadka/S8861CSO1/mri/orig.mgz... mri_add_xform_to_header -c /tmp/Skhadka/S8861CSO1/mri/transforms/talairach.xfm /tmp/Skhadka/S8861CSO1/mri/orig.mgz /tmp/Skhadka/S8861CSO1/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Wed Apr 25 15:14:40 EDT 2012 /tmp/Skhadka/S8861CSO1/mri talairach_avi --i orig.mgz --xfm transforms/talairach.auto.xfm cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Wed Apr 25 15:15:32 EDT 2012 /tmp/Skhadka/S8861CSO1/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.4562, pval=0.1049 >= threshold=0.0050) awk -f /opt/freesurfer/bin/extract_talairach_avi_QA.awk /tmp/Skhadka/S8861CSO1/mri/transforms/talairach_avi.log TalAviQA: 0.98038 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Wed Apr 25 15:15:32 EDT 2012 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /tmp/Skhadka/S8861CSO1/mri /opt/freesurfer/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 2011/03/02 20:16:39 nicks Exp $ Linux hhlxnrcas09 2.6.18-128.el5 #1 SMP Wed Jan 21 10:41:14 EST 2009 x86_64 x86_64 x86_64 GNU/Linux Wed Apr 25 15:15:32 EDT 2012 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 tmpdir is ./tmp.mri_nu_correct.mni.4599 /tmp/Skhadka/S8861CSO1/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.4599/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.4599/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.4599/nu0.mnc... -------------------------------------------------------- Iteration 1 Wed Apr 25 15:15:37 EDT 2012 nu_correct -clobber ./tmp.mri_nu_correct.mni.4599/nu0.mnc ./tmp.mri_nu_correct.mni.4599/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.4599/0/ [Skhadka@hhlxnrcas09:/tmp/Skhadka/S8861CSO1/mri/] [2012-04-25 15:15:37] running: /opt/freesurfer-5.0.0/mni/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.4599/0/ ./tmp.mri_nu_correct.mni.4599/nu0.mnc ./tmp.mri_nu_correct.mni.4599/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 17 CV of field change: 0.000951765 [Skhadka@hhlxnrcas09:/tmp/Skhadka/S8861CSO1/mri/] [2012-04-25 15:15:58] running: /opt/freesurfer-5.0.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.4599/nu0.mnc ./tmp.mri_nu_correct.mni.4599/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done -------------------------------------------------------- Iteration 2 Wed Apr 25 15:16:02 EDT 2012 nu_correct -clobber ./tmp.mri_nu_correct.mni.4599/nu1.mnc ./tmp.mri_nu_correct.mni.4599/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.4599/1/ [Skhadka@hhlxnrcas09:/tmp/Skhadka/S8861CSO1/mri/] [2012-04-25 15:16:02] running: /opt/freesurfer-5.0.0/mni/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.4599/1/ ./tmp.mri_nu_correct.mni.4599/nu1.mnc ./tmp.mri_nu_correct.mni.4599/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 11 CV of field change: 0.000946187 [Skhadka@hhlxnrcas09:/tmp/Skhadka/S8861CSO1/mri/] [2012-04-25 15:16:17] running: /opt/freesurfer-5.0.0/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.4599/nu1.mnc ./tmp.mri_nu_correct.mni.4599/1//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.4599/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.4599/ones.mgz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /tmp/Skhadka/S8861CSO1/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.4599/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.4599/ones.mgz sysname Linux hostname hhlxnrcas09 machine x86_64 user Skhadka input ./tmp.mri_nu_correct.mni.4599/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.4599/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.4599/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.4599/sum.junk --avgwf ./tmp.mri_nu_correct.mni.4599/input.mean.dat $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.4599/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.4599/sum.junk --avgwf ./tmp.mri_nu_correct.mni.4599/input.mean.dat sysname Linux hostname hhlxnrcas09 machine x86_64 user Skhadka Loading ./tmp.mri_nu_correct.mni.4599/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 1.67772e+07 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.4599/input.mean.dat mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.4599/ones.mgz --i ./tmp.mri_nu_correct.mni.4599/nu2.mnc --sum ./tmp.mri_nu_correct.mni.4599/sum.junk --avgwf ./tmp.mri_nu_correct.mni.4599/output.mean.dat $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.4599/ones.mgz --i ./tmp.mri_nu_correct.mni.4599/nu2.mnc --sum ./tmp.mri_nu_correct.mni.4599/sum.junk --avgwf ./tmp.mri_nu_correct.mni.4599/output.mean.dat sysname Linux hostname hhlxnrcas09 machine x86_64 user Skhadka Loading ./tmp.mri_nu_correct.mni.4599/ones.mgz Loading ./tmp.mri_nu_correct.mni.4599/nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 1.67772e+07 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.4599/output.mean.dat mris_calc -o ./tmp.mri_nu_correct.mni.4599/nu2.mnc ./tmp.mri_nu_correct.mni.4599/nu2.mnc mul .98785341751303870436 Saving result to './tmp.mri_nu_correct.mni.4599/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.4599/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.4599/nu2.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from ./tmp.mri_nu_correct.mni.4599/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) 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 14 seconds. mapping ( 8, 115) to ( 3, 110) Wed Apr 25 15:17:41 EDT 2012 mri_nu_correct.mni done #-------------------------------------------- #@# Intensity Normalization Wed Apr 25 15:17:41 EDT 2012 /tmp/Skhadka/S8861CSO1/mri mri_normalize -g 1 -mprage nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.031 -0.012 -0.002 -1.653; -0.014 0.866 0.449 -8.300; 0.007 -0.412 0.972 7.315; 0.000 0.000 0.000 1.000; assuming input volume is MGH (Van der Kouwe) MP-RAGE INFO: Modifying talairach volume c_(r,a,s) based on average_305 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 1 of 2 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 2 building Voronoi diagram... performing soap bubble smoothing... writing output to T1.mgz 3D bias adjustment took 3 minutes and 25 seconds. MRIsplineNormalize(): npeaks = 20 Starting OpenSpline(): npoints = 20 white matter peak found at 111 white matter peak found at 110 gm peak at 68 (68), valley at 25 (25) csf peak at 34, setting threshold to 56 white matter peak found at 111 white matter peak found at 110 gm peak at 70 (70), valley at 25 (25) csf peak at 35, setting threshold to 58 #-------------------------------------------- #@# Skull Stripping Wed Apr 25 15:21:07 EDT 2012 /tmp/Skhadka/S8861CSO1/mri mri_em_register -skull nu.mgz /opt/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 reading 1 input volumes... logging results to talairach_with_skull.log reading '/opt/freesurfer/average/RB_all_withskull_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu.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=6.0 skull bounding box = (40, 51, 0) --> (209, 219, 224) using (96, 107, 112) as brain centroid... mean wm in atlas = 126, using box (75,86,84) --> (116, 127,139) to find MRI wm before smoothing, mri peak at 110 after smoothing, mri peak at 110, scaling input intensities by 1.145 scaling channel 0 by 1.14545 initial log_p = -10378.9 ************************************************ First Search limited to translation only. ************************************************ Found translation: (-1.7, -18.8, 6.2): log p = -10318.617 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-10300.1, old_max_log_p =-10318.6 (thresh=-10308.3) 1.075 0.000 0.000 -11.264; 0.000 0.987 0.390 -55.872; 0.000 -0.371 0.850 65.683; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-10299.9, old_max_log_p =-10300.1 (thresh=-10289.8) 1.075 0.000 0.000 -11.264; 0.000 1.028 0.275 -49.091; 0.000 -0.257 0.960 45.694; 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=-10282.0, old_max_log_p =-10299.9 (thresh=-10289.6) 1.054 0.000 0.000 -8.599; 0.000 0.991 0.435 -60.058; 0.000 -0.407 0.868 71.887; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-10276.8, old_max_log_p =-10282.0 (thresh=-10271.8) 1.054 0.000 0.000 -8.599; 0.000 1.009 0.443 -63.455; 0.000 -0.391 0.836 73.167; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-10273.8, old_max_log_p =-10276.8 (thresh=-10266.5) 1.053 -0.002 0.024 -9.626; -0.009 0.997 0.471 -63.545; -0.026 -0.424 0.820 83.954; 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 1.05250 -0.00226 0.02397 -9.62592; -0.00863 0.99701 0.47062 -63.54471; -0.02584 -0.42364 0.81975 83.95404; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.05250 -0.00226 0.02397 -9.62592; -0.00863 0.99701 0.47062 -63.54471; -0.02584 -0.42364 0.81975 83.95404; 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: 007: -log(p) = 10273.8 tol 0.000010 Resulting transform: 1.053 -0.002 0.024 -9.626; -0.009 0.997 0.471 -63.545; -0.026 -0.424 0.820 83.954; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -10273.8 (old=-10378.9) transform before final EM align: 1.053 -0.002 0.024 -9.626; -0.009 0.997 0.471 -63.545; -0.026 -0.424 0.820 83.954; 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 1.05250 -0.00226 0.02397 -9.62592; -0.00863 0.99701 0.47062 -63.54471; -0.02584 -0.42364 0.81975 83.95404; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.05250 -0.00226 0.02397 -9.62592; -0.00863 0.99701 0.47062 -63.54471; -0.02584 -0.42364 0.81975 83.95404; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 008: -log(p) = 1144653.9 after pass:transform: ( 1.05, -0.00, 0.02, -9.63) ( -0.01, 1.00, 0.47, -63.54) ( -0.03, -0.42, 0.82, 83.95) 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 TOLERANCESpass 2 through quasi-newton minimization... 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) = 1144653.9 tol 0.000000 final transform: 1.053 -0.002 0.024 -9.626; -0.008 0.997 0.471 -63.545; -0.026 -0.424 0.820 83.954; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 32 minutes and 49 seconds. mri_watershed -T1 -brain_atlas /opt/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=127 y=130 z=106 r=79 first estimation of the main basin volume: 2082048 voxels Looking for seedpoints 2 found in the cerebellum 18 found in the rest of the brain global maximum in x=147, y=123, z=68, Imax=255 CSF=21, WM_intensity=110, WM_VARIANCE=5 WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 preflooding height equal to 10 percent done. Analyze... main basin size=25483196618 voxels, voxel volume =1.000 = 25483196618 mmm3 = 25483196.416 cm3 done. PostAnalyze...Basin Prior 221 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done. Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=126,y=135, z=99, r=11066 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=6, CSF_MAX=22 , nb = 45144 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=11 , nb = 2952 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=9 , nb = 2484 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=6, CSF_MAX=21 , nb = 19476 LEFT_BRAIN CSF_MIN=0, CSF_intensity=6, CSF_MAX=23 , nb = 19782 OTHER CSF_MIN=0, CSF_intensity=8, CSF_MAX=22 , nb = 450 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 22, 33, 46, 64 after analyzing : 22, 41, 46, 46 RIGHT_CER before analyzing : 11, 17, 41, 71 after analyzing : 11, 33, 41, 42 LEFT_CER before analyzing : 9, 15, 41, 69 after analyzing : 9, 32, 41, 41 RIGHT_BRAIN before analyzing : 21, 32, 45, 62 after analyzing : 21, 40, 45, 45 LEFT_BRAIN before analyzing : 23, 34, 46, 64 after analyzing : 23, 42, 46, 47 OTHER before analyzing : 22, 19, 9, 59 after analyzing : 19, 23, 25, 32 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...68 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.009 curvature mean = 75.346, std = 7.791 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 4.20, sigma = 7.13 after rotation: sse = 4.20, sigma = 7.13 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 6.32, its var is 11.72 before Erosion-Dilatation 5.27% of inacurate vertices after Erosion-Dilatation 4.14% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...42 iterations mri_strip_skull: done peeling brain Brain Size = 2068101 voxels, voxel volume = 1.000 mm3 = 2068101 mmm3 = 2068.101 cm3 ****************************** Saving brainmask.auto.mgz done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Wed Apr 25 15:54:45 EDT 2012 /tmp/Skhadka/S8861CSO1/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /opt/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta 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 '/opt/freesurfer/average/RB_all_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 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=22.0 skull bounding box = (56, 64, 19) --> (197, 211, 195) using (103, 113, 107) as brain centroid... mean wm in atlas = 107, using box (86,95,85) --> (120, 131,128) to find MRI wm before smoothing, mri peak at 110 after smoothing, mri peak at 110, scaling input intensities by 0.973 scaling channel 0 by 0.972727 initial log_p = -7415.9 ************************************************ First Search limited to translation only. ************************************************ Found translation: (-0.6, -17.6, 2.8): log p = -7184.498 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-7014.8, old_max_log_p =-7184.5 (thresh=-7177.3) 1.000 0.000 0.000 -0.568; 0.000 0.921 0.532 -61.373; 0.000 -0.457 0.791 86.579; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-6967.5, old_max_log_p =-7014.8 (thresh=-7007.7) 1.000 0.000 0.000 -0.568; 0.000 0.973 0.424 -57.384; 0.000 -0.333 0.854 63.214; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-6967.5, old_max_log_p =-6967.5 (thresh=-6960.5) 1.000 0.000 0.000 -0.568; 0.000 0.973 0.424 -57.384; 0.000 -0.333 0.854 63.214; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-6921.1, old_max_log_p =-6967.5 (thresh=-6960.5) 1.000 0.000 0.000 -0.568; 0.000 0.980 0.459 -60.083; 0.000 -0.372 0.854 70.438; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-6914.3, old_max_log_p =-6921.1 (thresh=-6914.2) 1.000 0.000 0.000 -2.443; 0.000 0.998 0.468 -65.314; 0.000 -0.365 0.838 71.092; 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=-6880.6, old_max_log_p =-6914.3 (thresh=-6907.4) 1.001 0.022 0.018 -6.410; -0.025 1.002 0.453 -60.144; -0.008 -0.350 0.848 70.009; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-6876.2, old_max_log_p =-6880.6 (thresh=-6873.7) 0.999 0.016 0.032 -6.838; -0.024 1.006 0.446 -60.059; -0.025 -0.342 0.852 70.221; 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 0.99939 0.01618 0.03198 -6.83764; -0.02446 1.00569 0.44634 -60.05866; -0.02478 -0.34218 0.85191 70.22090; 0.00000 0.00000 0.00000 1.00000; nsamples 2772 Quasinewton: input matrix 0.99939 0.01618 0.03198 -6.83764; -0.02446 1.00569 0.44634 -60.05866; -0.02478 -0.34218 0.85191 70.22090; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 008: -log(p) = 6875.5 after pass:transform: ( 1.00, 0.02, 0.03, -6.84) ( -0.02, 1.01, 0.45, -60.06) ( -0.02, -0.34, 0.85, 70.22) 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 TOLERANCESpass 2 through quasi-newton minimization... 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) = 6875.5 tol 0.000010 Resulting transform: 0.999 0.016 0.032 -6.838; -0.024 1.006 0.446 -60.059; -0.025 -0.342 0.852 70.221; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -6876.2 (old=-7415.9) transform before final EM align: 0.999 0.016 0.032 -6.838; -0.024 1.006 0.446 -60.059; -0.025 -0.342 0.852 70.221; 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 0.99939 0.01618 0.03198 -6.83764; -0.02446 1.00569 0.44634 -60.05866; -0.02478 -0.34218 0.85191 70.22090; 0.00000 0.00000 0.00000 1.00000; nsamples 312841 Quasinewton: input matrix 0.99939 0.01618 0.03198 -6.83764; -0.02446 1.00569 0.44634 -60.05866; -0.02478 -0.34218 0.85191 70.22090; 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) = 830418.6 tol 0.000000 final transform: 0.999 0.016 0.032 -6.838; -0.024 1.006 0.446 -60.059; -0.025 -0.342 0.852 70.221; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach.lta... registration took 38 minutes and 59 seconds. #-------------------------------------- #@# CA Normalize Wed Apr 25 16:33:44 EDT 2012 /tmp/Skhadka/S8861CSO1/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /opt/freesurfer/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 volumes reading atlas from '/opt/freesurfer/average/RB_all_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 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=22.0 skull bounding box = (56, 64, 19) --> (197, 211, 195) using (103, 113, 107) as brain centroid... mean wm in atlas = 107, using box (86,95,85) --> (120, 131,128) to find MRI wm before smoothing, mri peak at 110 after smoothing, mri peak at 110, scaling input intensities by 0.973 scaling channel 0 by 0.972727 using 244171 sample points... INFO: compute sample coordinates transform 0.999 0.016 0.032 -6.838; -0.024 1.006 0.446 -60.059; -0.025 -0.342 0.852 70.221; 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 (127, 72, 22) --> (193, 196, 193) Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 248.0 0 of 5080 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (63, 73, 21) --> (128, 188, 193) Right_Cerebral_White_Matter: limiting intensities to 97.0 --> 248.0 1 of 5069 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (129, 163, 57) --> (177, 207, 112) Left_Cerebellum_White_Matter: limiting intensities to 98.0 --> 248.0 0 of 106 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (81, 163, 53) --> (128, 206, 112) Right_Cerebellum_White_Matter: limiting intensities to 100.0 --> 248.0 0 of 76 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (110, 148, 89) --> (143, 212, 122) Brain_Stem: limiting intensities to 94.0 --> 248.0 0 of 324 (0.0%) samples deleted using 10655 total control points for intensity normalization... bias field = 1.014 +- 0.053 49 of 10654 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (127, 72, 22) --> (193, 196, 193) Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 240.0 0 of 5037 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (63, 73, 21) --> (128, 188, 193) Right_Cerebral_White_Matter: limiting intensities to 96.0 --> 240.0 1 of 5058 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (129, 163, 57) --> (177, 207, 112) Left_Cerebellum_White_Matter: limiting intensities to 90.0 --> 240.0 7 of 116 (6.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (81, 163, 53) --> (128, 206, 112) Right_Cerebellum_White_Matter: limiting intensities to 91.0 --> 240.0 0 of 74 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (110, 148, 89) --> (143, 212, 122) Brain_Stem: limiting intensities to 83.0 --> 240.0 0 of 325 (0.0%) samples deleted using 10610 total control points for intensity normalization... bias field = 1.022 +- 0.036 41 of 10602 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (127, 72, 22) --> (193, 196, 193) Left_Cerebral_White_Matter: limiting intensities to 97.0 --> 239.0 0 of 4938 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (63, 73, 21) --> (128, 188, 193) Right_Cerebral_White_Matter: limiting intensities to 96.0 --> 239.0 4 of 5015 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (129, 163, 57) --> (177, 207, 112) Left_Cerebellum_White_Matter: limiting intensities to 87.0 --> 239.0 20 of 89 (22.5%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (81, 163, 53) --> (128, 206, 112) Right_Cerebellum_White_Matter: limiting intensities to 87.0 --> 239.0 0 of 87 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (110, 148, 89) --> (143, 212, 122) Brain_Stem: limiting intensities to 77.0 --> 239.0 0 of 329 (0.0%) samples deleted using 10458 total control points for intensity normalization... bias field = 1.018 +- 0.028 24 of 10434 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 2 minutes and 39 seconds. #-------------------------------------- #@# CA Reg Wed Apr 25 16:36:23 EDT 2012 /tmp/Skhadka/S8861CSO1/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /opt/freesurfer/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 reading input volume 'norm.mgz'... reading GCA '/opt/freesurfer/average/RB_all_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 freeing gibbs priors...done. average std[0] = 5.0 label assignment complete, 0 changed (0.00%) det(m_affine) = 1.01 (predicted orig area = 7.9) label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.780, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 80203.047 ms 0001: dt=129.472000, rms=0.711 (8.833%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 80894.398 ms 0002: dt=221.952000, rms=0.691 (2.832%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 81969.812 ms 0003: dt=129.472000, rms=0.678 (1.865%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 79147.508 ms 0004: dt=129.472000, rms=0.676 (0.343%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 82106.891 ms 0005: dt=517.888000, rms=0.662 (2.022%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 80819.641 ms 0006: dt=32.368000, rms=0.661 (0.123%), neg=0, invalid=766 0007: dt=32.368000, rms=0.661 (0.058%), neg=0, invalid=766 0008: dt=32.368000, rms=0.661 (0.050%), neg=0, invalid=766 0009: dt=32.368000, rms=0.660 (0.060%), neg=0, invalid=766 0010: dt=32.368000, rms=0.660 (0.106%), neg=0, invalid=766 0011: dt=32.368000, rms=0.658 (0.204%), neg=0, invalid=766 0012: dt=32.368000, rms=0.656 (0.298%), neg=0, invalid=766 0013: dt=32.368000, rms=0.654 (0.340%), neg=0, invalid=766 0014: dt=32.368000, rms=0.652 (0.270%), neg=0, invalid=766 0015: dt=32.368000, rms=0.651 (0.216%), neg=0, invalid=766 0016: dt=32.368000, rms=0.650 (0.201%), neg=0, invalid=766 0017: dt=32.368000, rms=0.648 (0.188%), neg=0, invalid=766 0018: dt=32.368000, rms=0.647 (0.147%), neg=0, invalid=766 0019: dt=32.368000, rms=0.647 (0.124%), neg=0, invalid=766 0020: dt=32.368000, rms=0.646 (0.117%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 102358.281 ms 0021: dt=221.952000, rms=0.644 (0.226%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 98697.258 ms 0022: dt=73.984000, rms=0.644 (0.031%), neg=0, invalid=766 0023: dt=73.984000, rms=0.644 (0.041%), neg=0, invalid=766 0024: dt=73.984000, rms=0.644 (0.069%), neg=0, invalid=766 0025: dt=73.984000, rms=0.643 (0.101%), neg=0, invalid=766 0026: dt=73.984000, rms=0.642 (0.137%), neg=0, invalid=766 0027: dt=73.984000, rms=0.641 (0.148%), neg=0, invalid=766 0028: dt=73.984000, rms=0.640 (0.153%), neg=0, invalid=766 0029: dt=73.984000, rms=0.639 (0.143%), neg=0, invalid=766 0030: dt=73.984000, rms=0.638 (0.144%), neg=0, invalid=766 0031: dt=73.984000, rms=0.637 (0.186%), neg=0, invalid=766 0032: dt=73.984000, rms=0.636 (0.201%), neg=0, invalid=766 0033: dt=73.984000, rms=0.635 (0.195%), neg=0, invalid=766 0034: dt=73.984000, rms=0.633 (0.177%), neg=0, invalid=766 0035: dt=73.984000, rms=0.633 (0.138%), neg=0, invalid=766 0036: dt=73.984000, rms=0.632 (0.130%), neg=0, invalid=766 0037: dt=73.984000, rms=0.631 (0.150%), neg=0, invalid=766 0038: dt=73.984000, rms=0.630 (0.166%), neg=0, invalid=766 0039: dt=73.984000, rms=0.629 (0.150%), neg=0, invalid=766 0040: dt=73.984000, rms=0.628 (0.135%), neg=0, invalid=766 0041: dt=73.984000, rms=0.627 (0.131%), neg=0, invalid=766 0042: dt=73.984000, rms=0.626 (0.129%), neg=0, invalid=766 0043: dt=73.984000, rms=0.625 (0.129%), neg=0, invalid=766 0044: dt=73.984000, rms=0.625 (0.128%), neg=0, invalid=766 0045: dt=73.984000, rms=0.624 (0.107%), neg=0, invalid=766 0046: dt=73.984000, rms=0.624 (0.077%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 71504.352 ms 0047: dt=517.888000, rms=0.623 (0.013%), neg=0, invalid=766 0048: dt=517.888000, rms=0.623 (-0.084%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.623, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 58901.883 ms 0049: dt=129.472000, rms=0.623 (0.045%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 58924.102 ms 0050: dt=517.888000, rms=0.622 (0.202%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 58816.594 ms 0051: dt=32.368000, rms=0.622 (0.022%), neg=0, invalid=766 0052: dt=32.368000, rms=0.622 (0.016%), neg=0, invalid=766 0053: dt=32.368000, rms=0.622 (0.001%), neg=0, invalid=766 0054: dt=32.368000, rms=0.622 (-0.011%), neg=0, invalid=766 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.627, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 55013.957 ms 0055: dt=145.152000, rms=0.620 (1.173%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 57694.988 ms 0056: dt=62.208000, rms=0.616 (0.642%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 70436.312 ms 0057: dt=124.416000, rms=0.611 (0.843%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 63337.621 ms 0058: dt=36.288000, rms=0.608 (0.409%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 68640.258 ms 0059: dt=331.776000, rms=0.602 (1.054%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 64728.203 ms 0060: dt=20.736000, rms=0.598 (0.673%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 69616.883 ms 0061: dt=36.288000, rms=0.596 (0.207%), neg=0, invalid=766 0062: dt=36.288000, rms=0.596 (0.158%), neg=0, invalid=766 0063: dt=36.288000, rms=0.594 (0.247%), neg=0, invalid=766 0064: dt=36.288000, rms=0.592 (0.306%), neg=0, invalid=766 0065: dt=36.288000, rms=0.590 (0.324%), neg=0, invalid=766 0066: dt=36.288000, rms=0.588 (0.387%), neg=0, invalid=766 0067: dt=36.288000, rms=0.586 (0.398%), neg=0, invalid=766 0068: dt=36.288000, rms=0.584 (0.369%), neg=0, invalid=766 0069: dt=36.288000, rms=0.581 (0.358%), neg=0, invalid=766 0070: dt=36.288000, rms=0.580 (0.333%), neg=0, invalid=766 0071: dt=36.288000, rms=0.578 (0.337%), neg=0, invalid=766 0072: dt=36.288000, rms=0.576 (0.314%), neg=0, invalid=766 0073: dt=36.288000, rms=0.574 (0.260%), neg=0, invalid=766 0074: dt=36.288000, rms=0.573 (0.230%), neg=0, invalid=766 0075: dt=36.288000, rms=0.572 (0.219%), neg=0, invalid=766 0076: dt=36.288000, rms=0.571 (0.203%), neg=0, invalid=766 0077: dt=36.288000, rms=0.570 (0.167%), neg=0, invalid=766 0078: dt=36.288000, rms=0.569 (0.170%), neg=0, invalid=766 0079: dt=36.288000, rms=0.568 (0.167%), neg=0, invalid=766 0080: dt=36.288000, rms=0.567 (0.141%), neg=0, invalid=766 0081: dt=36.288000, rms=0.566 (0.111%), neg=0, invalid=766 0082: dt=36.288000, rms=0.566 (0.094%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 93177.898 ms 0083: dt=36.288000, rms=0.566 (0.008%), neg=0, invalid=766 0084: dt=36.288000, rms=0.566 (-0.007%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.566, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 88662.359 ms 0085: dt=36.288000, rms=0.565 (0.129%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 90567.398 ms 0086: dt=124.416000, rms=0.564 (0.143%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 82148.273 ms 0087: dt=36.288000, rms=0.564 (0.029%), neg=0, invalid=766 0088: dt=36.288000, rms=0.564 (0.021%), neg=0, invalid=766 0089: dt=36.288000, rms=0.564 (0.008%), neg=0, invalid=766 0090: dt=36.288000, rms=0.564 (0.004%), neg=0, invalid=766 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.590, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 80889.773 ms 0091: dt=2.800000, rms=0.590 (0.032%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 66678.953 ms 0092: dt=2.000000, rms=0.590 (0.010%), neg=0, invalid=766 0093: dt=2.000000, rms=0.590 (-0.008%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.590, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 65035.484 ms 0094: dt=0.500000, rms=0.590 (0.000%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 65609.742 ms 0095: dt=0.125000, rms=0.590 (-0.000%), neg=0, invalid=766 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.664, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 61167.016 ms 0096: dt=5.715877, rms=0.642 (3.406%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 59284.781 ms 0097: dt=3.559633, rms=0.640 (0.209%), neg=0, invalid=766 0098: dt=3.559633, rms=0.640 (-0.031%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.640, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 56238.293 ms 0099: dt=0.036000, rms=0.640 (0.000%), neg=0, invalid=766 0100: dt=0.036000, rms=0.640 (-0.000%), neg=0, invalid=766 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.706, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 53116.465 ms 0101: dt=1.176000, rms=0.702 (0.585%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 53415.355 ms 0102: dt=2.597315, rms=0.694 (1.097%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 53745.875 ms 0103: dt=0.384000, rms=0.693 (0.072%), neg=0, invalid=766 0104: dt=0.384000, rms=0.693 (0.022%), neg=0, invalid=766 0105: dt=0.384000, rms=0.693 (0.016%), neg=0, invalid=766 0106: dt=0.384000, rms=0.693 (0.043%), neg=0, invalid=766 0107: dt=0.384000, rms=0.692 (0.092%), neg=0, invalid=766 0108: dt=0.384000, rms=0.691 (0.112%), neg=0, invalid=766 0109: dt=0.384000, rms=0.691 (0.062%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 57878.980 ms 0110: dt=1.280000, rms=0.691 (0.023%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.691, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 58513.391 ms 0111: dt=1.536585, rms=0.689 (0.222%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 57534.258 ms 0112: dt=0.064000, rms=0.689 (-0.000%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.652, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 56578.812 ms 0113: dt=0.448000, rms=0.638 (2.194%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 50488.969 ms 0114: dt=0.000000, rms=0.638 (0.002%), neg=0, invalid=766 0115: dt=0.050000, rms=0.638 (-0.334%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.638, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 52718.336 ms 0116: dt=0.000000, rms=0.638 (0.000%), neg=0, invalid=766 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11725 (24) mri peak = 0.13434 (22) Left_Lateral_Ventricle (4): linear fit = 0.82 x + 0.0 (1681 voxels, overlap=0.355) Left_Lateral_Ventricle (4): linear fit = 0.82 x + 0.0 (1681 voxels, peak = 20), gca=19.8 gca peak = 0.14022 (22) mri peak = 0.14538 (21) Right_Lateral_Ventricle (43): linear fit = 0.80 x + 0.0 (1001 voxels, overlap=0.584) Right_Lateral_Ventricle (43): linear fit = 0.80 x + 0.0 (1001 voxels, peak = 18), gca=17.6 gca peak = 0.24234 (100) mri peak = 0.15038 (105) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (557 voxels, overlap=0.802) Right_Pallidum (52): linear fit = 1.02 x + 0.0 (557 voxels, peak = 102), gca=102.5 gca peak = 0.19192 (97) mri peak = 0.11877 (105) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (528 voxels, overlap=0.597) Left_Pallidum (13): linear fit = 1.05 x + 0.0 (528 voxels, peak = 102), gca=101.8 gca peak = 0.24007 (63) mri peak = 0.09412 (68) Right_Hippocampus (53): linear fit = 1.08 x + 0.0 (676 voxels, overlap=0.278) Right_Hippocampus (53): linear fit = 1.08 x + 0.0 (676 voxels, peak = 68), gca=67.7 gca peak = 0.29892 (64) mri peak = 0.12889 (68) Left_Hippocampus (17): linear fit = 1.05 x + 0.0 (640 voxels, overlap=0.552) Left_Hippocampus (17): linear fit = 1.05 x + 0.0 (640 voxels, peak = 67), gca=67.2 gca peak = 0.12541 (104) mri peak = 0.13247 (106) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (92896 voxels, overlap=0.633) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (92896 voxels, peak = 107), gca=106.6 gca peak = 0.13686 (104) mri peak = 0.11985 (107) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (94150 voxels, overlap=0.583) Left_Cerebral_White_Matter (2): linear fit = 1.05 x + 0.0 (94150 voxels, peak = 109), gca=109.2 gca peak = 0.11691 (63) mri peak = 0.03977 (65) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (42281 voxels, overlap=0.996) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (42281 voxels, peak = 65), gca=64.6 gca peak = 0.13270 (63) mri peak = 0.04227 (62) Right_Cerebral_Cortex (42): linear fit = 0.95 x + 0.0 (48943 voxels, overlap=0.996) Right_Cerebral_Cortex (42): linear fit = 0.95 x + 0.0 (48943 voxels, peak = 60), gca=59.8 gca peak = 0.15182 (70) mri peak = 0.15028 (75) Right_Caudate (50): linear fit = 1.05 x + 0.0 (883 voxels, overlap=0.787) Right_Caudate (50): linear fit = 1.05 x + 0.0 (883 voxels, peak = 74), gca=73.5 gca peak = 0.14251 (76) mri peak = 0.09424 (78) Left_Caudate (11): linear fit = 1.02 x + 0.0 (1011 voxels, overlap=0.967) Left_Caudate (11): linear fit = 1.02 x + 0.0 (1011 voxels, peak = 78), gca=77.9 gca peak = 0.12116 (60) mri peak = 0.03004 (68) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (25395 voxels, overlap=0.787) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (25395 voxels, peak = 62), gca=61.5 gca peak = 0.12723 (61) mri peak = 0.02589 (68) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (32017 voxels, overlap=0.180) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (32017 voxels, peak = 63), gca=62.5 gca peak = 0.22684 (88) mri peak = 0.08956 (96) Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (10137 voxels, overlap=0.000) Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (10137 voxels, peak = 95), gca=94.6 gca peak = 0.21067 (87) mri peak = 0.10685 (94) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (9287 voxels, overlap=0.007) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (9287 voxels, peak = 94), gca=93.5 gca peak = 0.25455 (62) mri peak = 0.09738 (75) Left_Amygdala (18): linear fit = 1.15 x + 0.0 (470 voxels, overlap=0.141) Left_Amygdala (18): linear fit = 1.15 x + 0.0 (470 voxels, peak = 71), gca=71.3 gca peak = 0.39668 (62) mri peak = 0.12308 (68) Right_Amygdala (54): linear fit = 1.15 x + 0.0 (419 voxels, overlap=0.001) Right_Amygdala (54): linear fit = 1.15 x + 0.0 (419 voxels, peak = 71), gca=71.3 gca peak = 0.10129 (93) mri peak = 0.06150 (95) Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (6587 voxels, overlap=0.956) Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (6587 voxels, peak = 95), gca=95.3 gca peak = 0.12071 (89) mri peak = 0.06039 (88) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (5351 voxels, overlap=0.978) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (5351 voxels, peak = 89), gca=89.0 gca peak = 0.13716 (82) mri peak = 0.06709 (88) Left_Putamen (12): linear fit = 1.02 x + 0.0 (3386 voxels, overlap=0.968) Left_Putamen (12): linear fit = 1.02 x + 0.0 (3386 voxels, peak = 84), gca=84.0 gca peak = 0.15214 (84) mri peak = 0.06167 (82) Right_Putamen (51): linear fit = 1.05 x + 0.0 (3361 voxels, overlap=0.988) Right_Putamen (51): linear fit = 1.05 x + 0.0 (3361 voxels, peak = 88), gca=88.2 gca peak = 0.08983 (85) mri peak = 0.08332 (92) Brain_Stem (16): linear fit = 1.08 x + 0.0 (13908 voxels, overlap=0.666) Brain_Stem (16): linear fit = 1.08 x + 0.0 (13908 voxels, peak = 91), gca=91.4 gca peak = 0.11809 (92) mri peak = 0.11367 (100) Right_VentralDC (60): linear fit = 1.08 x + 0.0 (1584 voxels, overlap=0.327) Right_VentralDC (60): linear fit = 1.08 x + 0.0 (1584 voxels, peak = 99), gca=98.9 gca peak = 0.12914 (94) mri peak = 0.13368 (101) Left_VentralDC (28): linear fit = 1.05 x + 0.0 (1654 voxels, overlap=0.321) Left_VentralDC (28): linear fit = 1.05 x + 0.0 (1654 voxels, peak = 99), gca=98.7 gca peak = 0.21100 (36) mri peak = 0.50000 (19) gca peak = 0.13542 (27) mri peak = 0.04712 (49) Fourth_Ventricle (15): linear fit = 1.65 x + 0.0 (665 voxels, overlap=0.021) Fourth_Ventricle (15): linear fit = 1.65 x + 0.0 (665 voxels, peak = 45), gca=44.5 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.21802 (40) gca peak Third_Ventricle = 0.21100 (36) gca peak Fourth_Ventricle = 0.13542 (27) 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_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) not using caudate to estimate GM means estimating mean gm scale to be 1.07 x + 0.0 estimating mean wm scale to be 1.04 x + 0.0 estimating mean csf scale to be 0.81 x + 0.0 saving intensity scales to talairach.label_intensities.txt label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.663, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 56249.590 ms 0117: dt=129.472000, rms=0.654 (1.389%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 53242.211 ms 0118: dt=129.472000, rms=0.651 (0.409%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 59823.191 ms 0119: dt=221.952000, rms=0.647 (0.623%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 62401.355 ms 0120: dt=55.488000, rms=0.646 (0.146%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 67439.516 ms 0121: dt=369.920000, rms=0.644 (0.307%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 61886.609 ms 0122: dt=110.976000, rms=0.641 (0.446%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 66754.648 ms 0123: dt=32.368000, rms=0.641 (0.038%), neg=0, invalid=766 0124: dt=32.368000, rms=0.641 (0.024%), neg=0, invalid=766 0125: dt=32.368000, rms=0.641 (0.037%), neg=0, invalid=766 0126: dt=32.368000, rms=0.640 (0.054%), neg=0, invalid=766 0127: dt=32.368000, rms=0.640 (0.099%), neg=0, invalid=766 0128: dt=32.368000, rms=0.639 (0.140%), neg=0, invalid=766 0129: dt=32.368000, rms=0.638 (0.156%), neg=0, invalid=766 0130: dt=32.368000, rms=0.637 (0.145%), neg=0, invalid=766 0131: dt=32.368000, rms=0.636 (0.127%), neg=0, invalid=766 0132: dt=32.368000, rms=0.635 (0.108%), neg=0, invalid=766 0133: dt=32.368000, rms=0.635 (0.101%), neg=0, invalid=766 0134: dt=32.368000, rms=0.634 (0.090%), neg=0, invalid=766 0135: dt=32.368000, rms=0.634 (0.093%), neg=0, invalid=766 0136: dt=32.368000, rms=0.633 (0.109%), neg=0, invalid=766 0137: dt=32.368000, rms=0.632 (0.123%), neg=0, invalid=766 0138: dt=32.368000, rms=0.631 (0.117%), neg=0, invalid=766 0139: dt=32.368000, rms=0.631 (0.117%), neg=0, invalid=766 0140: dt=32.368000, rms=0.630 (0.108%), neg=0, invalid=766 0141: dt=32.368000, rms=0.629 (0.101%), neg=0, invalid=766 0142: dt=32.368000, rms=0.629 (0.089%), neg=0, invalid=766 0143: dt=32.368000, rms=0.628 (0.088%), neg=0, invalid=766 0144: dt=32.368000, rms=0.628 (0.090%), neg=0, invalid=766 0145: dt=32.368000, rms=0.627 (0.091%), neg=0, invalid=766 0146: dt=32.368000, rms=0.626 (0.093%), neg=0, invalid=766 0147: dt=32.368000, rms=0.626 (0.089%), neg=0, invalid=766 0148: dt=32.368000, rms=0.625 (0.086%), neg=0, invalid=766 0149: dt=32.368000, rms=0.625 (0.075%), neg=0, invalid=766 0150: dt=32.368000, rms=0.624 (0.074%), neg=0, invalid=766 0151: dt=32.368000, rms=0.624 (0.074%), neg=0, invalid=766 0152: dt=32.368000, rms=0.624 (0.075%), neg=0, invalid=766 0153: dt=32.368000, rms=0.623 (0.078%), neg=0, invalid=766 0154: dt=32.368000, rms=0.623 (0.074%), neg=0, invalid=766 0155: dt=32.368000, rms=0.622 (0.073%), neg=0, invalid=766 0156: dt=32.368000, rms=0.622 (0.067%), neg=0, invalid=766 0157: dt=32.368000, rms=0.621 (0.061%), neg=0, invalid=766 0158: dt=32.368000, rms=0.621 (0.056%), neg=0, invalid=766 0159: dt=32.368000, rms=0.621 (0.054%), neg=0, invalid=766 0160: dt=32.368000, rms=0.620 (0.054%), neg=0, invalid=766 0161: dt=32.368000, rms=0.620 (0.053%), neg=0, invalid=766 0162: dt=32.368000, rms=0.620 (0.053%), neg=0, invalid=766 0163: dt=32.368000, rms=0.619 (0.048%), neg=0, invalid=766 0164: dt=32.368000, rms=0.619 (0.043%), neg=0, invalid=766 0165: dt=32.368000, rms=0.619 (0.040%), neg=0, invalid=766 0166: dt=32.368000, rms=0.619 (0.038%), neg=0, invalid=766 0167: dt=32.368000, rms=0.618 (0.038%), neg=0, invalid=766 0168: dt=32.368000, rms=0.618 (0.040%), neg=0, invalid=766 0169: dt=32.368000, rms=0.618 (0.037%), neg=0, invalid=766 0170: dt=32.368000, rms=0.618 (0.036%), neg=0, invalid=766 0171: dt=32.368000, rms=0.617 (0.036%), neg=0, invalid=766 0172: dt=32.368000, rms=0.617 (0.033%), neg=0, invalid=766 0173: dt=32.368000, rms=0.617 (0.035%), neg=0, invalid=766 0174: dt=32.368000, rms=0.617 (0.032%), neg=0, invalid=766 0175: dt=32.368000, rms=0.617 (0.031%), neg=0, invalid=766 0176: dt=32.368000, rms=0.616 (0.027%), neg=0, invalid=766 0177: dt=32.368000, rms=0.616 (0.027%), neg=0, invalid=766 0178: dt=32.368000, rms=0.616 (0.024%), neg=0, invalid=766 0179: dt=32.368000, rms=0.616 (0.027%), neg=0, invalid=766 0180: dt=32.368000, rms=0.616 (0.029%), neg=0, invalid=766 0181: dt=32.368000, rms=0.616 (0.029%), neg=0, invalid=766 0182: dt=32.368000, rms=0.615 (0.027%), neg=0, invalid=766 0183: dt=32.368000, rms=0.615 (0.027%), neg=0, invalid=766 0184: dt=32.368000, rms=0.615 (0.029%), neg=0, invalid=766 0185: dt=32.368000, rms=0.615 (0.030%), neg=0, invalid=766 0186: dt=32.368000, rms=0.615 (0.028%), neg=0, invalid=766 0187: dt=32.368000, rms=0.615 (0.026%), neg=0, invalid=766 0188: dt=32.368000, rms=0.614 (0.025%), neg=0, invalid=766 0189: dt=32.368000, rms=0.614 (0.024%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 68206.523 ms 0190: dt=517.888000, rms=0.614 (0.018%), neg=0, invalid=766 0191: dt=517.888000, rms=0.614 (-0.259%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.614, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 69016.984 ms 0192: dt=110.976000, rms=0.614 (0.081%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 64905.379 ms 0193: dt=443.904000, rms=0.613 (0.121%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 57138.961 ms 0194: dt=92.480000, rms=0.613 (0.035%), neg=0, invalid=766 0195: dt=92.480000, rms=0.613 (0.031%), neg=0, invalid=766 0196: dt=92.480000, rms=0.612 (0.026%), neg=0, invalid=766 0197: dt=92.480000, rms=0.612 (0.028%), neg=0, invalid=766 0198: dt=92.480000, rms=0.612 (0.020%), neg=0, invalid=766 0199: dt=92.480000, rms=0.612 (0.010%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 55629.898 ms 0200: dt=129.472000, rms=0.612 (0.009%), neg=0, invalid=766 0201: dt=129.472000, rms=0.612 (0.014%), neg=0, invalid=766 0202: dt=32.368000, rms=0.612 (0.004%), neg=0, invalid=766 0203: dt=16.184000, rms=0.612 (0.001%), neg=0, invalid=766 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.613, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 43998.027 ms 0204: dt=0.121500, rms=0.613 (0.001%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 36346.582 ms 0205: dt=0.008859, rms=0.613 (0.000%), neg=0, invalid=766 0206: dt=0.000069, rms=0.613 (0.000%), neg=0, invalid=766 0207: dt=0.000035, rms=0.613 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.613, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 27749.227 ms 0208: dt=0.000000, rms=0.613 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.616, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 27428.766 ms 0209: dt=0.000000, rms=0.616 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.616, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 27692.238 ms 0210: dt=0.000000, rms=0.616 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.627, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 60037.176 ms 0211: dt=4.032000, rms=0.606 (3.236%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 59582.227 ms 0212: dt=4.032000, rms=0.592 (2.408%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 59558.824 ms 0213: dt=4.032000, rms=0.581 (1.854%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 59325.766 ms 0214: dt=4.032000, rms=0.572 (1.454%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 63974.723 ms 0215: dt=16.128000, rms=0.548 (4.251%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 59466.578 ms 0216: dt=4.032000, rms=0.546 (0.300%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 58207.953 ms 0217: dt=4.032000, rms=0.545 (0.248%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 61993.422 ms 0218: dt=16.128000, rms=0.540 (0.872%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 62964.211 ms 0219: dt=4.032000, rms=0.540 (0.088%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 63479.738 ms 0220: dt=10.000000, rms=0.538 (0.308%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 63211.152 ms 0221: dt=3.456000, rms=0.538 (0.048%), neg=0, invalid=766 0222: dt=3.456000, rms=0.537 (0.111%), neg=0, invalid=766 0223: dt=3.456000, rms=0.537 (0.152%), neg=0, invalid=766 0224: dt=3.456000, rms=0.536 (0.045%), neg=0, invalid=766 0225: dt=3.456000, rms=0.536 (0.103%), neg=0, invalid=766 0226: dt=3.456000, rms=0.535 (0.150%), neg=0, invalid=766 0227: dt=3.456000, rms=0.534 (0.181%), neg=0, invalid=766 0228: dt=3.456000, rms=0.533 (0.183%), neg=0, invalid=766 0229: dt=3.456000, rms=0.532 (0.171%), neg=0, invalid=766 0230: dt=3.456000, rms=0.531 (0.168%), neg=0, invalid=766 0231: dt=3.456000, rms=0.530 (0.147%), neg=0, invalid=766 0232: dt=3.456000, rms=0.530 (0.123%), neg=0, invalid=766 0233: dt=3.456000, rms=0.529 (0.091%), neg=0, invalid=766 0234: dt=3.456000, rms=0.529 (0.072%), neg=0, invalid=766 0235: dt=3.456000, rms=0.529 (0.051%), neg=0, invalid=766 0236: dt=3.456000, rms=0.528 (0.046%), neg=0, invalid=766 0237: dt=3.456000, rms=0.528 (0.036%), neg=0, invalid=766 0238: dt=3.456000, rms=0.528 (0.026%), neg=0, invalid=766 0239: dt=3.456000, rms=0.528 (0.020%), neg=0, invalid=766 0240: dt=3.456000, rms=0.528 (0.018%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 59877.422 ms 0241: dt=4.032000, rms=0.528 (0.005%), neg=0, invalid=766 0242: dt=4.032000, rms=0.528 (0.002%), neg=0, invalid=766 0243: dt=4.032000, rms=0.528 (0.016%), neg=0, invalid=766 0244: dt=4.032000, rms=0.528 (0.012%), neg=0, invalid=766 0245: dt=4.032000, rms=0.528 (0.014%), neg=0, invalid=766 0246: dt=4.032000, rms=0.527 (0.014%), neg=0, invalid=766 0247: dt=4.032000, rms=0.527 (0.021%), neg=0, invalid=766 0248: dt=4.032000, rms=0.527 (0.022%), neg=0, invalid=766 0249: dt=4.032000, rms=0.527 (0.026%), neg=0, invalid=766 0250: dt=4.032000, rms=0.527 (0.024%), neg=0, invalid=766 0251: dt=4.032000, rms=0.527 (0.026%), neg=0, invalid=766 0252: dt=4.032000, rms=0.527 (0.018%), neg=0, invalid=766 0253: dt=4.032000, rms=0.527 (0.017%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 60619.590 ms 0254: dt=4.032000, rms=0.527 (0.013%), neg=0, invalid=766 0255: dt=4.032000, rms=0.527 (0.003%), neg=0, invalid=766 0256: dt=4.032000, rms=0.527 (0.004%), neg=0, invalid=766 0257: dt=4.032000, rms=0.527 (0.005%), neg=0, invalid=766 0258: dt=4.032000, rms=0.526 (0.015%), neg=0, invalid=766 0259: dt=4.032000, rms=0.526 (0.007%), neg=0, invalid=766 0260: dt=4.032000, rms=0.526 (0.018%), neg=0, invalid=766 0261: dt=4.032000, rms=0.526 (0.017%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.526, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 64661.652 ms 0262: dt=4.210526, rms=0.526 (0.073%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 69987.195 ms 0263: dt=0.252000, rms=0.526 (-0.002%), neg=0, invalid=766 0264: dt=0.252000, rms=0.526 (0.000%), neg=0, invalid=766 0265: dt=0.252000, rms=0.526 (-0.002%), neg=0, invalid=766 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.549, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 62221.723 ms 0266: dt=0.000000, rms=0.549 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.549, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 63035.566 ms 0267: dt=0.000000, rms=0.549 (0.000%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.510, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 58580.207 ms 0268: dt=0.148305, rms=0.505 (0.910%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 58612.863 ms 0269: dt=0.129870, rms=0.502 (0.569%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 63181.125 ms 0270: dt=0.320000, rms=0.497 (1.072%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 52464.871 ms 0271: dt=0.007000, rms=0.497 (0.010%), neg=0, invalid=766 0272: dt=0.007000, rms=0.497 (0.012%), neg=0, invalid=766 0273: dt=0.007000, rms=0.497 (0.022%), neg=0, invalid=766 0274: dt=0.007000, rms=0.497 (0.030%), neg=0, invalid=766 0275: dt=0.007000, rms=0.496 (0.037%), neg=0, invalid=766 0276: dt=0.007000, rms=0.496 (0.046%), neg=0, invalid=766 0277: dt=0.007000, rms=0.496 (0.048%), neg=0, invalid=766 0278: dt=0.007000, rms=0.496 (0.053%), neg=0, invalid=766 0279: dt=0.007000, rms=0.495 (0.058%), neg=0, invalid=766 0280: dt=0.007000, rms=0.495 (0.061%), neg=0, invalid=766 0281: dt=0.007000, rms=0.495 (0.064%), neg=0, invalid=766 0282: dt=0.007000, rms=0.494 (0.064%), neg=0, invalid=766 0283: dt=0.007000, rms=0.494 (0.063%), neg=0, invalid=766 0284: dt=0.007000, rms=0.494 (0.062%), neg=0, invalid=766 0285: dt=0.007000, rms=0.493 (0.063%), neg=0, invalid=766 0286: dt=0.007000, rms=0.493 (0.061%), neg=0, invalid=766 0287: dt=0.007000, rms=0.493 (0.063%), neg=0, invalid=766 0288: dt=0.007000, rms=0.493 (0.060%), neg=0, invalid=766 0289: dt=0.007000, rms=0.492 (0.057%), neg=0, invalid=766 0290: dt=0.007000, rms=0.492 (0.058%), neg=0, invalid=766 0291: dt=0.007000, rms=0.492 (0.056%), neg=0, invalid=766 0292: dt=0.007000, rms=0.491 (0.051%), neg=0, invalid=766 0293: dt=0.007000, rms=0.491 (0.049%), neg=0, invalid=766 0294: dt=0.007000, rms=0.491 (0.050%), neg=0, invalid=766 0295: dt=0.007000, rms=0.491 (0.044%), neg=0, invalid=766 0296: dt=0.007000, rms=0.491 (0.042%), neg=0, invalid=766 0297: dt=0.007000, rms=0.490 (0.038%), neg=0, invalid=766 0298: dt=0.007000, rms=0.490 (0.035%), neg=0, invalid=766 0299: dt=0.007000, rms=0.490 (0.037%), neg=0, invalid=766 0300: dt=0.007000, rms=0.490 (0.033%), neg=0, invalid=766 0301: dt=0.007000, rms=0.490 (0.031%), neg=0, invalid=766 0302: dt=0.007000, rms=0.490 (0.028%), neg=0, invalid=766 0303: dt=0.007000, rms=0.489 (0.026%), neg=0, invalid=766 0304: dt=0.007000, rms=0.489 (0.026%), neg=0, invalid=766 0305: dt=0.007000, rms=0.489 (0.024%), neg=0, invalid=766 0306: dt=0.007000, rms=0.489 (0.023%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 60705.734 ms 0307: dt=0.112000, rms=0.489 (0.013%), neg=0, invalid=766 0308: dt=0.112000, rms=0.489 (0.017%), neg=0, invalid=766 0309: dt=0.112000, rms=0.489 (0.038%), neg=0, invalid=766 0310: dt=0.112000, rms=0.489 (0.049%), neg=0, invalid=766 0311: dt=0.112000, rms=0.488 (0.064%), neg=0, invalid=766 0312: dt=0.112000, rms=0.488 (0.020%), neg=0, invalid=766 0313: dt=0.112000, rms=0.488 (0.022%), neg=0, invalid=766 0314: dt=0.056000, rms=0.488 (0.003%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 60599.320 ms 0315: dt=0.112000, rms=0.488 (0.025%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 56256.230 ms 0316: dt=0.028000, rms=0.488 (0.003%), neg=0, invalid=766 0317: dt=0.028000, rms=0.488 (0.005%), neg=0, invalid=766 0318: dt=0.028000, rms=0.488 (0.009%), neg=0, invalid=766 0319: dt=0.028000, rms=0.488 (0.014%), neg=0, invalid=766 0320: dt=0.028000, rms=0.488 (0.011%), neg=0, invalid=766 0321: dt=0.028000, rms=0.488 (0.005%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.488, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 62186.949 ms 0322: dt=0.112000, rms=0.486 (0.273%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 66215.430 ms 0323: dt=0.320000, rms=0.484 (0.562%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 52841.238 ms 0324: dt=0.007000, rms=0.484 (0.005%), neg=0, invalid=766 0325: dt=0.007000, rms=0.484 (0.005%), neg=0, invalid=766 0326: dt=0.007000, rms=0.483 (0.009%), neg=0, invalid=766 0327: dt=0.007000, rms=0.483 (0.011%), neg=0, invalid=766 0328: dt=0.007000, rms=0.483 (0.016%), neg=0, invalid=766 0329: dt=0.007000, rms=0.483 (0.016%), neg=0, invalid=766 0330: dt=0.007000, rms=0.483 (0.016%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 62260.777 ms 0331: dt=0.112000, rms=0.483 (0.053%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 65367.012 ms 0332: dt=0.320000, rms=0.482 (0.125%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 50974.496 ms 0333: dt=0.007000, rms=0.482 (-0.005%), neg=0, invalid=766 0334: dt=0.007000, rms=0.482 (0.001%), neg=0, invalid=766 0335: dt=0.007000, rms=0.482 (0.001%), neg=0, invalid=766 0336: dt=0.007000, rms=0.482 (0.007%), neg=0, invalid=766 0337: dt=0.007000, rms=0.482 (0.003%), neg=0, invalid=766 label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.480, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 74298.875 ms iter 0, gcam->neg = 32 after 9 iterations, nbhd size=1, neg = 0 0338: dt=44.800000, rms=0.470 (2.238%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 72424.102 ms iter 0, gcam->neg = 5 after 1 iterations, nbhd size=0, neg = 0 0339: dt=25.600000, rms=0.465 (0.969%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 73911.602 ms 0340: dt=12.163265, rms=0.463 (0.373%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 69670.867 ms iter 0, gcam->neg = 13 after 15 iterations, nbhd size=2, neg = 0 0341: dt=44.800000, rms=0.462 (0.366%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 72920.828 ms 0342: dt=8.736842, rms=0.460 (0.380%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 68554.711 ms 0343: dt=11.200000, rms=0.459 (0.148%), neg=0, invalid=766 0344: dt=11.200000, rms=0.459 (0.095%), neg=0, invalid=766 0345: dt=11.200000, rms=0.458 (0.166%), neg=0, invalid=766 0346: dt=11.200000, rms=0.457 (0.224%), neg=0, invalid=766 0347: dt=11.200000, rms=0.456 (0.257%), neg=0, invalid=766 0348: dt=11.200000, rms=0.455 (0.251%), neg=0, invalid=766 0349: dt=11.200000, rms=0.454 (0.217%), neg=0, invalid=766 0350: dt=11.200000, rms=0.453 (0.198%), neg=0, invalid=766 0351: dt=11.200000, rms=0.452 (0.188%), neg=0, invalid=766 0352: dt=11.200000, rms=0.451 (0.174%), neg=0, invalid=766 0353: dt=11.200000, rms=0.450 (0.165%), neg=0, invalid=766 0354: dt=11.200000, rms=0.450 (0.160%), neg=0, invalid=766 0355: dt=11.200000, rms=0.449 (0.135%), neg=0, invalid=766 0356: dt=11.200000, rms=0.448 (0.133%), neg=0, invalid=766 0357: dt=11.200000, rms=0.448 (0.115%), neg=0, invalid=766 0358: dt=11.200000, rms=0.447 (0.122%), neg=0, invalid=766 0359: dt=11.200000, rms=0.447 (0.112%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 69015.414 ms 0360: dt=25.600000, rms=0.447 (0.024%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0361: dt=25.600000, rms=0.447 (-0.044%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.447, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 72147.508 ms iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0362: dt=25.600000, rms=0.445 (0.464%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 76242.242 ms 0363: dt=8.952381, rms=0.444 (0.165%), neg=0, invalid=766 0364: dt=8.952381, rms=0.443 (0.119%), neg=0, invalid=766 0365: dt=8.952381, rms=0.443 (0.140%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 16 iterations, nbhd size=2, neg = 0 0366: dt=8.952381, rms=0.442 (0.162%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0367: dt=8.952381, rms=0.441 (0.146%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0368: dt=8.952381, rms=0.441 (0.080%), neg=0, invalid=766 0369: dt=8.952381, rms=0.441 (0.049%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 71236.305 ms 0370: dt=11.200000, rms=0.441 (0.059%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 71593.203 ms 0371: dt=11.200000, rms=0.440 (0.031%), neg=0, invalid=766 0372: dt=11.200000, rms=0.440 (0.014%), neg=0, invalid=766 0373: dt=11.200000, rms=0.440 (0.027%), neg=0, invalid=766 0374: dt=11.200000, rms=0.440 (0.039%), neg=0, invalid=766 0375: dt=11.200000, rms=0.440 (0.034%), neg=0, invalid=766 0376: dt=11.200000, rms=0.440 (0.038%), neg=0, invalid=766 0377: dt=11.200000, rms=0.440 (0.030%), neg=0, invalid=766 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.447, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 73528.648 ms 0378: dt=0.252000, rms=0.447 (0.002%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 73397.430 ms 0379: dt=0.063000, rms=0.447 (-0.003%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.447, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 73379.547 ms iter 0, gcam->neg = 2 after 21 iterations, nbhd size=3, neg = 0 0380: dt=3.456000, rms=0.447 (0.023%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 73388.492 ms iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0381: dt=1.008000, rms=0.447 (0.013%), neg=0, invalid=766 0382: dt=1.008000, rms=0.447 (0.006%), neg=0, invalid=766 0383: dt=1.008000, rms=0.447 (0.004%), neg=0, invalid=766 0384: dt=1.008000, rms=0.447 (-0.016%), neg=0, invalid=766 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.459, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 74240.359 ms 0385: dt=0.797203, rms=0.459 (0.077%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 75403.156 ms 0386: dt=0.256000, rms=0.459 (0.005%), neg=0, invalid=766 0387: dt=0.256000, rms=0.459 (-0.001%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.459, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 75718.773 ms iter 0, gcam->neg = 12 after 18 iterations, nbhd size=2, neg = 0 0388: dt=1.792000, rms=0.458 (0.239%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 76306.758 ms 0389: dt=0.312500, rms=0.458 (0.005%), neg=0, invalid=766 0390: dt=0.312500, rms=0.458 (0.015%), neg=0, invalid=766 0391: dt=0.312500, rms=0.458 (0.010%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0392: dt=0.312500, rms=0.458 (-0.002%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.447, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 104796.562 ms iter 0, gcam->neg = 527 after 21 iterations, nbhd size=2, neg = 0 0393: dt=1.765333, rms=0.420 (5.968%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 101911.297 ms 0394: dt=0.000250, rms=0.420 (-0.008%), neg=0, invalid=766 0395: dt=0.000250, rms=0.420 (0.000%), neg=0, invalid=766 0396: dt=0.000250, rms=0.420 (-0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.420, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 102875.781 ms 0397: dt=0.001500, rms=0.420 (0.001%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 100821.633 ms 0398: dt=0.003000, rms=0.420 (0.000%), neg=0, invalid=766 0399: dt=0.003000, rms=0.420 (0.001%), neg=0, invalid=766 0400: dt=0.003000, rms=0.420 (-0.000%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.408, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 104652.602 ms iter 0, gcam->neg = 330 after 14 iterations, nbhd size=1, neg = 0 0401: dt=0.661905, rms=0.399 (2.246%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 103162.977 ms 0402: dt=0.000438, rms=0.399 (-0.016%), neg=0, invalid=766 0403: dt=0.000438, rms=0.399 (0.001%), neg=0, invalid=766 0404: dt=0.000438, rms=0.399 (0.000%), neg=0, invalid=766 0405: dt=0.000438, rms=0.399 (-0.001%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.399, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 94105.336 ms iter 0, gcam->neg = 3 after 6 iterations, nbhd size=1, neg = 0 0406: dt=0.004000, rms=0.399 (0.005%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 96734.164 ms iter 0, gcam->neg = 3 after 6 iterations, nbhd size=1, neg = 0 0407: dt=0.007000, rms=0.399 (0.011%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 100524.797 ms iter 0, gcam->neg = 104 after 17 iterations, nbhd size=2, neg = 0 0408: dt=0.320000, rms=0.398 (0.360%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 105600.328 ms 0409: dt=0.001750, rms=0.397 (0.008%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0410: dt=0.001750, rms=0.397 (0.002%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0411: dt=0.001750, rms=0.397 (0.002%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0412: dt=0.001750, rms=0.397 (0.004%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0413: dt=0.001750, rms=0.397 (0.004%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 107316.688 ms iter 0, gcam->neg = 17 after 7 iterations, nbhd size=1, neg = 0 0414: dt=0.112000, rms=0.397 (0.073%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 104151.508 ms 0415: dt=0.001750, rms=0.397 (-0.004%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.396, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 94451.969 ms iter 0, gcam->neg = 64 after 26 iterations, nbhd size=3, neg = 0 0416: dt=0.096000, rms=0.395 (0.351%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 96010.117 ms iter 0, gcam->neg = 4 after 7 iterations, nbhd size=1, neg = 0 0417: dt=0.004000, rms=0.395 (0.005%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0418: dt=0.004000, rms=0.395 (0.012%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 0419: dt=0.004000, rms=0.395 (0.022%), neg=0, invalid=766 iter 0, gcam->neg = 6 after 8 iterations, nbhd size=1, neg = 0 0420: dt=0.004000, rms=0.395 (0.032%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 7 iterations, nbhd size=1, neg = 0 0421: dt=0.004000, rms=0.394 (0.041%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 22 iterations, nbhd size=3, neg = 0 0422: dt=0.004000, rms=0.394 (0.044%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 7 iterations, nbhd size=1, neg = 0 0423: dt=0.004000, rms=0.394 (0.050%), neg=0, invalid=766 iter 0, gcam->neg = 6 after 6 iterations, nbhd size=1, neg = 0 0424: dt=0.004000, rms=0.394 (0.054%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 6 iterations, nbhd size=1, neg = 0 0425: dt=0.004000, rms=0.394 (0.061%), neg=0, invalid=766 iter 0, gcam->neg = 7 after 15 iterations, nbhd size=2, neg = 0 0426: dt=0.004000, rms=0.393 (0.061%), neg=0, invalid=766 iter 0, gcam->neg = 6 after 14 iterations, nbhd size=2, neg = 0 0427: dt=0.004000, rms=0.393 (0.060%), neg=0, invalid=766 iter 0, gcam->neg = 8 after 9 iterations, nbhd size=1, neg = 0 0428: dt=0.004000, rms=0.393 (0.063%), neg=0, invalid=766 iter 0, gcam->neg = 7 after 8 iterations, nbhd size=1, neg = 0 0429: dt=0.004000, rms=0.393 (0.065%), neg=0, invalid=766 iter 0, gcam->neg = 9 after 9 iterations, nbhd size=1, neg = 0 0430: dt=0.004000, rms=0.392 (0.064%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 107352.680 ms iter 0, gcam->neg = 6 after 29 iterations, nbhd size=4, neg = 0 0431: dt=0.016000, rms=0.392 (0.014%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.392, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 94109.242 ms iter 0, gcam->neg = 92 after 66 iterations, nbhd size=1, neg = 0 0432: dt=0.192000, rms=0.390 (0.597%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 77881.227 ms 0433: dt=0.001750, rms=0.390 (0.011%), neg=0, invalid=766 0434: dt=0.001750, rms=0.390 (0.003%), neg=0, invalid=766 0435: dt=0.001750, rms=0.390 (0.011%), neg=0, invalid=766 0436: dt=0.001750, rms=0.390 (0.011%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0437: dt=0.001750, rms=0.390 (0.013%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 29 iterations, nbhd size=4, neg = 0 0438: dt=0.001750, rms=0.390 (0.015%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0439: dt=0.001750, rms=0.390 (0.018%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0440: dt=0.001750, rms=0.390 (0.018%), neg=0, invalid=766 0441: dt=0.001750, rms=0.390 (0.022%), neg=0, invalid=766 0442: dt=0.001750, rms=0.389 (0.023%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 7 iterations, nbhd size=1, neg = 0 0443: dt=0.001750, rms=0.389 (0.020%), neg=0, invalid=766 0444: dt=0.001750, rms=0.389 (0.025%), neg=0, invalid=766 0445: dt=0.001750, rms=0.389 (0.024%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 74180.922 ms iter 0, gcam->neg = 2 after 46 iterations, nbhd size=3, neg = 0 0446: dt=0.007000, rms=0.389 (0.012%), neg=0, invalid=766 label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* label assignment complete, 0 changed (0.00%) **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.389, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 71185.727 ms iter 0, gcam->neg = 8 after 200 iterations, nbhd size=1, neg = 2 starting rms=0.005, neg=2, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 41633.895 ms iter 1, dt=0.000000: new neg 2, old_neg 2, delta 0, rms=0.005 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0447: dt=2.800000, rms=0.389 (-0.159%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.389, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 69835.055 ms iter 0, gcam->neg = 108 after 200 iterations, nbhd size=2, neg = 6 starting rms=0.012, neg=6, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 55438.082 ms iter 1, dt=0.000000: new neg 6, old_neg 6, delta 0, rms=0.012 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0448: dt=25.600000, rms=0.389 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.389, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 109971.633 ms iter 0, gcam->neg = 36 after 200 iterations, nbhd size=2, neg = 1 starting rms=0.004, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 58140.184 ms iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.004 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0449: dt=0.864000, rms=0.389 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.389, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 100987.508 ms iter 0, gcam->neg = 150 after 200 iterations, nbhd size=4, neg = 2 starting rms=0.006, neg=2, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 55187.176 ms iter 1, dt=0.000000: new neg 2, old_neg 2, delta 0, rms=0.006 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0450: dt=4.032000, rms=0.389 (0.000%), neg=0, invalid=766 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.389, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 99018.805 ms iter 0, gcam->neg = 12 after 30 iterations, nbhd size=4, neg = 0 0451: dt=0.112000, rms=0.389 (0.052%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 107509.672 ms iter 0, gcam->neg = 111 after 200 iterations, nbhd size=1, neg = 2 starting rms=0.006, neg=2, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 55895.996 ms iter 1, dt=0.000000: new neg 2, old_neg 2, delta 0, rms=0.006 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0452: dt=1.192982, rms=0.389 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.389, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 108988.844 ms iter 0, gcam->neg = 178 after 200 iterations, nbhd size=1, neg = 1 starting rms=0.005, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 61122.160 ms iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.005 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0453: dt=1.792000, rms=0.389 (0.000%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.389, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 114871.508 ms 0454: dt=0.000250, rms=0.389 (0.001%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 115420.703 ms iter 0, gcam->neg = 3 after 6 iterations, nbhd size=1, neg = 0 0455: dt=0.003000, rms=0.389 (0.011%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 114985.219 ms iter 0, gcam->neg = 19 after 40 iterations, nbhd size=2, neg = 0 0456: dt=0.019979, rms=0.389 (0.070%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 115583.508 ms iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0457: dt=0.004000, rms=0.389 (0.014%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0458: dt=0.004000, rms=0.389 (0.014%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0459: dt=0.004000, rms=0.389 (0.026%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 75 iterations, nbhd size=4, neg = 0 0460: dt=0.004000, rms=0.388 (0.035%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 15 iterations, nbhd size=2, neg = 0 0461: dt=0.004000, rms=0.388 (0.044%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 15 iterations, nbhd size=2, neg = 0 0462: dt=0.004000, rms=0.388 (0.051%), neg=0, invalid=766 iter 0, gcam->neg = 6 after 8 iterations, nbhd size=1, neg = 0 0463: dt=0.004000, rms=0.388 (0.058%), neg=0, invalid=766 iter 0, gcam->neg = 9 after 19 iterations, nbhd size=2, neg = 0 0464: dt=0.004000, rms=0.388 (0.062%), neg=0, invalid=766 iter 0, gcam->neg = 8 after 20 iterations, nbhd size=2, neg = 0 0465: dt=0.004000, rms=0.387 (0.064%), neg=0, invalid=766 iter 0, gcam->neg = 8 after 25 iterations, nbhd size=3, neg = 0 0466: dt=0.004000, rms=0.387 (0.068%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 18 iterations, nbhd size=2, neg = 0 0467: dt=0.004000, rms=0.387 (0.071%), neg=0, invalid=766 iter 0, gcam->neg = 6 after 17 iterations, nbhd size=2, neg = 0 0468: dt=0.004000, rms=0.387 (0.071%), neg=0, invalid=766 iter 0, gcam->neg = 9 after 200 iterations, nbhd size=4, neg = 1 starting rms=0.006, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 62698.160 ms iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.006 (-0.000%) ---------- unfolding failed - restoring original position -------------------- 0469: dt=0.004000, rms=0.387 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.387, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 119857.078 ms iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0470: dt=0.001750, rms=0.387 (0.007%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 114801.914 ms 0471: dt=0.003000, rms=0.386 (0.012%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 106354.070 ms iter 0, gcam->neg = 3 after 200 iterations, nbhd size=4, neg = 1 starting rms=0.006, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 56620.590 ms iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.006 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0472: dt=0.007000, rms=0.386 (0.000%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.386, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 114938.539 ms 0473: dt=0.000250, rms=0.386 (0.001%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 113924.188 ms iter 0, gcam->neg = 3 after 6 iterations, nbhd size=1, neg = 0 0474: dt=0.005001, rms=0.386 (0.017%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 129113.672 ms iter 0, gcam->neg = 7 after 8 iterations, nbhd size=1, neg = 0 0475: dt=0.016000, rms=0.386 (0.055%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 111303.688 ms 0476: dt=0.001750, rms=0.386 (0.006%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0477: dt=0.001750, rms=0.386 (0.006%), neg=0, invalid=766 0478: dt=0.001750, rms=0.386 (0.011%), neg=0, invalid=766 0479: dt=0.001750, rms=0.386 (0.016%), neg=0, invalid=766 0480: dt=0.001750, rms=0.386 (0.020%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 7 iterations, nbhd size=1, neg = 0 0481: dt=0.001750, rms=0.386 (0.023%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 14 iterations, nbhd size=2, neg = 0 0482: dt=0.001750, rms=0.386 (0.026%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 14 iterations, nbhd size=2, neg = 0 0483: dt=0.001750, rms=0.386 (0.029%), neg=0, invalid=766 iter 0, gcam->neg = 6 after 16 iterations, nbhd size=2, neg = 0 0484: dt=0.001750, rms=0.385 (0.030%), neg=0, invalid=766 iter 0, gcam->neg = 8 after 15 iterations, nbhd size=2, neg = 0 0485: dt=0.001750, rms=0.385 (0.031%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 17 iterations, nbhd size=2, neg = 0 0486: dt=0.001750, rms=0.385 (0.033%), neg=0, invalid=766 iter 0, gcam->neg = 5 after 13 iterations, nbhd size=2, neg = 0 0487: dt=0.001750, rms=0.385 (0.035%), neg=0, invalid=766 iter 0, gcam->neg = 4 after 15 iterations, nbhd size=2, neg = 0 0488: dt=0.001750, rms=0.385 (0.036%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 7 iterations, nbhd size=1, neg = 0 0489: dt=0.001750, rms=0.385 (0.037%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0490: dt=0.001750, rms=0.385 (0.038%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 25 iterations, nbhd size=3, neg = 0 0491: dt=0.001750, rms=0.384 (0.034%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 7 iterations, nbhd size=1, neg = 0 0492: dt=0.001750, rms=0.384 (0.038%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 13 iterations, nbhd size=2, neg = 0 0493: dt=0.001750, rms=0.384 (0.038%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.384, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 149026.438 ms iter 0, gcam->neg = 1 after 14 iterations, nbhd size=2, neg = 0 0494: dt=0.001750, rms=0.384 (0.005%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 154765.406 ms 0495: dt=0.000375, rms=0.384 (0.001%), neg=0, invalid=766 0496: dt=0.000375, rms=0.384 (0.002%), neg=0, invalid=766 0497: dt=0.000375, rms=0.384 (0.003%), neg=0, invalid=766 0498: dt=0.000375, rms=0.384 (0.004%), neg=0, invalid=766 0499: dt=0.000375, rms=0.384 (0.005%), neg=0, invalid=766 0500: dt=0.000375, rms=0.384 (0.006%), neg=0, invalid=766 0501: dt=0.000375, rms=0.384 (0.007%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0502: dt=0.000375, rms=0.384 (0.008%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0503: dt=0.000375, rms=0.384 (0.009%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0504: dt=0.000375, rms=0.384 (0.009%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0505: dt=0.000375, rms=0.384 (0.010%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0506: dt=0.000375, rms=0.384 (0.010%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0507: dt=0.000375, rms=0.384 (0.011%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 16 iterations, nbhd size=2, neg = 0 0508: dt=0.000375, rms=0.384 (0.009%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0509: dt=0.000375, rms=0.384 (0.011%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 7 iterations, nbhd size=1, neg = 0 0510: dt=0.000375, rms=0.384 (0.012%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0511: dt=0.000375, rms=0.384 (0.012%), neg=0, invalid=766 0512: dt=0.000375, rms=0.384 (0.012%), neg=0, invalid=766 0513: dt=0.000375, rms=0.384 (0.012%), neg=0, invalid=766 0514: dt=0.000375, rms=0.384 (0.012%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 26 iterations, nbhd size=4, neg = 0 0515: dt=0.000375, rms=0.384 (0.008%), neg=0, invalid=766 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.383, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 148638.750 ms iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0516: dt=0.000313, rms=0.383 (0.001%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 163010.438 ms iter 0, gcam->neg = 2 after 8 iterations, nbhd size=1, neg = 0 0517: dt=0.004000, rms=0.383 (0.014%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 125227.117 ms iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0518: dt=0.007000, rms=0.383 (0.023%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 126186.758 ms iter 0, gcam->neg = 1 after 8 iterations, nbhd size=1, neg = 0 0519: dt=0.005000, rms=0.383 (0.016%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0520: dt=0.005000, rms=0.383 (0.016%), neg=0, invalid=766 iter 0, gcam->neg = 6 after 16 iterations, nbhd size=2, neg = 0 0521: dt=0.005000, rms=0.383 (0.030%), neg=0, invalid=766 iter 0, gcam->neg = 18 after 15 iterations, nbhd size=2, neg = 0 0522: dt=0.005000, rms=0.383 (0.041%), neg=0, invalid=766 iter 0, gcam->neg = 27 after 49 iterations, nbhd size=3, neg = 0 0523: dt=0.005000, rms=0.383 (0.048%), neg=0, invalid=766 iter 0, gcam->neg = 35 after 51 iterations, nbhd size=3, neg = 0 0524: dt=0.005000, rms=0.382 (0.058%), neg=0, invalid=766 iter 0, gcam->neg = 25 after 200 iterations, nbhd size=1, neg = 1 starting rms=0.001, neg=1, removing folds in lattice.... gcamFindOptimalTimeStep: Complete in 68733.172 ms iter 1, dt=0.000000: new neg 1, old_neg 1, delta 0, rms=0.001 (0.000%) ---------- unfolding failed - restoring original position -------------------- 0525: dt=0.005000, rms=0.382 (0.000%), neg=0, invalid=766 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.382, neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 126658.703 ms iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 0526: dt=0.001750, rms=0.382 (0.008%), neg=0, invalid=766 gcamFindOptimalTimeStep: Complete in 127903.117 ms 0527: dt=0.000438, rms=0.382 (0.002%), neg=0, invalid=766 0528: dt=0.000438, rms=0.382 (0.002%), neg=0, invalid=766 0529: dt=0.000438, rms=0.382 (0.004%), neg=0, invalid=766 0530: dt=0.000438, rms=0.382 (0.005%), neg=0, invalid=766 0531: dt=0.000438, rms=0.382 (0.007%), neg=0, invalid=766 iter 0, gcam->neg = 2 after 13 iterations, nbhd size=2, neg = 0 0532: dt=0.000438, rms=0.382 (0.008%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0533: dt=0.000438, rms=0.382 (0.009%), neg=0, invalid=766 0534: dt=0.000438, rms=0.382 (0.010%), neg=0, invalid=766 0535: dt=0.000438, rms=0.382 (0.011%), neg=0, invalid=766 0536: dt=0.000438, rms=0.382 (0.012%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0537: dt=0.000438, rms=0.382 (0.013%), neg=0, invalid=766 0538: dt=0.000438, rms=0.382 (0.013%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0539: dt=0.000438, rms=0.382 (0.014%), neg=0, invalid=766 iter 0, gcam->neg = 3 after 7 iterations, nbhd size=1, neg = 0 0540: dt=0.000438, rms=0.382 (0.014%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 13 iterations, nbhd size=2, neg = 0 0541: dt=0.000438, rms=0.382 (0.012%), neg=0, invalid=766 0542: dt=0.000438, rms=0.382 (0.015%), neg=0, invalid=766 iter 0, gcam->neg = 1 after 16 iterations, nbhd size=2, neg = 0 0543: dt=0.000438, rms=0.382 (0.015%), neg=0, invalid=766 writing output transformation to transforms/talairach.m3z... GCAMwrite GCAMwrite:: m3z loop GCAMwrite:: the command is: gzip -f -c > transforms/talairach.m3z registration took 9 hours, 42 minutes and 35 seconds. #-------------------------------------- #@# CA Reg Inv Thu Apr 26 02:18:59 EDT 2012 /tmp/Skhadka/S8861CSO1/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z zcat transforms/talairach.m3z Inverting GCAM Saving inverse #-------------------------------------- #@# Remove Neck Thu Apr 26 02:21:09 EDT 2012 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /opt/freesurfer/average/RB_all_2008-03-26.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/opt/freesurfer/average/RB_all_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... zcat transforms/talairach.m3z removing structures at least 25 mm from brain... 10508777 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 2 minutes and 33 seconds. #-------------------------------------- #@# SkullLTA Thu Apr 26 02:23:43 EDT 2012 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /opt/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta 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.log reading '/opt/freesurfer/average/RB_all_withskull_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 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=6.0 skull bounding box = (38, 51, 0) --> (211, 219, 223) using (96, 107, 112) as brain centroid... mean wm in atlas = 126, using box (75,86,84) --> (117, 127,139) to find MRI wm before smoothing, mri peak at 110 after smoothing, mri peak at 110, scaling input intensities by 1.145 scaling channel 0 by 1.14545 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-10288.7, old_max_log_p =-10356.4 (thresh=-10346.1) 0.999 0.016 0.032 -6.838; -0.026 1.070 0.475 -71.608; -0.025 -0.342 0.852 70.221; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-10288.7, old_max_log_p =-10288.7 (thresh=-10278.4) 0.999 0.016 0.032 -6.838; -0.026 1.070 0.475 -71.608; -0.025 -0.342 0.852 70.221; 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=-10273.8, old_max_log_p =-10288.7 (thresh=-10278.4) 0.999 -0.002 -0.039 2.865; 0.009 1.110 0.429 -74.970; 0.040 -0.280 0.896 50.779; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-10273.3, old_max_log_p =-10273.8 (thresh=-10263.5) 0.981 -0.002 -0.039 5.170; 0.008 1.089 0.421 -71.294; 0.039 -0.274 0.879 49.940; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-10271.4, old_max_log_p =-10273.3 (thresh=-10263.1) 0.983 -0.002 -0.039 4.887; 0.008 1.093 0.422 -71.971; 0.039 -0.275 0.881 49.809; 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 0.98281 -0.00159 -0.03868 4.88712; 0.00841 1.09270 0.42210 -71.97063; 0.03903 -0.27505 0.88130 49.80851; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 0.98281 -0.00159 -0.03868 4.88712; 0.00841 1.09270 0.42210 -71.97063; 0.03903 -0.27505 0.88130 49.80851; 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) = 10271.4 tol 0.000010 Resulting transform: 0.983 -0.002 -0.039 4.887; 0.008 1.093 0.422 -71.971; 0.039 -0.275 0.881 49.809; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -10271.4 (old=-10356.4) transform before final EM align: 0.983 -0.002 -0.039 4.887; 0.008 1.093 0.422 -71.971; 0.039 -0.275 0.881 49.809; 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 0.98281 -0.00159 -0.03868 4.88712; 0.00841 1.09270 0.42210 -71.97063; 0.03903 -0.27505 0.88130 49.80851; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 0.98281 -0.00159 -0.03868 4.88712; 0.00841 1.09270 0.42210 -71.97063; 0.03903 -0.27505 0.88130 49.80851; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 007: -log(p) = 1144535.2 after pass:transform: ( 0.98, -0.00, -0.04, 4.89) ( 0.01, 1.09, 0.42, -71.97) ( 0.04, -0.28, 0.88, 49.81) 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 TOLERANCESpass 2 through quasi-newton minimization... 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: 009: -log(p) = 1144535.2 tol 0.000000 final transform: 0.984 -0.001 -0.038 4.887; 0.009 1.093 0.422 -71.971; 0.038 -0.276 0.881 49.809; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 46 minutes and 14 seconds. #-------------------------------------- #@# SubCort Seg Thu Apr 26 03:09:56 EDT 2012 mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z /opt/freesurfer/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 not handling expanded ventricles... reading 1 input volumes... reading classifier array from /opt/freesurfer/average/RB_all_2008-03-26.gca... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 reading input volume from norm.mgz... average std[0] = 6.9 reading transform from transforms/talairach.m3z... zcat transforms/talairach.m3z Atlas used for the 3D morph was /opt/freesurfer/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 = 0.12895 (22) Left_Lateral_Ventricle (4): linear fit = 0.82 x + 0.0 (710 voxels, overlap=0.563) Left_Lateral_Ventricle (4): linear fit = 0.82 x + 0.0 (710 voxels, peak = 22), gca=22.3 gca peak = 0.14982 (20) mri peak = 0.16418 (21) Right_Lateral_Ventricle (43): linear fit = 0.90 x + 0.0 (602 voxels, overlap=0.597) Right_Lateral_Ventricle (43): linear fit = 0.90 x + 0.0 (602 voxels, peak = 18), gca=18.0 gca peak = 0.28003 (97) mri peak = 0.19144 (103) Right_Pallidum (52): linear fit = 1.05 x + 0.0 (592 voxels, overlap=0.518) Right_Pallidum (52): linear fit = 1.05 x + 0.0 (592 voxels, peak = 102), gca=101.8 gca peak = 0.18160 (96) mri peak = 0.14974 (106) Left_Pallidum (13): linear fit = 1.08 x + 0.0 (613 voxels, overlap=0.559) Left_Pallidum (13): linear fit = 1.08 x + 0.0 (613 voxels, peak = 103), gca=103.2 gca peak = 0.27536 (62) mri peak = 0.12919 (68) Right_Hippocampus (53): linear fit = 1.08 x + 0.0 (1072 voxels, overlap=0.304) Right_Hippocampus (53): linear fit = 1.08 x + 0.0 (1072 voxels, peak = 67), gca=66.7 gca peak = 0.32745 (63) mri peak = 0.14464 (70) Left_Hippocampus (17): linear fit = 1.08 x + 0.0 (1276 voxels, overlap=0.514) Left_Hippocampus (17): linear fit = 1.08 x + 0.0 (1276 voxels, peak = 68), gca=67.7 gca peak = 0.08597 (105) mri peak = 0.14200 (106) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (68687 voxels, overlap=0.598) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (68687 voxels, peak = 108), gca=107.6 gca peak = 0.09209 (106) mri peak = 0.13180 (107) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (55572 voxels, overlap=0.607) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (55572 voxels, peak = 109), gca=108.6 gca peak = 0.07826 (63) mri peak = 0.04672 (63) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (71055 voxels, overlap=0.971) Left_Cerebral_Cortex (3): linear fit = 1.02 x + 0.0 (71055 voxels, peak = 65), gca=64.6 gca peak = 0.08598 (64) mri peak = 0.04722 (63) Right_Cerebral_Cortex (42): linear fit = 0.98 x + 0.0 (70241 voxels, overlap=0.911) Right_Cerebral_Cortex (42): linear fit = 0.98 x + 0.0 (70241 voxels, peak = 62), gca=62.4 gca peak = 0.24164 (71) mri peak = 0.16314 (78) Right_Caudate (50): linear fit = 1.05 x + 0.0 (940 voxels, overlap=0.592) Right_Caudate (50): linear fit = 1.05 x + 0.0 (940 voxels, peak = 75), gca=74.5 gca peak = 0.18227 (75) mri peak = 0.13589 (79) Left_Caudate (11): linear fit = 1.02 x + 0.0 (1144 voxels, overlap=0.988) Left_Caudate (11): linear fit = 1.02 x + 0.0 (1144 voxels, peak = 77), gca=76.9 gca peak = 0.10629 (62) mri peak = 0.04696 (62) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (26769 voxels, overlap=0.976) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (26769 voxels, peak = 64), gca=63.5 gca peak = 0.11668 (59) mri peak = 0.04367 (64) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (27975 voxels, overlap=0.989) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (27975 voxels, peak = 60), gca=60.5 gca peak = 0.17849 (88) mri peak = 0.16781 (96) Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (7693 voxels, overlap=0.120) Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (7693 voxels, peak = 95), gca=94.6 gca peak = 0.16819 (86) mri peak = 0.15881 (94) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (7949 voxels, overlap=0.169) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (7949 voxels, peak = 92), gca=92.5 gca peak = 0.41688 (64) mri peak = 0.13037 (68) Left_Amygdala (18): linear fit = 1.10 x + 0.0 (671 voxels, overlap=0.100) Left_Amygdala (18): linear fit = 1.10 x + 0.0 (671 voxels, peak = 70), gca=70.4 gca peak = 0.42394 (62) mri peak = 0.15705 (68) Right_Amygdala (54): linear fit = 1.08 x + 0.0 (623 voxels, overlap=0.434) Right_Amygdala (54): linear fit = 1.08 x + 0.0 (623 voxels, peak = 67), gca=66.7 gca peak = 0.10041 (96) mri peak = 0.07758 (94) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (6239 voxels, overlap=0.973) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (6239 voxels, peak = 96), gca=96.0 gca peak = 0.13978 (88) mri peak = 0.07367 (92) Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (5649 voxels, overlap=0.987) Right_Thalamus_Proper (49): linear fit = 1.02 x + 0.0 (5649 voxels, peak = 90), gca=90.2 gca peak = 0.08514 (81) mri peak = 0.07760 (83) Left_Putamen (12): linear fit = 1.05 x + 0.0 (3394 voxels, overlap=0.831) Left_Putamen (12): linear fit = 1.05 x + 0.0 (3394 voxels, peak = 85), gca=85.0 gca peak = 0.09624 (82) mri peak = 0.08487 (82) Right_Putamen (51): linear fit = 1.05 x + 0.0 (3417 voxels, overlap=0.815) Right_Putamen (51): linear fit = 1.05 x + 0.0 (3417 voxels, peak = 86), gca=86.1 gca peak = 0.07543 (88) mri peak = 0.08825 (93) Brain_Stem (16): linear fit = 1.05 x + 0.0 (13849 voxels, overlap=0.599) Brain_Stem (16): linear fit = 1.05 x + 0.0 (13849 voxels, peak = 92), gca=92.4 gca peak = 0.12757 (95) mri peak = 0.13182 (103) Right_VentralDC (60): linear fit = 1.08 x + 0.0 (1918 voxels, overlap=0.275) Right_VentralDC (60): linear fit = 1.08 x + 0.0 (1918 voxels, peak = 102), gca=102.1 gca peak = 0.17004 (92) mri peak = 0.14807 (103) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1944 voxels, overlap=0.330) Left_VentralDC (28): linear fit = 1.08 x + 0.0 (1944 voxels, peak = 99), gca=98.9 gca peak = 0.21361 (36) mri peak = 0.10279 (19) gca peak = 0.26069 (23) mri peak = 0.13415 (17) Fourth_Ventricle (15): linear fit = 0.70 x + 0.0 (165 voxels, overlap=0.313) Fourth_Ventricle (15): linear fit = 0.70 x + 0.0 (165 voxels, peak = 16), gca=16.1 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 1.05 x + 0.0 estimating mean wm scale to be 1.02 x + 0.0 estimating mean csf scale to be 0.81 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.14550 (23) mri peak = 0.12895 (22) Left_Lateral_Ventricle (4): linear fit = 0.98 x + 0.0 (710 voxels, overlap=0.920) Left_Lateral_Ventricle (4): linear fit = 0.98 x + 0.0 (710 voxels, peak = 22), gca=22.4 gca peak = 0.15072 (19) mri peak = 0.16418 (21) Right_Lateral_Ventricle (43): linear fit = 0.98 x + 0.0 (602 voxels, overlap=0.756) Right_Lateral_Ventricle (43): linear fit = 0.98 x + 0.0 (602 voxels, peak = 19), gca=18.5 gca peak = 0.27005 (102) mri peak = 0.19144 (103) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (592 voxels, overlap=0.959) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (592 voxels, peak = 102), gca=102.0 gca peak = 0.17360 (104) mri peak = 0.14974 (106) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (613 voxels, overlap=0.761) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (613 voxels, peak = 104), gca=104.0 gca peak = 0.28672 (67) mri peak = 0.12919 (68) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1072 voxels, overlap=0.999) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1072 voxels, peak = 67), gca=67.0 gca peak = 0.34175 (68) mri peak = 0.14464 (70) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (1276 voxels, overlap=1.000) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (1276 voxels, peak = 68), gca=68.0 gca peak = 0.08345 (108) mri peak = 0.14200 (106) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (68687 voxels, overlap=0.646) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (68687 voxels, peak = 108), gca=108.0 gca peak = 0.08544 (108) mri peak = 0.13180 (107) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (55572 voxels, overlap=0.658) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (55572 voxels, peak = 108), gca=108.0 gca peak = 0.07458 (65) mri peak = 0.04672 (63) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (71055 voxels, overlap=0.932) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (71055 voxels, peak = 65), gca=65.0 gca peak = 0.08941 (62) mri peak = 0.04722 (63) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (70241 voxels, overlap=0.951) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (70241 voxels, peak = 64), gca=63.5 gca peak = 0.23838 (77) mri peak = 0.16314 (78) Right_Caudate (50): linear fit = 1.00 x + 0.0 (940 voxels, overlap=1.000) Right_Caudate (50): linear fit = 1.00 x + 0.0 (940 voxels, peak = 77), gca=77.0 gca peak = 0.18199 (77) mri peak = 0.13589 (79) Left_Caudate (11): linear fit = 1.00 x + 0.0 (1144 voxels, overlap=0.866) Left_Caudate (11): linear fit = 1.00 x + 0.0 (1144 voxels, peak = 77), gca=77.0 gca peak = 0.10271 (63) mri peak = 0.04696 (62) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (26769 voxels, overlap=0.992) Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (26769 voxels, peak = 65), gca=64.6 gca peak = 0.12579 (61) mri peak = 0.04367 (64) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (27975 voxels, overlap=0.997) Right_Cerebellum_Cortex (47): linear fit = 1.02 x + 0.0 (27975 voxels, peak = 63), gca=62.5 gca peak = 0.17137 (94) mri peak = 0.16781 (96) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (7693 voxels, overlap=0.885) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (7693 voxels, peak = 94), gca=94.0 gca peak = 0.15715 (93) mri peak = 0.15881 (94) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (7949 voxels, overlap=0.903) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (7949 voxels, peak = 93), gca=93.0 gca peak = 0.30057 (70) mri peak = 0.13037 (68) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (671 voxels, overlap=1.000) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (671 voxels, peak = 70), gca=70.0 gca peak = 0.39849 (67) mri peak = 0.15705 (68) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (623 voxels, overlap=0.999) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (623 voxels, peak = 67), gca=67.0 gca peak = 0.10547 (96) mri peak = 0.07758 (94) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (6239 voxels, overlap=0.970) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (6239 voxels, peak = 96), gca=96.0 gca peak = 0.12515 (90) mri peak = 0.07367 (92) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (5649 voxels, overlap=0.940) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (5649 voxels, peak = 90), gca=90.0 gca peak = 0.08410 (85) mri peak = 0.07760 (83) Left_Putamen (12): linear fit = 1.00 x + 0.0 (3394 voxels, overlap=0.988) Left_Putamen (12): linear fit = 1.00 x + 0.0 (3394 voxels, peak = 85), gca=85.0 gca peak = 0.09525 (80) mri peak = 0.08487 (82) Right_Putamen (51): linear fit = 1.00 x + 0.0 (3417 voxels, overlap=0.953) Right_Putamen (51): linear fit = 1.00 x + 0.0 (3417 voxels, peak = 80), gca=80.0 gca peak = 0.07205 (90) mri peak = 0.08825 (93) Brain_Stem (16): linear fit = 1.02 x + 0.0 (13849 voxels, overlap=0.761) Brain_Stem (16): linear fit = 1.02 x + 0.0 (13849 voxels, peak = 92), gca=92.2 gca peak = 0.13180 (98) mri peak = 0.13182 (103) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1918 voxels, overlap=0.724) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (1918 voxels, peak = 98), gca=98.0 gca peak = 0.14842 (99) mri peak = 0.14807 (103) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1944 voxels, overlap=0.844) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1944 voxels, peak = 99), gca=99.0 gca peak = 0.21394 (29) mri peak = 0.10279 (19) gca peak = 0.30880 (16) mri peak = 0.13415 (17) Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (165 voxels, overlap=0.806) Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (165 voxels, peak = 16), gca=16.4 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.26806 (38) gca peak Third_Ventricle = 0.21394 (29) gca peak CSF = 0.21620 (31) gca peak Left_Accumbens_area = 0.37763 (71) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.65116 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.30892 (34) gca peak Right_Accumbens_area = 0.30055 (75) gca peak Right_vessel = 0.83457 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.81716 (34) gca peak WM_hypointensities = 0.14724 (84) gca peak non_WM_hypointensities = 0.11940 (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 0.99 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 16917 gm and wm labels changed (%24 to gray, %76 to white out of all changed labels) 319 hippocampal voxels changed. 6 amygdala voxels changed. pass 1: 92123 changed. image ll: -2.264, PF=1.000 pass 2: 16415 changed. image ll: -2.261, PF=1.000 pass 3: 5997 changed. pass 4: 2533 changed. writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 39 minutes and 39 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /tmp/Skhadka/S8861CSO1/mri/transforms/cc_up.lta S8861CSO1 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /tmp/Skhadka/S8861CSO1/mri/transforms/cc_up.lta reading aseg from /tmp/Skhadka/S8861CSO1/mri/aseg.auto_noCCseg.mgz reading norm from /tmp/Skhadka/S8861CSO1/mri/norm.mgz 34078 voxels in left wm, 47648 in right wm, xrange [123, 130] searching rotation angles z=[-7 7], y=[-7 7] searching scale 1 Z rot -7.0 searching scale 1 Z rot -6.7 searching scale 1 Z rot -6.5 searching scale 1 Z rot -6.2 searching scale 1 Z rot -6.0 searching scale 1 Z rot -5.7 searching scale 1 Z rot -5.5 searching scale 1 Z rot -5.2 searching scale 1 Z rot -5.0 searching scale 1 Z rot -4.7 searching scale 1 Z rot -4.5 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 global minimum found at slice 126.5, rotations (0.27, 0.05) final transformation (x=126.5, yr=0.272, zr=0.047): 1.000 -0.001 0.005 1.131; 0.001 1.000 0.000 9.896; -0.005 -0.000 1.000 30.601; 0.000 0.000 0.000 1.000; updating x range to be [126, 130] in xformed coordinates best xformed slice 129 cc center is found at 129 155 118 eigenvectors: -0.004 0.004 1.000; -0.302 -0.953 0.003; 0.953 -0.302 0.005; writing aseg with callosum to /tmp/Skhadka/S8861CSO1/mri/aseg.auto.mgz... corpus callosum matter segmentation took 1.3 minutes #-------------------------------------- #@# Merge ASeg Thu Apr 26 03:50:56 EDT 2012 cp aseg.auto.mgz aseg.mgz #-------------------------------------------- #@# Intensity Normalization2 Thu Apr 26 03:50:56 EDT 2012 /tmp/Skhadka/S8861CSO1/mri mri_normalize -mprage -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz using segmentation for initial intensity normalization reading from norm.mgz... normalizing image... removing outliers in the aseg WM... 816 control points removed building Voronoi diagram... performing soap bubble smoothing... building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 1 of 2 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 2 building Voronoi diagram... performing soap bubble smoothing... writing output to brain.mgz 3D bias adjustment took 5 minutes and 58 seconds. assuming input volume is MGH (Van der Kouwe) MP-RAGE using MR volume brainmask.mgz to mask input volume... white matter peak found at 111 white matter peak found at 110 gm peak at 70 (70), valley at 41 (41) csf peak at 35, setting threshold to 58 white matter peak found at 111 white matter peak found at 110 gm peak at 71 (71), valley at 25 (25) csf peak at 36, setting threshold to 59 #-------------------------------------------- #@# Mask BFS Thu Apr 26 03:57:01 EDT 2012 /tmp/Skhadka/S8861CSO1/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 2025390 voxels in mask Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Thu Apr 26 03:57:07 EDT 2012 mri_segment -mprage brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (105.0): 104.8 +- 6.7 [79.0 --> 125.0] GM (73.0) : 71.4 +- 10.1 [30.0 --> 95.0] setting bottom of white matter range to 81.5 setting top of gray matter range to 91.6 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... 8798 sparsely connected voxels removed... thickening thin strands.... 20 segments, 4938 filled 7217 bright non-wm voxels segmented. 3776 diagonally connected voxels added... white matter segmentation took 2.8 minutes writing output to wm.seg.mgz... assuming input volume is MGH (Van der Kouwe) MP-RAGE 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 0.99 minutes reading wm segmentation from wm.seg.mgz... 23 voxels added to wm to prevent paths from MTL structures to cortex 1318 additional wm voxels added 0 additional wm voxels added SEG EDIT: 30756 voxels turned on, 45725 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 110 new 110 115,126,128 old 110 new 110 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 13 found - 13 modified | TOTAL: 13 pass 2 (xy+): 0 found - 13 modified | TOTAL: 13 pass 1 (xy-): 27 found - 27 modified | TOTAL: 40 pass 2 (xy-): 0 found - 27 modified | TOTAL: 40 pass 1 (yz+): 48 found - 48 modified | TOTAL: 88 pass 2 (yz+): 0 found - 48 modified | TOTAL: 88 pass 1 (yz-): 16 found - 16 modified | TOTAL: 104 pass 2 (yz-): 0 found - 16 modified | TOTAL: 104 pass 1 (xz+): 19 found - 19 modified | TOTAL: 123 pass 2 (xz+): 0 found - 19 modified | TOTAL: 123 pass 1 (xz-): 19 found - 19 modified | TOTAL: 142 pass 2 (xz-): 0 found - 19 modified | TOTAL: 142 Iteration Number : 1 pass 1 (+++): 30 found - 30 modified | TOTAL: 30 pass 2 (+++): 0 found - 30 modified | TOTAL: 30 pass 1 (+++): 21 found - 21 modified | TOTAL: 51 pass 2 (+++): 0 found - 21 modified | TOTAL: 51 pass 1 (+++): 31 found - 31 modified | TOTAL: 82 pass 2 (+++): 0 found - 31 modified | TOTAL: 82 pass 1 (+++): 26 found - 26 modified | TOTAL: 108 pass 2 (+++): 0 found - 26 modified | TOTAL: 108 Iteration Number : 1 pass 1 (++): 144 found - 144 modified | TOTAL: 144 pass 2 (++): 0 found - 144 modified | TOTAL: 144 pass 1 (+-): 187 found - 187 modified | TOTAL: 331 pass 2 (+-): 0 found - 187 modified | TOTAL: 331 pass 1 (--): 153 found - 153 modified | TOTAL: 484 pass 2 (--): 0 found - 153 modified | TOTAL: 484 pass 1 (-+): 126 found - 126 modified | TOTAL: 610 pass 2 (-+): 0 found - 126 modified | TOTAL: 610 Iteration Number : 2 pass 1 (xy+): 6 found - 6 modified | TOTAL: 6 pass 2 (xy+): 0 found - 6 modified | TOTAL: 6 pass 1 (xy-): 5 found - 5 modified | TOTAL: 11 pass 2 (xy-): 0 found - 5 modified | TOTAL: 11 pass 1 (yz+): 5 found - 5 modified | TOTAL: 16 pass 2 (yz+): 0 found - 5 modified | TOTAL: 16 pass 1 (yz-): 5 found - 5 modified | TOTAL: 21 pass 2 (yz-): 0 found - 5 modified | TOTAL: 21 pass 1 (xz+): 2 found - 2 modified | TOTAL: 23 pass 2 (xz+): 0 found - 2 modified | TOTAL: 23 pass 1 (xz-): 7 found - 7 modified | TOTAL: 30 pass 2 (xz-): 0 found - 7 modified | TOTAL: 30 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 2 found - 2 modified | TOTAL: 4 pass 2 (+++): 0 found - 2 modified | TOTAL: 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 4 Iteration Number : 2 pass 1 (++): 4 found - 4 modified | TOTAL: 4 pass 2 (++): 0 found - 4 modified | TOTAL: 4 pass 1 (+-): 1 found - 1 modified | TOTAL: 5 pass 2 (+-): 0 found - 1 modified | TOTAL: 5 pass 1 (--): 3 found - 3 modified | TOTAL: 8 pass 2 (--): 0 found - 3 modified | TOTAL: 8 pass 1 (-+): 2 found - 2 modified | TOTAL: 10 pass 2 (-+): 0 found - 2 modified | TOTAL: 10 Iteration Number : 3 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-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 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 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 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 = 905 (out of 640666: 0.141259) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Thu Apr 26 04:01:09 EDT 2012 /tmp/Skhadka/S8861CSO1/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 0.999 0.016 0.032 -6.838; -0.024 1.006 0.446 -60.059; -0.025 -0.342 0.852 70.221; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 0.999 0.016 0.032 -6.838; -0.024 1.006 0.446 -60.059; -0.025 -0.342 0.852 70.221; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 2418 (min = 350, max = 1400), aspect = 1.42 (min = 0.10, max = 0.75) need search nearby using seed (127, 120, 149), TAL = (1.0, 21.0, 8.0) talairach voxel to voxel transform 0.999 -0.024 -0.025 7.097; 0.010 0.844 -0.442 81.800; 0.033 0.338 0.995 -49.365; 0.000 0.000 0.000 1.000; segmentation indicates cc at (127, 120, 149) --> (1.0, 21.0, 8.0) done. writing output to filled.mgz... filling took 1.5 minutes talairach cc position changed to (1.00, 21.00, 8.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(19.00, 21.00, 8.00) SRC: (109.41, 118.18, 143.12) search lh wm seed point around talairach space (-17.00, 21.00, 8.00), SRC: (145.39, 118.53, 144.31) 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 Thu Apr 26 04:02:38 EDT 2012 /tmp/Skhadka/S8861CSO1/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+): 3 found - 3 modified | TOTAL: 4 pass 2 (yz+): 0 found - 3 modified | TOTAL: 4 pass 1 (yz-): 2 found - 2 modified | TOTAL: 6 pass 2 (yz-): 0 found - 2 modified | TOTAL: 6 pass 1 (xz+): 1 found - 1 modified | TOTAL: 7 pass 2 (xz+): 0 found - 1 modified | TOTAL: 7 pass 1 (xz-): 1 found - 1 modified | TOTAL: 8 pass 2 (xz-): 0 found - 1 modified | TOTAL: 8 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 (+-): 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 (-+): 0 found - 0 modified | TOTAL: 3 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 1 found - 1 modified | TOTAL: 1 pass 2 (yz+): 0 found - 1 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 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 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+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 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 (+++): 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 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 12 (out of 309885: 0.003872) 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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ slice 30: 2149 vertices, 2349 faces slice 40: 11301 vertices, 11725 faces slice 50: 24760 vertices, 25272 faces slice 60: 39890 vertices, 40404 faces slice 70: 54241 vertices, 54750 faces slice 80: 68012 vertices, 68444 faces slice 90: 81007 vertices, 81483 faces slice 100: 93459 vertices, 93920 faces slice 110: 105078 vertices, 105540 faces slice 120: 115972 vertices, 116384 faces slice 130: 126958 vertices, 127431 faces slice 140: 137380 vertices, 137768 faces slice 150: 147317 vertices, 147743 faces slice 160: 155651 vertices, 155970 faces slice 170: 161909 vertices, 162185 faces slice 180: 166603 vertices, 166802 faces slice 190: 169180 vertices, 169307 faces slice 200: 169340 vertices, 169426 faces slice 210: 169340 vertices, 169426 faces slice 220: 169340 vertices, 169426 faces slice 230: 169340 vertices, 169426 faces slice 240: 169340 vertices, 169426 faces slice 250: 169340 vertices, 169426 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... 169340 voxel in cpt #1: X=-86 [v=169340,e=508278,f=338852] located at (-26.494467, -32.086372, -2.601222) For the whole surface: X=-86 [v=169340,e=508278,f=338852] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Thu Apr 26 04:02:59 EDT 2012 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /tmp/Skhadka/S8861CSO1/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 Thu Apr 26 04:03:08 EDT 2012 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /tmp/Skhadka/S8861CSO1/scripts avg radius = 51.5 mm, total surface area = 89169 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 1.5 minutes Not saving sulc step 000: RMS=0.103 (target=0.015) step 005: RMS=0.077 (target=0.015) step 010: RMS=0.059 (target=0.015) step 015: RMS=0.050 (target=0.015) step 020: RMS=0.043 (target=0.015) step 025: RMS=0.039 (target=0.015) step 030: RMS=0.036 (target=0.015) step 035: RMS=0.033 (target=0.015) step 040: RMS=0.031 (target=0.015) step 045: RMS=0.030 (target=0.015) step 050: RMS=0.030 (target=0.015) step 055: RMS=0.029 (target=0.015) step 060: RMS=0.029 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh Thu Apr 26 04:04:41 EDT 2012 /tmp/Skhadka/S8861CSO1/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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.88 +- 0.56 (0.00-->6.91) (max @ vno 125481 --> 126645) face area 0.02 +- 0.03 (-0.20-->0.69) scaling brain by 0.295... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.365, avgs=0 005/300: dt: 0.9000, rms radial error=175.111, avgs=0 010/300: dt: 0.9000, rms radial error=174.564, avgs=0 015/300: dt: 0.9000, rms radial error=173.845, avgs=0 020/300: dt: 0.9000, rms radial error=173.027, avgs=0 025/300: dt: 0.9000, rms radial error=172.152, avgs=0 030/300: dt: 0.9000, rms radial error=171.245, avgs=0 035/300: dt: 0.9000, rms radial error=170.320, avgs=0 040/300: dt: 0.9000, rms radial error=169.387, avgs=0 045/300: dt: 0.9000, rms radial error=168.451, avgs=0 050/300: dt: 0.9000, rms radial error=167.514, avgs=0 055/300: dt: 0.9000, rms radial error=166.580, avgs=0 060/300: dt: 0.9000, rms radial error=165.648, avgs=0 065/300: dt: 0.9000, rms radial error=164.720, avgs=0 070/300: dt: 0.9000, rms radial error=163.796, avgs=0 075/300: dt: 0.9000, rms radial error=162.876, avgs=0 080/300: dt: 0.9000, rms radial error=161.960, avgs=0 085/300: dt: 0.9000, rms radial error=161.049, avgs=0 090/300: dt: 0.9000, rms radial error=160.143, avgs=0 095/300: dt: 0.9000, rms radial error=159.241, avgs=0 100/300: dt: 0.9000, rms radial error=158.344, avgs=0 105/300: dt: 0.9000, rms radial error=157.451, avgs=0 110/300: dt: 0.9000, rms radial error=156.563, avgs=0 115/300: dt: 0.9000, rms radial error=155.679, avgs=0 120/300: dt: 0.9000, rms radial error=154.800, avgs=0 125/300: dt: 0.9000, rms radial error=153.926, avgs=0 130/300: dt: 0.9000, rms radial error=153.055, avgs=0 135/300: dt: 0.9000, rms radial error=152.191, avgs=0 140/300: dt: 0.9000, rms radial error=151.331, avgs=0 145/300: dt: 0.9000, rms radial error=150.479, avgs=0 150/300: dt: 0.9000, rms radial error=149.632, avgs=0 155/300: dt: 0.9000, rms radial error=148.790, avgs=0 160/300: dt: 0.9000, rms radial error=147.952, avgs=0 165/300: dt: 0.9000, rms radial error=147.118, avgs=0 170/300: dt: 0.9000, rms radial error=146.289, avgs=0 175/300: dt: 0.9000, rms radial error=145.465, avgs=0 180/300: dt: 0.9000, rms radial error=144.645, avgs=0 185/300: dt: 0.9000, rms radial error=143.830, avgs=0 190/300: dt: 0.9000, rms radial error=143.020, avgs=0 195/300: dt: 0.9000, rms radial error=142.215, avgs=0 200/300: dt: 0.9000, rms radial error=141.414, avgs=0 205/300: dt: 0.9000, rms radial error=140.618, avgs=0 210/300: dt: 0.9000, rms radial error=139.826, avgs=0 215/300: dt: 0.9000, rms radial error=139.038, avgs=0 220/300: dt: 0.9000, rms radial error=138.255, avgs=0 225/300: dt: 0.9000, rms radial error=137.476, avgs=0 230/300: dt: 0.9000, rms radial error=136.701, avgs=0 235/300: dt: 0.9000, rms radial error=135.931, avgs=0 240/300: dt: 0.9000, rms radial error=135.166, avgs=0 245/300: dt: 0.9000, rms radial error=134.404, avgs=0 250/300: dt: 0.9000, rms radial error=133.647, avgs=0 255/300: dt: 0.9000, rms radial error=132.894, avgs=0 260/300: dt: 0.9000, rms radial error=132.145, avgs=0 265/300: dt: 0.9000, rms radial error=131.401, avgs=0 270/300: dt: 0.9000, rms radial error=130.660, avgs=0 275/300: dt: 0.9000, rms radial error=129.924, avgs=0 280/300: dt: 0.9000, rms radial error=129.192, avgs=0 285/300: dt: 0.9000, rms radial error=128.464, avgs=0 290/300: dt: 0.9000, rms radial error=127.740, avgs=0 295/300: dt: 0.9000, rms radial error=127.020, avgs=0 300/300: dt: 0.9000, rms radial error=126.305, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 20176.40 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00012 epoch 2 (K=40.0), pass 1, starting sse = 3535.63 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00001 epoch 3 (K=160.0), pass 1, starting sse = 407.33 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.05/10 = 0.00527 epoch 4 (K=640.0), pass 1, starting sse = 32.06 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.13/13 = 0.00997 final writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.19 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology lh Thu Apr 26 04:15:58 EDT 2012 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated /tmp/Skhadka/S8861CSO1/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 S8861CSO1 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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ before topology correction, eno=-86 (nv=169340, nf=338852, ne=508278, g=44) 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... 5202 ambiguous faces found in tessellation segmenting defects... 54 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 8 into 7 -merging segment 31 into 28 -merging segment 45 into 38 51 defects to be corrected 0 vertices coincident reading input surface /tmp/Skhadka/S8861CSO1/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.3772 (-4.6886) -vertex loglikelihood: -6.3407 (-3.1703) -normal dot loglikelihood: -3.5087 (-3.5087) -quad curv loglikelihood: -6.3433 (-3.1716) Total Loglikelihood : -25.5698 CORRECTING DEFECT 0 (vertices=21, convex hull=59) After retessellation of defect 0, euler #=-49 (166113,496882,330720) : difference with theory (-48) = 1 CORRECTING DEFECT 1 (vertices=44, convex hull=60) After retessellation of defect 1, euler #=-48 (166120,496926,330758) : difference with theory (-47) = 1 CORRECTING DEFECT 2 (vertices=6, convex hull=32) After retessellation of defect 2, euler #=-47 (166122,496944,330775) : difference with theory (-46) = 1 CORRECTING DEFECT 3 (vertices=80, convex hull=96) After retessellation of defect 3, euler #=-46 (166133,497013,330834) : difference with theory (-45) = 1 CORRECTING DEFECT 4 (vertices=33, convex hull=67) After retessellation of defect 4, euler #=-45 (166142,497068,330881) : difference with theory (-44) = 1 CORRECTING DEFECT 5 (vertices=38, convex hull=95) After retessellation of defect 5, euler #=-44 (166163,497173,330966) : difference with theory (-43) = 1 CORRECTING DEFECT 6 (vertices=25, convex hull=71) After retessellation of defect 6, euler #=-43 (166171,497230,331016) : difference with theory (-42) = 1 CORRECTING DEFECT 7 (vertices=51, convex hull=122) After retessellation of defect 7, euler #=-41 (166199,497360,331120) : difference with theory (-41) = 0 CORRECTING DEFECT 8 (vertices=40, convex hull=70) After retessellation of defect 8, euler #=-40 (166222,497456,331194) : difference with theory (-40) = 0 CORRECTING DEFECT 9 (vertices=55, convex hull=74) After retessellation of defect 9, euler #=-39 (166239,497540,331262) : difference with theory (-39) = 0 CORRECTING DEFECT 10 (vertices=36, convex hull=74) After retessellation of defect 10, euler #=-38 (166253,497611,331320) : difference with theory (-38) = 0 CORRECTING DEFECT 11 (vertices=22, convex hull=49) After retessellation of defect 11, euler #=-37 (166262,497656,331357) : difference with theory (-37) = 0 CORRECTING DEFECT 12 (vertices=25, convex hull=57) After retessellation of defect 12, euler #=-36 (166277,497723,331410) : difference with theory (-36) = 0 CORRECTING DEFECT 13 (vertices=21, convex hull=28) After retessellation of defect 13, euler #=-35 (166286,497758,331437) : difference with theory (-35) = 0 CORRECTING DEFECT 14 (vertices=41, convex hull=54) After retessellation of defect 14, euler #=-34 (166306,497838,331498) : difference with theory (-34) = 0 CORRECTING DEFECT 15 (vertices=47, convex hull=44) After retessellation of defect 15, euler #=-33 (166312,497874,331529) : difference with theory (-33) = 0 CORRECTING DEFECT 16 (vertices=6, convex hull=29) After retessellation of defect 16, euler #=-32 (166313,497888,331543) : difference with theory (-32) = 0 CORRECTING DEFECT 17 (vertices=45, convex hull=62) After retessellation of defect 17, euler #=-31 (166323,497942,331588) : difference with theory (-31) = 0 CORRECTING DEFECT 18 (vertices=56, convex hull=56) After retessellation of defect 18, euler #=-30 (166335,498001,331636) : difference with theory (-30) = 0 CORRECTING DEFECT 19 (vertices=29, convex hull=60) After retessellation of defect 19, euler #=-29 (166350,498071,331692) : difference with theory (-29) = 0 CORRECTING DEFECT 20 (vertices=18, convex hull=40) After retessellation of defect 20, euler #=-28 (166360,498113,331725) : difference with theory (-28) = 0 CORRECTING DEFECT 21 (vertices=40, convex hull=21) After retessellation of defect 21, euler #=-27 (166361,498121,331733) : difference with theory (-27) = 0 CORRECTING DEFECT 22 (vertices=126, convex hull=61) After retessellation of defect 22, euler #=-26 (166398,498262,331838) : difference with theory (-26) = 0 CORRECTING DEFECT 23 (vertices=27, convex hull=49) After retessellation of defect 23, euler #=-25 (166410,498316,331881) : difference with theory (-25) = 0 CORRECTING DEFECT 24 (vertices=92, convex hull=64) After retessellation of defect 24, euler #=-25 (166436,498423,331962) : difference with theory (-24) = 1 CORRECTING DEFECT 25 (vertices=74, convex hull=66) After retessellation of defect 25, euler #=-24 (166461,498530,332045) : difference with theory (-23) = 1 CORRECTING DEFECT 26 (vertices=41, convex hull=79) After retessellation of defect 26, euler #=-23 (166481,498626,332122) : difference with theory (-22) = 1 CORRECTING DEFECT 27 (vertices=229, convex hull=179) After retessellation of defect 27, euler #=-21 (166563,498966,332382) : difference with theory (-21) = 0 CORRECTING DEFECT 28 (vertices=79, convex hull=28) After retessellation of defect 28, euler #=-20 (166570,498995,332405) : difference with theory (-20) = 0 CORRECTING DEFECT 29 (vertices=252, convex hull=58) After retessellation of defect 29, euler #=-19 (166589,499079,332471) : difference with theory (-19) = 0 CORRECTING DEFECT 30 (vertices=21, convex hull=55) After retessellation of defect 30, euler #=-18 (166600,499135,332517) : difference with theory (-18) = 0 CORRECTING DEFECT 31 (vertices=51, convex hull=74) After retessellation of defect 31, euler #=-17 (166632,499263,332614) : difference with theory (-17) = 0 CORRECTING DEFECT 32 (vertices=55, convex hull=35) After retessellation of defect 32, euler #=-16 (166637,499290,332637) : difference with theory (-16) = 0 CORRECTING DEFECT 33 (vertices=8, convex hull=33) After retessellation of defect 33, euler #=-15 (166638,499302,332649) : difference with theory (-15) = 0 CORRECTING DEFECT 34 (vertices=6, convex hull=19) After retessellation of defect 34, euler #=-14 (166639,499310,332657) : difference with theory (-14) = 0 CORRECTING DEFECT 35 (vertices=20, convex hull=49) After retessellation of defect 35, euler #=-13 (166648,499354,332693) : difference with theory (-13) = 0 CORRECTING DEFECT 36 (vertices=512, convex hull=247) After retessellation of defect 36, euler #=-11 (166703,499649,332935) : difference with theory (-12) = -1 CORRECTING DEFECT 37 (vertices=5, convex hull=18) After retessellation of defect 37, euler #=-10 (166704,499656,332942) : difference with theory (-11) = -1 CORRECTING DEFECT 38 (vertices=5, convex hull=27) After retessellation of defect 38, euler #=-9 (166706,499669,332954) : difference with theory (-10) = -1 CORRECTING DEFECT 39 (vertices=29, convex hull=21) After retessellation of defect 39, euler #=-8 (166707,499678,332963) : difference with theory (-9) = -1 CORRECTING DEFECT 40 (vertices=48, convex hull=61) After retessellation of defect 40, euler #=-7 (166718,499735,333010) : difference with theory (-8) = -1 CORRECTING DEFECT 41 (vertices=77, convex hull=64) After retessellation of defect 41, euler #=-6 (166734,499810,333070) : difference with theory (-7) = -1 CORRECTING DEFECT 42 (vertices=57, convex hull=97) After retessellation of defect 42, euler #=-5 (166760,499932,333167) : difference with theory (-6) = -1 CORRECTING DEFECT 43 (vertices=8, convex hull=20) After retessellation of defect 43, euler #=-4 (166763,499946,333179) : difference with theory (-5) = -1 CORRECTING DEFECT 44 (vertices=320, convex hull=276) After retessellation of defect 44, euler #=-4 (166868,500411,333539) : difference with theory (-4) = 0 CORRECTING DEFECT 45 (vertices=52, convex hull=80) After retessellation of defect 45, euler #=-3 (166893,500520,333624) : difference with theory (-3) = 0 CORRECTING DEFECT 46 (vertices=14, convex hull=56) After retessellation of defect 46, euler #=-2 (166900,500560,333658) : difference with theory (-2) = 0 CORRECTING DEFECT 47 (vertices=39, convex hull=39) After retessellation of defect 47, euler #=-1 (166905,500594,333688) : difference with theory (-1) = 0 CORRECTING DEFECT 48 (vertices=87, convex hull=96) After retessellation of defect 48, euler #=0 (166923,500690,333767) : difference with theory (0) = 0 CORRECTING DEFECT 49 (vertices=85, convex hull=116) After retessellation of defect 49, euler #=1 (166957,500853,333897) : difference with theory (1) = 0 CORRECTING DEFECT 50 (vertices=36, convex hull=32) After retessellation of defect 50, euler #=2 (166963,500883,333922) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.23 (0.02-->7.74) (max @ vno 16071 --> 27263) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.23 (0.02-->7.74) (max @ vno 16071 --> 27263) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 141 mutations (32.1%), 298 crossovers (67.9%), 177 vertices were eliminated building final representation... 2377 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=166963, nf=333922, ne=500883, g=0) writing corrected surface to /tmp/Skhadka/S8861CSO1/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 57.5 minutes 0 defective edges removing intersecting faces 000: 313 intersecting 001: 9 intersecting mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 166963 - 500883 + 333922 = 2 --> 0 holes F =2V-4: 333922 = 333926-4 (0) 2E=3F: 1001766 = 1001766 (0) total defect index = 0 /tmp/Skhadka/S8861CSO1/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 47 intersecting 001: 7 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Thu Apr 26 05:13:44 EDT 2012 /tmp/Skhadka/S8861CSO1/scripts mris_make_surfaces -noaparc -mgz -T1 brain.finalsurfs S8861CSO1 lh 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 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading volume /tmp/Skhadka/S8861CSO1/mri/filled.mgz... reading volume /tmp/Skhadka/S8861CSO1/mri/brain.finalsurfs.mgz... reading volume /tmp/Skhadka/S8861CSO1/mri/wm.mgz... 17993 bright wm thresholded. 7285 bright non-wm voxels segmented. reading original surface position from /tmp/Skhadka/S8861CSO1/surf/lh.orig... computing class statistics... border white: 300698 voxels (1.79%) border gray 353688 voxels (2.11%) WM (96.0): 96.9 +- 8.3 [70.0 --> 110.0] GM (83.0) : 81.2 +- 11.3 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 59.7 (was 70) setting MAX_BORDER_WHITE to 115.3 (was 105) setting MIN_BORDER_WHITE to 71.0 (was 85) setting MAX_CSF to 48.4 (was 40) setting MAX_GRAY to 98.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 65.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 37.2 (was 40) repositioning cortical surface to gray/white boundary reading volume /tmp/Skhadka/S8861CSO1/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.02-->3.12) (max @ vno 152078 --> 166767) face area 0.28 +- 0.13 (0.00-->3.47) mean absolute distance = 0.66 +- 0.80 5205 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... intensity peaks found at WM=107, GM=71 using class modes intead of means.... mean inside = 96.5, mean outside = 78.3 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=82.6, 92 (92) missing vertices, mean dist 0.3 [0.5 (%34.8)->0.7 (%65.2))] %77 local maxima, %18 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=hhlxn, 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 smoothing T1 volume with sigma = 1.000 vertex spacing 0.91 +- 0.26 (0.09-->3.87) (max @ vno 90018 --> 85227) face area 0.28 +- 0.14 (0.00-->3.01) mean absolute distance = 0.36 +- 0.55 5585 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5851758.0, rms=9.42 001: dt: 0.5000, sse=7467958.5, rms=6.63 002: dt: 0.5000, sse=8214030.5, rms=5.22 003: dt: 0.5000, sse=8563017.0, rms=4.45 004: dt: 0.5000, sse=8838934.0, rms=3.99 005: dt: 0.5000, sse=8941146.0, rms=3.77 006: dt: 0.5000, sse=9079610.0, rms=3.61 007: dt: 0.5000, sse=9065686.0, rms=3.55 008: dt: 0.5000, sse=9165234.0, rms=3.47 rms = 3.46, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=9100352.0, rms=3.46 010: dt: 0.2500, sse=5703069.5, rms=2.41 011: dt: 0.2500, sse=5345097.0, rms=2.08 012: dt: 0.2500, sse=5077540.5, rms=1.99 013: dt: 0.2500, sse=5020151.0, rms=1.93 rms = 1.92, time step reduction 2 of 3 to 0.125... 014: dt: 0.2500, sse=4957149.0, rms=1.92 015: dt: 0.1250, sse=4852609.0, rms=1.85 rms = 1.85, time step reduction 3 of 3 to 0.062... 016: dt: 0.1250, sse=4821892.0, rms=1.85 positioning took 3.3 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 4 vertex label from ripped group mean border=86.1, 98 (25) missing vertices, mean dist -0.2 [0.4 (%77.4)->0.3 (%22.6))] %86 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=hhlxn, 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 (0.08-->4.09) (max @ vno 90018 --> 85227) face area 0.34 +- 0.17 (0.00-->3.56) mean absolute distance = 0.24 +- 0.39 4483 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5598271.0, rms=4.81 017: dt: 0.5000, sse=5984006.5, rms=3.22 rms = 3.41, time step reduction 1 of 3 to 0.250... 018: dt: 0.2500, sse=5608487.0, rms=2.53 019: dt: 0.2500, sse=5532649.0, rms=2.07 020: dt: 0.2500, sse=5431774.5, rms=1.83 021: dt: 0.2500, sse=5397988.0, rms=1.73 022: dt: 0.2500, sse=5339272.0, rms=1.67 rms = 1.63, time step reduction 2 of 3 to 0.125... 023: dt: 0.2500, sse=5348050.5, rms=1.63 024: dt: 0.1250, sse=5250713.0, rms=1.57 rms = 1.57, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=5219487.0, rms=1.57 positioning took 2.0 minutes inhibiting deformation at non-cortical midline structures... removing 2 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 removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 1 vertex label from ripped group mean border=87.9, 103 (7) missing vertices, mean dist -0.1 [0.2 (%69.0)->0.2 (%31.0))] %90 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=hhlxn, 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-->4.21) (max @ vno 90018 --> 85227) face area 0.33 +- 0.16 (0.00-->3.32) mean absolute distance = 0.20 +- 0.33 4052 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5369833.0, rms=2.81 026: dt: 0.5000, sse=5924358.0, rms=2.67 rms = 3.16, time step reduction 1 of 3 to 0.250... 027: dt: 0.2500, sse=5558767.0, rms=1.88 028: dt: 0.2500, sse=5590452.5, rms=1.57 029: dt: 0.2500, sse=5482738.5, rms=1.49 rms = 1.49, time step reduction 2 of 3 to 0.125... 030: dt: 0.2500, sse=5481923.5, rms=1.49 031: dt: 0.1250, sse=5381061.0, rms=1.42 rms = 1.43, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=5381061.0, rms=1.42 positioning took 1.5 minutes inhibiting deformation at non-cortical midline structures... removing 2 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 removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 1 vertex label from ripped group mean border=88.5, 98 (3) missing vertices, mean dist -0.0 [0.2 (%55.3)->0.2 (%44.7))] %92 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=hhlxn, 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 /tmp/Skhadka/S8861CSO1/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=5386278.0, rms=1.57 rms = 1.70, time step reduction 1 of 3 to 0.250... 033: dt: 0.2500, sse=5558166.0, rms=1.22 034: dt: 0.2500, sse=5836879.5, rms=1.08 rms = 1.11, time step reduction 2 of 3 to 0.125... rms = 1.08, time step reduction 3 of 3 to 0.062... 035: dt: 0.1250, sse=5833192.5, rms=1.08 positioning took 0.9 minutes inhibiting deformation at non-cortical midline structures... generating cortex label... 19 non-cortical segments detected only using segment with 2612 vertices erasing segment 1 (vno[0] = 74589) erasing segment 2 (vno[0] = 105217) erasing segment 3 (vno[0] = 108558) erasing segment 4 (vno[0] = 114636) erasing segment 5 (vno[0] = 120189) erasing segment 6 (vno[0] = 123275) erasing segment 7 (vno[0] = 124162) erasing segment 8 (vno[0] = 127500) erasing segment 9 (vno[0] = 128619) erasing segment 10 (vno[0] = 129613) erasing segment 11 (vno[0] = 129657) erasing segment 12 (vno[0] = 129690) erasing segment 13 (vno[0] = 129710) erasing segment 14 (vno[0] = 130707) erasing segment 15 (vno[0] = 131649) erasing segment 16 (vno[0] = 131689) erasing segment 17 (vno[0] = 132643) erasing segment 18 (vno[0] = 132660) writing cortex label to /tmp/Skhadka/S8861CSO1/label/lh.cortex.label... LabelWrite: saving to /tmp/Skhadka/S8861CSO1/label/lh.cortex.label writing curvature file /tmp/Skhadka/S8861CSO1/surf/lh.curv writing smoothed area to lh.area writing curvature file /tmp/Skhadka/S8861CSO1/surf/lh.area vertex spacing 0.89 +- 0.25 (0.05-->4.25) (max @ vno 90018 --> 85227) face area 0.33 +- 0.16 (0.00-->3.26) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... smoothing surface for 5 iterations... mean border=61.7, 176 (176) missing vertices, mean dist 1.8 [0.1 (%0.0)->3.0 (%100.0))] %15 local maxima, %41 large gradients and %40 min vals, 3635 gradients ignored tol=1.0e-04, sigma=2.0, host=hhlxn, 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=26001500.0, rms=26.63 001: dt: 0.5000, sse=19603762.0, rms=22.58 002: dt: 0.5000, sse=15194537.0, rms=19.32 003: dt: 0.5000, sse=12258880.0, rms=16.77 004: dt: 0.5000, sse=10396171.0, rms=14.79 005: dt: 0.5000, sse=9214622.0, rms=13.25 006: dt: 0.5000, sse=8520365.0, rms=12.03 007: dt: 0.5000, sse=8120760.5, rms=11.00 008: dt: 0.5000, sse=7871306.5, rms=10.07 009: dt: 0.5000, sse=7701433.0, rms=9.20 010: dt: 0.5000, sse=7624119.5, rms=8.40 011: dt: 0.5000, sse=7606754.0, rms=7.68 012: dt: 0.5000, sse=7653069.0, rms=7.04 013: dt: 0.5000, sse=7737149.5, rms=6.45 014: dt: 0.5000, sse=7867976.5, rms=5.94 015: dt: 0.5000, sse=7996599.0, rms=5.48 016: dt: 0.5000, sse=8125278.5, rms=5.11 017: dt: 0.5000, sse=8241435.0, rms=4.80 018: dt: 0.5000, sse=8318303.0, rms=4.56 019: dt: 0.5000, sse=8383227.0, rms=4.37 020: dt: 0.5000, sse=8481787.0, rms=4.24 021: dt: 0.5000, sse=8512491.0, rms=4.14 022: dt: 0.5000, sse=8546015.0, rms=4.06 023: dt: 0.5000, sse=8562214.0, rms=3.99 rms = 3.95, time step reduction 1 of 3 to 0.250... 024: dt: 0.5000, sse=8595722.0, rms=3.95 025: dt: 0.2500, sse=6410866.0, rms=3.45 026: dt: 0.2500, sse=6271421.5, rms=3.30 rms = 3.29, time step reduction 2 of 3 to 0.125... 027: dt: 0.2500, sse=6140568.0, rms=3.29 028: dt: 0.1250, sse=5871548.5, rms=3.19 rms = 3.17, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=5841277.0, rms=3.17 positioning took 6.0 minutes mean border=59.7, 2141 (78) missing vertices, mean dist 0.2 [0.2 (%42.3)->0.6 (%57.7))] %38 local maxima, %25 large gradients and %32 min vals, 1782 gradients ignored tol=1.0e-04, sigma=1.0, host=hhlxn, 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=6586351.0, rms=4.76 030: dt: 0.5000, sse=6862220.0, rms=4.27 031: dt: 0.5000, sse=8742032.0, rms=4.11 rms = 4.13, time step reduction 1 of 3 to 0.250... 032: dt: 0.2500, sse=7431947.5, rms=3.62 033: dt: 0.2500, sse=6819378.0, rms=3.43 rms = 3.39, time step reduction 2 of 3 to 0.125... 034: dt: 0.2500, sse=6843748.0, rms=3.39 035: dt: 0.1250, sse=6557859.5, rms=3.26 rms = 3.23, time step reduction 3 of 3 to 0.062... 036: dt: 0.1250, sse=6546865.0, rms=3.23 positioning took 1.6 minutes mean border=58.5, 2637 (68) missing vertices, mean dist 0.1 [0.2 (%38.6)->0.4 (%61.4))] %50 local maxima, %13 large gradients and %32 min vals, 1909 gradients ignored tol=1.0e-04, sigma=0.5, host=hhlxn, 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=6678541.0, rms=3.70 rms = 3.93, time step reduction 1 of 3 to 0.250... 037: dt: 0.2500, sse=6494382.5, rms=3.42 038: dt: 0.2500, sse=6623686.0, rms=3.29 039: dt: 0.2500, sse=6846025.5, rms=3.24 rms = 3.20, time step reduction 2 of 3 to 0.125... 040: dt: 0.2500, sse=7020381.0, rms=3.20 041: dt: 0.1250, sse=6807590.5, rms=3.09 rms = 3.05, time step reduction 3 of 3 to 0.062... 042: dt: 0.1250, sse=6834540.0, rms=3.05 positioning took 1.5 minutes mean border=57.9, 5665 (66) missing vertices, mean dist 0.1 [0.2 (%45.4)->0.3 (%54.6))] %52 local maxima, %11 large gradients and %31 min vals, 1536 gradients ignored tol=1.0e-04, sigma=0.2, host=hhlxn, 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 /tmp/Skhadka/S8861CSO1/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=6863461.5, rms=3.17 rms = 3.52, time step reduction 1 of 3 to 0.250... 043: dt: 0.2500, sse=6799017.5, rms=3.05 044: dt: 0.2500, sse=7122425.0, rms=3.00 rms = 2.98, time step reduction 2 of 3 to 0.125... 045: dt: 0.2500, sse=7232861.5, rms=2.98 046: dt: 0.1250, sse=7107959.5, rms=2.87 rms = 2.84, time step reduction 3 of 3 to 0.062... 047: dt: 0.1250, sse=7148902.0, rms=2.84 positioning took 1.3 minutes writing curvature file /tmp/Skhadka/S8861CSO1/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /tmp/Skhadka/S8861CSO1/surf/lh.area.pial vertex spacing 1.03 +- 0.47 (0.05-->6.65) (max @ vno 120110 --> 119020) face area 0.42 +- 0.35 (0.00-->5.10) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 166963 vertices processed 25000 of 166963 vertices processed 50000 of 166963 vertices processed 75000 of 166963 vertices processed 100000 of 166963 vertices processed 125000 of 166963 vertices processed 150000 of 166963 vertices processed 0 of 166963 vertices processed 25000 of 166963 vertices processed 50000 of 166963 vertices processed 75000 of 166963 vertices processed 100000 of 166963 vertices processed 125000 of 166963 vertices processed 150000 of 166963 vertices processed thickness calculation complete, 4673:7227 truncations. 54549 vertices at 0 distance 81932 vertices at 1 distance 87018 vertices at 2 distance 53476 vertices at 3 distance 25208 vertices at 4 distance 10710 vertices at 5 distance 4452 vertices at 6 distance 2023 vertices at 7 distance 1000 vertices at 8 distance 500 vertices at 9 distance 311 vertices at 10 distance 233 vertices at 11 distance 163 vertices at 12 distance 108 vertices at 13 distance 84 vertices at 14 distance 66 vertices at 15 distance 61 vertices at 16 distance 62 vertices at 17 distance 46 vertices at 18 distance 49 vertices at 19 distance 39 vertices at 20 distance writing curvature file /tmp/Skhadka/S8861CSO1/surf/lh.thickness positioning took 24.7 minutes #-------------------------------------------- #@# Smooth2 lh Thu Apr 26 05:38:27 EDT 2012 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /tmp/Skhadka/S8861CSO1/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 Thu Apr 26 05:38:37 EDT 2012 /tmp/Skhadka/S8861CSO1/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 51.8 mm, total surface area = 100638 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.115 (target=0.015) step 005: RMS=0.081 (target=0.015) step 010: RMS=0.060 (target=0.015) step 015: RMS=0.048 (target=0.015) step 020: RMS=0.040 (target=0.015) step 025: RMS=0.034 (target=0.015) step 030: RMS=0.029 (target=0.015) step 035: RMS=0.024 (target=0.015) step 040: RMS=0.021 (target=0.015) step 045: RMS=0.019 (target=0.015) step 050: RMS=0.017 (target=0.015) step 055: RMS=0.016 (target=0.015) step 060: RMS=0.015 (target=0.015) inflation complete. inflation took 1.6 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 357 vertices thresholded to be in k1 ~ [-0.28 0.35], k2 ~ [-0.10 0.06] total integrated curvature = 0.498*4pi (6.254) --> 1 handles ICI = 1.7, FI = 13.5, variation=218.418 204 vertices thresholded to be in [-0.01 0.02] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 200 vertices thresholded to be in [-0.17 0.16] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.016, std = 0.025 done. #-------------------------------------------- #@# Tessellate rh Thu Apr 26 05:43:16 EDT 2012 /tmp/Skhadka/S8861CSO1/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.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+): 3 found - 3 modified | TOTAL: 4 pass 2 (yz+): 0 found - 3 modified | TOTAL: 4 pass 1 (yz-): 1 found - 1 modified | TOTAL: 5 pass 2 (yz-): 0 found - 1 modified | TOTAL: 5 pass 1 (xz+): 1 found - 1 modified | TOTAL: 6 pass 2 (xz+): 0 found - 1 modified | TOTAL: 6 pass 1 (xz-): 1 found - 1 modified | TOTAL: 7 pass 2 (xz-): 0 found - 1 modified | TOTAL: 7 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 (-+): 3 found - 3 modified | TOTAL: 3 pass 2 (-+): 0 found - 3 modified | TOTAL: 3 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 = 10 (out of 307381: 0.003253) 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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ slice 30: 1537 vertices, 1690 faces slice 40: 9578 vertices, 9925 faces slice 50: 21993 vertices, 22491 faces slice 60: 36774 vertices, 37321 faces slice 70: 51634 vertices, 52153 faces slice 80: 65214 vertices, 65659 faces slice 90: 78195 vertices, 78665 faces slice 100: 91118 vertices, 91584 faces slice 110: 103042 vertices, 103501 faces slice 120: 114402 vertices, 114898 faces slice 130: 125002 vertices, 125489 faces slice 140: 135564 vertices, 135990 faces slice 150: 144920 vertices, 145389 faces slice 160: 154001 vertices, 154401 faces slice 170: 159974 vertices, 160286 faces slice 180: 165033 vertices, 165315 faces slice 190: 167927 vertices, 168114 faces slice 200: 168188 vertices, 168324 faces slice 210: 168188 vertices, 168324 faces slice 220: 168188 vertices, 168324 faces slice 230: 168188 vertices, 168324 faces slice 240: 168188 vertices, 168324 faces slice 250: 168188 vertices, 168324 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... 168188 voxel in cpt #1: X=-136 [v=168188,e=504972,f=336648] located at (29.265892, -30.671921, -0.994138) For the whole surface: X=-136 [v=168188,e=504972,f=336648] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 rh Thu Apr 26 05:43:35 EDT 2012 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix /tmp/Skhadka/S8861CSO1/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 Thu Apr 26 05:43:44 EDT 2012 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix /tmp/Skhadka/S8861CSO1/scripts avg radius = 50.7 mm, total surface area = 87116 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 1.4 minutes Not saving sulc step 000: RMS=0.107 (target=0.015) step 005: RMS=0.080 (target=0.015) step 010: RMS=0.062 (target=0.015) step 015: RMS=0.054 (target=0.015) step 020: RMS=0.048 (target=0.015) step 025: RMS=0.044 (target=0.015) step 030: RMS=0.040 (target=0.015) step 035: RMS=0.038 (target=0.015) step 040: RMS=0.036 (target=0.015) step 045: RMS=0.035 (target=0.015) step 050: RMS=0.034 (target=0.015) step 055: RMS=0.034 (target=0.015) step 060: RMS=0.035 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere rh Thu Apr 26 05:45:11 EDT 2012 /tmp/Skhadka/S8861CSO1/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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.88 +- 0.56 (0.00-->6.47) (max @ vno 106174 --> 106203) face area 0.02 +- 0.03 (-0.22-->0.51) scaling brain by 0.298... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=175.586, avgs=0 005/300: dt: 0.9000, rms radial error=175.332, avgs=0 010/300: dt: 0.9000, rms radial error=174.786, avgs=0 015/300: dt: 0.9000, rms radial error=174.067, avgs=0 020/300: dt: 0.9000, rms radial error=173.248, avgs=0 025/300: dt: 0.9000, rms radial error=172.371, avgs=0 030/300: dt: 0.9000, rms radial error=171.462, avgs=0 035/300: dt: 0.9000, rms radial error=170.534, avgs=0 040/300: dt: 0.9000, rms radial error=169.599, avgs=0 045/300: dt: 0.9000, rms radial error=168.660, avgs=0 050/300: dt: 0.9000, rms radial error=167.721, avgs=0 055/300: dt: 0.9000, rms radial error=166.787, avgs=0 060/300: dt: 0.9000, rms radial error=165.855, avgs=0 065/300: dt: 0.9000, rms radial error=164.927, avgs=0 070/300: dt: 0.9000, rms radial error=164.003, avgs=0 075/300: dt: 0.9000, rms radial error=163.083, avgs=0 080/300: dt: 0.9000, rms radial error=162.168, avgs=0 085/300: dt: 0.9000, rms radial error=161.256, avgs=0 090/300: dt: 0.9000, rms radial error=160.348, avgs=0 095/300: dt: 0.9000, rms radial error=159.445, avgs=0 100/300: dt: 0.9000, rms radial error=158.546, avgs=0 105/300: dt: 0.9000, rms radial error=157.651, avgs=0 110/300: dt: 0.9000, rms radial error=156.761, avgs=0 115/300: dt: 0.9000, rms radial error=155.875, avgs=0 120/300: dt: 0.9000, rms radial error=154.998, avgs=0 125/300: dt: 0.9000, rms radial error=154.125, avgs=0 130/300: dt: 0.9000, rms radial error=153.258, avgs=0 135/300: dt: 0.9000, rms radial error=152.395, avgs=0 140/300: dt: 0.9000, rms radial error=151.537, avgs=0 145/300: dt: 0.9000, rms radial error=150.684, avgs=0 150/300: dt: 0.9000, rms radial error=149.835, avgs=0 155/300: dt: 0.9000, rms radial error=148.992, avgs=0 160/300: dt: 0.9000, rms radial error=148.153, avgs=0 165/300: dt: 0.9000, rms radial error=147.319, avgs=0 170/300: dt: 0.9000, rms radial error=146.491, avgs=0 175/300: dt: 0.9000, rms radial error=145.667, avgs=0 180/300: dt: 0.9000, rms radial error=144.848, avgs=0 185/300: dt: 0.9000, rms radial error=144.033, avgs=0 190/300: dt: 0.9000, rms radial error=143.223, avgs=0 195/300: dt: 0.9000, rms radial error=142.417, avgs=0 200/300: dt: 0.9000, rms radial error=141.616, avgs=0 205/300: dt: 0.9000, rms radial error=140.819, avgs=0 210/300: dt: 0.9000, rms radial error=140.026, avgs=0 215/300: dt: 0.9000, rms radial error=139.238, avgs=0 220/300: dt: 0.9000, rms radial error=138.455, avgs=0 225/300: dt: 0.9000, rms radial error=137.676, avgs=0 230/300: dt: 0.9000, rms radial error=136.903, avgs=0 235/300: dt: 0.9000, rms radial error=136.133, avgs=0 240/300: dt: 0.9000, rms radial error=135.368, avgs=0 245/300: dt: 0.9000, rms radial error=134.607, avgs=0 250/300: dt: 0.9000, rms radial error=133.850, avgs=0 255/300: dt: 0.9000, rms radial error=133.097, avgs=0 260/300: dt: 0.9000, rms radial error=132.349, avgs=0 265/300: dt: 0.9000, rms radial error=131.604, avgs=0 270/300: dt: 0.9000, rms radial error=130.864, avgs=0 275/300: dt: 0.9000, rms radial error=130.129, avgs=0 280/300: dt: 0.9000, rms radial error=129.398, avgs=0 285/300: dt: 0.9000, rms radial error=128.670, avgs=0 290/300: dt: 0.9000, rms radial error=127.947, avgs=0 295/300: dt: 0.9000, rms radial error=127.228, avgs=0 300/300: dt: 0.9000, rms radial error=126.513, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 20060.71 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00016 epoch 2 (K=40.0), pass 1, starting sse = 3534.50 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00011 epoch 3 (K=160.0), pass 1, starting sse = 423.66 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.05/10 = 0.00454 epoch 4 (K=640.0), pass 1, starting sse = 38.11 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.07/11 = 0.00645 final writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.16 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology rh Thu Apr 26 05:54:41 EDT 2012 cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated /tmp/Skhadka/S8861CSO1/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 S8861CSO1 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 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ before topology correction, eno=-136 (nv=168188, nf=336648, ne=504972, g=69) 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 7 iterations marking ambiguous vertices... 11029 ambiguous faces found in tessellation segmenting defects... 70 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 11 into 8 -merging segment 56 into 48 68 defects to be corrected 0 vertices coincident reading input surface /tmp/Skhadka/S8861CSO1/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.4230 (-4.7115) -vertex loglikelihood: -6.3668 (-3.1834) -normal dot loglikelihood: -3.6030 (-3.6030) -quad curv loglikelihood: -6.3657 (-3.1828) Total Loglikelihood : -25.7585 CORRECTING DEFECT 0 (vertices=48, convex hull=89) After retessellation of defect 0, euler #=-67 (161637,482595,320891) : difference with theory (-65) = 2 CORRECTING DEFECT 1 (vertices=64, convex hull=110) After retessellation of defect 1, euler #=-66 (161677,482765,321022) : difference with theory (-64) = 2 CORRECTING DEFECT 2 (vertices=72, convex hull=62) After retessellation of defect 2, euler #=-65 (161686,482815,321064) : difference with theory (-63) = 2 CORRECTING DEFECT 3 (vertices=44, convex hull=75) After retessellation of defect 3, euler #=-64 (161705,482898,321129) : difference with theory (-62) = 2 CORRECTING DEFECT 4 (vertices=6, convex hull=22) After retessellation of defect 4, euler #=-63 (161706,482908,321139) : difference with theory (-61) = 2 CORRECTING DEFECT 5 (vertices=30, convex hull=66) After retessellation of defect 5, euler #=-62 (161721,482979,321196) : difference with theory (-60) = 2 CORRECTING DEFECT 6 (vertices=39, convex hull=48) After retessellation of defect 6, euler #=-61 (161728,483019,321230) : difference with theory (-59) = 2 CORRECTING DEFECT 7 (vertices=6, convex hull=21) After retessellation of defect 7, euler #=-60 (161730,483030,321240) : difference with theory (-58) = 2 CORRECTING DEFECT 8 (vertices=461, convex hull=290) After retessellation of defect 8, euler #=-58 (161804,483415,321553) : difference with theory (-57) = 1 CORRECTING DEFECT 9 (vertices=25, convex hull=69) After retessellation of defect 9, euler #=-57 (161818,483487,321612) : difference with theory (-56) = 1 CORRECTING DEFECT 10 (vertices=51, convex hull=48) After retessellation of defect 10, euler #=-56 (161830,483545,321659) : difference with theory (-55) = 1 CORRECTING DEFECT 11 (vertices=57, convex hull=70) After retessellation of defect 11, euler #=-55 (161849,483627,321723) : difference with theory (-54) = 1 CORRECTING DEFECT 12 (vertices=40, convex hull=56) After retessellation of defect 12, euler #=-54 (161856,483671,321761) : difference with theory (-53) = 1 CORRECTING DEFECT 13 (vertices=60, convex hull=82) After retessellation of defect 13, euler #=-53 (161891,483810,321866) : difference with theory (-52) = 1 CORRECTING DEFECT 14 (vertices=31, convex hull=64) After retessellation of defect 14, euler #=-52 (161902,483868,321914) : difference with theory (-51) = 1 CORRECTING DEFECT 15 (vertices=66, convex hull=109) After retessellation of defect 15, euler #=-51 (161918,483964,321995) : difference with theory (-50) = 1 CORRECTING DEFECT 16 (vertices=76, convex hull=100) After retessellation of defect 16, euler #=-50 (161935,484055,322070) : difference with theory (-49) = 1 CORRECTING DEFECT 17 (vertices=12, convex hull=37) After retessellation of defect 17, euler #=-49 (161937,484077,322091) : difference with theory (-48) = 1 CORRECTING DEFECT 18 (vertices=50, convex hull=117) After retessellation of defect 18, euler #=-48 (161965,484208,322195) : difference with theory (-47) = 1 CORRECTING DEFECT 19 (vertices=50, convex hull=73) After retessellation of defect 19, euler #=-47 (161981,484287,322259) : difference with theory (-46) = 1 CORRECTING DEFECT 20 (vertices=357, convex hull=238) normal vector of length zero at vertex 163148 with 3 faces normal vector of length zero at vertex 163148 with 3 faces normal vector of length zero at vertex 163148 with 3 faces normal vector of length zero at vertex 163148 with 3 faces normal vector of length zero at vertex 163148 with 3 faces After retessellation of defect 20, euler #=-46 (162009,484492,322437) : difference with theory (-45) = 1 CORRECTING DEFECT 21 (vertices=34, convex hull=57) After retessellation of defect 21, euler #=-45 (162018,484544,322481) : difference with theory (-44) = 1 CORRECTING DEFECT 22 (vertices=28, convex hull=43) After retessellation of defect 22, euler #=-44 (162027,484587,322516) : difference with theory (-43) = 1 CORRECTING DEFECT 23 (vertices=169, convex hull=134) After retessellation of defect 23, euler #=-43 (162076,484793,322674) : difference with theory (-42) = 1 CORRECTING DEFECT 24 (vertices=43, convex hull=92) After retessellation of defect 24, euler #=-42 (162095,484887,322750) : difference with theory (-41) = 1 CORRECTING DEFECT 25 (vertices=210, convex hull=106) After retessellation of defect 25, euler #=-41 (162117,485001,322843) : difference with theory (-40) = 1 CORRECTING DEFECT 26 (vertices=589, convex hull=417) After retessellation of defect 26, euler #=-40 (162292,485741,323409) : difference with theory (-39) = 1 CORRECTING DEFECT 27 (vertices=21, convex hull=60) After retessellation of defect 27, euler #=-39 (162301,485787,323447) : difference with theory (-38) = 1 CORRECTING DEFECT 28 (vertices=22, convex hull=26) After retessellation of defect 28, euler #=-38 (162304,485803,323461) : difference with theory (-37) = 1 CORRECTING DEFECT 29 (vertices=129, convex hull=35) After retessellation of defect 29, euler #=-37 (162313,485842,323492) : difference with theory (-36) = 1 CORRECTING DEFECT 30 (vertices=15, convex hull=22) After retessellation of defect 30, euler #=-36 (162317,485860,323507) : difference with theory (-35) = 1 CORRECTING DEFECT 31 (vertices=32, convex hull=63) After retessellation of defect 31, euler #=-35 (162326,485911,323550) : difference with theory (-34) = 1 CORRECTING DEFECT 32 (vertices=23, convex hull=47) After retessellation of defect 32, euler #=-34 (162341,485973,323598) : difference with theory (-33) = 1 CORRECTING DEFECT 33 (vertices=26, convex hull=66) After retessellation of defect 33, euler #=-33 (162351,486027,323643) : difference with theory (-32) = 1 CORRECTING DEFECT 34 (vertices=24, convex hull=31) Warning - incorrect dp selected!!!!(-76.287563 >= -76.287568 ) After retessellation of defect 34, euler #=-32 (162355,486048,323661) : difference with theory (-31) = 1 CORRECTING DEFECT 35 (vertices=35, convex hull=53) After retessellation of defect 35, euler #=-31 (162368,486114,323715) : difference with theory (-30) = 1 CORRECTING DEFECT 36 (vertices=297, convex hull=70) After retessellation of defect 36, euler #=-30 (162396,486230,323804) : difference with theory (-29) = 1 CORRECTING DEFECT 37 (vertices=162, convex hull=73) After retessellation of defect 37, euler #=-29 (162421,486334,323884) : difference with theory (-28) = 1 CORRECTING DEFECT 38 (vertices=51, convex hull=88) After retessellation of defect 38, euler #=-28 (162433,486403,323942) : difference with theory (-27) = 1 CORRECTING DEFECT 39 (vertices=327, convex hull=112) After retessellation of defect 39, euler #=-27 (162481,486600,324092) : difference with theory (-26) = 1 CORRECTING DEFECT 40 (vertices=84, convex hull=100) After retessellation of defect 40, euler #=-26 (162519,486760,324215) : difference with theory (-25) = 1 CORRECTING DEFECT 41 (vertices=13, convex hull=20) After retessellation of defect 41, euler #=-25 (162521,486772,324226) : difference with theory (-24) = 1 CORRECTING DEFECT 42 (vertices=86, convex hull=67) After retessellation of defect 42, euler #=-24 (162542,486866,324300) : difference with theory (-23) = 1 CORRECTING DEFECT 43 (vertices=24, convex hull=56) After retessellation of defect 43, euler #=-23 (162555,486926,324348) : difference with theory (-22) = 1 CORRECTING DEFECT 44 (vertices=21, convex hull=42) After retessellation of defect 44, euler #=-22 (162560,486957,324375) : difference with theory (-21) = 1 CORRECTING DEFECT 45 (vertices=72, convex hull=44) After retessellation of defect 45, euler #=-21 (162569,487008,324418) : difference with theory (-20) = 1 CORRECTING DEFECT 46 (vertices=17, convex hull=33) After retessellation of defect 46, euler #=-20 (162572,487029,324437) : difference with theory (-19) = 1 CORRECTING DEFECT 47 (vertices=212, convex hull=129) After retessellation of defect 47, euler #=-18 (162582,487121,324521) : difference with theory (-18) = 0 CORRECTING DEFECT 48 (vertices=43, convex hull=61) After retessellation of defect 48, euler #=-17 (162599,487200,324584) : difference with theory (-17) = 0 CORRECTING DEFECT 49 (vertices=5, convex hull=15) After retessellation of defect 49, euler #=-16 (162599,487204,324589) : difference with theory (-16) = 0 CORRECTING DEFECT 50 (vertices=8, convex hull=24) After retessellation of defect 50, euler #=-15 (162601,487217,324601) : difference with theory (-15) = 0 CORRECTING DEFECT 51 (vertices=32, convex hull=64) After retessellation of defect 51, euler #=-14 (162613,487276,324649) : difference with theory (-14) = 0 CORRECTING DEFECT 52 (vertices=5, convex hull=20) After retessellation of defect 52, euler #=-13 (162615,487286,324658) : difference with theory (-13) = 0 CORRECTING DEFECT 53 (vertices=583, convex hull=281) After retessellation of defect 53, euler #=-12 (162705,487701,324984) : difference with theory (-12) = 0 CORRECTING DEFECT 54 (vertices=303, convex hull=51) After retessellation of defect 54, euler #=-11 (162721,487772,325040) : difference with theory (-11) = 0 CORRECTING DEFECT 55 (vertices=521, convex hull=157) After retessellation of defect 55, euler #=-10 (162748,487930,325172) : difference with theory (-10) = 0 CORRECTING DEFECT 56 (vertices=20, convex hull=45) After retessellation of defect 56, euler #=-9 (162756,487974,325209) : difference with theory (-9) = 0 CORRECTING DEFECT 57 (vertices=19, convex hull=24) After retessellation of defect 57, euler #=-8 (162758,487988,325222) : difference with theory (-8) = 0 CORRECTING DEFECT 58 (vertices=70, convex hull=100) After retessellation of defect 58, euler #=-7 (162775,488083,325301) : difference with theory (-7) = 0 CORRECTING DEFECT 59 (vertices=12, convex hull=17) After retessellation of defect 59, euler #=-6 (162775,488087,325306) : difference with theory (-6) = 0 CORRECTING DEFECT 60 (vertices=36, convex hull=26) After retessellation of defect 60, euler #=-5 (162778,488106,325323) : difference with theory (-5) = 0 CORRECTING DEFECT 61 (vertices=161, convex hull=57) After retessellation of defect 61, euler #=-4 (162797,488185,325384) : difference with theory (-4) = 0 CORRECTING DEFECT 62 (vertices=122, convex hull=120) After retessellation of defect 62, euler #=-3 (162834,488347,325510) : difference with theory (-3) = 0 CORRECTING DEFECT 63 (vertices=57, convex hull=80) After retessellation of defect 63, euler #=-2 (162848,488427,325577) : difference with theory (-2) = 0 CORRECTING DEFECT 64 (vertices=43, convex hull=59) After retessellation of defect 64, euler #=-1 (162868,488513,325644) : difference with theory (-1) = 0 CORRECTING DEFECT 65 (vertices=44, convex hull=64) After retessellation of defect 65, euler #=0 (162885,488591,325706) : difference with theory (0) = 0 CORRECTING DEFECT 66 (vertices=23, convex hull=60) After retessellation of defect 66, euler #=1 (162896,488646,325751) : difference with theory (1) = 0 CORRECTING DEFECT 67 (vertices=45, convex hull=76) After retessellation of defect 67, euler #=2 (162916,488742,325828) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.26 (0.06-->10.29) (max @ vno 27998 --> 38442) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.26 (0.06-->10.29) (max @ vno 27998 --> 38442) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 288 mutations (34.8%), 540 crossovers (65.2%), 621 vertices were eliminated building final representation... 5272 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=162916, nf=325828, ne=488742, g=0) writing corrected surface to /tmp/Skhadka/S8861CSO1/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 109.4 minutes 0 defective edges removing intersecting faces 000: 565 intersecting 001: 6 intersecting 002: 8 intersecting 003: 4 intersecting mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 162916 - 488742 + 325828 = 2 --> 0 holes F =2V-4: 325828 = 325832-4 (0) 2E=3F: 977484 = 977484 (0) total defect index = 0 /tmp/Skhadka/S8861CSO1/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 72 intersecting 001: 3 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf rh Thu Apr 26 07:44:19 EDT 2012 /tmp/Skhadka/S8861CSO1/scripts mris_make_surfaces -noaparc -mgz -T1 brain.finalsurfs S8861CSO1 rh 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 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.2 2011/04/27 19:21:05 nicks Exp $ reading volume /tmp/Skhadka/S8861CSO1/mri/filled.mgz... reading volume /tmp/Skhadka/S8861CSO1/mri/brain.finalsurfs.mgz... reading volume /tmp/Skhadka/S8861CSO1/mri/wm.mgz... 17186 bright wm thresholded. 7293 bright non-wm voxels segmented. reading original surface position from /tmp/Skhadka/S8861CSO1/surf/rh.orig... computing class statistics... border white: 300698 voxels (1.79%) border gray 353688 voxels (2.11%) WM (96.0): 96.9 +- 8.1 [70.0 --> 110.0] GM (83.0) : 81.3 +- 11.6 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 59.4 (was 70) setting MAX_BORDER_WHITE to 115.1 (was 105) setting MIN_BORDER_WHITE to 71.0 (was 85) setting MAX_CSF to 47.9 (was 40) setting MAX_GRAY to 98.9 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 65.2 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 36.3 (was 40) repositioning cortical surface to gray/white boundary reading volume /tmp/Skhadka/S8861CSO1/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.23 (0.03-->5.79) (max @ vno 162174 --> 162241) face area 0.28 +- 0.14 (0.00-->6.79) mean absolute distance = 0.66 +- 0.83 5175 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... intensity peaks found at WM=107, GM=71 using class modes intead of means.... mean inside = 96.2, mean outside = 78.1 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group mean border=82.9, 66 (66) missing vertices, mean dist 0.3 [0.5 (%37.8)->0.7 (%62.2))] %79 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=hhlxn, 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 smoothing T1 volume with sigma = 1.000 vertex spacing 0.91 +- 0.27 (0.11-->6.12) (max @ vno 162182 --> 162248) face area 0.28 +- 0.15 (0.00-->6.73) mean absolute distance = 0.34 +- 0.56 4860 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5912348.0, rms=9.55 001: dt: 0.5000, sse=7651812.0, rms=6.89 002: dt: 0.5000, sse=8486307.0, rms=5.56 003: dt: 0.5000, sse=8793131.0, rms=4.81 004: dt: 0.5000, sse=9126438.0, rms=4.32 005: dt: 0.5000, sse=9169421.0, rms=4.05 006: dt: 0.5000, sse=9323874.0, rms=3.85 007: dt: 0.5000, sse=9262514.0, rms=3.76 008: dt: 0.5000, sse=9367922.0, rms=3.65 rms = 3.62, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=9291327.0, rms=3.62 010: dt: 0.2500, sse=5982766.5, rms=2.60 011: dt: 0.2500, sse=5613437.5, rms=2.26 012: dt: 0.2500, sse=5347141.5, rms=2.17 rms = 2.12, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=5289078.0, rms=2.12 014: dt: 0.1250, sse=5138699.5, rms=2.04 rms = 2.03, time step reduction 3 of 3 to 0.062... 015: dt: 0.1250, sse=5092735.0, rms=2.03 positioning took 3.0 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 1 vertex label from ripped group mean border=85.8, 99 (20) missing vertices, mean dist -0.2 [0.4 (%74.0)->0.3 (%26.0))] %87 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=hhlxn, 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 +- 0.27 (0.08-->6.59) (max @ vno 162184 --> 162240) face area 0.34 +- 0.18 (0.00-->8.54) mean absolute distance = 0.25 +- 0.42 4644 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5684286.5, rms=4.33 016: dt: 0.5000, sse=6258415.0, rms=3.12 rms = 3.40, time step reduction 1 of 3 to 0.250... 017: dt: 0.2500, sse=5854890.5, rms=2.44 018: dt: 0.2500, sse=5804919.0, rms=2.07 019: dt: 0.2500, sse=5699720.0, rms=1.90 020: dt: 0.2500, sse=5670729.5, rms=1.82 rms = 1.79, time step reduction 2 of 3 to 0.125... 021: dt: 0.2500, sse=5634349.5, rms=1.79 022: dt: 0.1250, sse=5564761.0, rms=1.72 rms = 1.70, time step reduction 3 of 3 to 0.062... 023: dt: 0.1250, sse=5510305.5, rms=1.70 positioning took 1.7 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 1 vertex label from ripped group mean border=87.5, 87 (14) missing vertices, mean dist -0.1 [0.3 (%66.9)->0.2 (%33.1))] %91 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=hhlxn, 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 +- 0.26 (0.07-->7.09) (max @ vno 162184 --> 162240) face area 0.34 +- 0.18 (0.00-->9.05) mean absolute distance = 0.22 +- 0.36 4547 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5643799.5, rms=2.78 024: dt: 0.5000, sse=6251123.5, rms=2.66 rms = 3.16, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=5882549.5, rms=1.95 026: dt: 0.2500, sse=5917392.0, rms=1.68 027: dt: 0.2500, sse=5799667.0, rms=1.62 rms = 1.61, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=5808492.0, rms=1.61 029: dt: 0.1250, sse=5699814.5, rms=1.54 rms = 1.55, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=5699814.5, rms=1.54 positioning took 1.5 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 2 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 removing 1 vertex label from ripped group mean border=88.0, 115 (11) missing vertices, mean dist -0.0 [0.2 (%54.9)->0.2 (%45.1))] %92 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=hhlxn, 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 /tmp/Skhadka/S8861CSO1/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=5704980.5, rms=1.67 rms = 1.77, time step reduction 1 of 3 to 0.250... 031: dt: 0.2500, sse=5884671.0, rms=1.34 032: dt: 0.2500, sse=6190899.5, rms=1.19 rms = 1.21, time step reduction 2 of 3 to 0.125... rms = 1.18, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=6190632.5, rms=1.18 positioning took 0.8 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 2 vertex label from ripped group generating cortex label... 19 non-cortical segments detected only using segment with 2201 vertices erasing segment 0 (vno[0] = 67452) erasing segment 2 (vno[0] = 81206) erasing segment 3 (vno[0] = 82427) erasing segment 4 (vno[0] = 97964) erasing segment 5 (vno[0] = 106526) erasing segment 6 (vno[0] = 120049) erasing segment 7 (vno[0] = 120051) erasing segment 8 (vno[0] = 121004) erasing segment 9 (vno[0] = 121013) erasing segment 10 (vno[0] = 122045) erasing segment 11 (vno[0] = 125107) erasing segment 12 (vno[0] = 125211) erasing segment 13 (vno[0] = 126351) erasing segment 14 (vno[0] = 127362) erasing segment 15 (vno[0] = 130965) erasing segment 16 (vno[0] = 131217) erasing segment 17 (vno[0] = 133702) erasing segment 18 (vno[0] = 133718) writing cortex label to /tmp/Skhadka/S8861CSO1/label/rh.cortex.label... LabelWrite: saving to /tmp/Skhadka/S8861CSO1/label/rh.cortex.label writing curvature file /tmp/Skhadka/S8861CSO1/surf/rh.curv writing smoothed area to rh.area writing curvature file /tmp/Skhadka/S8861CSO1/surf/rh.area vertex spacing 0.89 +- 0.26 (0.08-->7.19) (max @ vno 162184 --> 162240) face area 0.33 +- 0.18 (0.00-->9.06) repositioning cortical surface to gray/csf boundary. smoothing T1 volume with sigma = 2.000 averaging target values for 5 iterations... smoothing surface for 5 iterations... mean border=61.6, 137 (137) missing vertices, mean dist 1.7 [0.2 (%0.0)->3.2 (%100.0))] %15 local maxima, %36 large gradients and %46 min vals, 4478 gradients ignored tol=1.0e-04, sigma=2.0, host=hhlxn, 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=24907252.0, rms=26.21 001: dt: 0.5000, sse=18938884.0, rms=22.29 002: dt: 0.5000, sse=14811120.0, rms=19.14 003: dt: 0.5000, sse=12042455.0, rms=16.66 004: dt: 0.5000, sse=10271379.0, rms=14.72 005: dt: 0.5000, sse=9119310.0, rms=13.17 006: dt: 0.5000, sse=8411594.0, rms=11.93 007: dt: 0.5000, sse=7917719.5, rms=10.86 008: dt: 0.5000, sse=7675540.0, rms=9.92 009: dt: 0.5000, sse=7467597.0, rms=9.05 010: dt: 0.5000, sse=7402642.5, rms=8.27 011: dt: 0.5000, sse=7374392.0, rms=7.56 012: dt: 0.5000, sse=7477525.5, rms=6.95 013: dt: 0.5000, sse=7557438.5, rms=6.38 014: dt: 0.5000, sse=7709303.0, rms=5.89 015: dt: 0.5000, sse=7755836.0, rms=5.46 016: dt: 0.5000, sse=7979782.0, rms=5.11 017: dt: 0.5000, sse=8031666.0, rms=4.82 018: dt: 0.5000, sse=8202959.5, rms=4.60 019: dt: 0.5000, sse=8185450.0, rms=4.42 020: dt: 0.5000, sse=8339801.5, rms=4.27 021: dt: 0.5000, sse=8276153.5, rms=4.15 022: dt: 0.5000, sse=8409447.0, rms=4.07 023: dt: 0.5000, sse=8362873.0, rms=4.00 rms = 3.96, time step reduction 1 of 3 to 0.250... 024: dt: 0.5000, sse=8437879.0, rms=3.96 025: dt: 0.2500, sse=6531600.0, rms=3.52 026: dt: 0.2500, sse=6424304.0, rms=3.40 rms = 3.41, time step reduction 2 of 3 to 0.125... rms = 3.36, time step reduction 3 of 3 to 0.062... 027: dt: 0.1250, sse=6309732.0, rms=3.36 positioning took 5.6 minutes mean border=59.7, 2541 (57) missing vertices, mean dist 0.2 [0.2 (%42.4)->0.7 (%57.6))] %34 local maxima, %24 large gradients and %37 min vals, 1922 gradients ignored tol=1.0e-04, sigma=1.0, host=hhlxn, 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=7009212.5, rms=4.78 028: dt: 0.5000, sse=7219290.5, rms=4.31 029: dt: 0.5000, sse=8761107.0, rms=4.09 rms = 4.10, time step reduction 1 of 3 to 0.250... 030: dt: 0.2500, sse=7546080.5, rms=3.67 031: dt: 0.2500, sse=6961413.5, rms=3.52 rms = 3.48, time step reduction 2 of 3 to 0.125... 032: dt: 0.2500, sse=6964528.5, rms=3.48 033: dt: 0.1250, sse=6704204.5, rms=3.35 rms = 3.32, time step reduction 3 of 3 to 0.062... 034: dt: 0.1250, sse=6707858.5, rms=3.32 positioning took 1.6 minutes mean border=58.9, 3114 (51) missing vertices, mean dist 0.1 [0.2 (%41.2)->0.5 (%58.8))] %45 local maxima, %13 large gradients and %37 min vals, 2073 gradients ignored tol=1.0e-04, sigma=0.5, host=hhlxn, 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=6809330.0, rms=3.67 rms = 3.85, time step reduction 1 of 3 to 0.250... 035: dt: 0.2500, sse=6653614.5, rms=3.46 036: dt: 0.2500, sse=6777817.0, rms=3.35 rms = 3.31, time step reduction 2 of 3 to 0.125... 037: dt: 0.2500, sse=6988413.0, rms=3.31 038: dt: 0.1250, sse=6830173.5, rms=3.20 rms = 3.16, time step reduction 3 of 3 to 0.062... 039: dt: 0.1250, sse=6875155.5, rms=3.16 positioning took 1.2 minutes mean border=58.3, 6228 (45) missing vertices, mean dist 0.1 [0.2 (%45.9)->0.4 (%54.1))] %47 local maxima, %11 large gradients and %35 min vals, 1859 gradients ignored tol=1.0e-04, sigma=0.2, host=hhlxn, 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 /tmp/Skhadka/S8861CSO1/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=6899009.0, rms=3.26 rms = 3.48, time step reduction 1 of 3 to 0.250... 040: dt: 0.2500, sse=6848448.5, rms=3.15 041: dt: 0.2500, sse=7181155.5, rms=3.08 rms = 3.05, time step reduction 2 of 3 to 0.125... 042: dt: 0.2500, sse=7300521.5, rms=3.05 043: dt: 0.1250, sse=7189040.5, rms=2.94 rms = 2.91, time step reduction 3 of 3 to 0.062... 044: dt: 0.1250, sse=7237433.0, rms=2.91 positioning took 1.2 minutes writing curvature file /tmp/Skhadka/S8861CSO1/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /tmp/Skhadka/S8861CSO1/surf/rh.area.pial vertex spacing 1.03 +- 0.49 (0.07-->9.45) (max @ vno 162198 --> 162240) face area 0.42 +- 0.37 (0.00-->12.34) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 162916 vertices processed 25000 of 162916 vertices processed 50000 of 162916 vertices processed 75000 of 162916 vertices processed 100000 of 162916 vertices processed 125000 of 162916 vertices processed 150000 of 162916 vertices processed 0 of 162916 vertices processed 25000 of 162916 vertices processed 50000 of 162916 vertices processed 75000 of 162916 vertices processed 100000 of 162916 vertices processed 125000 of 162916 vertices processed 150000 of 162916 vertices processed thickness calculation complete, 5592:7261 truncations. 51277 vertices at 0 distance 73205 vertices at 1 distance 85798 vertices at 2 distance 56181 vertices at 3 distance 26924 vertices at 4 distance 11432 vertices at 5 distance 4679 vertices at 6 distance 2089 vertices at 7 distance 1014 vertices at 8 distance 581 vertices at 9 distance 368 vertices at 10 distance 245 vertices at 11 distance 152 vertices at 12 distance 140 vertices at 13 distance 115 vertices at 14 distance 109 vertices at 15 distance 82 vertices at 16 distance 98 vertices at 17 distance 76 vertices at 18 distance 67 vertices at 19 distance 60 vertices at 20 distance writing curvature file /tmp/Skhadka/S8861CSO1/surf/rh.thickness positioning took 23.0 minutes #-------------------------------------------- #@# Smooth2 rh Thu Apr 26 08:07:20 EDT 2012 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm /tmp/Skhadka/S8861CSO1/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 Thu Apr 26 08:07:28 EDT 2012 /tmp/Skhadka/S8861CSO1/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated avg radius = 51.0 mm, total surface area = 98663 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.119 (target=0.015) step 005: RMS=0.083 (target=0.015) step 010: RMS=0.060 (target=0.015) step 015: RMS=0.050 (target=0.015) step 020: RMS=0.041 (target=0.015) step 025: RMS=0.035 (target=0.015) step 030: RMS=0.029 (target=0.015) step 035: RMS=0.025 (target=0.015) step 040: RMS=0.021 (target=0.015) step 045: RMS=0.018 (target=0.015) step 050: RMS=0.017 (target=0.015) step 055: RMS=0.015 (target=0.015) inflation complete. inflation took 1.2 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 338 vertices thresholded to be in k1 ~ [-0.29 0.27], k2 ~ [-0.13 0.06] total integrated curvature = 0.456*4pi (5.736) --> 1 handles ICI = 1.7, FI = 13.9, variation=224.641 186 vertices thresholded to be in [-0.01 0.02] writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 192 vertices thresholded to be in [-0.15 0.14] done. writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.016, std = 0.025 done. #-------------------------------------------- #@# ASeg Stats Thu Apr 26 08:11:29 EDT 2012 INFO: mri_segstats will not calculate Supratentorial due to missing ribbon.mgz file /tmp/Skhadka/S8861CSO1 mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /opt/freesurfer/ASegStatsLUT.txt --subject S8861CSO1 $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --excludeid 0 --excl-ctxgmwm --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab /opt/freesurfer/ASegStatsLUT.txt --subject S8861CSO1 sysname Linux hostname hhlxnrcas09 machine x86_64 user Skhadka atlas_icv (eTIV) = 1840397 mm^3 (det: 1.058524 ) Loading mri/aseg.mgz Getting Cerebral WM volumes from surface lh white matter volume 282167 rh white matter volume 281113 Getting Cerebral GM and WM volumes from surfaces lh surface-based volumes (mm3): wTot = 302809.975931, pTot = 662179.899194 c = 359369.923263 rh surface-based volumes (mm3): wTot = 301529.113626, pTot = 653162.366820 c = 351633.253194 Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 50 segmentations Computing statistics for each segmentation 3 4 Left-Lateral-Ventricle 4062 4062 4 5 Left-Inf-Lat-Vent 223 223 5 7 Left-Cerebellum-White-Matter 16066 16066 6 8 Left-Cerebellum-Cortex 60337 60337 7 10 Left-Thalamus-Proper 9659 9659 8 11 Left-Caudate 4647 4647 9 12 Left-Putamen 8374 8374 10 13 Left-Pallidum 1953 1953 11 14 3rd-Ventricle 1012 1012 12 15 4th-Ventricle 1342 1342 13 16 Brain-Stem 21932 21932 14 17 Left-Hippocampus 4941 4941 15 18 Left-Amygdala 2274 2274 16 24 CSF 1412 1412 17 26 Left-Accumbens-area 937 937 18 28 Left-VentralDC 5028 5028 19 30 Left-vessel 44 44 20 31 Left-choroid-plexus 1157 1157 23 43 Right-Lateral-Ventricle 3204 3204 24 44 Right-Inf-Lat-Vent 147 147 25 46 Right-Cerebellum-White-Matter 16813 16813 26 47 Right-Cerebellum-Cortex 60406 60406 27 49 Right-Thalamus-Proper 9428 9428 28 50 Right-Caudate 4278 4278 29 51 Right-Putamen 8458 8458 30 52 Right-Pallidum 2018 2018 31 53 Right-Hippocampus 5175 5175 32 54 Right-Amygdala 2411 2411 33 58 Right-Accumbens-area 893 893 34 60 Right-VentralDC 5148 5148 35 62 Right-vessel 66 66 36 63 Right-choroid-plexus 1531 1531 37 72 5th-Ventricle 0 38 77 WM-hypointensities 2723 2723 39 78 Left-WM-hypointensities 0 40 79 Right-WM-hypointensities 0 41 80 non-WM-hypointensities 6 6 42 81 Left-non-WM-hypointensities 0 43 82 Right-non-WM-hypointensities 0 44 85 Optic-Chiasm 229 229 45 251 CC_Posterior 765 765 46 252 CC_Mid_Posterior 430 430 47 253 CC_Central 559 559 48 254 CC_Mid_Anterior 508 508 49 255 CC_Anterior 836 836 Reporting on 45 segmentations SubCortGrayVol = 218297 #-------------------------------------------- #@# Hippocampal Subfields processing Thu Apr 26 08:26:42 EDT 2012 mkdir -p /tmp/Skhadka/S8861CSO1/tmp/subfieldResults kvlSegmentHippocampalSubfields.sh S8861CSO1 left /tmp/Skhadka /tmp/Skhadka/S8861CSO1/tmp/subfieldResults kvlSegmentHippocampalSubfields.sh S8861CSO1 right /tmp/Skhadka /tmp/Skhadka/S8861CSO1/tmp/subfieldResults cp /tmp/Skhadka/S8861CSO1/tmp/subfieldResults/S8861CSO1/left/segmentationWithoutPartialVolumingLog/posterior_left* /tmp/Skhadka/S8861CSO1/mri cp /tmp/Skhadka/S8861CSO1/tmp/subfieldResults/S8861CSO1/left/segmentationWithoutPartialVolumingLog/posterior_Left* /tmp/Skhadka/S8861CSO1/mri cp /tmp/Skhadka/S8861CSO1/tmp/subfieldResults/S8861CSO1/right/segmentationWithoutPartialVolumingLog/posterior_right* /tmp/Skhadka/S8861CSO1/mri cp /tmp/Skhadka/S8861CSO1/tmp/subfieldResults/S8861CSO1/right/segmentationWithoutPartialVolumingLog/posterior_Right* /tmp/Skhadka/S8861CSO1/mri rm -rf /tmp/Skhadka/S8861CSO1/tmp/subfieldResults #------------------------------------------ recon-all -s S8861CSO1 finished without error at Thu Apr 26 12:28:41 EDT 2012