Wed May 22 11:34:05 JST 2013 /home/yamamoto/freesurfer/5.3.0/dist/subjects/test /usr/local/freesurfer/5.3.0/dist/bin/recon-all -s test -i sample-001.mgz -i sample-002.mgz -autorecon1 -autorecon2 -openmp 8 subjid test setenv SUBJECTS_DIR /home/yamamoto/freesurfer/5.3.0/dist/subjects FREESURFER_HOME /usr/local/freesurfer/5.3.0/dist Actual FREESURFER_HOME /home/yamamoto/freesurfer/5.3.0/dist build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux dhcp006.tkl.iis.u-tokyo.ac.jp 2.6.32-358.6.2.el6.x86_64 #1 SMP Thu May 16 20:59:36 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 1024 total used free shared buffers cached Mem: 16292132 1352952 14939180 0 51904 833720 -/+ buffers/cache: 467328 15824804 Swap: 8216568 0 8216568 ######################################## program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/22-02:34:05-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: yamamoto Machine: dhcp006.tkl.iis.u-tokyo.ac.jp Platform: Linux PlatformVersion: 2.6.32-358.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/22-02:34:05-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: yamamoto Machine: dhcp006.tkl.iis.u-tokyo.ac.jp Platform: Linux PlatformVersion: 2.6.32-358.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/22-02:34:05-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: yamamoto Machine: dhcp006.tkl.iis.u-tokyo.ac.jp Platform: Linux PlatformVersion: 2.6.32-358.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/22-02:34:05-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: yamamoto Machine: dhcp006.tkl.iis.u-tokyo.ac.jp Platform: Linux PlatformVersion: 2.6.32-358.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/22-02:34:06-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: yamamoto Machine: dhcp006.tkl.iis.u-tokyo.ac.jp Platform: Linux PlatformVersion: 2.6.32-358.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/22-02:34:06-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: yamamoto Machine: dhcp006.tkl.iis.u-tokyo.ac.jp Platform: Linux PlatformVersion: 2.6.32-358.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/22-02:34:06-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: yamamoto Machine: dhcp006.tkl.iis.u-tokyo.ac.jp Platform: Linux PlatformVersion: 2.6.32-358.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/22-02:34:06-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: yamamoto Machine: dhcp006.tkl.iis.u-tokyo.ac.jp Platform: Linux PlatformVersion: 2.6.32-358.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 8 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/22-02:34:06-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: yamamoto Machine: dhcp006.tkl.iis.u-tokyo.ac.jp Platform: Linux PlatformVersion: 2.6.32-358.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/22-02:34:06-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: yamamoto Machine: dhcp006.tkl.iis.u-tokyo.ac.jp Platform: Linux PlatformVersion: 2.6.32-358.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/22-02:34:06-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: yamamoto Machine: dhcp006.tkl.iis.u-tokyo.ac.jp Platform: Linux PlatformVersion: 2.6.32-358.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/22-02:34:06-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: yamamoto Machine: dhcp006.tkl.iis.u-tokyo.ac.jp Platform: Linux PlatformVersion: 2.6.32-358.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/22-02:34:06-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: yamamoto Machine: dhcp006.tkl.iis.u-tokyo.ac.jp Platform: Linux PlatformVersion: 2.6.32-358.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/22-02:34:06-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: yamamoto Machine: dhcp006.tkl.iis.u-tokyo.ac.jp Platform: Linux PlatformVersion: 2.6.32-358.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/22-02:34:06-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: yamamoto Machine: dhcp006.tkl.iis.u-tokyo.ac.jp Platform: Linux PlatformVersion: 2.6.32-358.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/22-02:34:06-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: yamamoto Machine: dhcp006.tkl.iis.u-tokyo.ac.jp Platform: Linux PlatformVersion: 2.6.32-358.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/22-02:34:06-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: yamamoto Machine: dhcp006.tkl.iis.u-tokyo.ac.jp Platform: Linux PlatformVersion: 2.6.32-358.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/22-02:34:06-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: yamamoto Machine: dhcp006.tkl.iis.u-tokyo.ac.jp Platform: Linux PlatformVersion: 2.6.32-358.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/22-02:34:06-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: yamamoto Machine: dhcp006.tkl.iis.u-tokyo.ac.jp Platform: Linux PlatformVersion: 2.6.32-358.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/22-02:34:06-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: yamamoto Machine: dhcp006.tkl.iis.u-tokyo.ac.jp Platform: Linux PlatformVersion: 2.6.32-358.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/22-02:34:06-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: yamamoto Machine: dhcp006.tkl.iis.u-tokyo.ac.jp Platform: Linux PlatformVersion: 2.6.32-358.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/22-02:34:06-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: yamamoto Machine: dhcp006.tkl.iis.u-tokyo.ac.jp Platform: Linux PlatformVersion: 2.6.32-358.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/22-02:34:06-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: yamamoto Machine: dhcp006.tkl.iis.u-tokyo.ac.jp Platform: Linux PlatformVersion: 2.6.32-358.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/22-02:34:07-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: yamamoto Machine: dhcp006.tkl.iis.u-tokyo.ac.jp Platform: Linux PlatformVersion: 2.6.32-358.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/22-02:34:07-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: yamamoto Machine: dhcp006.tkl.iis.u-tokyo.ac.jp Platform: Linux PlatformVersion: 2.6.32-358.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/22-02:34:07-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: yamamoto Machine: dhcp006.tkl.iis.u-tokyo.ac.jp Platform: Linux PlatformVersion: 2.6.32-358.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/22-02:34:07-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: yamamoto Machine: dhcp006.tkl.iis.u-tokyo.ac.jp Platform: Linux PlatformVersion: 2.6.32-358.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/22-02:34:07-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: yamamoto Machine: dhcp006.tkl.iis.u-tokyo.ac.jp Platform: Linux PlatformVersion: 2.6.32-358.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/22-02:34:07-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: yamamoto Machine: dhcp006.tkl.iis.u-tokyo.ac.jp Platform: Linux PlatformVersion: 2.6.32-358.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/22-02:34:07-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: yamamoto Machine: dhcp006.tkl.iis.u-tokyo.ac.jp Platform: Linux PlatformVersion: 2.6.32-358.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/22-02:34:07-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: yamamoto Machine: dhcp006.tkl.iis.u-tokyo.ac.jp Platform: Linux PlatformVersion: 2.6.32-358.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/22-02:34:07-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: yamamoto Machine: dhcp006.tkl.iis.u-tokyo.ac.jp Platform: Linux PlatformVersion: 2.6.32-358.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/22-02:34:07-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: yamamoto Machine: dhcp006.tkl.iis.u-tokyo.ac.jp Platform: Linux PlatformVersion: 2.6.32-358.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/22-02:34:07-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: yamamoto Machine: dhcp006.tkl.iis.u-tokyo.ac.jp Platform: Linux PlatformVersion: 2.6.32-358.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/22-02:34:07-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: yamamoto Machine: dhcp006.tkl.iis.u-tokyo.ac.jp Platform: Linux PlatformVersion: 2.6.32-358.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/22-02:34:07-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: yamamoto Machine: dhcp006.tkl.iis.u-tokyo.ac.jp Platform: Linux PlatformVersion: 2.6.32-358.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/22-02:34:07-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: yamamoto Machine: dhcp006.tkl.iis.u-tokyo.ac.jp Platform: Linux PlatformVersion: 2.6.32-358.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/22-02:34:07-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: yamamoto Machine: dhcp006.tkl.iis.u-tokyo.ac.jp Platform: Linux PlatformVersion: 2.6.32-358.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer/5.3.0/dist/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /usr/local/freesurfer/5.3.0/dist/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /home/yamamoto/freesurfer/5.3.0/dist/subjects/test mri_convert /home/yamamoto/freesurfer/5.3.0/dist/subjects/sample-001.mgz /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri/orig/001.mgz mri_convert /home/yamamoto/freesurfer/5.3.0/dist/subjects/sample-001.mgz /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/yamamoto/freesurfer/5.3.0/dist/subjects/sample-001.mgz... TR=7.25, TE=3.22, TI=600.00, flip angle=7.00 i_ras = (-0, -1, -0) j_ras = (-0, 0, -1) k_ras = (-1, 0, 0) writing to /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri/orig/001.mgz... /home/yamamoto/freesurfer/5.3.0/dist/subjects/test mri_convert /home/yamamoto/freesurfer/5.3.0/dist/subjects/sample-002.mgz /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri/orig/002.mgz mri_convert /home/yamamoto/freesurfer/5.3.0/dist/subjects/sample-002.mgz /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri/orig/002.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/yamamoto/freesurfer/5.3.0/dist/subjects/sample-002.mgz... TR=7.25, TE=3.22, TI=600.00, flip angle=7.00 i_ras = (-0, -1, -0) j_ras = (-0, 0, -1) k_ras = (-1, 0, 0) writing to /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri/orig/002.mgz... #-------------------------------------------- #@# MotionCor Wed May 22 11:34:17 JST 2013 Found 2 runs /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri/orig/001.mgz /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri/orig/002.mgz Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... /home/yamamoto/freesurfer/5.3.0/dist/subjects/test mri_robust_template --mov /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri/orig/001.mgz /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri/orig/002.mgz --average 1 --template /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri/rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --iscaleout /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri/orig/001-iscale.txt /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri/orig/002-iscale.txt --subsample 200 --lta /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri/orig/001.lta /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri/orig/002.lta $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ --mov: Using /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri/orig/001.mgz as movable/source volume. --mov: Using /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri/orig/002.mgz as movable/source volume. Total: 2 input volumes --average: Using method 1 for template computation. --template: Using /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri/rawavg.mgz as template output volume. --satit: Will estimate SAT iteratively! --inittp: Using TP 1 as target for initialization --fixtp: Will map everything to init TP! --noit: Will output only first template (no iterations)! --iscale: Enableing intensity scaling! --iscaleout: Will perform intensity scaling and output results --subsample: Will subsample if size is larger than 200 on all axes! --lta: Will output LTA transforms reading source '/home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri/orig/001.mgz'... converting source '/home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri/orig/001.mgz' to bspline ... MRItoBSpline degree 3 reading source '/home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri/orig/002.mgz'... converting source '/home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri/orig/002.mgz' to bspline ... MRItoBSpline degree 3 MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) : [init] ========================= TP 2 to TP 1 ============================== Register TP 2 ( /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri/orig/002.mgz ) to TP 1 ( /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri/orig/001.mgz ) -- Original : (1, 1, 1.32812) mm size and (256, 256, 128) voxels. -- Resampled: (1, 1, 1) mm size and (256, 256, 170) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3 -- Original : (1, 1, 1.32812) mm size and (256, 256, 128) voxels. -- Resampled: (1, 1, 1) mm size and (256, 256, 170) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3 - Max Resolution used: 2 -- gpS ( 64 , 64 , 42 ) -- gpT ( 64 , 64 , 42 ) - running loop to estimate saturation parameter: Adjusting final transform due to non isotropic voxels ... Adjusting final transform due to non isotropic voxels ... mapping movs and creating initial template... allow intensity scaling using median Writing final template: /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri/rawavg.mgz Writing final transforms (warps etc.)... Determinant( lta[ 0 ]) : 1 Determinant( lta[ 1 ]) : 1 registration took 1 minutes and 40 seconds. Thank you for using RobustTemplate! If you find it useful and use it for a publication, please cite: Within-Subject Template Estimation for Unbiased Longitudinal Image Analysis M. Reuter, N.J. Schmansky, H.D. Rosas, B. Fischl. NeuroImage 2012. http://dx.doi.org/10.1016/j.neuroimage.2012.02.084 http://reuter.mit.edu/papers/reuter-long12.pdf /home/yamamoto/freesurfer/5.3.0/dist/subjects/test mri_convert /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri/rawavg.mgz /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri/orig.mgz --conform mri_convert /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri/rawavg.mgz /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri/rawavg.mgz... TR=7.25, TE=3.22, TI=600.00, flip angle=7.00 i_ras = (-0, -1, -0) j_ras = (-0, 0, -1) k_ras = (-1, 0, 0) Original Data has (1, 1, 1.32812) mm size and (256, 256, 128) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri/orig.mgz... mri_add_xform_to_header -c /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri/transforms/talairach.xfm /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri/orig.mgz /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Wed May 22 11:36:03 JST 2013 /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Wed May 22 11:37:03 JST 2013 /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7197, pval=0.4932 >= threshold=0.0050) awk -f /usr/local/freesurfer/5.3.0/dist/bin/extract_talairach_avi_QA.awk /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri/transforms/talairach_avi.log tal_QC_AZS /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri/transforms/talairach_avi.log TalAviQA: 0.98354 z-score: 1 #-------------------------------------------- #@# Nu Intensity Correction Wed May 22 11:37:03 JST 2013 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri /usr/local/freesurfer/5.3.0/dist/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ Linux dhcp006.tkl.iis.u-tokyo.ac.jp 2.6.32-358.6.2.el6.x86_64 #1 SMP Thu May 16 20:59:36 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux Wed May 22 11:37:03 JST 2013 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.6019 /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.6019/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.6019/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig.mgz... TR=7.25, TE=3.22, TI=600.00, flip angle=7.00 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.6019/nu0.mnc... -------------------------------------------------------- Iteration 1 Wed May 22 11:37:04 JST 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.6019/nu0.mnc ./tmp.mri_nu_correct.mni.6019/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.6019/0/ [yamamoto@dhcp006.tkl.iis.u-tokyo.ac.jp:/home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri/] [2013-05-22 11:37:04] running: /usr/local/freesurfer/5.3.0/dist/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.6019/0/ ./tmp.mri_nu_correct.mni.6019/nu0.mnc ./tmp.mri_nu_correct.mni.6019/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 Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 24 CV of field change: 0.000960512 [yamamoto@dhcp006.tkl.iis.u-tokyo.ac.jp:/home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri/] [2013-05-22 11:37:17] running: /usr/local/freesurfer/5.3.0/dist/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.6019/nu0.mnc ./tmp.mri_nu_correct.mni.6019/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done -------------------------------------------------------- Iteration 2 Wed May 22 11:37:19 JST 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.6019/nu1.mnc ./tmp.mri_nu_correct.mni.6019/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.6019/1/ [yamamoto@dhcp006.tkl.iis.u-tokyo.ac.jp:/home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri/] [2013-05-22 11:37:19] running: /usr/local/freesurfer/5.3.0/dist/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.6019/1/ ./tmp.mri_nu_correct.mni.6019/nu1.mnc ./tmp.mri_nu_correct.mni.6019/nu2.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 Processing:.................................................................Done Number of iterations: 18 CV of field change: 0.000952646 [yamamoto@dhcp006.tkl.iis.u-tokyo.ac.jp:/home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri/] [2013-05-22 11:37:29] running: /usr/local/freesurfer/5.3.0/dist/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.6019/nu1.mnc ./tmp.mri_nu_correct.mni.6019/1//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.6019/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.6019/ones.mgz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.6019/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.6019/ones.mgz sysname Linux hostname dhcp006.tkl.iis.u-tokyo.ac.jp machine x86_64 user yamamoto input ./tmp.mri_nu_correct.mni.6019/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.6019/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.6019/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.6019/sum.junk --avgwf ./tmp.mri_nu_correct.mni.6019/input.mean.dat $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.6019/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.6019/sum.junk --avgwf ./tmp.mri_nu_correct.mni.6019/input.mean.dat sysname Linux hostname dhcp006.tkl.iis.u-tokyo.ac.jp machine x86_64 user yamamoto UseRobust 0 Loading ./tmp.mri_nu_correct.mni.6019/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 16777216.000 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.6019/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.6019/ones.mgz --i ./tmp.mri_nu_correct.mni.6019/nu2.mnc --sum ./tmp.mri_nu_correct.mni.6019/sum.junk --avgwf ./tmp.mri_nu_correct.mni.6019/output.mean.dat $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.6019/ones.mgz --i ./tmp.mri_nu_correct.mni.6019/nu2.mnc --sum ./tmp.mri_nu_correct.mni.6019/sum.junk --avgwf ./tmp.mri_nu_correct.mni.6019/output.mean.dat sysname Linux hostname dhcp006.tkl.iis.u-tokyo.ac.jp machine x86_64 user yamamoto UseRobust 0 Loading ./tmp.mri_nu_correct.mni.6019/ones.mgz Loading ./tmp.mri_nu_correct.mni.6019/nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 16777216.000 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.6019/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.6019/nu2.mnc ./tmp.mri_nu_correct.mni.6019/nu2.mnc mul 1.03893033372461743569 Saving result to './tmp.mri_nu_correct.mni.6019/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.6019/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.6019/nu2.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.6019/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 6 seconds. mapping (13, 164) to ( 3, 110) Wed May 22 11:37:56 JST 2013 mri_nu_correct.mni done mri_add_xform_to_header -c /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Wed May 22 11:37:57 JST 2013 /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.105 -0.009 -0.015 -5.386; -0.008 0.948 0.290 -46.903; 0.014 -0.258 1.062 24.150; 0.000 0.000 0.000 1.000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 20 Starting OpenSpline(): npoints = 20 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 111 white matter peak found at 108 gm peak at 59 (59), valley at 36 (36) csf peak at 29, setting threshold to 49 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 58 (58), valley at 21 (21) csf peak at 29, setting threshold to 48 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 1 minutes and 32 seconds. #-------------------------------------------- #@# Skull Stripping Wed May 22 11:39:29 JST 2013 /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri mri_em_register -skull nu.mgz /usr/local/freesurfer/5.3.0/dist/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta ======= NUMBER OF OPENMP THREADS = 8 ======= aligning to atlas containing skull, setting unknown_nbr_spacing = 5 reading 1 input volumes... logging results to talairach_with_skull.log reading '/usr/local/freesurfer/5.3.0/dist/average/RB_all_withskull_2008-03-26.gca'... average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu.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=5.0 skull bounding box = (45, 44, 16) --> (211, 255, 240) using (100, 114, 128) as brain centroid... mean wm in atlas = 126, using box (80,88,100) --> (120, 140,155) to find MRI wm before smoothing, mri peak at 105 after smoothing, mri peak at 105, scaling input intensities by 1.200 scaling channel 0 by 1.2 initial log_p = -4.6 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.413473 @ (-9.091, -27.273, -9.091) max log p = -4.284189 @ (4.545, 13.636, -4.545) max log p = -4.261134 @ (2.273, -2.273, 2.273) max log p = -4.239956 @ (-1.136, -3.409, 1.136) max log p = -4.214496 @ (1.705, 1.705, 1.705) max log p = -4.214496 @ (0.000, 0.000, 0.000) Found translation: (-1.7, -17.6, -8.5): log p = -4.214 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-4.2 (thresh=-4.2) 1.150 0.000 0.000 -20.824; 0.000 1.038 0.278 -47.310; 0.000 -0.259 0.966 31.285; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.9, old_max_log_p =-4.0 (thresh=-3.9) 1.064 0.000 0.000 -9.830; 0.000 1.194 0.320 -72.574; 0.000 -0.259 0.966 31.285; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.064 0.000 0.000 -9.830; 0.000 1.194 0.320 -72.574; 0.000 -0.259 0.966 31.285; 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=-3.8, old_max_log_p =-3.9 (thresh=-3.9) 1.103 -0.043 -0.012 -9.644; 0.031 1.170 0.314 -74.623; 0.000 -0.254 0.948 30.812; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 1.103 -0.043 -0.012 -9.644; 0.031 1.170 0.314 -74.623; 0.000 -0.254 0.948 30.812; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 1.107 -0.046 -0.004 -10.747; 0.031 1.168 0.305 -73.318; -0.009 -0.245 0.953 30.607; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 1.107 -0.046 -0.004 -10.747; 0.031 1.167 0.304 -73.090; -0.009 -0.245 0.953 30.607; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 1.107 -0.046 -0.004 -10.747; 0.031 1.167 0.304 -73.090; -0.009 -0.245 0.953 30.607; 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 1.10672 -0.04562 -0.00388 -10.74661; 0.03133 1.16700 0.30446 -73.08980; -0.00878 -0.24455 0.95265 30.60730; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.10672 -0.04562 -0.00388 -10.74661; 0.03133 1.16700 0.30446 -73.08980; -0.00878 -0.24455 0.95265 30.60730; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.107 -0.046 -0.004 -10.747; 0.031 1.167 0.304 -73.090; -0.009 -0.245 0.953 30.607; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.8 (old=-4.6) transform before final EM align: 1.107 -0.046 -0.004 -10.747; 0.031 1.167 0.304 -73.090; -0.009 -0.245 0.953 30.607; 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 1.10672 -0.04562 -0.00388 -10.74661; 0.03133 1.16700 0.30446 -73.08980; -0.00878 -0.24455 0.95265 30.60730; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.10672 -0.04562 -0.00388 -10.74661; 0.03133 1.16700 0.30446 -73.08980; -0.00878 -0.24455 0.95265 30.60730; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 012: -log(p) = 4.2 tol 0.000000 final transform: 1.107 -0.046 -0.004 -10.747; 0.031 1.167 0.304 -73.090; -0.009 -0.245 0.953 30.607; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 7 minutes and 58 seconds. mri_watershed -T1 -brain_atlas /usr/local/freesurfer/5.3.0/dist/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) ********************************************************* 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=129 y=123 z=120 r=88 first estimation of the main basin volume: 2905514 voxels Looking for seedpoints 2 found in the cerebellum 17 found in the rest of the brain global maximum in x=150, y=116, z=78, Imax=255 CSF=15, 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=21469392614 voxels, voxel volume =1.000 = 21469392614 mmm3 = 21469392.896 cm3 done. PostAnalyze...Basin Prior 126 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=128,y=129, z=113, r=10568 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=5, CSF_MAX=44 , nb = 42256 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=23 , nb = -1029805253 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=21 , nb = 1107860192 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=41 , nb = 1083351462 LEFT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=48 , nb = 1082267792 OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=53 , nb = 1065932874 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 44, 38, 35, 57 after analyzing : 29, 38, 38, 42 RIGHT_CER before analyzing : 23, 30, 38, 57 after analyzing : 23, 35, 38, 40 LEFT_CER before analyzing : 21, 29, 38, 59 after analyzing : 21, 35, 38, 41 RIGHT_BRAIN before analyzing : 41, 36, 34, 57 after analyzing : 29, 36, 36, 41 LEFT_BRAIN before analyzing : 48, 39, 35, 57 after analyzing : 31, 39, 39, 43 OTHER before analyzing : 53, 68, 75, 95 after analyzing : 53, 72, 75, 77 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...63 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.012 curvature mean = 70.153, std = 8.679 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 0.85, sigma = 1.56 after rotation: sse = 0.85, sigma = 1.56 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 0.85, its var is 1.26 before Erosion-Dilatation 0.00% of inacurate vertices after Erosion-Dilatation 0.00% 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...52 iterations mri_strip_skull: done peeling brain Brain Size = 1687406 voxels, voxel volume = 1.000 mm3 = 1687406 mmm3 = 1687.406 cm3 ****************************** Saving brainmask.auto.mgz done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Wed May 22 11:47:45 JST 2013 /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /usr/local/freesurfer/5.3.0/dist/average/RB_all_2008-03-26.gca transforms/talairach.lta ======= NUMBER OF OPENMP THREADS = 8 ======= aligning to atlas containing skull, setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/usr/local/freesurfer/5.3.0/dist/average/RB_all_2008-03-26.gca'... average std = 6.9 using min determinant for regularization = 4.7 0 singular and 1812 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 14.9 or > 790.2 total sample mean = 84.4 (994 zeros) ************************************************ spacing=8, using 2772 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2772, passno 0, spacing 8 resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=22.1 skull bounding box = (63, 69, 36) --> (192, 210, 204) using (106, 116, 120) as brain centroid... mean wm in atlas = 107, using box (90,99,99) --> (121, 133,140) to find MRI wm before smoothing, mri peak at 107 after smoothing, mri peak at 106, scaling input intensities by 1.009 scaling channel 0 by 1.00943 initial log_p = -4.2 ************************************************ First Search limited to translation only. ************************************************ max log p = -3.914970 @ (-9.091, -9.091, -9.091) max log p = -3.832740 @ (4.545, -4.545, -4.545) max log p = -3.754328 @ (2.273, 2.273, 2.273) max log p = -3.754328 @ (0.000, 0.000, 0.000) max log p = -3.744413 @ (0.568, 0.568, -0.568) max log p = -3.744413 @ (0.000, 0.000, 0.000) Found translation: (-1.7, -10.8, -11.9): log p = -3.744 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.5, old_max_log_p =-3.7 (thresh=-3.7) 1.064 0.000 0.000 -9.897; 0.000 1.111 0.298 -60.064; 0.000 -0.236 0.883 39.996; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.5, old_max_log_p =-3.5 (thresh=-3.5) 1.064 0.000 0.000 -9.897; 0.000 1.111 0.298 -60.064; 0.000 -0.254 0.949 35.097; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.5, old_max_log_p =-3.5 (thresh=-3.5) 1.064 0.000 0.000 -9.897; 0.000 1.111 0.298 -60.064; 0.000 -0.254 0.949 35.097; 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=-3.3, old_max_log_p =-3.5 (thresh=-3.5) 1.103 -0.008 0.031 -19.243; 0.000 1.089 0.292 -56.584; -0.037 -0.259 0.966 34.728; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.2, old_max_log_p =-3.3 (thresh=-3.3) 1.103 -0.008 0.031 -19.243; 0.002 1.125 0.232 -54.787; -0.035 -0.180 0.946 26.476; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 5 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.2, old_max_log_p =-3.2 (thresh=-3.2) 1.103 -0.008 0.031 -19.243; 0.002 1.125 0.232 -54.787; -0.035 -0.180 0.946 26.476; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.2, old_max_log_p =-3.2 (thresh=-3.2) 1.107 0.002 0.025 -19.617; -0.007 1.117 0.247 -54.719; -0.026 -0.198 0.940 27.850; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 7 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.2, old_max_log_p =-3.2 (thresh=-3.2) 1.108 0.002 0.026 -19.788; -0.007 1.119 0.247 -54.922; -0.026 -0.198 0.940 27.850; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 8 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.2, old_max_log_p =-3.2 (thresh=-3.2) 1.108 0.002 0.026 -19.788; -0.007 1.119 0.247 -54.922; -0.026 -0.198 0.940 27.850; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2772 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.10846 0.00244 0.02551 -19.78843; -0.00718 1.11879 0.24699 -54.92196; -0.02624 -0.19803 0.94032 27.84964; 0.00000 0.00000 0.00000 1.00000; nsamples 2772 Quasinewton: input matrix 1.10846 0.00244 0.02551 -19.78843; -0.00718 1.11879 0.24699 -54.92196; -0.02624 -0.19803 0.94032 27.84964; 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: 011: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.108 0.002 0.026 -19.788; -0.007 1.119 0.247 -54.922; -0.026 -0.198 0.940 27.850; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.2 (old=-4.2) transform before final EM align: 1.108 0.002 0.026 -19.788; -0.007 1.119 0.247 -54.922; -0.026 -0.198 0.940 27.850; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 312841 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.10846 0.00244 0.02551 -19.78843; -0.00718 1.11879 0.24699 -54.92196; -0.02624 -0.19803 0.94032 27.84964; 0.00000 0.00000 0.00000 1.00000; nsamples 312841 Quasinewton: input matrix 1.10846 0.00244 0.02551 -19.78843; -0.00718 1.11879 0.24699 -54.92196; -0.02624 -0.19803 0.94032 27.84964; 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: 013: -log(p) = 3.8 tol 0.000000 final transform: 1.108 0.002 0.026 -19.788; -0.007 1.119 0.247 -54.922; -0.026 -0.198 0.940 27.850; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach.lta... registration took 6 minutes and 49 seconds. #-------------------------------------- #@# CA Normalize Wed May 22 11:54:34 JST 2013 /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /usr/local/freesurfer/5.3.0/dist/average/RB_all_2008-03-26.gca transforms/talairach.lta norm.mgz writing control point volume to ctrl_pts.mgz using MR volume brainmask.mgz to mask input volume... reading 1 input volume reading atlas from '/usr/local/freesurfer/5.3.0/dist/average/RB_all_2008-03-26.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=22.1 skull bounding box = (63, 69, 36) --> (192, 210, 204) using (106, 116, 120) as brain centroid... mean wm in atlas = 107, using box (90,99,99) --> (121, 133,140) to find MRI wm before smoothing, mri peak at 107 after smoothing, mri peak at 106, scaling input intensities by 1.009 scaling channel 0 by 1.00943 using 244171 sample points... INFO: compute sample coordinates transform 1.108 0.002 0.026 -19.788; -0.007 1.119 0.247 -54.922; -0.026 -0.198 0.940 27.850; 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 (128, 72, 35) --> (188, 175, 206) Left_Cerebral_White_Matter: limiting intensities to 98.0 --> 181.0 0 of 18 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (71, 73, 33) --> (129, 171, 205) Right_Cerebral_White_Matter: limiting intensities to 107.0 --> 181.0 1 of 9 (11.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (131, 151, 63) --> (174, 191, 118) Left_Cerebellum_White_Matter: limiting intensities to 98.0 --> 181.0 0 of 8 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (87, 151, 60) --> (129, 190, 118) Right_Cerebellum_White_Matter: limiting intensities to 96.0 --> 181.0 0 of 13 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (114, 141, 98) --> (143, 203, 129) Brain_Stem: limiting intensities to 85.0 --> 181.0 0 of 9 (0.0%) samples deleted using 57 total control points for intensity normalization... bias field = 0.927 +- 0.081 0 of 56 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (128, 72, 35) --> (188, 175, 206) Left_Cerebral_White_Matter: limiting intensities to 92.0 --> 172.0 0 of 94 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (71, 73, 33) --> (129, 171, 205) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 172.0 0 of 87 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (131, 151, 63) --> (174, 191, 118) Left_Cerebellum_White_Matter: limiting intensities to 95.0 --> 172.0 8 of 34 (23.5%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (87, 151, 60) --> (129, 190, 118) Right_Cerebellum_White_Matter: limiting intensities to 82.0 --> 172.0 0 of 34 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (114, 141, 98) --> (143, 203, 129) Brain_Stem: limiting intensities to 87.0 --> 172.0 35 of 78 (44.9%) samples deleted using 327 total control points for intensity normalization... bias field = 0.993 +- 0.059 0 of 284 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (128, 72, 35) --> (188, 175, 206) Left_Cerebral_White_Matter: limiting intensities to 87.0 --> 174.0 0 of 204 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (71, 73, 33) --> (129, 171, 205) Right_Cerebral_White_Matter: limiting intensities to 91.0 --> 174.0 0 of 210 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (131, 151, 63) --> (174, 191, 118) Left_Cerebellum_White_Matter: limiting intensities to 80.0 --> 174.0 0 of 36 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (87, 151, 60) --> (129, 190, 118) Right_Cerebellum_White_Matter: limiting intensities to 78.0 --> 174.0 0 of 53 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (114, 141, 98) --> (143, 203, 129) Brain_Stem: limiting intensities to 84.0 --> 174.0 59 of 127 (46.5%) samples deleted using 630 total control points for intensity normalization... bias field = 1.004 +- 0.046 0 of 571 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 11 seconds. #-------------------------------------- #@# CA Reg Wed May 22 11:55:45 JST 2013 /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /usr/local/freesurfer/5.3.0/dist/average/RB_all_2008-03-26.gca transforms/talairach.m3z not handling expanded ventricles... using previously computed transform transforms/talairach.lta renormalizing sequences with structure alignment, equivalent to: -renormalize -regularize_mean 0.500 -regularize 0.500 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log ======= NUMBER OF OPENMP THREADS = 8 ======= reading input volume 'norm.mgz'... reading GCA '/usr/local/freesurfer/5.3.0/dist/average/RB_all_2008-03-26.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.22 (predicted orig area = 6.6) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.039 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.808, neg=0, invalid=96777 0001: dt=129.472000, rms=0.759 (6.141%), neg=0, invalid=96777 0002: dt=295.936000, rms=0.735 (3.089%), neg=0, invalid=96777 0003: dt=110.976000, rms=0.721 (1.964%), neg=0, invalid=96777 0004: dt=129.472000, rms=0.717 (0.506%), neg=0, invalid=96777 0005: dt=517.888000, rms=0.708 (1.335%), neg=0, invalid=96777 0006: dt=73.984000, rms=0.704 (0.558%), neg=0, invalid=96777 0007: dt=517.888000, rms=0.700 (0.509%), neg=0, invalid=96777 0008: dt=129.472000, rms=0.697 (0.474%), neg=0, invalid=96777 0009: dt=129.472000, rms=0.696 (0.126%), neg=0, invalid=96777 0010: dt=129.472000, rms=0.695 (0.187%), neg=0, invalid=96777 0011: dt=129.472000, rms=0.693 (0.277%), neg=0, invalid=96777 0012: dt=129.472000, rms=0.690 (0.336%), neg=0, invalid=96777 0013: dt=129.472000, rms=0.688 (0.363%), neg=0, invalid=96777 0014: dt=129.472000, rms=0.685 (0.419%), neg=0, invalid=96777 0015: dt=129.472000, rms=0.682 (0.407%), neg=0, invalid=96777 0016: dt=129.472000, rms=0.680 (0.345%), neg=0, invalid=96777 0017: dt=129.472000, rms=0.678 (0.282%), neg=0, invalid=96777 0018: dt=129.472000, rms=0.676 (0.263%), neg=0, invalid=96777 0019: dt=129.472000, rms=0.674 (0.291%), neg=0, invalid=96777 0020: dt=129.472000, rms=0.672 (0.267%), neg=0, invalid=96777 0021: dt=129.472000, rms=0.671 (0.233%), neg=0, invalid=96777 0022: dt=129.472000, rms=0.669 (0.204%), neg=0, invalid=96777 0023: dt=129.472000, rms=0.668 (0.188%), neg=0, invalid=96777 0024: dt=129.472000, rms=0.667 (0.204%), neg=0, invalid=96777 0025: dt=129.472000, rms=0.666 (0.176%), neg=0, invalid=96777 0026: dt=129.472000, rms=0.665 (0.147%), neg=0, invalid=96777 0027: dt=129.472000, rms=0.664 (0.145%), neg=0, invalid=96777 0028: dt=129.472000, rms=0.663 (0.172%), neg=0, invalid=96777 0029: dt=129.472000, rms=0.661 (0.182%), neg=0, invalid=96777 0030: dt=129.472000, rms=0.660 (0.144%), neg=0, invalid=96777 0031: dt=129.472000, rms=0.660 (0.105%), neg=0, invalid=96777 0032: dt=129.472000, rms=0.659 (0.127%), neg=0, invalid=96777 0033: dt=129.472000, rms=0.658 (0.155%), neg=0, invalid=96777 0034: dt=129.472000, rms=0.657 (0.127%), neg=0, invalid=96777 0035: dt=129.472000, rms=0.657 (0.071%), neg=0, invalid=96777 0036: dt=129.472000, rms=0.656 (0.065%), neg=0, invalid=96777 0037: dt=129.472000, rms=0.656 (0.073%), neg=0, invalid=96777 0038: dt=0.000000, rms=0.656 (-0.001%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.656, neg=0, invalid=96777 0039: dt=32.368000, rms=0.656 (0.012%), neg=0, invalid=96777 0040: dt=55.488000, rms=0.656 (0.009%), neg=0, invalid=96777 0041: dt=55.488000, rms=0.655 (0.011%), neg=0, invalid=96777 0042: dt=55.488000, rms=0.655 (0.019%), neg=0, invalid=96777 0043: dt=55.488000, rms=0.655 (0.007%), neg=0, invalid=96777 0044: dt=55.488000, rms=0.655 (0.015%), neg=0, invalid=96777 0045: dt=55.488000, rms=0.655 (0.037%), neg=0, invalid=96777 0046: dt=55.488000, rms=0.655 (0.050%), neg=0, invalid=96777 0047: dt=55.488000, rms=0.654 (0.060%), neg=0, invalid=96777 0048: dt=55.488000, rms=0.654 (0.061%), neg=0, invalid=96777 0049: dt=55.488000, rms=0.654 (0.045%), neg=0, invalid=96777 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.659, neg=0, invalid=96777 0050: dt=145.152000, rms=0.652 (1.067%), neg=0, invalid=96777 0051: dt=103.680000, rms=0.647 (0.745%), neg=0, invalid=96777 0052: dt=62.208000, rms=0.643 (0.723%), neg=0, invalid=96777 0053: dt=25.920000, rms=0.642 (0.100%), neg=0, invalid=96777 0054: dt=25.920000, rms=0.641 (0.156%), neg=0, invalid=96777 0055: dt=25.920000, rms=0.639 (0.265%), neg=0, invalid=96777 0056: dt=25.920000, rms=0.637 (0.352%), neg=0, invalid=96777 0057: dt=25.920000, rms=0.634 (0.410%), neg=0, invalid=96777 0058: dt=25.920000, rms=0.631 (0.457%), neg=0, invalid=96777 0059: dt=25.920000, rms=0.628 (0.483%), neg=0, invalid=96777 0060: dt=25.920000, rms=0.625 (0.473%), neg=0, invalid=96777 0061: dt=25.920000, rms=0.623 (0.443%), neg=0, invalid=96777 0062: dt=25.920000, rms=0.620 (0.406%), neg=0, invalid=96777 0063: dt=25.920000, rms=0.618 (0.380%), neg=0, invalid=96777 0064: dt=25.920000, rms=0.616 (0.355%), neg=0, invalid=96777 0065: dt=25.920000, rms=0.613 (0.339%), neg=0, invalid=96777 0066: dt=25.920000, rms=0.611 (0.319%), neg=0, invalid=96777 0067: dt=25.920000, rms=0.610 (0.260%), neg=0, invalid=96777 0068: dt=25.920000, rms=0.609 (0.207%), neg=0, invalid=96777 0069: dt=25.920000, rms=0.608 (0.167%), neg=0, invalid=96777 0070: dt=25.920000, rms=0.607 (0.165%), neg=0, invalid=96777 0071: dt=25.920000, rms=0.605 (0.189%), neg=0, invalid=96777 0072: dt=25.920000, rms=0.605 (0.156%), neg=0, invalid=96777 0073: dt=25.920000, rms=0.604 (0.132%), neg=0, invalid=96777 0074: dt=25.920000, rms=0.603 (0.098%), neg=0, invalid=96777 0075: dt=25.920000, rms=0.603 (0.080%), neg=0, invalid=96777 0076: dt=145.152000, rms=0.602 (0.068%), neg=0, invalid=96777 0077: dt=145.152000, rms=0.602 (-0.580%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.602, neg=0, invalid=96777 0078: dt=31.104000, rms=0.602 (0.061%), neg=0, invalid=96777 0079: dt=82.944000, rms=0.601 (0.105%), neg=0, invalid=96777 0080: dt=36.288000, rms=0.601 (0.012%), neg=0, invalid=96777 0081: dt=36.288000, rms=0.601 (0.010%), neg=0, invalid=96777 0082: dt=36.288000, rms=0.601 (-0.005%), neg=0, invalid=96777 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.622, neg=0, invalid=96777 0083: dt=1.600000, rms=0.622 (0.004%), neg=0, invalid=96777 0084: dt=0.175000, rms=0.622 (0.001%), neg=0, invalid=96777 0085: dt=0.175000, rms=0.622 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.622, neg=0, invalid=96777 0086: dt=0.000000, rms=0.622 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.683, neg=0, invalid=96777 0087: dt=5.388379, rms=0.665 (2.663%), neg=0, invalid=96777 0088: dt=1.375000, rms=0.665 (0.030%), neg=0, invalid=96777 0089: dt=1.375000, rms=0.665 (-0.010%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.665, neg=0, invalid=96777 0090: dt=0.000000, rms=0.665 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 5.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.729, neg=0, invalid=96777 0091: dt=1.325527, rms=0.723 (0.798%), neg=0, invalid=96777 0092: dt=2.070000, rms=0.716 (0.924%), neg=0, invalid=96777 0093: dt=0.448000, rms=0.716 (0.073%), neg=0, invalid=96777 0094: dt=0.448000, rms=0.716 (0.023%), neg=0, invalid=96777 0095: dt=0.448000, rms=0.716 (0.010%), neg=0, invalid=96777 0096: dt=0.448000, rms=0.716 (-0.006%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.716, neg=0, invalid=96777 0097: dt=1.792000, rms=0.713 (0.328%), neg=0, invalid=96777 0098: dt=0.096000, rms=0.713 (-0.000%), neg=0, invalid=96777 0099: dt=0.096000, rms=0.713 (0.002%), neg=0, invalid=96777 0100: dt=0.096000, rms=0.713 (-0.000%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 10.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.672, neg=0, invalid=96777 0101: dt=0.320000, rms=0.656 (2.333%), neg=0, invalid=96777 0102: dt=0.000000, rms=0.656 (0.001%), neg=0, invalid=96777 0103: dt=0.050000, rms=0.656 (-0.446%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.656, neg=0, invalid=96777 0104: dt=0.000000, rms=0.656 (0.000%), neg=0, invalid=96777 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11725 (24) mri peak = 0.15859 ( 6) Left_Lateral_Ventricle (4): linear fit = 0.20 x + 0.0 (1090 voxels, overlap=0.006) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (1090 voxels, peak = 5), gca=9.6 gca peak = 0.14022 (22) mri peak = 0.15911 ( 6) Right_Lateral_Ventricle (43): linear fit = 0.22 x + 0.0 (437 voxels, overlap=0.007) Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (437 voxels, peak = 5), gca=8.8 gca peak = 0.24234 (100) mri peak = 0.09735 (99) Right_Pallidum (52): linear fit = 0.98 x + 0.0 (340 voxels, overlap=0.910) Right_Pallidum (52): linear fit = 0.98 x + 0.0 (340 voxels, peak = 98), gca=97.5 gca peak = 0.19192 (97) mri peak = 0.06173 (91) Left_Pallidum (13): linear fit = 0.94 x + 0.0 (263 voxels, overlap=0.621) Left_Pallidum (13): linear fit = 0.94 x + 0.0 (263 voxels, peak = 91), gca=90.7 gca peak = 0.24007 (63) mri peak = 0.08008 (58) Right_Hippocampus (53): linear fit = 0.90 x + 0.0 (443 voxels, overlap=0.941) Right_Hippocampus (53): linear fit = 0.90 x + 0.0 (443 voxels, peak = 57), gca=57.0 gca peak = 0.29892 (64) mri peak = 0.08500 (56) Left_Hippocampus (17): linear fit = 0.88 x + 0.0 (570 voxels, overlap=0.713) Left_Hippocampus (17): linear fit = 0.88 x + 0.0 (570 voxels, peak = 56), gca=56.0 gca peak = 0.12541 (104) mri peak = 0.07075 (109) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (68600 voxels, overlap=0.760) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (68600 voxels, peak = 110), gca=109.7 gca peak = 0.13686 (104) mri peak = 0.06712 (106) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (71378 voxels, overlap=0.772) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (71378 voxels, peak = 109), gca=108.7 gca peak = 0.11691 (63) mri peak = 0.04693 (56) Left_Cerebral_Cortex (3): linear fit = 0.85 x + 0.0 (18103 voxels, overlap=0.496) Left_Cerebral_Cortex (3): linear fit = 0.85 x + 0.0 (18103 voxels, peak = 53), gca=53.2 gca peak = 0.13270 (63) mri peak = 0.04410 (55) Right_Cerebral_Cortex (42): linear fit = 0.86 x + 0.0 (19606 voxels, overlap=0.382) Right_Cerebral_Cortex (42): linear fit = 0.86 x + 0.0 (19606 voxels, peak = 54), gca=53.9 gca peak = 0.15182 (70) mri peak = 0.07947 (69) Right_Caudate (50): linear fit = 0.94 x + 0.0 (628 voxels, overlap=0.893) Right_Caudate (50): linear fit = 0.94 x + 0.0 (628 voxels, peak = 65), gca=65.4 gca peak = 0.14251 (76) mri peak = 0.07000 (69) Left_Caudate (11): linear fit = 0.89 x + 0.0 (622 voxels, overlap=0.637) Left_Caudate (11): linear fit = 0.89 x + 0.0 (622 voxels, peak = 68), gca=68.0 gca peak = 0.12116 (60) mri peak = 0.03914 (56) Left_Cerebellum_Cortex (8): linear fit = 0.92 x + 0.0 (11159 voxels, overlap=0.732) Left_Cerebellum_Cortex (8): linear fit = 0.92 x + 0.0 (11159 voxels, peak = 55), gca=54.9 gca peak = 0.12723 (61) mri peak = 0.04309 (56) Right_Cerebellum_Cortex (47): linear fit = 0.92 x + 0.0 (11912 voxels, overlap=0.845) Right_Cerebellum_Cortex (47): linear fit = 0.92 x + 0.0 (11912 voxels, peak = 56), gca=55.8 gca peak = 0.22684 (88) mri peak = 0.06006 (95) Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (5994 voxels, overlap=0.582) Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (5994 voxels, peak = 95), gca=95.5 gca peak = 0.21067 (87) mri peak = 0.07853 (91) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (6150 voxels, overlap=0.807) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (6150 voxels, peak = 94), gca=93.5 gca peak = 0.25455 (62) mri peak = 0.10082 (61) Left_Amygdala (18): linear fit = 0.96 x + 0.0 (369 voxels, overlap=0.992) Left_Amygdala (18): linear fit = 0.96 x + 0.0 (369 voxels, peak = 60), gca=59.8 gca peak = 0.39668 (62) mri peak = 0.08832 (64) Right_Amygdala (54): linear fit = 0.95 x + 0.0 (389 voxels, overlap=0.993) Right_Amygdala (54): linear fit = 0.95 x + 0.0 (389 voxels, peak = 59), gca=59.2 gca peak = 0.10129 (93) mri peak = 0.05457 (99) Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (5284 voxels, overlap=0.748) Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (5284 voxels, peak = 99), gca=99.0 gca peak = 0.12071 (89) mri peak = 0.05516 (96) Right_Thalamus_Proper (49): linear fit = 1.08 x + 0.0 (4253 voxels, overlap=0.710) Right_Thalamus_Proper (49): linear fit = 1.08 x + 0.0 (4253 voxels, peak = 96), gca=95.7 gca peak = 0.13716 (82) mri peak = 0.04947 (85) Left_Putamen (12): linear fit = 1.05 x + 0.0 (2110 voxels, overlap=1.002) Left_Putamen (12): linear fit = 1.05 x + 0.0 (2110 voxels, peak = 87), gca=86.5 gca peak = 0.15214 (84) mri peak = 0.04170 (90) Right_Putamen (51): linear fit = 0.99 x + 0.0 (2090 voxels, overlap=0.980) Right_Putamen (51): linear fit = 0.99 x + 0.0 (2090 voxels, peak = 83), gca=82.7 gca peak = 0.08983 (85) mri peak = 0.06366 (89) Brain_Stem (16): linear fit = 1.03 x + 0.0 (12295 voxels, overlap=0.778) Brain_Stem (16): linear fit = 1.03 x + 0.0 (12295 voxels, peak = 88), gca=88.0 gca peak = 0.11809 (92) mri peak = 0.06699 (93) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (915 voxels, overlap=0.729) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (915 voxels, peak = 101), gca=100.7 gca peak = 0.12914 (94) mri peak = 0.06524 (103) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (1084 voxels, overlap=0.799) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (1084 voxels, peak = 102), gca=102.0 gca peak = 0.21100 (36) mri peak = 0.11271 (53) gca peak = 0.13542 (27) mri peak = 0.21409 ( 6) Fourth_Ventricle (15): linear fit = 0.19 x + 0.0 (207 voxels, overlap=0.013) Fourth_Ventricle (15): linear fit = 0.19 x + 0.0 (207 voxels, peak = 5), gca=5.0 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) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means estimating mean gm scale to be 0.90 x + 0.0 estimating mean wm scale to be 1.05 x + 0.0 estimating mean csf scale to be 0.40 x + 0.0 saving intensity scales to talairach.label_intensities.txt **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.703, neg=0, invalid=96777 0105: dt=129.472000, rms=0.696 (0.925%), neg=0, invalid=96777 0106: dt=129.472000, rms=0.694 (0.392%), neg=0, invalid=96777 0107: dt=129.472000, rms=0.692 (0.231%), neg=0, invalid=96777 0108: dt=110.976000, rms=0.691 (0.209%), neg=0, invalid=96777 0109: dt=110.976000, rms=0.690 (0.133%), neg=0, invalid=96777 0110: dt=129.472000, rms=0.688 (0.171%), neg=0, invalid=96777 0111: dt=92.480000, rms=0.688 (0.072%), neg=0, invalid=96777 0112: dt=221.952000, rms=0.687 (0.191%), neg=0, invalid=96777 0113: dt=32.368000, rms=0.686 (0.057%), neg=0, invalid=96777 0114: dt=129.472000, rms=0.686 (0.065%), neg=0, invalid=96777 0115: dt=129.472000, rms=0.685 (0.103%), neg=0, invalid=96777 0116: dt=32.368000, rms=0.685 (0.029%), neg=0, invalid=96777 0117: dt=32.368000, rms=0.685 (0.021%), neg=0, invalid=96777 0118: dt=32.368000, rms=0.685 (0.032%), neg=0, invalid=96777 0119: dt=32.368000, rms=0.684 (0.040%), neg=0, invalid=96777 0120: dt=32.368000, rms=0.684 (0.061%), neg=0, invalid=96777 0121: dt=32.368000, rms=0.683 (0.073%), neg=0, invalid=96777 0122: dt=32.368000, rms=0.683 (0.073%), neg=0, invalid=96777 0123: dt=32.368000, rms=0.682 (0.076%), neg=0, invalid=96777 0124: dt=32.368000, rms=0.682 (0.071%), neg=0, invalid=96777 0125: dt=32.368000, rms=0.681 (0.070%), neg=0, invalid=96777 0126: dt=32.368000, rms=0.681 (0.067%), neg=0, invalid=96777 0127: dt=32.368000, rms=0.680 (0.068%), neg=0, invalid=96777 0128: dt=32.368000, rms=0.680 (0.063%), neg=0, invalid=96777 0129: dt=32.368000, rms=0.680 (0.064%), neg=0, invalid=96777 0130: dt=32.368000, rms=0.679 (0.060%), neg=0, invalid=96777 0131: dt=32.368000, rms=0.679 (0.059%), neg=0, invalid=96777 0132: dt=32.368000, rms=0.678 (0.055%), neg=0, invalid=96777 0133: dt=32.368000, rms=0.678 (0.056%), neg=0, invalid=96777 0134: dt=32.368000, rms=0.678 (0.052%), neg=0, invalid=96777 0135: dt=32.368000, rms=0.677 (0.046%), neg=0, invalid=96777 0136: dt=32.368000, rms=0.677 (0.045%), neg=0, invalid=96777 0137: dt=32.368000, rms=0.677 (0.045%), neg=0, invalid=96777 0138: dt=32.368000, rms=0.676 (0.045%), neg=0, invalid=96777 0139: dt=32.368000, rms=0.676 (0.043%), neg=0, invalid=96777 0140: dt=32.368000, rms=0.676 (0.044%), neg=0, invalid=96777 0141: dt=32.368000, rms=0.676 (0.047%), neg=0, invalid=96777 0142: dt=32.368000, rms=0.675 (0.044%), neg=0, invalid=96777 0143: dt=32.368000, rms=0.675 (0.045%), neg=0, invalid=96777 0144: dt=32.368000, rms=0.675 (0.040%), neg=0, invalid=96777 0145: dt=32.368000, rms=0.674 (0.035%), neg=0, invalid=96777 0146: dt=32.368000, rms=0.674 (0.037%), neg=0, invalid=96777 0147: dt=32.368000, rms=0.674 (0.029%), neg=0, invalid=96777 0148: dt=32.368000, rms=0.674 (0.029%), neg=0, invalid=96777 0149: dt=32.368000, rms=0.674 (0.033%), neg=0, invalid=96777 0150: dt=32.368000, rms=0.673 (0.030%), neg=0, invalid=96777 0151: dt=32.368000, rms=0.673 (0.030%), neg=0, invalid=96777 0152: dt=32.368000, rms=0.673 (0.025%), neg=0, invalid=96777 0153: dt=32.368000, rms=0.673 (0.028%), neg=0, invalid=96777 0154: dt=32.368000, rms=0.673 (0.029%), neg=0, invalid=96777 0155: dt=32.368000, rms=0.672 (0.031%), neg=0, invalid=96777 0156: dt=32.368000, rms=0.672 (0.026%), neg=0, invalid=96777 0157: dt=32.368000, rms=0.672 (0.025%), neg=0, invalid=96777 0158: dt=32.368000, rms=0.672 (0.029%), neg=0, invalid=96777 0159: dt=32.368000, rms=0.672 (0.028%), neg=0, invalid=96777 0160: dt=32.368000, rms=0.671 (0.027%), neg=0, invalid=96777 0161: dt=32.368000, rms=0.671 (0.028%), neg=0, invalid=96777 0162: dt=32.368000, rms=0.671 (0.031%), neg=0, invalid=96777 0163: dt=32.368000, rms=0.671 (0.033%), neg=0, invalid=96777 0164: dt=32.368000, rms=0.671 (0.031%), neg=0, invalid=96777 0165: dt=32.368000, rms=0.670 (0.027%), neg=0, invalid=96777 0166: dt=32.368000, rms=0.670 (0.027%), neg=0, invalid=96777 0167: dt=32.368000, rms=0.670 (0.022%), neg=0, invalid=96777 0168: dt=32.368000, rms=0.670 (0.021%), neg=0, invalid=96777 0169: dt=517.888000, rms=0.670 (0.047%), neg=0, invalid=96777 0170: dt=13.872000, rms=0.670 (-0.003%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.670, neg=0, invalid=96777 0171: dt=92.480000, rms=0.669 (0.049%), neg=0, invalid=96777 0172: dt=295.936000, rms=0.669 (0.099%), neg=0, invalid=96777 0173: dt=92.480000, rms=0.668 (0.048%), neg=0, invalid=96777 0174: dt=92.480000, rms=0.668 (0.055%), neg=0, invalid=96777 0175: dt=92.480000, rms=0.668 (0.044%), neg=0, invalid=96777 0176: dt=92.480000, rms=0.667 (0.041%), neg=0, invalid=96777 0177: dt=92.480000, rms=0.667 (0.024%), neg=0, invalid=96777 0178: dt=92.480000, rms=0.667 (0.051%), neg=0, invalid=96777 0179: dt=92.480000, rms=0.667 (0.056%), neg=0, invalid=96777 0180: dt=92.480000, rms=0.666 (0.048%), neg=0, invalid=96777 0181: dt=92.480000, rms=0.666 (0.041%), neg=0, invalid=96777 0182: dt=92.480000, rms=0.666 (0.043%), neg=0, invalid=96777 0183: dt=92.480000, rms=0.665 (0.058%), neg=0, invalid=96777 0184: dt=92.480000, rms=0.665 (0.042%), neg=0, invalid=96777 0185: dt=92.480000, rms=0.665 (0.042%), neg=0, invalid=96777 0186: dt=92.480000, rms=0.665 (0.033%), neg=0, invalid=96777 0187: dt=92.480000, rms=0.664 (0.053%), neg=0, invalid=96777 0188: dt=92.480000, rms=0.664 (0.064%), neg=0, invalid=96777 0189: dt=92.480000, rms=0.663 (0.039%), neg=0, invalid=96777 0190: dt=92.480000, rms=0.663 (0.039%), neg=0, invalid=96777 0191: dt=92.480000, rms=0.663 (0.025%), neg=0, invalid=96777 0192: dt=92.480000, rms=0.663 (0.039%), neg=0, invalid=96777 0193: dt=92.480000, rms=0.663 (0.037%), neg=0, invalid=96777 0194: dt=92.480000, rms=0.662 (0.023%), neg=0, invalid=96777 0195: dt=92.480000, rms=0.662 (0.030%), neg=0, invalid=96777 0196: dt=92.480000, rms=0.662 (0.040%), neg=0, invalid=96777 0197: dt=92.480000, rms=0.662 (0.042%), neg=0, invalid=96777 0198: dt=92.480000, rms=0.662 (0.017%), neg=0, invalid=96777 0199: dt=92.480000, rms=0.661 (0.029%), neg=0, invalid=96777 0200: dt=92.480000, rms=0.661 (0.042%), neg=0, invalid=96777 0201: dt=92.480000, rms=0.661 (0.025%), neg=0, invalid=96777 0202: dt=92.480000, rms=0.661 (0.012%), neg=0, invalid=96777 0203: dt=92.480000, rms=0.661 (0.031%), neg=0, invalid=96777 0204: dt=92.480000, rms=0.660 (0.049%), neg=0, invalid=96777 0205: dt=92.480000, rms=0.660 (0.035%), neg=0, invalid=96777 0206: dt=92.480000, rms=0.660 (0.024%), neg=0, invalid=96777 0207: dt=92.480000, rms=0.660 (0.019%), neg=0, invalid=96777 0208: dt=92.480000, rms=0.660 (0.006%), neg=0, invalid=96777 0209: dt=92.480000, rms=0.660 (-0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.660, neg=0, invalid=96777 0210: dt=103.680000, rms=0.656 (0.646%), neg=0, invalid=96777 0211: dt=36.288000, rms=0.654 (0.363%), neg=0, invalid=96777 0212: dt=145.152000, rms=0.647 (0.988%), neg=0, invalid=96777 0213: dt=20.736000, rms=0.646 (0.158%), neg=0, invalid=96777 0214: dt=145.152000, rms=0.642 (0.579%), neg=0, invalid=96777 0215: dt=36.288000, rms=0.641 (0.241%), neg=0, invalid=96777 0216: dt=145.152000, rms=0.638 (0.437%), neg=0, invalid=96777 0217: dt=2.268000, rms=0.638 (0.032%), neg=0, invalid=96777 0218: dt=0.283500, rms=0.638 (0.015%), neg=0, invalid=96777 0219: dt=0.070875, rms=0.638 (0.000%), neg=0, invalid=96777 0220: dt=0.004430, rms=0.638 (0.000%), neg=0, invalid=96777 0221: dt=0.001107, rms=0.638 (0.000%), neg=0, invalid=96777 0222: dt=0.000000, rms=0.638 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.638, neg=0, invalid=96777 0223: dt=0.000000, rms=0.638 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.640, neg=0, invalid=96777 0224: dt=0.000000, rms=0.640 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.640, neg=0, invalid=96777 0225: dt=0.000000, rms=0.640 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.649, neg=0, invalid=96777 0226: dt=1.008000, rms=0.644 (0.800%), neg=0, invalid=96777 0227: dt=2.880000, rms=0.630 (2.094%), neg=0, invalid=96777 0228: dt=11.520000, rms=0.591 (6.273%), neg=0, invalid=96777 0229: dt=11.520000, rms=0.578 (2.162%), neg=0, invalid=96777 0230: dt=16.128000, rms=0.570 (1.374%), neg=0, invalid=96777 0231: dt=3.287356, rms=0.569 (0.258%), neg=0, invalid=96777 0232: dt=8.666667, rms=0.567 (0.333%), neg=0, invalid=96777 0233: dt=3.456000, rms=0.566 (0.117%), neg=0, invalid=96777 0234: dt=8.266667, rms=0.565 (0.231%), neg=0, invalid=96777 0235: dt=4.032000, rms=0.564 (0.087%), neg=0, invalid=96777 0236: dt=6.222222, rms=0.564 (0.145%), neg=0, invalid=96777 0237: dt=4.032000, rms=0.563 (0.082%), neg=0, invalid=96777 0238: dt=11.520000, rms=0.562 (0.139%), neg=0, invalid=96777 0239: dt=2.680000, rms=0.562 (0.103%), neg=0, invalid=96777 0240: dt=13.824000, rms=0.561 (0.148%), neg=0, invalid=96777 0241: dt=3.741935, rms=0.560 (0.095%), neg=0, invalid=96777 0242: dt=6.912000, rms=0.560 (0.077%), neg=0, invalid=96777 0243: dt=4.032000, rms=0.560 (0.042%), neg=0, invalid=96777 0244: dt=4.032000, rms=0.559 (0.055%), neg=0, invalid=96777 0245: dt=4.032000, rms=0.559 (0.068%), neg=0, invalid=96777 0246: dt=4.032000, rms=0.558 (0.101%), neg=0, invalid=96777 0247: dt=4.032000, rms=0.558 (0.103%), neg=0, invalid=96777 0248: dt=4.032000, rms=0.557 (0.141%), neg=0, invalid=96777 0249: dt=4.032000, rms=0.556 (0.132%), neg=0, invalid=96777 0250: dt=4.032000, rms=0.556 (0.130%), neg=0, invalid=96777 0251: dt=4.032000, rms=0.555 (0.127%), neg=0, invalid=96777 0252: dt=4.032000, rms=0.554 (0.113%), neg=0, invalid=96777 0253: dt=4.032000, rms=0.554 (0.094%), neg=0, invalid=96777 0254: dt=4.032000, rms=0.553 (0.094%), neg=0, invalid=96777 0255: dt=4.032000, rms=0.553 (0.083%), neg=0, invalid=96777 0256: dt=4.032000, rms=0.552 (0.062%), neg=0, invalid=96777 0257: dt=4.032000, rms=0.552 (0.063%), neg=0, invalid=96777 0258: dt=4.032000, rms=0.552 (0.042%), neg=0, invalid=96777 0259: dt=4.032000, rms=0.552 (0.050%), neg=0, invalid=96777 0260: dt=4.032000, rms=0.551 (0.049%), neg=0, invalid=96777 0261: dt=4.032000, rms=0.551 (0.041%), neg=0, invalid=96777 0262: dt=4.032000, rms=0.551 (0.036%), neg=0, invalid=96777 0263: dt=4.032000, rms=0.551 (0.049%), neg=0, invalid=96777 0264: dt=4.032000, rms=0.550 (0.040%), neg=0, invalid=96777 0265: dt=4.032000, rms=0.550 (0.038%), neg=0, invalid=96777 0266: dt=4.032000, rms=0.550 (0.050%), neg=0, invalid=96777 0267: dt=4.032000, rms=0.550 (0.029%), neg=0, invalid=96777 0268: dt=4.032000, rms=0.550 (0.023%), neg=0, invalid=96777 0269: dt=4.032000, rms=0.549 (0.031%), neg=0, invalid=96777 0270: dt=4.032000, rms=0.549 (0.010%), neg=0, invalid=96777 0271: dt=4.032000, rms=0.549 (0.023%), neg=0, invalid=96777 0272: dt=4.032000, rms=0.549 (0.016%), neg=0, invalid=96777 0273: dt=4.032000, rms=0.549 (0.027%), neg=0, invalid=96777 0274: dt=2.304000, rms=0.549 (0.003%), neg=0, invalid=96777 0275: dt=2.304000, rms=0.549 (-0.004%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.549, neg=0, invalid=96777 0276: dt=0.720000, rms=0.549 (0.001%), neg=0, invalid=96777 0277: dt=0.000000, rms=0.549 (0.004%), neg=0, invalid=96777 0278: dt=0.000000, rms=0.549 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.569, neg=0, invalid=96777 0279: dt=0.000000, rms=0.569 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.569, neg=0, invalid=96777 0280: dt=0.000000, rms=0.569 (0.000%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.536, neg=0, invalid=96777 0281: dt=0.174797, rms=0.528 (1.477%), neg=0, invalid=96777 0282: dt=0.007000, rms=0.527 (0.034%), neg=0, invalid=96777 0283: dt=0.007000, rms=0.527 (0.039%), neg=0, invalid=96777 0284: dt=0.007000, rms=0.527 (0.076%), neg=0, invalid=96777 0285: dt=0.007000, rms=0.526 (0.101%), neg=0, invalid=96777 0286: dt=0.007000, rms=0.526 (0.127%), neg=0, invalid=96777 0287: dt=0.007000, rms=0.525 (0.154%), neg=0, invalid=96777 0288: dt=0.007000, rms=0.524 (0.166%), neg=0, invalid=96777 0289: dt=0.007000, rms=0.523 (0.177%), neg=0, invalid=96777 0290: dt=0.007000, rms=0.522 (0.190%), neg=0, invalid=96777 0291: dt=0.007000, rms=0.521 (0.195%), neg=0, invalid=96777 0292: dt=0.007000, rms=0.520 (0.201%), neg=0, invalid=96777 0293: dt=0.007000, rms=0.519 (0.193%), neg=0, invalid=96777 0294: dt=0.007000, rms=0.518 (0.199%), neg=0, invalid=96777 0295: dt=0.007000, rms=0.517 (0.194%), neg=0, invalid=96777 0296: dt=0.007000, rms=0.516 (0.186%), neg=0, invalid=96777 0297: dt=0.007000, rms=0.515 (0.179%), neg=0, invalid=96777 0298: dt=0.007000, rms=0.514 (0.173%), neg=0, invalid=96777 0299: dt=0.007000, rms=0.513 (0.161%), neg=0, invalid=96777 0300: dt=0.007000, rms=0.513 (0.005%), neg=0, invalid=96777 0301: dt=0.007000, rms=0.513 (0.006%), neg=0, invalid=96777 0302: dt=0.007000, rms=0.513 (0.012%), neg=0, invalid=96777 0303: dt=0.007000, rms=0.513 (0.019%), neg=0, invalid=96777 0304: dt=0.007000, rms=0.513 (0.024%), neg=0, invalid=96777 0305: dt=0.007000, rms=0.513 (0.022%), neg=0, invalid=96777 0306: dt=0.448000, rms=0.511 (0.332%), neg=0, invalid=96777 0307: dt=0.005001, rms=0.511 (0.005%), neg=0, invalid=96777 0308: dt=0.005001, rms=0.511 (0.003%), neg=0, invalid=96777 0309: dt=0.005001, rms=0.511 (0.005%), neg=0, invalid=96777 0310: dt=0.005001, rms=0.511 (0.008%), neg=0, invalid=96777 0311: dt=0.005001, rms=0.511 (0.009%), neg=0, invalid=96777 0312: dt=0.005001, rms=0.511 (0.009%), neg=0, invalid=96777 0313: dt=0.005001, rms=0.511 (0.003%), neg=0, invalid=96777 0314: dt=0.112000, rms=0.511 (0.064%), neg=0, invalid=96777 0315: dt=0.028000, rms=0.511 (0.014%), neg=0, invalid=96777 0316: dt=0.028000, rms=0.510 (0.011%), neg=0, invalid=96777 0317: dt=0.028000, rms=0.510 (0.028%), neg=0, invalid=96777 0318: dt=0.028000, rms=0.510 (0.036%), neg=0, invalid=96777 0319: dt=0.014000, rms=0.510 (0.009%), neg=0, invalid=96777 0320: dt=0.014000, rms=0.510 (0.005%), neg=0, invalid=96777 0321: dt=0.112000, rms=0.510 (0.050%), neg=0, invalid=96777 0322: dt=0.112000, rms=0.510 (0.044%), neg=0, invalid=96777 0323: dt=0.056000, rms=0.509 (0.025%), neg=0, invalid=96777 0324: dt=0.056000, rms=0.509 (0.044%), neg=0, invalid=96777 0325: dt=0.028000, rms=0.509 (0.004%), neg=0, invalid=96777 0326: dt=0.007000, rms=0.509 (-0.001%), neg=0, invalid=96777 0327: dt=0.007000, rms=0.509 (0.002%), neg=0, invalid=96777 0328: dt=0.112000, rms=0.509 (0.040%), neg=0, invalid=96777 0329: dt=0.112000, rms=0.509 (0.039%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.509, neg=0, invalid=96777 0330: dt=0.115919, rms=0.507 (0.368%), neg=0, invalid=96777 0331: dt=0.007000, rms=0.507 (0.019%), neg=0, invalid=96777 0332: dt=0.007000, rms=0.507 (0.015%), neg=0, invalid=96777 0333: dt=0.007000, rms=0.507 (0.035%), neg=0, invalid=96777 0334: dt=0.007000, rms=0.506 (0.042%), neg=0, invalid=96777 0335: dt=0.007000, rms=0.506 (0.058%), neg=0, invalid=96777 0336: dt=0.007000, rms=0.506 (0.063%), neg=0, invalid=96777 0337: dt=0.007000, rms=0.505 (0.069%), neg=0, invalid=96777 0338: dt=0.007000, rms=0.505 (0.075%), neg=0, invalid=96777 0339: dt=0.007000, rms=0.505 (0.082%), neg=0, invalid=96777 0340: dt=0.007000, rms=0.504 (0.083%), neg=0, invalid=96777 0341: dt=0.007000, rms=0.504 (0.081%), neg=0, invalid=96777 0342: dt=0.007000, rms=0.503 (0.082%), neg=0, invalid=96777 0343: dt=0.007000, rms=0.503 (0.079%), neg=0, invalid=96777 0344: dt=0.007000, rms=0.503 (0.080%), neg=0, invalid=96777 0345: dt=0.007000, rms=0.502 (0.076%), neg=0, invalid=96777 0346: dt=0.007000, rms=0.502 (0.072%), neg=0, invalid=96777 0347: dt=0.007000, rms=0.502 (0.063%), neg=0, invalid=96777 0348: dt=0.007000, rms=0.501 (0.062%), neg=0, invalid=96777 0349: dt=0.007000, rms=0.501 (0.054%), neg=0, invalid=96777 0350: dt=0.007000, rms=0.501 (0.049%), neg=0, invalid=96777 0351: dt=0.007000, rms=0.501 (0.042%), neg=0, invalid=96777 0352: dt=0.007000, rms=0.500 (0.039%), neg=0, invalid=96777 0353: dt=0.007000, rms=0.500 (0.037%), neg=0, invalid=96777 0354: dt=0.007000, rms=0.500 (0.033%), neg=0, invalid=96777 0355: dt=0.007000, rms=0.500 (0.022%), neg=0, invalid=96777 0356: dt=0.007000, rms=0.500 (0.020%), neg=0, invalid=96777 0357: dt=0.000000, rms=0.500 (-0.000%), neg=0, invalid=96777 label assignment complete, 0 changed (0.00%) ********************************************************************************************* ********************************************************************************************* ********************************************************************************************* ********************* ALLOWING NEGATIVE NODES IN DEFORMATION ******************************** ********************************************************************************************* ********************************************************************************************* ********************************************************************************************* **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.498, neg=0, invalid=96777 0358: dt=0.027094, rms=0.498 (0.000%), neg=0, invalid=96777 0359: dt=0.027094, rms=0.498 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.498, neg=0, invalid=96777 0360: dt=129.472000, rms=0.497 (0.068%), neg=0, invalid=96777 0361: dt=129.472000, rms=0.497 (0.037%), neg=0, invalid=96777 0362: dt=129.472000, rms=0.497 (0.020%), neg=0, invalid=96777 0363: dt=129.472000, rms=0.497 (0.038%), neg=0, invalid=96777 0364: dt=129.472000, rms=0.497 (0.039%), neg=0, invalid=96777 0365: dt=129.472000, rms=0.497 (0.016%), neg=0, invalid=96777 0366: dt=129.472000, rms=0.497 (0.028%), neg=0, invalid=96777 0367: dt=129.472000, rms=0.497 (0.003%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.497, neg=0, invalid=96777 0368: dt=36.288000, rms=0.496 (0.127%), neg=0, invalid=96777 0369: dt=36.288000, rms=0.496 (0.064%), neg=0, invalid=96777 0370: dt=36.288000, rms=0.495 (0.036%), neg=0, invalid=96777 0371: dt=36.288000, rms=0.495 (0.043%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0372: dt=36.288000, rms=0.495 (-0.025%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.495, neg=0, invalid=96777 0373: dt=36.288000, rms=0.494 (0.236%), neg=0, invalid=96777 0374: dt=36.288000, rms=0.494 (0.110%), neg=0, invalid=96777 0375: dt=36.288000, rms=0.493 (0.096%), neg=0, invalid=96777 0376: dt=36.288000, rms=0.492 (0.143%), neg=0, invalid=96777 0377: dt=36.288000, rms=0.492 (0.148%), neg=0, invalid=96777 0378: dt=36.288000, rms=0.491 (0.154%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0379: dt=36.288000, rms=0.490 (0.162%), neg=0, invalid=96777 0380: dt=36.288000, rms=0.489 (0.116%), neg=0, invalid=96777 0381: dt=36.288000, rms=0.489 (0.119%), neg=0, invalid=96777 0382: dt=36.288000, rms=0.488 (0.091%), neg=0, invalid=96777 0383: dt=25.920000, rms=0.488 (0.017%), neg=0, invalid=96777 0384: dt=25.920000, rms=0.488 (0.019%), neg=0, invalid=96777 0385: dt=25.920000, rms=0.488 (0.021%), neg=0, invalid=96777 0386: dt=25.920000, rms=0.488 (0.027%), neg=0, invalid=96777 0387: dt=25.920000, rms=0.488 (0.028%), neg=0, invalid=96777 0388: dt=25.920000, rms=0.488 (0.027%), neg=0, invalid=96777 0389: dt=25.920000, rms=0.488 (0.046%), neg=0, invalid=96777 0390: dt=25.920000, rms=0.487 (0.031%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.488, neg=0, invalid=96777 iter 0, gcam->neg = 5 after 6 iterations, nbhd size=1, neg = 0 0391: dt=38.400000, rms=0.485 (0.542%), neg=0, invalid=96777 iter 0, gcam->neg = 11 after 7 iterations, nbhd size=1, neg = 0 0392: dt=38.400000, rms=0.483 (0.394%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 0393: dt=11.200000, rms=0.482 (0.201%), neg=0, invalid=96777 0394: dt=11.200000, rms=0.481 (0.149%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 6 iterations, nbhd size=1, neg = 0 0395: dt=11.200000, rms=0.481 (0.185%), neg=0, invalid=96777 iter 0, gcam->neg = 4 after 7 iterations, nbhd size=1, neg = 0 0396: dt=11.200000, rms=0.480 (0.224%), neg=0, invalid=96777 iter 0, gcam->neg = 6 after 1 iterations, nbhd size=0, neg = 0 0397: dt=11.200000, rms=0.479 (0.205%), neg=0, invalid=96777 iter 0, gcam->neg = 5 after 9 iterations, nbhd size=1, neg = 0 0398: dt=11.200000, rms=0.477 (0.252%), neg=0, invalid=96777 0399: dt=11.200000, rms=0.476 (0.248%), neg=0, invalid=96777 0400: dt=11.200000, rms=0.475 (0.224%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 0401: dt=11.200000, rms=0.474 (0.150%), neg=0, invalid=96777 0402: dt=11.200000, rms=0.474 (0.158%), neg=0, invalid=96777 0403: dt=11.200000, rms=0.473 (0.127%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0404: dt=11.200000, rms=0.472 (0.157%), neg=0, invalid=96777 0405: dt=11.200000, rms=0.472 (0.114%), neg=0, invalid=96777 0406: dt=11.200000, rms=0.471 (0.118%), neg=0, invalid=96777 0407: dt=11.200000, rms=0.470 (0.155%), neg=0, invalid=96777 0408: dt=11.200000, rms=0.470 (0.138%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 7 iterations, nbhd size=1, neg = 0 0409: dt=11.200000, rms=0.469 (0.122%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 9 iterations, nbhd size=1, neg = 0 0410: dt=11.200000, rms=0.469 (0.082%), neg=0, invalid=96777 0411: dt=11.200000, rms=0.469 (0.065%), neg=0, invalid=96777 0412: dt=11.200000, rms=0.468 (0.014%), neg=0, invalid=96777 0413: dt=11.200000, rms=0.468 (0.010%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 35 iterations, nbhd size=4, neg = 0 0414: dt=11.200000, rms=0.468 (-0.034%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.468, neg=0, invalid=96777 0415: dt=38.400000, rms=0.465 (0.629%), neg=0, invalid=96777 0416: dt=8.412371, rms=0.465 (0.179%), neg=0, invalid=96777 0417: dt=8.412371, rms=0.464 (0.090%), neg=0, invalid=96777 0418: dt=8.412371, rms=0.464 (0.129%), neg=0, invalid=96777 0419: dt=8.412371, rms=0.463 (0.127%), neg=0, invalid=96777 0420: dt=8.412371, rms=0.462 (0.124%), neg=0, invalid=96777 0421: dt=8.412371, rms=0.462 (0.132%), neg=0, invalid=96777 0422: dt=8.412371, rms=0.461 (0.106%), neg=0, invalid=96777 0423: dt=8.412371, rms=0.461 (0.061%), neg=0, invalid=96777 0424: dt=11.200000, rms=0.461 (0.024%), neg=0, invalid=96777 0425: dt=11.200000, rms=0.461 (0.043%), neg=0, invalid=96777 0426: dt=11.200000, rms=0.461 (0.023%), neg=0, invalid=96777 0427: dt=11.200000, rms=0.460 (0.027%), neg=0, invalid=96777 0428: dt=11.200000, rms=0.460 (0.033%), neg=0, invalid=96777 0429: dt=11.200000, rms=0.460 (0.063%), neg=0, invalid=96777 0430: dt=11.200000, rms=0.460 (0.046%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.465, neg=0, invalid=96777 0431: dt=1.008000, rms=0.465 (0.014%), neg=0, invalid=96777 0432: dt=0.432000, rms=0.465 (-0.003%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.465, neg=0, invalid=96777 0433: dt=3.456000, rms=0.465 (0.037%), neg=0, invalid=96777 0434: dt=2.880000, rms=0.465 (0.012%), neg=0, invalid=96777 0435: dt=2.880000, rms=0.465 (-0.009%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.474, neg=0, invalid=96777 0436: dt=0.320000, rms=0.474 (0.013%), neg=0, invalid=96777 0437: dt=0.320000, rms=0.474 (0.007%), neg=0, invalid=96777 0438: dt=0.320000, rms=0.474 (-0.010%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.474, neg=0, invalid=96777 iter 0, gcam->neg = 8 after 1 iterations, nbhd size=0, neg = 0 0439: dt=1.280000, rms=0.473 (0.166%), neg=0, invalid=96777 0440: dt=0.001000, rms=0.473 (0.011%), neg=0, invalid=96777 0441: dt=0.001000, rms=0.473 (0.000%), neg=0, invalid=96777 0442: dt=0.001000, rms=0.473 (0.000%), neg=0, invalid=96777 0443: dt=0.001000, rms=0.473 (-0.000%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.463, neg=0, invalid=96777 iter 0, gcam->neg = 858 after 24 iterations, nbhd size=2, neg = 0 0444: dt=1.694374, rms=0.424 (8.289%), neg=0, invalid=96777 0445: dt=0.000078, rms=0.424 (-0.001%), neg=0, invalid=96777 0446: dt=0.000078, rms=0.424 (0.001%), neg=0, invalid=96777 0447: dt=0.000078, rms=0.424 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.424, neg=0, invalid=96777 0448: dt=0.000438, rms=0.424 (0.001%), neg=0, invalid=96777 0449: dt=0.000000, rms=0.424 (0.000%), neg=0, invalid=96777 label assignment complete, 0 changed (0.00%) label assignment complete, 0 changed (0.00%) ***************** morphing with label term set to 0 ******************************* **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.411, neg=0, invalid=96777 0450: dt=0.000000, rms=0.412 (-0.318%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.412, neg=0, invalid=96777 0451: dt=55.488000, rms=0.412 (0.014%), neg=0, invalid=96777 0452: dt=73.984000, rms=0.412 (0.003%), neg=0, invalid=96777 0453: dt=73.984000, rms=0.412 (0.000%), neg=0, invalid=96777 0454: dt=73.984000, rms=0.412 (-0.002%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.413, neg=0, invalid=96777 0455: dt=0.000000, rms=0.413 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.413, neg=0, invalid=96777 0456: dt=36.288000, rms=0.412 (0.024%), neg=0, invalid=96777 0457: dt=103.680000, rms=0.412 (0.027%), neg=0, invalid=96777 0458: dt=3.888000, rms=0.412 (0.001%), neg=0, invalid=96777 0459: dt=3.888000, rms=0.412 (0.002%), neg=0, invalid=96777 0460: dt=3.888000, rms=0.412 (0.003%), neg=0, invalid=96777 0461: dt=3.888000, rms=0.412 (0.004%), neg=0, invalid=96777 0462: dt=3.888000, rms=0.412 (0.005%), neg=0, invalid=96777 0463: dt=3.888000, rms=0.412 (0.005%), neg=0, invalid=96777 0464: dt=3.888000, rms=0.412 (0.005%), neg=0, invalid=96777 0465: dt=3.888000, rms=0.412 (0.005%), neg=0, invalid=96777 0466: dt=3.888000, rms=0.412 (0.005%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.413, neg=0, invalid=96777 iter 0, gcam->neg = 7 after 32 iterations, nbhd size=3, neg = 0 0467: dt=9.600000, rms=0.413 (0.043%), neg=0, invalid=96777 0468: dt=0.043750, rms=0.413 (0.000%), neg=0, invalid=96777 0469: dt=0.043750, rms=0.413 (0.000%), neg=0, invalid=96777 0470: dt=0.043750, rms=0.413 (0.000%), neg=0, invalid=96777 0471: dt=0.043750, rms=0.413 (0.000%), neg=0, invalid=96777 0472: dt=0.043750, rms=0.413 (0.001%), neg=0, invalid=96777 0473: dt=0.043750, rms=0.413 (0.001%), neg=0, invalid=96777 0474: dt=0.043750, rms=0.413 (0.001%), neg=0, invalid=96777 0475: dt=0.043750, rms=0.413 (0.001%), neg=0, invalid=96777 0476: dt=0.043750, rms=0.413 (0.001%), neg=0, invalid=96777 0477: dt=0.043750, rms=0.413 (0.001%), neg=0, invalid=96777 0478: dt=0.043750, rms=0.413 (0.001%), neg=0, invalid=96777 0479: dt=0.043750, rms=0.413 (0.001%), neg=0, invalid=96777 0480: dt=0.043750, rms=0.413 (0.001%), neg=0, invalid=96777 0481: dt=0.043750, rms=0.413 (0.001%), neg=0, invalid=96777 0482: dt=0.043750, rms=0.413 (0.001%), neg=0, invalid=96777 0483: dt=0.043750, rms=0.413 (0.001%), neg=0, invalid=96777 0484: dt=0.043750, rms=0.413 (0.001%), neg=0, invalid=96777 0485: dt=0.043750, rms=0.413 (0.001%), neg=0, invalid=96777 0486: dt=0.043750, rms=0.413 (0.001%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.413, neg=0, invalid=96777 iter 0, gcam->neg = 10 after 17 iterations, nbhd size=2, neg = 0 0487: dt=44.800000, rms=0.411 (0.413%), neg=0, invalid=96777 0488: dt=2.800000, rms=0.411 (0.013%), neg=0, invalid=96777 0489: dt=2.800000, rms=0.411 (0.028%), neg=0, invalid=96777 0490: dt=2.800000, rms=0.410 (0.048%), neg=0, invalid=96777 0491: dt=2.800000, rms=0.410 (0.057%), neg=0, invalid=96777 0492: dt=2.800000, rms=0.410 (0.052%), neg=0, invalid=96777 0493: dt=2.800000, rms=0.410 (0.051%), neg=0, invalid=96777 iter 0, gcam->neg = 14 after 200 iterations, nbhd size=1, neg = 2 starting rms=0.004, neg=2, removing folds in lattice.... iter 1, dt=0.000219: new neg 0, old_neg 2, delta 2, rms=0.003 (32.861%) 0494: dt=44.800000, rms=0.410 (0.037%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.412, neg=0, invalid=96777 iter 0, gcam->neg = 41 after 200 iterations, nbhd size=4, neg = 4 starting rms=0.004, neg=4, removing folds in lattice.... iter 1, dt=0.000219: new neg 0, old_neg 4, delta 4, rms=0.002 (44.683%) 0495: dt=4.166667, rms=0.411 (0.136%), neg=0, invalid=96777 iter 0, gcam->neg = 23 after 200 iterations, nbhd size=2, neg = 4 starting rms=0.004, neg=4, removing folds in lattice.... iter 1, dt=0.000219: new neg 0, old_neg 4, delta 4, rms=0.002 (45.425%) 0496: dt=4.032000, rms=0.411 (0.098%), neg=0, invalid=96777 iter 0, gcam->neg = 15 after 200 iterations, nbhd size=4, neg = 4 starting rms=0.004, neg=4, removing folds in lattice.... iter 1, dt=0.000125: new neg 0, old_neg 4, delta 4, rms=0.002 (49.453%) 0497: dt=4.032000, rms=0.410 (0.106%), neg=0, invalid=96777 iter 0, gcam->neg = 22 after 200 iterations, nbhd size=1, neg = 4 starting rms=0.005, neg=4, removing folds in lattice.... iter 1, dt=0.000156: new neg 0, old_neg 4, delta 4, rms=0.002 (52.609%) 0498: dt=4.032000, rms=0.410 (0.010%), neg=0, invalid=96777 iter 0, gcam->neg = 19 after 200 iterations, nbhd size=2, neg = 4 starting rms=0.005, neg=4, removing folds in lattice.... iter 1, dt=0.000156: new neg 0, old_neg 4, delta 4, rms=0.002 (56.189%) 0499: dt=4.032000, rms=0.410 (0.043%), neg=0, invalid=96777 iter 0, gcam->neg = 15 after 38 iterations, nbhd size=4, neg = 0 0500: dt=4.032000, rms=0.410 (0.052%), neg=0, invalid=96777 iter 0, gcam->neg = 341 after 200 iterations, nbhd size=1, neg = 2 starting rms=0.004, neg=2, removing folds in lattice.... iter 1, dt=0.000219: new neg 0, old_neg 2, delta 2, rms=0.003 (23.571%) 0501: dt=4.032000, rms=0.410 (-0.316%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.410, neg=0, invalid=96777 0502: dt=0.000984, rms=0.410 (0.000%), neg=0, invalid=96777 iter 0, gcam->neg = 13 after 200 iterations, nbhd size=4, neg = 2 starting rms=0.003, neg=2, removing folds in lattice.... iter 1, dt=0.000750: new neg 0, old_neg 2, delta 2, rms=0.002 (31.808%) 0503: dt=2.880000, rms=0.410 (0.073%), neg=0, invalid=96777 iter 0, gcam->neg = 61 after 200 iterations, nbhd size=2, neg = 2 starting rms=0.004, neg=2, removing folds in lattice.... iter 1, dt=0.000055: new neg 0, old_neg 2, delta 2, rms=0.002 (37.096%) 0504: dt=11.520000, rms=0.408 (0.518%), neg=0, invalid=96777 0505: dt=0.002250, rms=0.408 (0.000%), neg=0, invalid=96777 0506: dt=0.002250, rms=0.408 (0.000%), neg=0, invalid=96777 0507: dt=0.002250, rms=0.408 (0.000%), neg=0, invalid=96777 0508: dt=0.002250, rms=0.408 (0.000%), neg=0, invalid=96777 0509: dt=0.002250, rms=0.408 (0.000%), neg=0, invalid=96777 0510: dt=0.002250, rms=0.408 (0.000%), neg=0, invalid=96777 0511: dt=0.002250, rms=0.408 (0.000%), neg=0, invalid=96777 0512: dt=0.002250, rms=0.408 (0.000%), neg=0, invalid=96777 0513: dt=0.002250, rms=0.408 (0.000%), neg=0, invalid=96777 0514: dt=0.002250, rms=0.408 (0.000%), neg=0, invalid=96777 0515: dt=0.002250, rms=0.408 (0.000%), neg=0, invalid=96777 0516: dt=0.002250, rms=0.408 (0.000%), neg=0, invalid=96777 0517: dt=0.002250, rms=0.408 (0.000%), neg=0, invalid=96777 0518: dt=0.002250, rms=0.408 (0.000%), neg=0, invalid=96777 0519: dt=0.002250, rms=0.408 (0.000%), neg=0, invalid=96777 0520: dt=0.002250, rms=0.408 (0.000%), neg=0, invalid=96777 0521: dt=0.002250, rms=0.408 (0.000%), neg=0, invalid=96777 0522: dt=0.002250, rms=0.408 (0.000%), neg=0, invalid=96777 0523: dt=0.002250, rms=0.408 (0.000%), neg=0, invalid=96777 0524: dt=0.002250, rms=0.408 (0.000%), neg=0, invalid=96777 0525: dt=0.002250, rms=0.408 (0.000%), neg=0, invalid=96777 0526: dt=0.002250, rms=0.408 (0.000%), neg=0, invalid=96777 0527: dt=0.002250, rms=0.408 (0.000%), neg=0, invalid=96777 0528: dt=0.002250, rms=0.408 (0.001%), neg=0, invalid=96777 0529: dt=0.002250, rms=0.408 (0.001%), neg=0, invalid=96777 0530: dt=0.002250, rms=0.408 (0.001%), neg=0, invalid=96777 0531: dt=0.002250, rms=0.408 (0.001%), neg=0, invalid=96777 0532: dt=0.002250, rms=0.408 (0.001%), neg=0, invalid=96777 0533: dt=0.002250, rms=0.408 (0.001%), neg=0, invalid=96777 0534: dt=0.002250, rms=0.408 (0.001%), neg=0, invalid=96777 0535: dt=0.002250, rms=0.408 (0.001%), neg=0, invalid=96777 0536: dt=0.002250, rms=0.408 (0.001%), neg=0, invalid=96777 0537: dt=0.002250, rms=0.408 (0.001%), neg=0, invalid=96777 0538: dt=0.002250, rms=0.408 (0.001%), neg=0, invalid=96777 0539: dt=0.002250, rms=0.408 (0.001%), neg=0, invalid=96777 0540: dt=0.002250, rms=0.407 (0.001%), neg=0, invalid=96777 0541: dt=0.002250, rms=0.407 (0.001%), neg=0, invalid=96777 0542: dt=0.002250, rms=0.407 (0.001%), neg=0, invalid=96777 0543: dt=0.002250, rms=0.407 (0.001%), neg=0, invalid=96777 0544: dt=0.002250, rms=0.407 (0.001%), neg=0, invalid=96777 0545: dt=0.002250, rms=0.407 (0.001%), neg=0, invalid=96777 0546: dt=0.002250, rms=0.407 (0.001%), neg=0, invalid=96777 0547: dt=0.002250, rms=0.407 (0.001%), neg=0, invalid=96777 0548: dt=0.002250, rms=0.407 (0.001%), neg=0, invalid=96777 0549: dt=0.002250, rms=0.407 (0.001%), neg=0, invalid=96777 0550: dt=0.002250, rms=0.407 (0.001%), neg=0, invalid=96777 iter 0, gcam->neg = 44 after 200 iterations, nbhd size=4, neg = 1 starting rms=0.003, neg=1, removing folds in lattice.... iter 1, dt=0.000094: new neg 0, old_neg 1, delta 1, rms=0.002 (35.827%) 0551: dt=13.824000, rms=0.407 (0.233%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 6 iterations, nbhd size=1, neg = 0 0552: dt=1.008000, rms=0.407 (0.006%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.412, neg=0, invalid=96777 0553: dt=0.000000, rms=0.412 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.412, neg=0, invalid=96777 0554: dt=0.000000, rms=0.412 (0.000%), neg=0, invalid=96777 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.403, neg=0, invalid=96777 iter 0, gcam->neg = 584 after 36 iterations, nbhd size=4, neg = 0 0555: dt=0.782297, rms=0.390 (3.296%), neg=0, invalid=96777 0556: dt=0.000000, rms=0.390 (0.000%), neg=0, invalid=96777 iter 0, gcam->neg = 647 after 10 iterations, nbhd size=1, neg = 0 0557: dt=0.050000, rms=0.390 (-0.352%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.390, neg=0, invalid=96777 0558: dt=0.000000, rms=0.390 (0.000%), neg=0, invalid=96777 writing output transformation to transforms/talairach.m3z... GCAMwrite registration took 0 hours, 49 minutes and 8 seconds. #-------------------------------------- #@# CA Reg Inv Wed May 22 12:44:53 JST 2013 /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z Inverting GCAM Saving inverse #-------------------------------------- #@# Remove Neck Wed May 22 12:45:33 JST 2013 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /usr/local/freesurfer/5.3.0/dist/average/RB_all_2008-03-26.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/usr/local/freesurfer/5.3.0/dist/average/RB_all_2008-03-26.gca'... reading input volume 'nu.mgz'... reading transform 'transforms/talairach.m3z'... removing structures at least 25 mm from brain... 10996188 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 0 minutes and 40 seconds. #-------------------------------------- #@# SkullLTA Wed May 22 12:46:13 JST 2013 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /usr/local/freesurfer/5.3.0/dist/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull_2.lta ======= NUMBER OF OPENMP THREADS = 8 ======= aligning to atlas containing skull, setting unknown_nbr_spacing = 5 using previously computed transform transforms/talairach.lta reading 1 input volumes... logging results to talairach_with_skull_2.log reading '/usr/local/freesurfer/5.3.0/dist/average/RB_all_withskull_2008-03-26.gca'... average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu_noneck.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=6.0 skull bounding box = (40, 44, 16) --> (214, 235, 234) using (98, 108, 125) as brain centroid... mean wm in atlas = 126, using box (77,84,98) --> (119, 131,151) to find MRI wm before smoothing, mri peak at 105 after smoothing, mri peak at 105, scaling input intensities by 1.200 scaling channel 0 by 1.2 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.9, old_max_log_p =-4.0 (thresh=-4.0) 1.108 0.002 0.026 -19.788; -0.007 1.119 0.247 -54.922; -0.028 -0.211 1.000 22.865; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.108 0.002 0.026 -19.788; -0.007 1.119 0.247 -54.922; -0.028 -0.211 1.000 22.865; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.8, old_max_log_p =-3.9 (thresh=-3.9) 1.087 0.002 0.025 -16.957; -0.008 1.153 0.289 -62.272; -0.027 -0.244 0.973 32.207; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 1.087 0.002 0.025 -16.957; -0.008 1.153 0.289 -62.272; -0.027 -0.244 0.973 32.207; 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=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 1.090 0.007 0.051 -21.823; -0.016 1.165 0.249 -57.431; -0.054 -0.197 0.983 27.885; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 1.089 -0.001 0.041 -19.074; -0.007 1.165 0.249 -58.627; -0.045 -0.197 0.984 26.119; 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 1.08884 -0.00100 0.04131 -19.07375; -0.00711 1.16495 0.24949 -58.62693; -0.04542 -0.19679 0.98435 26.11882; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.08884 -0.00100 0.04131 -19.07375; -0.00711 1.16495 0.24949 -58.62693; -0.04542 -0.19679 0.98435 26.11882; 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) = -0.0 tol 0.000010 Resulting transform: 1.089 -0.001 0.041 -19.074; -0.007 1.165 0.249 -58.627; -0.045 -0.197 0.984 26.119; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.8 (old=-4.0) transform before final EM align: 1.089 -0.001 0.041 -19.074; -0.007 1.165 0.249 -58.627; -0.045 -0.197 0.984 26.119; 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 1.08884 -0.00100 0.04131 -19.07375; -0.00711 1.16495 0.24949 -58.62693; -0.04542 -0.19679 0.98435 26.11882; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.08884 -0.00100 0.04131 -19.07375; -0.00711 1.16495 0.24949 -58.62693; -0.04542 -0.19679 0.98435 26.11882; 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: 009: -log(p) = 4.2 tol 0.000000 final transform: 1.089 -0.001 0.041 -19.074; -0.007 1.165 0.249 -58.627; -0.045 -0.197 0.984 26.119; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull_2.lta... registration took 6 minutes and 13 seconds. #-------------------------------------- #@# SubCort Seg Wed May 22 12:52:26 JST 2013 mri_ca_label -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/5.3.0/dist/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz sysname Linux hostname dhcp006.tkl.iis.u-tokyo.ac.jp machine x86_64 setenv SUBJECTS_DIR /home/yamamoto/freesurfer/5.3.0/dist/subjects cd /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri mri_ca_label -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/5.3.0/dist/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz renormalizing sequences with structure alignment, equivalent to: -renormalize -renormalize_mean 0.500 -regularize 0.500 reading 1 input volumes... reading classifier array from /usr/local/freesurfer/5.3.0/dist/average/RB_all_2008-03-26.gca... reading input volume from norm.mgz... average std[0] = 6.9 reading transform from transforms/talairach.m3z... Atlas used for the 3D morph was /usr/local/freesurfer/5.3.0/dist/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 = 0.14704 ( 4) Left_Lateral_Ventricle (4): linear fit = 0.12 x + 0.0 (431 voxels, overlap=0.006) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (431 voxels, peak = 3), gca=10.8 gca peak = 0.14982 (20) mri peak = 0.16421 ( 4) Right_Lateral_Ventricle (43): linear fit = 0.05 x + 0.0 (426 voxels, overlap=0.008) Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (426 voxels, peak = 1), gca=8.0 gca peak = 0.28003 (97) mri peak = 0.11985 (99) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (265 voxels, overlap=0.910) Right_Pallidum (52): linear fit = 1.01 x + 0.0 (265 voxels, peak = 98), gca=98.5 gca peak = 0.18160 (96) mri peak = 0.08209 (98) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (256 voxels, overlap=1.030) Left_Pallidum (13): linear fit = 1.02 x + 0.0 (256 voxels, peak = 98), gca=98.4 gca peak = 0.27536 (62) mri peak = 0.08446 (59) Right_Hippocampus (53): linear fit = 0.92 x + 0.0 (439 voxels, overlap=0.474) Right_Hippocampus (53): linear fit = 0.92 x + 0.0 (439 voxels, peak = 57), gca=56.7 gca peak = 0.32745 (63) mri peak = 0.10170 (56) Left_Hippocampus (17): linear fit = 0.88 x + 0.0 (524 voxels, overlap=0.280) Left_Hippocampus (17): linear fit = 0.88 x + 0.0 (524 voxels, peak = 55), gca=55.1 gca peak = 0.08597 (105) mri peak = 0.07097 (109) Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (45951 voxels, overlap=0.701) Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (45951 voxels, peak = 110), gca=109.7 gca peak = 0.09209 (106) mri peak = 0.06732 (111) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (47636 voxels, overlap=0.709) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (47636 voxels, peak = 110), gca=109.7 gca peak = 0.07826 (63) mri peak = 0.04470 (56) Left_Cerebral_Cortex (3): linear fit = 0.88 x + 0.0 (15274 voxels, overlap=0.523) Left_Cerebral_Cortex (3): linear fit = 0.88 x + 0.0 (15274 voxels, peak = 55), gca=55.1 gca peak = 0.08598 (64) mri peak = 0.04273 (54) Right_Cerebral_Cortex (42): linear fit = 0.86 x + 0.0 (16313 voxels, overlap=0.509) Right_Cerebral_Cortex (42): linear fit = 0.86 x + 0.0 (16313 voxels, peak = 55), gca=54.7 gca peak = 0.24164 (71) mri peak = 0.07986 (69) Right_Caudate (50): linear fit = 0.94 x + 0.0 (520 voxels, overlap=1.013) Right_Caudate (50): linear fit = 0.94 x + 0.0 (520 voxels, peak = 67), gca=67.1 gca peak = 0.18227 (75) mri peak = 0.10234 (71) Left_Caudate (11): linear fit = 0.90 x + 0.0 (806 voxels, overlap=0.598) Left_Caudate (11): linear fit = 0.90 x + 0.0 (806 voxels, peak = 68), gca=67.9 gca peak = 0.10629 (62) mri peak = 0.05000 (56) Left_Cerebellum_Cortex (8): linear fit = 0.92 x + 0.0 (11453 voxels, overlap=0.927) Left_Cerebellum_Cortex (8): linear fit = 0.92 x + 0.0 (11453 voxels, peak = 57), gca=56.7 gca peak = 0.11668 (59) mri peak = 0.05275 (56) Right_Cerebellum_Cortex (47): linear fit = 0.92 x + 0.0 (10794 voxels, overlap=0.913) Right_Cerebellum_Cortex (47): linear fit = 0.92 x + 0.0 (10794 voxels, peak = 54), gca=54.0 gca peak = 0.17849 (88) mri peak = 0.08849 (95) Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (3806 voxels, overlap=0.722) Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (3806 voxels, peak = 95), gca=94.6 gca peak = 0.16819 (86) mri peak = 0.09270 (91) Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (3903 voxels, overlap=0.896) Right_Cerebellum_White_Matter (46): linear fit = 1.04 x + 0.0 (3903 voxels, peak = 90), gca=89.9 gca peak = 0.41688 (64) mri peak = 0.10840 (64) Left_Amygdala (18): linear fit = 0.99 x + 0.0 (286 voxels, overlap=1.037) Left_Amygdala (18): linear fit = 0.99 x + 0.0 (286 voxels, peak = 63), gca=63.0 gca peak = 0.42394 (62) mri peak = 0.10830 (64) Right_Amygdala (54): linear fit = 1.03 x + 0.0 (274 voxels, overlap=1.041) Right_Amygdala (54): linear fit = 1.03 x + 0.0 (274 voxels, peak = 64), gca=64.2 gca peak = 0.10041 (96) mri peak = 0.07478 (96) Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (3564 voxels, overlap=0.862) Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (3564 voxels, peak = 98), gca=98.4 gca peak = 0.13978 (88) mri peak = 0.06460 (96) Right_Thalamus_Proper (49): linear fit = 1.09 x + 0.0 (3588 voxels, overlap=0.794) Right_Thalamus_Proper (49): linear fit = 1.09 x + 0.0 (3588 voxels, peak = 95), gca=95.5 gca peak = 0.08514 (81) mri peak = 0.04390 (72) Left_Putamen (12): linear fit = 0.96 x + 0.0 (2415 voxels, overlap=0.992) Left_Putamen (12): linear fit = 0.96 x + 0.0 (2415 voxels, peak = 78), gca=78.2 gca peak = 0.09624 (82) mri peak = 0.04283 (77) Right_Putamen (51): linear fit = 0.93 x + 0.0 (2093 voxels, overlap=0.916) Right_Putamen (51): linear fit = 0.93 x + 0.0 (2093 voxels, peak = 76), gca=75.8 gca peak = 0.07543 (88) mri peak = 0.06535 (89) Brain_Stem (16): linear fit = 1.03 x + 0.0 (10128 voxels, overlap=0.765) Brain_Stem (16): linear fit = 1.03 x + 0.0 (10128 voxels, peak = 91), gca=91.1 gca peak = 0.12757 (95) mri peak = 0.05683 (104) Right_VentralDC (60): linear fit = 1.11 x + 0.0 (883 voxels, overlap=0.717) Right_VentralDC (60): linear fit = 1.11 x + 0.0 (883 voxels, peak = 105), gca=105.0 gca peak = 0.17004 (92) mri peak = 0.07350 (103) Left_VentralDC (28): linear fit = 1.11 x + 0.0 (965 voxels, overlap=0.878) Left_VentralDC (28): linear fit = 1.11 x + 0.0 (965 voxels, peak = 102), gca=101.7 gca peak = 0.21361 (36) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.26069 (23) mri peak = 0.27711 ( 6) Fourth_Ventricle (15): linear fit = 0.22 x + 0.0 (75 voxels, overlap=0.020) Fourth_Ventricle (15): linear fit = 0.22 x + 0.0 (75 voxels, peak = 5), gca=4.9 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.31795 (35) gca peak Third_Ventricle = 0.21361 (36) gca peak Fourth_Ventricle = 0.26069 (23) 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 0.92 x + 0.0 estimating mean wm scale to be 1.04 x + 0.0 estimating mean csf scale to be 0.40 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.31600 (11) mri peak = 0.14704 ( 4) Left_Lateral_Ventricle (4): linear fit = 0.28 x + 0.0 (431 voxels, overlap=0.226) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (431 voxels, peak = 3), gca=4.4 gca peak = 0.29325 ( 9) mri peak = 0.16421 ( 4) Right_Lateral_Ventricle (43): linear fit = 0.34 x + 0.0 (426 voxels, overlap=0.798) Right_Lateral_Ventricle (43): linear fit = 0.40 x + 0.0 (426 voxels, peak = 3), gca=3.6 gca peak = 0.32701 (99) mri peak = 0.11985 (99) Right_Pallidum (52): linear fit = 0.98 x + 0.0 (265 voxels, overlap=0.833) Right_Pallidum (52): linear fit = 0.98 x + 0.0 (265 voxels, peak = 97), gca=96.5 gca peak = 0.16494 (98) mri peak = 0.08209 (98) Left_Pallidum (13): linear fit = 0.99 x + 0.0 (256 voxels, overlap=0.941) Left_Pallidum (13): linear fit = 0.99 x + 0.0 (256 voxels, peak = 97), gca=96.5 gca peak = 0.28673 (57) mri peak = 0.08446 (59) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (439 voxels, overlap=1.005) Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (439 voxels, peak = 57), gca=57.0 gca peak = 0.32450 (55) mri peak = 0.10170 (56) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (524 voxels, overlap=1.008) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (524 voxels, peak = 55), gca=55.0 gca peak = 0.08169 (110) mri peak = 0.07097 (109) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (45951 voxels, overlap=0.835) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (45951 voxels, peak = 110), gca=110.0 gca peak = 0.08542 (110) mri peak = 0.06732 (111) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (47636 voxels, overlap=0.814) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (47636 voxels, peak = 110), gca=110.0 gca peak = 0.09007 (55) mri peak = 0.04470 (56) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (15274 voxels, overlap=0.965) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (15274 voxels, peak = 54), gca=54.2 gca peak = 0.10286 (55) mri peak = 0.04273 (54) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (16313 voxels, overlap=0.979) Right_Cerebral_Cortex (42): linear fit = 1.02 x + 0.0 (16313 voxels, peak = 56), gca=56.4 gca peak = 0.23254 (69) mri peak = 0.07986 (69) Right_Caudate (50): linear fit = 1.00 x + 0.0 (520 voxels, overlap=1.007) Right_Caudate (50): linear fit = 1.00 x + 0.0 (520 voxels, peak = 69), gca=69.0 gca peak = 0.17958 (68) mri peak = 0.10234 (71) Left_Caudate (11): linear fit = 1.00 x + 0.0 (806 voxels, overlap=0.996) Left_Caudate (11): linear fit = 1.00 x + 0.0 (806 voxels, peak = 68), gca=68.0 gca peak = 0.11904 (56) mri peak = 0.05000 (56) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (11453 voxels, overlap=1.000) Left_Cerebellum_Cortex (8): linear fit = 0.99 x + 0.0 (11453 voxels, peak = 55), gca=55.2 gca peak = 0.13000 (55) mri peak = 0.05275 (56) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (10794 voxels, overlap=1.000) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (10794 voxels, peak = 55), gca=54.7 gca peak = 0.17137 (94) mri peak = 0.08849 (95) Left_Cerebellum_White_Matter (7): linear fit = 0.99 x + 0.0 (3806 voxels, overlap=0.989) Left_Cerebellum_White_Matter (7): linear fit = 0.99 x + 0.0 (3806 voxels, peak = 93), gca=92.6 gca peak = 0.15955 (90) mri peak = 0.09270 (91) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (3903 voxels, overlap=0.994) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (3903 voxels, peak = 90), gca=89.6 gca peak = 0.49383 (63) mri peak = 0.10840 (64) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (286 voxels, overlap=1.024) Left_Amygdala (18): linear fit = 1.00 x + 0.0 (286 voxels, peak = 63), gca=63.0 gca peak = 0.40643 (65) mri peak = 0.10830 (64) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (274 voxels, overlap=1.018) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (274 voxels, peak = 65), gca=65.0 gca peak = 0.09901 (97) mri peak = 0.07478 (96) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3564 voxels, overlap=0.961) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (3564 voxels, peak = 97), gca=97.5 gca peak = 0.11706 (95) mri peak = 0.06460 (96) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3588 voxels, overlap=0.893) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (3588 voxels, peak = 95), gca=95.0 gca peak = 0.08887 (78) mri peak = 0.04390 (72) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2415 voxels, overlap=0.929) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2415 voxels, peak = 78), gca=77.6 gca peak = 0.12036 (70) mri peak = 0.04283 (77) Right_Putamen (51): linear fit = 1.09 x + 0.0 (2093 voxels, overlap=0.950) Right_Putamen (51): linear fit = 1.09 x + 0.0 (2093 voxels, peak = 76), gca=76.0 gca peak = 0.07055 (91) mri peak = 0.06535 (89) Brain_Stem (16): linear fit = 0.99 x + 0.0 (10128 voxels, overlap=0.835) Brain_Stem (16): linear fit = 0.99 x + 0.0 (10128 voxels, peak = 90), gca=89.6 gca peak = 0.11344 (105) mri peak = 0.05683 (104) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (883 voxels, overlap=0.842) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (883 voxels, peak = 106), gca=105.5 gca peak = 0.14357 (102) mri peak = 0.07350 (103) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (965 voxels, overlap=0.910) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (965 voxels, peak = 102), gca=102.0 gca peak = 0.35640 (14) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.33827 ( 9) mri peak = 0.27711 ( 6) Fourth_Ventricle (15): linear fit = 0.54 x + 0.0 (75 voxels, overlap=0.300) Fourth_Ventricle (15): linear fit = 0.54 x + 0.0 (75 voxels, peak = 5), gca=4.8 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.27467 (31) gca peak Third_Ventricle = 0.35640 (14) gca peak Fourth_Ventricle = 0.33827 ( 9) gca peak CSF = 0.30128 (18) gca peak Left_Accumbens_area = 0.53589 (63) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.39369 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.34941 (29) gca peak Right_Accumbens_area = 0.31095 (68) gca peak Right_vessel = 0.52700 (60) gca peak Right_choroid_plexus = 0.10273 (48) gca peak Fifth_Ventricle = 0.45329 (19) gca peak WM_hypointensities = 0.17107 (85) gca peak non_WM_hypointensities = 0.12132 (55) gca peak Optic_Chiasm = 0.34840 (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 0.40 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 16299 gm and wm labels changed (%12 to gray, %88 to white out of all changed labels) 238 hippocampal voxels changed. 1 amygdala voxels changed. pass 1: 92546 changed. image ll: -2.232, PF=1.000 pass 2: 15754 changed. image ll: -2.229, PF=1.000 pass 3: 5653 changed. pass 4: 2464 changed. writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 10 minutes and 20 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri/transforms/cc_up.lta test will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri/transforms/cc_up.lta reading aseg from /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri/aseg.auto_noCCseg.mgz reading norm from /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri/norm.mgz 29110 voxels in left wm, 21396 in right wm, xrange [126, 132] searching rotation angles z=[-6 8], y=[-7 7] searching scale 1 Z rot -6.0 searching scale 1 Z rot -5.8 searching scale 1 Z rot -5.5 searching scale 1 Z rot -5.3 searching scale 1 Z rot -5.0 searching scale 1 Z rot -4.8 searching scale 1 Z rot -4.5 searching scale 1 Z rot -4.3 searching scale 1 Z rot -4.0 searching scale 1 Z rot -3.8 searching scale 1 Z rot -3.5 searching scale 1 Z rot -3.3 searching scale 1 Z rot -3.0 searching scale 1 Z rot -2.8 searching scale 1 Z rot -2.5 searching scale 1 Z rot -2.3 searching scale 1 Z rot -2.0 searching scale 1 Z rot -1.8 searching scale 1 Z rot -1.5 searching scale 1 Z rot -1.3 searching scale 1 Z rot -1.0 searching scale 1 Z rot -0.8 searching scale 1 Z rot -0.5 searching scale 1 Z rot -0.3 searching scale 1 Z rot -0.0 searching scale 1 Z rot 0.2 searching scale 1 Z rot 0.5 searching scale 1 Z rot 0.7 searching scale 1 Z rot 1.0 searching scale 1 Z rot 1.2 searching scale 1 Z rot 1.5 searching scale 1 Z rot 1.7 searching scale 1 Z rot 2.0 searching scale 1 Z rot 2.2 searching scale 1 Z rot 2.5 searching scale 1 Z rot 2.7 searching scale 1 Z rot 3.0 searching scale 1 Z rot 3.2 searching scale 1 Z rot 3.5 searching scale 1 Z rot 3.7 searching scale 1 Z rot 4.0 searching scale 1 Z rot 4.2 searching scale 1 Z rot 4.5 searching scale 1 Z rot 4.7 searching scale 1 Z rot 5.0 searching scale 1 Z rot 5.2 searching scale 1 Z rot 5.5 searching scale 1 Z rot 5.7 searching scale 1 Z rot 6.0 searching scale 1 Z rot 6.2 searching scale 1 Z rot 6.5 searching scale 1 Z rot 6.7 searching scale 1 Z rot 7.0 searching scale 1 Z rot 7.2 searching scale 1 Z rot 7.5 global minimum found at slice 128.0, rotations (0.70, 0.72) final transformation (x=128.0, yr=0.702, zr=0.718): 1.000 -0.013 0.012 0.063; 0.013 1.000 0.000 12.388; -0.012 0.000 1.000 16.577; 0.000 0.000 0.000 1.000; updating x range to be [126, 132] in xformed coordinates best xformed slice 129 cc center is found at 129 150 111 eigenvectors: -0.001 -0.002 1.000; -0.062 -0.998 -0.002; 0.998 -0.062 0.001; error in mid anterior detected - correcting... writing aseg with callosum to /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri/aseg.auto.mgz... corpus callosum matter segmentation took 0.4 minutes #-------------------------------------- #@# Merge ASeg Wed May 22 13:03:09 JST 2013 cp aseg.auto.mgz aseg.mgz #-------------------------------------------- #@# Intensity Normalization2 Wed May 22 13:03:09 JST 2013 /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading from norm.mgz... Reading aseg aseg.mgz normalizing image... processing with aseg removing outliers in the aseg WM... 4897 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 111 white matter peak found at 109 gm peak at 57 (57), valley at 30 (30) csf peak at 28, setting threshold to 47 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 58 (58), valley at 21 (21) csf peak at 29, setting threshold to 48 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 2 minutes and 18 seconds. #-------------------------------------------- #@# Mask BFS Wed May 22 13:05:28 JST 2013 /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1644351 voxels in mask (pct= 9.80) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Wed May 22 13:05:29 JST 2013 mri_segment brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (107.0): 107.4 +- 5.2 [80.0 --> 125.0] GM (68.0) : 66.6 +- 10.5 [30.0 --> 96.0] setting bottom of white matter range to 77.0 setting top of gray matter range to 87.5 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... 8339 sparsely connected voxels removed... thickening thin strands.... 20 segments, 6112 filled 5201 bright non-wm voxels segmented. 4108 diagonally connected voxels added... white matter segmentation took 1.1 minutes writing output to wm.seg.mgz... mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.36 minutes reading wm segmentation from wm.seg.mgz... 58 voxels added to wm to prevent paths from MTL structures to cortex 1985 additional wm voxels added 0 additional wm voxels added SEG EDIT: 46759 voxels turned on, 38375 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+): 28 found - 28 modified | TOTAL: 28 pass 2 (xy+): 0 found - 28 modified | TOTAL: 28 pass 1 (xy-): 21 found - 21 modified | TOTAL: 49 pass 2 (xy-): 0 found - 21 modified | TOTAL: 49 pass 1 (yz+): 31 found - 31 modified | TOTAL: 80 pass 2 (yz+): 0 found - 31 modified | TOTAL: 80 pass 1 (yz-): 30 found - 30 modified | TOTAL: 110 pass 2 (yz-): 0 found - 30 modified | TOTAL: 110 pass 1 (xz+): 27 found - 27 modified | TOTAL: 137 pass 2 (xz+): 0 found - 27 modified | TOTAL: 137 pass 1 (xz-): 29 found - 29 modified | TOTAL: 166 pass 2 (xz-): 0 found - 29 modified | TOTAL: 166 Iteration Number : 1 pass 1 (+++): 26 found - 26 modified | TOTAL: 26 pass 2 (+++): 0 found - 26 modified | TOTAL: 26 pass 1 (+++): 34 found - 34 modified | TOTAL: 60 pass 2 (+++): 0 found - 34 modified | TOTAL: 60 pass 1 (+++): 21 found - 21 modified | TOTAL: 81 pass 2 (+++): 0 found - 21 modified | TOTAL: 81 pass 1 (+++): 25 found - 25 modified | TOTAL: 106 pass 2 (+++): 0 found - 25 modified | TOTAL: 106 Iteration Number : 1 pass 1 (++): 163 found - 163 modified | TOTAL: 163 pass 2 (++): 0 found - 163 modified | TOTAL: 163 pass 1 (+-): 140 found - 140 modified | TOTAL: 303 pass 2 (+-): 0 found - 140 modified | TOTAL: 303 pass 1 (--): 146 found - 146 modified | TOTAL: 449 pass 2 (--): 0 found - 146 modified | TOTAL: 449 pass 1 (-+): 119 found - 119 modified | TOTAL: 568 pass 2 (-+): 0 found - 119 modified | TOTAL: 568 Iteration Number : 2 pass 1 (xy+): 7 found - 7 modified | TOTAL: 7 pass 2 (xy+): 0 found - 7 modified | TOTAL: 7 pass 1 (xy-): 9 found - 9 modified | TOTAL: 16 pass 2 (xy-): 0 found - 9 modified | TOTAL: 16 pass 1 (yz+): 9 found - 9 modified | TOTAL: 25 pass 2 (yz+): 0 found - 9 modified | TOTAL: 25 pass 1 (yz-): 12 found - 12 modified | TOTAL: 37 pass 2 (yz-): 0 found - 12 modified | TOTAL: 37 pass 1 (xz+): 7 found - 7 modified | TOTAL: 44 pass 2 (xz+): 0 found - 7 modified | TOTAL: 44 pass 1 (xz-): 9 found - 9 modified | TOTAL: 53 pass 2 (xz-): 0 found - 9 modified | TOTAL: 53 Iteration Number : 2 pass 1 (+++): 2 found - 2 modified | TOTAL: 2 pass 2 (+++): 0 found - 2 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 2 Iteration Number : 2 pass 1 (++): 8 found - 8 modified | TOTAL: 8 pass 2 (++): 0 found - 8 modified | TOTAL: 8 pass 1 (+-): 4 found - 4 modified | TOTAL: 12 pass 2 (+-): 0 found - 4 modified | TOTAL: 12 pass 1 (--): 5 found - 5 modified | TOTAL: 17 pass 2 (--): 0 found - 5 modified | TOTAL: 17 pass 1 (-+): 4 found - 4 modified | TOTAL: 21 pass 2 (-+): 0 found - 4 modified | TOTAL: 21 Iteration Number : 3 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-): 1 found - 1 modified | TOTAL: 2 pass 2 (xz-): 0 found - 1 modified | TOTAL: 2 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 (-+): 1 found - 1 modified | TOTAL: 1 pass 2 (-+): 0 found - 1 modified | TOTAL: 1 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 919 (out of 618184: 0.148661) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Wed May 22 13:06:59 JST 2013 /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.auto_noCCseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.108 0.002 0.026 -19.788; -0.007 1.119 0.247 -54.922; -0.026 -0.198 0.940 27.850; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 1.108 0.002 0.026 -19.788; -0.007 1.119 0.247 -54.922; -0.026 -0.198 0.940 27.850; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 1312 (min = 350, max = 1400), aspect = 0.47 (min = 0.10, max = 0.75) no need to search using seed (126, 105, 94), TAL = (2.0, -34.0, 23.0) talairach voxel to voxel transform 0.902 -0.006 -0.023 18.147; 0.000 0.854 -0.224 53.162; 0.025 0.180 1.016 -17.915; 0.000 0.000 0.000 1.000; segmentation indicates cc at (126, 105, 94) --> (2.0, -34.0, 23.0) done. writing output to filled.mgz... filling took 0.5 minutes talairach cc position changed to (2.00, -34.00, 23.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, -34.00, 23.00) SRC: (112.74, 121.78, 99.14) search lh wm seed point around talairach space (-16.00, -34.00, 23.00), SRC: (145.19, 121.79, 100.05) 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 Wed May 22 13:07:28 JST 2013 /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 0 found - 0 modified | TOTAL: 1 pass 1 (yz+): 1 found - 1 modified | TOTAL: 2 pass 2 (yz+): 0 found - 1 modified | TOTAL: 2 pass 1 (yz-): 0 found - 0 modified | TOTAL: 2 pass 1 (xz+): 2 found - 2 modified | TOTAL: 4 pass 2 (xz+): 0 found - 2 modified | TOTAL: 4 pass 1 (xz-): 2 found - 2 modified | TOTAL: 6 pass 2 (xz-): 0 found - 2 modified | TOTAL: 6 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 1 found - 1 modified | TOTAL: 1 pass 2 (++): 0 found - 1 modified | TOTAL: 1 pass 1 (+-): 0 found - 0 modified | TOTAL: 1 pass 1 (--): 0 found - 0 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 7 (out of 296738: 0.002359) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ slice 40: 1695 vertices, 1859 faces slice 50: 8637 vertices, 8944 faces slice 60: 18773 vertices, 19160 faces slice 70: 30596 vertices, 31050 faces slice 80: 41845 vertices, 42235 faces slice 90: 54279 vertices, 54642 faces slice 100: 66475 vertices, 66898 faces slice 110: 78437 vertices, 78850 faces slice 120: 89643 vertices, 90060 faces slice 130: 99993 vertices, 100370 faces slice 140: 110026 vertices, 110418 faces slice 150: 119509 vertices, 119850 faces slice 160: 127692 vertices, 128020 faces slice 170: 135200 vertices, 135488 faces slice 180: 141589 vertices, 141826 faces slice 190: 147207 vertices, 147417 faces slice 200: 151331 vertices, 151484 faces slice 210: 152516 vertices, 152570 faces slice 220: 152516 vertices, 152570 faces slice 230: 152516 vertices, 152570 faces slice 240: 152516 vertices, 152570 faces slice 250: 152516 vertices, 152570 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... 152516 voxel in cpt #1: X=-54 [v=152516,e=457710,f=305140] located at (-26.627855, -17.293831, 5.686944) For the whole surface: X=-54 [v=152516,e=457710,f=305140] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Wed May 22 13:07:32 JST 2013 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/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 Wed May 22 13:07:35 JST 2013 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/scripts avg radius = 50.1 mm, total surface area = 79788 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.3 minutes Not saving sulc step 000: RMS=0.102 (target=0.015) step 005: RMS=0.074 (target=0.015) step 010: RMS=0.054 (target=0.015) step 015: RMS=0.044 (target=0.015) step 020: RMS=0.038 (target=0.015) step 025: RMS=0.033 (target=0.015) step 030: RMS=0.029 (target=0.015) step 035: RMS=0.026 (target=0.015) step 040: RMS=0.024 (target=0.015) step 045: RMS=0.022 (target=0.015) step 050: RMS=0.022 (target=0.015) step 055: RMS=0.021 (target=0.015) step 060: RMS=0.020 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh Wed May 22 13:07:55 JST 2013 /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.93 +- 0.57 (0.00-->5.89) (max @ vno 112868 --> 112882) face area 0.02 +- 0.03 (-0.08-->0.53) scaling brain by 0.288... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.923, avgs=0 005/300: dt: 0.9000, rms radial error=176.663, avgs=0 010/300: dt: 0.9000, rms radial error=176.105, avgs=0 015/300: dt: 0.9000, rms radial error=175.370, avgs=0 020/300: dt: 0.9000, rms radial error=174.534, avgs=0 025/300: dt: 0.9000, rms radial error=173.638, avgs=0 030/300: dt: 0.9000, rms radial error=172.709, avgs=0 035/300: dt: 0.9000, rms radial error=171.763, avgs=0 040/300: dt: 0.9000, rms radial error=170.817, avgs=0 045/300: dt: 0.9000, rms radial error=169.870, avgs=0 050/300: dt: 0.9000, rms radial error=168.923, avgs=0 055/300: dt: 0.9000, rms radial error=167.978, avgs=0 060/300: dt: 0.9000, rms radial error=167.038, avgs=0 065/300: dt: 0.9000, rms radial error=166.101, avgs=0 070/300: dt: 0.9000, rms radial error=165.169, avgs=0 075/300: dt: 0.9000, rms radial error=164.242, avgs=0 080/300: dt: 0.9000, rms radial error=163.320, avgs=0 085/300: dt: 0.9000, rms radial error=162.403, avgs=0 090/300: dt: 0.9000, rms radial error=161.491, avgs=0 095/300: dt: 0.9000, rms radial error=160.584, avgs=0 100/300: dt: 0.9000, rms radial error=159.682, avgs=0 105/300: dt: 0.9000, rms radial error=158.785, avgs=0 110/300: dt: 0.9000, rms radial error=157.892, avgs=0 115/300: dt: 0.9000, rms radial error=157.005, avgs=0 120/300: dt: 0.9000, rms radial error=156.122, avgs=0 125/300: dt: 0.9000, rms radial error=155.244, avgs=0 130/300: dt: 0.9000, rms radial error=154.371, avgs=0 135/300: dt: 0.9000, rms radial error=153.502, avgs=0 140/300: dt: 0.9000, rms radial error=152.638, avgs=0 145/300: dt: 0.9000, rms radial error=151.779, avgs=0 150/300: dt: 0.9000, rms radial error=150.925, avgs=0 155/300: dt: 0.9000, rms radial error=150.075, avgs=0 160/300: dt: 0.9000, rms radial error=149.229, avgs=0 165/300: dt: 0.9000, rms radial error=148.389, avgs=0 170/300: dt: 0.9000, rms radial error=147.553, avgs=0 175/300: dt: 0.9000, rms radial error=146.722, avgs=0 180/300: dt: 0.9000, rms radial error=145.895, avgs=0 185/300: dt: 0.9000, rms radial error=145.073, avgs=0 190/300: dt: 0.9000, rms radial error=144.256, avgs=0 195/300: dt: 0.9000, rms radial error=143.443, avgs=0 200/300: dt: 0.9000, rms radial error=142.635, avgs=0 205/300: dt: 0.9000, rms radial error=141.831, avgs=0 210/300: dt: 0.9000, rms radial error=141.032, avgs=0 215/300: dt: 0.9000, rms radial error=140.237, avgs=0 220/300: dt: 0.9000, rms radial error=139.446, avgs=0 225/300: dt: 0.9000, rms radial error=138.660, avgs=0 230/300: dt: 0.9000, rms radial error=137.879, avgs=0 235/300: dt: 0.9000, rms radial error=137.102, avgs=0 240/300: dt: 0.9000, rms radial error=136.329, avgs=0 245/300: dt: 0.9000, rms radial error=135.561, avgs=0 250/300: dt: 0.9000, rms radial error=134.797, avgs=0 255/300: dt: 0.9000, rms radial error=134.038, avgs=0 260/300: dt: 0.9000, rms radial error=133.283, avgs=0 265/300: dt: 0.9000, rms radial error=132.531, avgs=0 270/300: dt: 0.9000, rms radial error=131.784, avgs=0 275/300: dt: 0.9000, rms radial error=131.041, avgs=0 280/300: dt: 0.9000, rms radial error=130.302, avgs=0 285/300: dt: 0.9000, rms radial error=129.567, avgs=0 290/300: dt: 0.9000, rms radial error=128.837, avgs=0 295/300: dt: 0.9000, rms radial error=128.111, avgs=0 300/300: dt: 0.9000, rms radial error=127.388, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 18303.42 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00020 epoch 2 (K=40.0), pass 1, starting sse = 3247.93 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00007 epoch 3 (K=160.0), pass 1, starting sse = 383.20 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.09/12 = 0.00764 epoch 4 (K=640.0), pass 1, starting sse = 26.04 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.13/15 = 0.00873 final writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.05 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology lh Wed May 22 13:10:57 JST 2013 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 test lh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ before topology correction, eno=-54 (nv=152516, nf=305140, ne=457710, g=28) 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 11 iterations marking ambiguous vertices... 3161 ambiguous faces found in tessellation segmenting defects... 37 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 12 into 11 36 defects to be corrected 0 vertices coincident reading input surface /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.4519 (-4.7260) -vertex loglikelihood: -6.6206 (-3.3103) -normal dot loglikelihood: -3.5357 (-3.5357) -quad curv loglikelihood: -6.5617 (-3.2809) Total Loglikelihood : -26.1699 CORRECTING DEFECT 0 (vertices=23, convex hull=39) After retessellation of defect 0, euler #=-33 (150539,450695,300123) : difference with theory (-33) = 0 CORRECTING DEFECT 1 (vertices=23, convex hull=26) After retessellation of defect 1, euler #=-32 (150541,450708,300135) : difference with theory (-32) = 0 CORRECTING DEFECT 2 (vertices=26, convex hull=42) After retessellation of defect 2, euler #=-31 (150550,450749,300168) : difference with theory (-31) = 0 CORRECTING DEFECT 3 (vertices=29, convex hull=63) After retessellation of defect 3, euler #=-30 (150561,450807,300216) : difference with theory (-30) = 0 CORRECTING DEFECT 4 (vertices=11, convex hull=32) After retessellation of defect 4, euler #=-29 (150564,450828,300235) : difference with theory (-29) = 0 CORRECTING DEFECT 5 (vertices=24, convex hull=64) After retessellation of defect 5, euler #=-28 (150576,450888,300284) : difference with theory (-28) = 0 CORRECTING DEFECT 6 (vertices=9, convex hull=27) After retessellation of defect 6, euler #=-27 (150579,450904,300298) : difference with theory (-27) = 0 CORRECTING DEFECT 7 (vertices=32, convex hull=75) After retessellation of defect 7, euler #=-26 (150597,450986,300363) : difference with theory (-26) = 0 CORRECTING DEFECT 8 (vertices=50, convex hull=98) After retessellation of defect 8, euler #=-25 (150609,451066,300432) : difference with theory (-25) = 0 CORRECTING DEFECT 9 (vertices=23, convex hull=44) After retessellation of defect 9, euler #=-24 (150623,451122,300475) : difference with theory (-24) = 0 CORRECTING DEFECT 10 (vertices=199, convex hull=147) After retessellation of defect 10, euler #=-23 (150699,451420,300698) : difference with theory (-23) = 0 CORRECTING DEFECT 11 (vertices=65, convex hull=68) After retessellation of defect 11, euler #=-21 (150708,451475,300746) : difference with theory (-22) = -1 CORRECTING DEFECT 12 (vertices=7, convex hull=34) After retessellation of defect 12, euler #=-20 (150710,451490,300760) : difference with theory (-21) = -1 CORRECTING DEFECT 13 (vertices=153, convex hull=60) After retessellation of defect 13, euler #=-19 (150728,451571,300824) : difference with theory (-20) = -1 CORRECTING DEFECT 14 (vertices=22, convex hull=47) After retessellation of defect 14, euler #=-18 (150737,451618,300863) : difference with theory (-19) = -1 CORRECTING DEFECT 15 (vertices=17, convex hull=22) After retessellation of defect 15, euler #=-17 (150739,451629,300873) : difference with theory (-18) = -1 CORRECTING DEFECT 16 (vertices=20, convex hull=34) After retessellation of defect 16, euler #=-16 (150747,451664,300901) : difference with theory (-17) = -1 CORRECTING DEFECT 17 (vertices=60, convex hull=45) After retessellation of defect 17, euler #=-15 (150753,451701,300933) : difference with theory (-16) = -1 CORRECTING DEFECT 18 (vertices=79, convex hull=117) After retessellation of defect 18, euler #=-15 (150801,451908,301092) : difference with theory (-15) = 0 CORRECTING DEFECT 19 (vertices=482, convex hull=107) After retessellation of defect 19, euler #=-14 (150839,452073,301220) : difference with theory (-14) = 0 CORRECTING DEFECT 20 (vertices=31, convex hull=55) After retessellation of defect 20, euler #=-13 (150854,452139,301272) : difference with theory (-13) = 0 CORRECTING DEFECT 21 (vertices=117, convex hull=104) After retessellation of defect 21, euler #=-12 (150899,452318,301407) : difference with theory (-12) = 0 CORRECTING DEFECT 22 (vertices=48, convex hull=94) After retessellation of defect 22, euler #=-11 (150929,452448,301508) : difference with theory (-11) = 0 CORRECTING DEFECT 23 (vertices=29, convex hull=70) After retessellation of defect 23, euler #=-10 (150948,452532,301574) : difference with theory (-10) = 0 CORRECTING DEFECT 24 (vertices=59, convex hull=91) After retessellation of defect 24, euler #=-9 (150975,452652,301668) : difference with theory (-9) = 0 CORRECTING DEFECT 25 (vertices=32, convex hull=73) After retessellation of defect 25, euler #=-8 (150993,452735,301734) : difference with theory (-8) = 0 CORRECTING DEFECT 26 (vertices=20, convex hull=57) After retessellation of defect 26, euler #=-7 (151002,452785,301776) : difference with theory (-7) = 0 CORRECTING DEFECT 27 (vertices=5, convex hull=28) Warning - incorrect dp selected!!!!(-71.248173 >= -71.248180 ) After retessellation of defect 27, euler #=-6 (151003,452794,301785) : difference with theory (-6) = 0 CORRECTING DEFECT 28 (vertices=46, convex hull=66) After retessellation of defect 28, euler #=-5 (151016,452861,301840) : difference with theory (-5) = 0 CORRECTING DEFECT 29 (vertices=47, convex hull=83) After retessellation of defect 29, euler #=-4 (151048,452991,301939) : difference with theory (-4) = 0 CORRECTING DEFECT 30 (vertices=28, convex hull=61) After retessellation of defect 30, euler #=-3 (151060,453053,301990) : difference with theory (-3) = 0 CORRECTING DEFECT 31 (vertices=22, convex hull=48) After retessellation of defect 31, euler #=-2 (151066,453090,302022) : difference with theory (-2) = 0 CORRECTING DEFECT 32 (vertices=20, convex hull=58) After retessellation of defect 32, euler #=-1 (151077,453143,302065) : difference with theory (-1) = 0 CORRECTING DEFECT 33 (vertices=21, convex hull=43) After retessellation of defect 33, euler #=0 (151084,453177,302093) : difference with theory (0) = 0 CORRECTING DEFECT 34 (vertices=18, convex hull=74) After retessellation of defect 34, euler #=1 (151093,453229,302137) : difference with theory (1) = 0 CORRECTING DEFECT 35 (vertices=82, convex hull=102) After retessellation of defect 35, euler #=2 (151121,453357,302238) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.22 (0.08-->6.83) (max @ vno 47949 --> 54017) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.22 (0.08-->6.83) (max @ vno 47949 --> 54017) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 119 mutations (33.3%), 238 crossovers (66.7%), 82 vertices were eliminated building final representation... 1395 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=151121, nf=302238, ne=453357, g=0) writing corrected surface to /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 13.0 minutes 0 defective edges removing intersecting faces 000: 243 intersecting mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 151121 - 453357 + 302238 = 2 --> 0 holes F =2V-4: 302238 = 302242-4 (0) 2E=3F: 906714 = 906714 (0) total defect index = 0 /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 9 intersecting 001: 3 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Wed May 22 13:24:04 JST 2013 /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/scripts mris_make_surfaces -noaparc -mgz -T1 brain.finalsurfs test 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 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri/filled.mgz... reading volume /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri/brain.finalsurfs.mgz... reading volume /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri/wm.mgz... 20084 bright wm thresholded. 5996 bright non-wm voxels segmented. reading original surface position from /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/surf/lh.orig... computing class statistics... border white: 285437 voxels (1.70%) border gray 325958 voxels (1.94%) WM (92.0): 93.1 +- 9.3 [70.0 --> 110.0] GM (77.0) : 74.7 +- 13.2 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 48.8 (was 70) setting MAX_BORDER_WHITE to 112.3 (was 105) setting MIN_BORDER_WHITE to 62.0 (was 85) setting MAX_CSF to 35.7 (was 40) setting MAX_GRAY to 93.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 55.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 22.5 (was 40) repositioning cortical surface to gray/white boundary reading volume /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.22 (0.03-->4.26) (max @ vno 65844 --> 150695) face area 0.28 +- 0.12 (0.00-->1.82) mean absolute distance = 0.73 +- 0.93 3696 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=103, GM=62 mean inside = 92.6, mean outside = 70.6 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group mean border=75.0, 25 (25) missing vertices, mean dist 0.3 [0.6 (%33.0)->0.8 (%67.0))] %68 local maxima, %27 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=dhcp0, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.26 (0.09-->4.69) (max @ vno 150693 --> 150677) face area 0.28 +- 0.13 (0.00-->2.16) mean absolute distance = 0.36 +- 0.59 3998 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=7327668.5, rms=12.62 001: dt: 0.5000, sse=7639011.5, rms=9.053 (0.000%) 002: dt: 0.5000, sse=8093604.5, rms=6.960 (0.000%) 003: dt: 0.5000, sse=8384604.0, rms=5.677 (0.000%) 004: dt: 0.5000, sse=8754246.0, rms=4.914 (0.000%) 005: dt: 0.5000, sse=8858062.0, rms=4.529 (0.000%) 006: dt: 0.5000, sse=9088583.0, rms=4.306 (0.000%) 007: dt: 0.5000, sse=9092950.0, rms=4.203 (0.000%) 008: dt: 0.5000, sse=9166653.0, rms=4.109 (0.000%) rms = 4.07, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=9118690.0, rms=4.073 (0.000%) 010: dt: 0.2500, sse=5744214.0, rms=2.855 (0.000%) 011: dt: 0.2500, sse=5245197.0, rms=2.443 (0.000%) 012: dt: 0.2500, sse=4966902.5, rms=2.332 (0.000%) 013: dt: 0.2500, sse=4875130.0, rms=2.252 (0.000%) rms = 2.21, time step reduction 2 of 3 to 0.125... 014: dt: 0.2500, sse=4803458.0, rms=2.211 (0.000%) 015: dt: 0.1250, sse=4636186.5, rms=2.080 (0.000%) rms = 2.06, time step reduction 3 of 3 to 0.062... 016: dt: 0.1250, sse=4594459.0, rms=2.064 (0.000%) positioning took 1.2 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group mean border=78.8, 41 (6) missing vertices, mean dist -0.2 [0.4 (%72.8)->0.2 (%27.2))] %77 local maxima, %17 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=dhcp0, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.25 (0.09-->3.83) (max @ vno 99848 --> 99851) face area 0.35 +- 0.17 (0.00-->2.67) mean absolute distance = 0.27 +- 0.42 4100 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5441016.5, rms=5.37 017: dt: 0.5000, sse=5815892.5, rms=3.597 (0.000%) rms = 3.95, time step reduction 1 of 3 to 0.250... 018: dt: 0.2500, sse=5327664.0, rms=2.665 (0.000%) 019: dt: 0.2500, sse=5153605.0, rms=2.129 (0.000%) 020: dt: 0.2500, sse=5044537.0, rms=1.846 (0.000%) 021: dt: 0.2500, sse=4995722.5, rms=1.790 (0.000%) rms = 1.74, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=4939615.5, rms=1.742 (0.000%) 023: dt: 0.1250, sse=4840590.5, rms=1.639 (0.000%) rms = 1.64, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=4794897.0, rms=1.636 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 1 vertex label from ripped group mean border=81.7, 25 (4) missing vertices, mean dist -0.2 [0.3 (%70.8)->0.2 (%29.2))] %86 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=dhcp0, 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 (0.04-->4.11) (max @ vno 99848 --> 99851) face area 0.34 +- 0.16 (0.00-->2.43) mean absolute distance = 0.23 +- 0.33 3468 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5130742.0, rms=3.91 025: dt: 0.5000, sse=5533413.0, rms=3.414 (0.000%) rms = 3.81, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=5084697.5, rms=2.258 (0.000%) 027: dt: 0.2500, sse=4997347.0, rms=1.804 (0.000%) 028: dt: 0.2500, sse=4997775.5, rms=1.609 (0.000%) rms = 1.62, time step reduction 2 of 3 to 0.125... 029: dt: 0.1250, sse=4940582.5, rms=1.538 (0.000%) 030: dt: 0.1250, sse=4858876.0, rms=1.446 (0.000%) rms = 1.45, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=4858876.0, rms=1.446 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 1 vertex label from ripped group mean border=82.7, 45 (4) missing vertices, mean dist -0.1 [0.2 (%56.6)->0.2 (%43.4))] %89 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=dhcp0, 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 /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=4895950.5, rms=1.95 rms = 2.46, time step reduction 1 of 3 to 0.250... 032: dt: 0.2500, sse=4982885.0, rms=1.357 (0.000%) 033: dt: 0.2500, sse=5171754.0, rms=1.099 (0.000%) rms = 1.10, time step reduction 2 of 3 to 0.125... rms = 1.09, time step reduction 3 of 3 to 0.062... 034: dt: 0.1250, sse=5165083.0, rms=1.092 (0.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... generating cortex label... 15 non-cortical segments detected only using segment with 2181 vertices erasing segment 1 (vno[0] = 69270) erasing segment 2 (vno[0] = 88668) erasing segment 3 (vno[0] = 102908) erasing segment 4 (vno[0] = 107784) erasing segment 5 (vno[0] = 108735) erasing segment 6 (vno[0] = 108788) erasing segment 7 (vno[0] = 109844) erasing segment 8 (vno[0] = 109955) erasing segment 9 (vno[0] = 112007) erasing segment 10 (vno[0] = 112813) erasing segment 11 (vno[0] = 117074) erasing segment 12 (vno[0] = 117116) erasing segment 13 (vno[0] = 117132) erasing segment 14 (vno[0] = 150737) writing cortex label to /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/label/lh.cortex.label... writing curvature file /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/surf/lh.curv writing smoothed area to lh.area writing curvature file /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/surf/lh.area vertex spacing 0.89 +- 0.25 (0.04-->4.06) (max @ vno 99848 --> 99851) face area 0.33 +- 0.16 (0.00-->2.42) 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=51.2, 42 (42) missing vertices, mean dist 1.7 [0.1 (%0.0)->2.3 (%100.0))] %17 local maxima, %55 large gradients and %24 min vals, 2331 gradients ignored tol=1.0e-04, sigma=2.0, host=dhcp0, 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=31063846.0, rms=31.17 001: dt: 0.5000, sse=22973182.0, rms=26.298 (0.000%) 002: dt: 0.5000, sse=17177792.0, rms=22.187 (0.000%) 003: dt: 0.5000, sse=13292335.0, rms=18.834 (0.000%) 004: dt: 0.5000, sse=10997074.0, rms=16.136 (0.000%) 005: dt: 0.5000, sse=9610738.0, rms=13.973 (0.000%) 006: dt: 0.5000, sse=8739952.0, rms=12.204 (0.000%) 007: dt: 0.5000, sse=8115812.5, rms=10.653 (0.000%) 008: dt: 0.5000, sse=7728543.0, rms=9.234 (0.000%) 009: dt: 0.5000, sse=7461184.5, rms=7.929 (0.000%) 010: dt: 0.5000, sse=7389792.5, rms=6.798 (0.000%) 011: dt: 0.5000, sse=7437587.5, rms=5.901 (0.000%) 012: dt: 0.5000, sse=7588469.0, rms=5.241 (0.000%) 013: dt: 0.5000, sse=7725253.0, rms=4.809 (0.000%) 014: dt: 0.5000, sse=7860558.5, rms=4.573 (0.000%) 015: dt: 0.5000, sse=7935308.0, rms=4.428 (0.000%) 016: dt: 0.5000, sse=8035019.0, rms=4.361 (0.000%) 017: dt: 0.5000, sse=8074084.5, rms=4.293 (0.000%) rms = 4.27, time step reduction 1 of 3 to 0.250... 018: dt: 0.5000, sse=8111806.0, rms=4.267 (0.000%) 019: dt: 0.2500, sse=5566488.0, rms=3.416 (0.000%) 020: dt: 0.2500, sse=5366555.5, rms=3.177 (0.000%) rms = 3.16, time step reduction 2 of 3 to 0.125... 021: dt: 0.2500, sse=5198831.5, rms=3.160 (0.000%) 022: dt: 0.1250, sse=4905612.0, rms=2.960 (0.000%) rms = 2.93, time step reduction 3 of 3 to 0.062... 023: dt: 0.1250, sse=4865296.5, rms=2.934 (0.000%) positioning took 1.6 minutes mean border=49.2, 1025 (12) missing vertices, mean dist 0.1 [0.2 (%49.9)->0.5 (%50.1))] %36 local maxima, %40 large gradients and %19 min vals, 802 gradients ignored tol=1.0e-04, sigma=1.0, host=dhcp0, 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=5503690.5, rms=4.71 024: dt: 0.5000, sse=5972977.5, rms=4.170 (0.000%) rms = 4.24, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=5469198.0, rms=3.445 (0.000%) 026: dt: 0.2500, sse=5518545.0, rms=3.171 (0.000%) 027: dt: 0.2500, sse=5470086.0, rms=3.082 (0.000%) rms = 3.04, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=5529128.5, rms=3.040 (0.000%) 029: dt: 0.1250, sse=5286373.5, rms=2.833 (0.000%) rms = 2.80, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=5269306.5, rms=2.797 (0.000%) positioning took 0.5 minutes mean border=47.3, 1169 (9) missing vertices, mean dist 0.1 [0.2 (%43.1)->0.4 (%56.9))] %53 local maxima, %23 large gradients and %19 min vals, 928 gradients ignored tol=1.0e-04, sigma=0.5, host=dhcp0, 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=5494655.5, rms=3.86 rms = 4.11, time step reduction 1 of 3 to 0.250... 031: dt: 0.2500, sse=5287646.5, rms=3.321 (0.000%) 032: dt: 0.2500, sse=5303519.5, rms=3.021 (0.000%) 033: dt: 0.2500, sse=5546572.5, rms=2.950 (0.000%) rms = 2.96, time step reduction 2 of 3 to 0.125... 034: dt: 0.1250, sse=5464162.0, rms=2.879 (0.000%) 035: dt: 0.1250, sse=5393984.0, rms=2.777 (0.000%) rms = 2.76, time step reduction 3 of 3 to 0.062... 036: dt: 0.1250, sse=5387472.0, rms=2.757 (0.000%) positioning took 0.5 minutes mean border=46.2, 2360 (8) missing vertices, mean dist 0.1 [0.2 (%48.2)->0.3 (%51.8))] %57 local maxima, %18 large gradients and %19 min vals, 775 gradients ignored tol=1.0e-04, sigma=0.2, host=dhcp0, 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 /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=5441063.5, rms=3.08 rms = 3.76, time step reduction 1 of 3 to 0.250... 037: dt: 0.2500, sse=5327975.5, rms=2.825 (0.000%) 038: dt: 0.2500, sse=5569510.5, rms=2.720 (0.000%) rms = 2.70, time step reduction 2 of 3 to 0.125... 039: dt: 0.2500, sse=5681605.0, rms=2.700 (0.000%) 040: dt: 0.1250, sse=5592720.5, rms=2.556 (0.000%) rms = 2.53, time step reduction 3 of 3 to 0.062... 041: dt: 0.1250, sse=5601125.5, rms=2.527 (0.000%) positioning took 0.4 minutes writing curvature file /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/surf/lh.area.pial vertex spacing 1.00 +- 0.41 (0.02-->6.97) (max @ vno 98951 --> 97972) face area 0.40 +- 0.29 (0.00-->7.35) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 151121 vertices processed 25000 of 151121 vertices processed 50000 of 151121 vertices processed 75000 of 151121 vertices processed 100000 of 151121 vertices processed 125000 of 151121 vertices processed 150000 of 151121 vertices processed 0 of 151121 vertices processed 25000 of 151121 vertices processed 50000 of 151121 vertices processed 75000 of 151121 vertices processed 100000 of 151121 vertices processed 125000 of 151121 vertices processed 150000 of 151121 vertices processed thickness calculation complete, 262:659 truncations. 35640 vertices at 0 distance 108448 vertices at 1 distance 95525 vertices at 2 distance 36564 vertices at 3 distance 9791 vertices at 4 distance 2357 vertices at 5 distance 655 vertices at 6 distance 217 vertices at 7 distance 100 vertices at 8 distance 47 vertices at 9 distance 22 vertices at 10 distance 21 vertices at 11 distance 17 vertices at 12 distance 15 vertices at 13 distance 16 vertices at 14 distance 13 vertices at 15 distance 7 vertices at 16 distance 3 vertices at 17 distance 8 vertices at 18 distance 5 vertices at 19 distance 9 vertices at 20 distance writing curvature file /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/surf/lh.thickness positioning took 9.2 minutes #-------------------------------------------- #@# Smooth2 lh Wed May 22 13:33:16 JST 2013 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/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 Wed May 22 13:33:19 JST 2013 /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 50.2 mm, total surface area = 90996 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.116 (target=0.015) step 005: RMS=0.081 (target=0.015) step 010: RMS=0.058 (target=0.015) step 015: RMS=0.047 (target=0.015) step 020: RMS=0.039 (target=0.015) step 025: RMS=0.033 (target=0.015) step 030: RMS=0.027 (target=0.015) step 035: RMS=0.023 (target=0.015) step 040: RMS=0.020 (target=0.015) step 045: RMS=0.018 (target=0.015) step 050: RMS=0.016 (target=0.015) step 055: RMS=0.015 (target=0.015) inflation complete. inflation took 0.3 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 199 vertices thresholded to be in k1 ~ [-0.28 2.36], k2 ~ [-0.12 0.11] total integrated curvature = 0.563*4pi (7.069) --> 0 handles ICI = 1.6, FI = 11.5, variation=191.571 142 vertices thresholded to be in [-0.04 0.02] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 108 vertices thresholded to be in [-0.16 0.26] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.016, std = 0.023 done. #----------------------------------------- #@# Curvature Stats lh Wed May 22 13:34:36 JST 2013 /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm test lh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/lh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ test/lh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 310 ] Gb_filter = 0 WARN: S lookup min: -0.683132 WARN: S explicit min: 0.000000 vertex = 136 #-------------------------------------------- #@# Tessellate rh Wed May 22 13:34:38 JST 2013 /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 3 found - 3 modified | TOTAL: 3 pass 2 (xy+): 0 found - 3 modified | TOTAL: 3 pass 1 (xy-): 0 found - 0 modified | TOTAL: 3 pass 1 (yz+): 1 found - 1 modified | TOTAL: 4 pass 2 (yz+): 0 found - 1 modified | TOTAL: 4 pass 1 (yz-): 0 found - 0 modified | TOTAL: 4 pass 1 (xz+): 2 found - 2 modified | TOTAL: 6 pass 2 (xz+): 0 found - 2 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 (-+): 1 found - 1 modified | TOTAL: 1 pass 2 (-+): 0 found - 1 modified | TOTAL: 1 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 8 (out of 298635: 0.002679) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ slice 40: 708 vertices, 792 faces slice 50: 5836 vertices, 6100 faces slice 60: 15402 vertices, 15763 faces slice 70: 27465 vertices, 27880 faces slice 80: 39792 vertices, 40236 faces slice 90: 51773 vertices, 52175 faces slice 100: 63631 vertices, 64027 faces slice 110: 75515 vertices, 75931 faces slice 120: 86949 vertices, 87364 faces slice 130: 97874 vertices, 98313 faces slice 140: 108597 vertices, 109001 faces slice 150: 118607 vertices, 118925 faces slice 160: 126929 vertices, 127280 faces slice 170: 135052 vertices, 135358 faces slice 180: 141870 vertices, 142132 faces slice 190: 147946 vertices, 148181 faces slice 200: 151870 vertices, 152043 faces slice 210: 153074 vertices, 153130 faces slice 220: 153074 vertices, 153130 faces slice 230: 153074 vertices, 153130 faces slice 240: 153074 vertices, 153130 faces slice 250: 153074 vertices, 153130 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... 153074 voxel in cpt #1: X=-56 [v=153074,e=459390,f=306260] located at (26.387413, -15.180201, 5.867678) For the whole surface: X=-56 [v=153074,e=459390,f=306260] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 rh Wed May 22 13:34:43 JST 2013 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/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 Wed May 22 13:34:45 JST 2013 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/scripts avg radius = 49.3 mm, total surface area = 79630 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.3 minutes Not saving sulc step 000: RMS=0.102 (target=0.015) step 005: RMS=0.074 (target=0.015) step 010: RMS=0.054 (target=0.015) step 015: RMS=0.046 (target=0.015) step 020: RMS=0.039 (target=0.015) step 025: RMS=0.034 (target=0.015) step 030: RMS=0.031 (target=0.015) step 035: RMS=0.028 (target=0.015) step 040: RMS=0.026 (target=0.015) step 045: RMS=0.024 (target=0.015) step 050: RMS=0.023 (target=0.015) step 055: RMS=0.022 (target=0.015) step 060: RMS=0.022 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere rh Wed May 22 13:35:05 JST 2013 /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.94 +- 0.57 (0.00-->6.22) (max @ vno 58544 --> 59748) face area 0.02 +- 0.03 (-0.12-->0.57) scaling brain by 0.294... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=176.654, avgs=0 005/300: dt: 0.9000, rms radial error=176.392, avgs=0 010/300: dt: 0.9000, rms radial error=175.829, avgs=0 015/300: dt: 0.9000, rms radial error=175.091, avgs=0 020/300: dt: 0.9000, rms radial error=174.250, avgs=0 025/300: dt: 0.9000, rms radial error=173.354, avgs=0 030/300: dt: 0.9000, rms radial error=172.431, avgs=0 035/300: dt: 0.9000, rms radial error=171.494, avgs=0 040/300: dt: 0.9000, rms radial error=170.549, avgs=0 045/300: dt: 0.9000, rms radial error=169.602, avgs=0 050/300: dt: 0.9000, rms radial error=168.657, avgs=0 055/300: dt: 0.9000, rms radial error=167.714, avgs=0 060/300: dt: 0.9000, rms radial error=166.774, avgs=0 065/300: dt: 0.9000, rms radial error=165.839, avgs=0 070/300: dt: 0.9000, rms radial error=164.909, avgs=0 075/300: dt: 0.9000, rms radial error=163.984, avgs=0 080/300: dt: 0.9000, rms radial error=163.064, avgs=0 085/300: dt: 0.9000, rms radial error=162.148, avgs=0 090/300: dt: 0.9000, rms radial error=161.238, avgs=0 095/300: dt: 0.9000, rms radial error=160.332, avgs=0 100/300: dt: 0.9000, rms radial error=159.432, avgs=0 105/300: dt: 0.9000, rms radial error=158.536, avgs=0 110/300: dt: 0.9000, rms radial error=157.646, avgs=0 115/300: dt: 0.9000, rms radial error=156.760, avgs=0 120/300: dt: 0.9000, rms radial error=155.879, avgs=0 125/300: dt: 0.9000, rms radial error=155.004, avgs=0 130/300: dt: 0.9000, rms radial error=154.134, avgs=0 135/300: dt: 0.9000, rms radial error=153.268, avgs=0 140/300: dt: 0.9000, rms radial error=152.407, avgs=0 145/300: dt: 0.9000, rms radial error=151.551, avgs=0 150/300: dt: 0.9000, rms radial error=150.700, avgs=0 155/300: dt: 0.9000, rms radial error=149.854, avgs=0 160/300: dt: 0.9000, rms radial error=149.012, avgs=0 165/300: dt: 0.9000, rms radial error=148.175, avgs=0 170/300: dt: 0.9000, rms radial error=147.343, avgs=0 175/300: dt: 0.9000, rms radial error=146.514, avgs=0 180/300: dt: 0.9000, rms radial error=145.691, avgs=0 185/300: dt: 0.9000, rms radial error=144.872, avgs=0 190/300: dt: 0.9000, rms radial error=144.058, avgs=0 195/300: dt: 0.9000, rms radial error=143.248, avgs=0 200/300: dt: 0.9000, rms radial error=142.442, avgs=0 205/300: dt: 0.9000, rms radial error=141.641, avgs=0 210/300: dt: 0.9000, rms radial error=140.845, avgs=0 215/300: dt: 0.9000, rms radial error=140.052, avgs=0 220/300: dt: 0.9000, rms radial error=139.265, avgs=0 225/300: dt: 0.9000, rms radial error=138.481, avgs=0 230/300: dt: 0.9000, rms radial error=137.702, avgs=0 235/300: dt: 0.9000, rms radial error=136.928, avgs=0 240/300: dt: 0.9000, rms radial error=136.157, avgs=0 245/300: dt: 0.9000, rms radial error=135.392, avgs=0 250/300: dt: 0.9000, rms radial error=134.630, avgs=0 255/300: dt: 0.9000, rms radial error=133.872, avgs=0 260/300: dt: 0.9000, rms radial error=133.119, avgs=0 265/300: dt: 0.9000, rms radial error=132.370, avgs=0 270/300: dt: 0.9000, rms radial error=131.625, avgs=0 275/300: dt: 0.9000, rms radial error=130.885, avgs=0 280/300: dt: 0.9000, rms radial error=130.148, avgs=0 285/300: dt: 0.9000, rms radial error=129.415, avgs=0 290/300: dt: 0.9000, rms radial error=128.687, avgs=0 295/300: dt: 0.9000, rms radial error=127.962, avgs=0 300/300: dt: 0.9000, rms radial error=127.241, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 18289.01 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 = 3211.82 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00003 epoch 3 (K=160.0), pass 1, starting sse = 359.14 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.07/11 = 0.00597 epoch 4 (K=640.0), pass 1, starting sse = 23.89 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.12/14 = 0.00845 final writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.05 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology rh Wed May 22 13:38:04 JST 2013 cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 test rh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ before topology correction, eno=-56 (nv=153074, nf=306260, ne=459390, g=29) 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 10 iterations marking ambiguous vertices... 4099 ambiguous faces found in tessellation segmenting defects... 34 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 16 into 14 33 defects to be corrected 0 vertices coincident reading input surface /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.5876 (-4.7938) -vertex loglikelihood: -6.6365 (-3.3182) -normal dot loglikelihood: -3.6258 (-3.6258) -quad curv loglikelihood: -6.5889 (-3.2944) Total Loglikelihood : -26.4388 CORRECTING DEFECT 0 (vertices=46, convex hull=76) After retessellation of defect 0, euler #=-31 (150646,451033,300356) : difference with theory (-30) = 1 CORRECTING DEFECT 1 (vertices=26, convex hull=51) After retessellation of defect 1, euler #=-30 (150657,451086,300399) : difference with theory (-29) = 1 CORRECTING DEFECT 2 (vertices=18, convex hull=55) After retessellation of defect 2, euler #=-29 (150666,451132,300437) : difference with theory (-28) = 1 CORRECTING DEFECT 3 (vertices=53, convex hull=60) After retessellation of defect 3, euler #=-28 (150675,451184,300481) : difference with theory (-27) = 1 CORRECTING DEFECT 4 (vertices=69, convex hull=96) After retessellation of defect 4, euler #=-27 (150706,451316,300583) : difference with theory (-26) = 1 CORRECTING DEFECT 5 (vertices=19, convex hull=42) After retessellation of defect 5, euler #=-26 (150715,451356,300615) : difference with theory (-25) = 1 CORRECTING DEFECT 6 (vertices=485, convex hull=233) After retessellation of defect 6, euler #=-25 (150752,451578,300801) : difference with theory (-24) = 1 CORRECTING DEFECT 7 (vertices=5, convex hull=22) After retessellation of defect 7, euler #=-24 (150754,451590,300812) : difference with theory (-23) = 1 CORRECTING DEFECT 8 (vertices=11, convex hull=29) After retessellation of defect 8, euler #=-23 (150756,451604,300825) : difference with theory (-22) = 1 CORRECTING DEFECT 9 (vertices=11, convex hull=21) After retessellation of defect 9, euler #=-22 (150758,451614,300834) : difference with theory (-21) = 1 CORRECTING DEFECT 10 (vertices=275, convex hull=152) After retessellation of defect 10, euler #=-21 (150783,451759,300955) : difference with theory (-20) = 1 CORRECTING DEFECT 11 (vertices=21, convex hull=43) After retessellation of defect 11, euler #=-20 (150791,451799,300988) : difference with theory (-19) = 1 CORRECTING DEFECT 12 (vertices=73, convex hull=45) After retessellation of defect 12, euler #=-19 (150796,451832,301017) : difference with theory (-18) = 1 CORRECTING DEFECT 13 (vertices=28, convex hull=51) After retessellation of defect 13, euler #=-18 (150815,451906,301073) : difference with theory (-17) = 1 CORRECTING DEFECT 14 (vertices=74, convex hull=39) After retessellation of defect 14, euler #=-16 (150823,451942,301103) : difference with theory (-16) = 0 CORRECTING DEFECT 15 (vertices=540, convex hull=107) After retessellation of defect 15, euler #=-15 (150840,452046,301191) : difference with theory (-15) = 0 CORRECTING DEFECT 16 (vertices=64, convex hull=95) After retessellation of defect 16, euler #=-14 (150864,452165,301287) : difference with theory (-14) = 0 CORRECTING DEFECT 17 (vertices=14, convex hull=28) After retessellation of defect 17, euler #=-13 (150867,452185,301305) : difference with theory (-13) = 0 CORRECTING DEFECT 18 (vertices=72, convex hull=112) After retessellation of defect 18, euler #=-12 (150912,452371,301447) : difference with theory (-12) = 0 CORRECTING DEFECT 19 (vertices=5, convex hull=19) After retessellation of defect 19, euler #=-11 (150913,452379,301455) : difference with theory (-11) = 0 CORRECTING DEFECT 20 (vertices=52, convex hull=66) After retessellation of defect 20, euler #=-10 (150925,452445,301510) : difference with theory (-10) = 0 CORRECTING DEFECT 21 (vertices=36, convex hull=83) After retessellation of defect 21, euler #=-9 (150945,452541,301587) : difference with theory (-9) = 0 CORRECTING DEFECT 22 (vertices=50, convex hull=65) After retessellation of defect 22, euler #=-8 (150963,452620,301649) : difference with theory (-8) = 0 CORRECTING DEFECT 23 (vertices=40, convex hull=57) After retessellation of defect 23, euler #=-7 (150985,452707,301715) : difference with theory (-7) = 0 CORRECTING DEFECT 24 (vertices=15, convex hull=31) After retessellation of defect 24, euler #=-6 (150985,452718,301727) : difference with theory (-6) = 0 CORRECTING DEFECT 25 (vertices=25, convex hull=47) After retessellation of defect 25, euler #=-5 (150993,452763,301765) : difference with theory (-5) = 0 CORRECTING DEFECT 26 (vertices=17, convex hull=39) After retessellation of defect 26, euler #=-4 (151000,452798,301794) : difference with theory (-4) = 0 CORRECTING DEFECT 27 (vertices=55, convex hull=63) After retessellation of defect 27, euler #=-3 (151015,452868,301850) : difference with theory (-3) = 0 CORRECTING DEFECT 28 (vertices=39, convex hull=82) After retessellation of defect 28, euler #=-2 (151040,452976,301934) : difference with theory (-2) = 0 CORRECTING DEFECT 29 (vertices=27, convex hull=61) After retessellation of defect 29, euler #=-1 (151051,453032,301980) : difference with theory (-1) = 0 CORRECTING DEFECT 30 (vertices=69, convex hull=105) After retessellation of defect 30, euler #=0 (151067,453121,302054) : difference with theory (0) = 0 CORRECTING DEFECT 31 (vertices=38, convex hull=81) After retessellation of defect 31, euler #=1 (151089,453219,302131) : difference with theory (1) = 0 CORRECTING DEFECT 32 (vertices=81, convex hull=98) After retessellation of defect 32, euler #=2 (151126,453372,302248) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.88 +- 0.24 (0.10-->12.99) (max @ vno 63944 --> 64040) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.88 +- 0.24 (0.10-->12.99) (max @ vno 63944 --> 64040) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 128 mutations (35.3%), 235 crossovers (64.7%), 283 vertices were eliminated building final representation... 1948 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=151126, nf=302248, ne=453372, g=0) writing corrected surface to /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 17.0 minutes 0 defective edges removing intersecting faces 000: 202 intersecting mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 151126 - 453372 + 302248 = 2 --> 0 holes F =2V-4: 302248 = 302252-4 (0) 2E=3F: 906744 = 906744 (0) total defect index = 0 /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 7 intersecting 001: 2 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf rh Wed May 22 13:55:10 JST 2013 /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/scripts mris_make_surfaces -noaparc -mgz -T1 brain.finalsurfs test 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 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri/filled.mgz... reading volume /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri/brain.finalsurfs.mgz... reading volume /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri/wm.mgz... 20986 bright wm thresholded. 6012 bright non-wm voxels segmented. reading original surface position from /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/surf/rh.orig... computing class statistics... border white: 285437 voxels (1.70%) border gray 325958 voxels (1.94%) WM (92.0): 93.0 +- 9.3 [70.0 --> 110.0] GM (77.0) : 74.7 +- 13.1 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 47.9 (was 70) setting MAX_BORDER_WHITE to 112.3 (was 105) setting MIN_BORDER_WHITE to 61.0 (was 85) setting MAX_CSF to 34.8 (was 40) setting MAX_GRAY to 93.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 54.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 21.6 (was 40) repositioning cortical surface to gray/white boundary reading volume /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.22 (0.01-->5.94) (max @ vno 63944 --> 63945) face area 0.28 +- 0.13 (0.00-->4.91) mean absolute distance = 0.72 +- 0.89 4230 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=103, GM=61 mean inside = 92.5, mean outside = 70.7 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group mean border=75.1, 20 (20) missing vertices, mean dist 0.3 [0.6 (%33.5)->0.8 (%66.5))] %73 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=dhcp0, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.92 +- 0.27 (0.04-->6.12) (max @ vno 63944 --> 64040) face area 0.28 +- 0.14 (0.00-->4.53) mean absolute distance = 0.36 +- 0.59 3609 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=7352738.0, rms=12.58 001: dt: 0.5000, sse=7781044.0, rms=9.076 (0.000%) 002: dt: 0.5000, sse=8270974.0, rms=7.019 (0.000%) 003: dt: 0.5000, sse=8558652.0, rms=5.710 (0.000%) 004: dt: 0.5000, sse=8892391.0, rms=4.924 (0.000%) 005: dt: 0.5000, sse=9045343.0, rms=4.479 (0.000%) 006: dt: 0.5000, sse=9238084.0, rms=4.244 (0.000%) 007: dt: 0.5000, sse=9267146.0, rms=4.116 (0.000%) 008: dt: 0.5000, sse=9356278.0, rms=4.043 (0.000%) rms = 4.00, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=9318011.0, rms=3.996 (0.000%) 010: dt: 0.2500, sse=5915003.5, rms=2.777 (0.000%) 011: dt: 0.2500, sse=5408477.0, rms=2.371 (0.000%) 012: dt: 0.2500, sse=5127127.0, rms=2.274 (0.000%) 013: dt: 0.2500, sse=5043927.0, rms=2.201 (0.000%) rms = 2.18, time step reduction 2 of 3 to 0.125... 014: dt: 0.2500, sse=4966217.5, rms=2.175 (0.000%) 015: dt: 0.1250, sse=4804173.5, rms=2.039 (0.000%) rms = 2.03, time step reduction 3 of 3 to 0.062... 016: dt: 0.1250, sse=4764513.0, rms=2.026 (0.000%) positioning took 1.2 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group mean border=78.7, 26 (6) missing vertices, mean dist -0.2 [0.4 (%71.6)->0.3 (%28.4))] %80 local maxima, %15 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=dhcp0, 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 +- 0.26 (0.06-->6.51) (max @ vno 63944 --> 64040) face area 0.35 +- 0.17 (0.00-->6.59) mean absolute distance = 0.28 +- 0.42 4512 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5618840.5, rms=5.32 017: dt: 0.5000, sse=6052593.5, rms=3.554 (0.000%) rms = 3.92, time step reduction 1 of 3 to 0.250... 018: dt: 0.2500, sse=5552037.0, rms=2.636 (0.000%) 019: dt: 0.2500, sse=5360172.5, rms=2.132 (0.000%) 020: dt: 0.2500, sse=5240290.0, rms=1.872 (0.000%) 021: dt: 0.2500, sse=5208777.5, rms=1.819 (0.000%) rms = 1.78, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=5147106.5, rms=1.780 (0.000%) 023: dt: 0.1250, sse=5042121.0, rms=1.669 (0.000%) rms = 1.67, time step reduction 3 of 3 to 0.062... 024: dt: 0.1250, sse=4999598.0, rms=1.667 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 3 vertex label from ripped group mean border=81.5, 36 (5) missing vertices, mean dist -0.2 [0.3 (%70.0)->0.2 (%30.0))] %88 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=dhcp0, 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-->6.71) (max @ vno 63944 --> 64040) face area 0.34 +- 0.17 (0.00-->6.96) mean absolute distance = 0.24 +- 0.34 3971 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5324669.0, rms=3.86 025: dt: 0.5000, sse=5733026.0, rms=3.378 (0.000%) rms = 3.81, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=5276934.0, rms=2.260 (0.000%) 027: dt: 0.2500, sse=5201913.0, rms=1.847 (0.000%) 028: dt: 0.2500, sse=5197759.0, rms=1.658 (0.000%) rms = 1.67, time step reduction 2 of 3 to 0.125... 029: dt: 0.1250, sse=5138836.0, rms=1.586 (0.000%) 030: dt: 0.1250, sse=5049672.0, rms=1.488 (0.000%) rms = 1.49, time step reduction 3 of 3 to 0.062... 031: dt: 0.1250, sse=5049672.0, rms=1.488 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 3 vertex label from ripped group mean border=82.4, 44 (4) missing vertices, mean dist -0.1 [0.3 (%56.9)->0.2 (%43.1))] %90 local maxima, % 5 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=dhcp0, 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 /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=5084280.5, rms=1.96 rms = 2.49, time step reduction 1 of 3 to 0.250... 032: dt: 0.2500, sse=5181331.5, rms=1.378 (0.000%) 033: dt: 0.2500, sse=5384961.5, rms=1.129 (0.000%) rms = 1.13, time step reduction 2 of 3 to 0.125... rms = 1.12, time step reduction 3 of 3 to 0.062... 034: dt: 0.1250, sse=5381820.0, rms=1.119 (0.000%) positioning took 0.3 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 1 vertex label from ripped group generating cortex label... 13 non-cortical segments detected only using segment with 2269 vertices erasing segment 1 (vno[0] = 63973) erasing segment 2 (vno[0] = 72154) erasing segment 3 (vno[0] = 93213) erasing segment 4 (vno[0] = 95275) erasing segment 5 (vno[0] = 105019) erasing segment 6 (vno[0] = 109241) erasing segment 7 (vno[0] = 112200) erasing segment 8 (vno[0] = 114085) erasing segment 9 (vno[0] = 116797) erasing segment 10 (vno[0] = 116803) erasing segment 11 (vno[0] = 117647) erasing segment 12 (vno[0] = 119117) writing cortex label to /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/label/rh.cortex.label... writing curvature file /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/surf/rh.curv writing smoothed area to rh.area writing curvature file /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/surf/rh.area vertex spacing 0.89 +- 0.26 (0.08-->6.67) (max @ vno 63944 --> 64040) face area 0.33 +- 0.16 (0.00-->6.37) 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=50.5, 32 (32) missing vertices, mean dist 1.7 [0.1 (%0.0)->2.5 (%100.0))] %15 local maxima, %50 large gradients and %31 min vals, 2362 gradients ignored tol=1.0e-04, sigma=2.0, host=dhcp0, 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=32033526.0, rms=31.59 001: dt: 0.5000, sse=23819060.0, rms=26.744 (0.000%) 002: dt: 0.5000, sse=17880274.0, rms=22.635 (0.000%) 003: dt: 0.5000, sse=13838837.0, rms=19.264 (0.000%) 004: dt: 0.5000, sse=11342854.0, rms=16.516 (0.000%) 005: dt: 0.5000, sse=9787623.0, rms=14.251 (0.000%) 006: dt: 0.5000, sse=8781440.0, rms=12.401 (0.000%) 007: dt: 0.5000, sse=8164389.0, rms=10.789 (0.000%) 008: dt: 0.5000, sse=7750554.0, rms=9.357 (0.000%) 009: dt: 0.5000, sse=7540142.0, rms=8.050 (0.000%) 010: dt: 0.5000, sse=7461331.0, rms=6.907 (0.000%) 011: dt: 0.5000, sse=7463322.5, rms=5.952 (0.000%) 012: dt: 0.5000, sse=7638576.5, rms=5.252 (0.000%) 013: dt: 0.5000, sse=7796853.0, rms=4.817 (0.000%) 014: dt: 0.5000, sse=7985792.5, rms=4.574 (0.000%) 015: dt: 0.5000, sse=8064076.5, rms=4.416 (0.000%) 016: dt: 0.5000, sse=8200499.5, rms=4.340 (0.000%) rms = 4.29, time step reduction 1 of 3 to 0.250... 017: dt: 0.5000, sse=8199462.0, rms=4.292 (0.000%) 018: dt: 0.2500, sse=5747654.5, rms=3.490 (0.000%) 019: dt: 0.2500, sse=5542956.5, rms=3.266 (0.000%) rms = 3.25, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=5368658.0, rms=3.245 (0.000%) 021: dt: 0.1250, sse=5074490.5, rms=3.044 (0.000%) rms = 3.02, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=5044423.0, rms=3.018 (0.000%) positioning took 1.6 minutes mean border=48.6, 1239 (11) missing vertices, mean dist 0.1 [0.2 (%50.8)->0.5 (%49.2))] %34 local maxima, %37 large gradients and %25 min vals, 722 gradients ignored tol=1.0e-04, sigma=1.0, host=dhcp0, 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=5625308.0, rms=4.58 023: dt: 0.5000, sse=6143260.5, rms=4.135 (0.000%) rms = 4.21, time step reduction 1 of 3 to 0.250... 024: dt: 0.2500, sse=5641547.0, rms=3.451 (0.000%) 025: dt: 0.2500, sse=5731530.0, rms=3.199 (0.000%) 026: dt: 0.2500, sse=5664827.5, rms=3.114 (0.000%) rms = 3.09, time step reduction 2 of 3 to 0.125... 027: dt: 0.2500, sse=5744919.5, rms=3.092 (0.000%) 028: dt: 0.1250, sse=5479673.5, rms=2.891 (0.000%) rms = 2.86, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=5472025.0, rms=2.857 (0.000%) positioning took 0.6 minutes mean border=46.9, 1475 (11) missing vertices, mean dist 0.1 [0.2 (%44.2)->0.4 (%55.8))] %49 local maxima, %21 large gradients and %25 min vals, 860 gradients ignored tol=1.0e-04, sigma=0.5, host=dhcp0, 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=5658978.0, rms=3.74 rms = 4.09, time step reduction 1 of 3 to 0.250... 030: dt: 0.2500, sse=5467204.0, rms=3.266 (0.000%) 031: dt: 0.2500, sse=5533208.0, rms=3.058 (0.000%) 032: dt: 0.2500, sse=5774706.5, rms=3.002 (0.000%) rms = 3.00, time step reduction 2 of 3 to 0.125... 033: dt: 0.1250, sse=5692706.0, rms=2.931 (0.000%) 034: dt: 0.1250, sse=5615832.0, rms=2.826 (0.000%) rms = 2.80, time step reduction 3 of 3 to 0.062... 035: dt: 0.1250, sse=5604183.5, rms=2.805 (0.000%) positioning took 0.5 minutes mean border=46.0, 2730 (11) missing vertices, mean dist 0.1 [0.2 (%48.8)->0.3 (%51.2))] %53 local maxima, %17 large gradients and %24 min vals, 720 gradients ignored tol=1.0e-04, sigma=0.2, host=dhcp0, 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 /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=5658586.0, rms=3.12 rms = 3.77, time step reduction 1 of 3 to 0.250... 036: dt: 0.2500, sse=5553045.5, rms=2.897 (0.000%) 037: dt: 0.2500, sse=5821264.0, rms=2.814 (0.000%) rms = 2.81, time step reduction 2 of 3 to 0.125... 038: dt: 0.2500, sse=5938199.5, rms=2.809 (0.000%) 039: dt: 0.1250, sse=5831911.0, rms=2.664 (0.000%) rms = 2.64, time step reduction 3 of 3 to 0.062... 040: dt: 0.1250, sse=5853027.5, rms=2.635 (0.000%) positioning took 0.4 minutes writing curvature file /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/surf/rh.area.pial vertex spacing 1.00 +- 0.42 (0.07-->7.78) (max @ vno 68724 --> 71056) face area 0.39 +- 0.29 (0.00-->7.33) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 151126 vertices processed 25000 of 151126 vertices processed 50000 of 151126 vertices processed 75000 of 151126 vertices processed 100000 of 151126 vertices processed 125000 of 151126 vertices processed 150000 of 151126 vertices processed 0 of 151126 vertices processed 25000 of 151126 vertices processed 50000 of 151126 vertices processed 75000 of 151126 vertices processed 100000 of 151126 vertices processed 125000 of 151126 vertices processed 150000 of 151126 vertices processed thickness calculation complete, 146:616 truncations. 34086 vertices at 0 distance 104194 vertices at 1 distance 97623 vertices at 2 distance 39039 vertices at 3 distance 11339 vertices at 4 distance 3001 vertices at 5 distance 813 vertices at 6 distance 264 vertices at 7 distance 108 vertices at 8 distance 43 vertices at 9 distance 20 vertices at 10 distance 14 vertices at 11 distance 22 vertices at 12 distance 19 vertices at 13 distance 8 vertices at 14 distance 14 vertices at 15 distance 10 vertices at 16 distance 8 vertices at 17 distance 3 vertices at 18 distance 8 vertices at 19 distance 8 vertices at 20 distance writing curvature file /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/surf/rh.thickness positioning took 9.3 minutes #-------------------------------------------- #@# Smooth2 rh Wed May 22 14:04:28 JST 2013 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/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 Wed May 22 14:04:30 JST 2013 /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated avg radius = 49.5 mm, total surface area = 91356 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.118 (target=0.015) step 005: RMS=0.081 (target=0.015) step 010: RMS=0.058 (target=0.015) step 015: RMS=0.048 (target=0.015) step 020: RMS=0.039 (target=0.015) step 025: RMS=0.033 (target=0.015) step 030: RMS=0.028 (target=0.015) step 035: RMS=0.023 (target=0.015) step 040: RMS=0.020 (target=0.015) step 045: RMS=0.018 (target=0.015) step 050: RMS=0.016 (target=0.015) inflation complete. inflation took 0.3 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/rh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 200 vertices thresholded to be in k1 ~ [-0.24 0.31], k2 ~ [-0.10 0.05] total integrated curvature = 0.556*4pi (6.982) --> 0 handles ICI = 1.7, FI = 12.4, variation=206.150 129 vertices thresholded to be in [-0.01 0.01] writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 157 vertices thresholded to be in [-0.13 0.15] done. writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.015, std = 0.024 done. #----------------------------------------- #@# Curvature Stats rh Wed May 22 14:05:47 JST 2013 /home/yamamoto/freesurfer/5.3.0/dist/subjects/test/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm test rh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/rh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ test/rh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 262 ] Gb_filter = 0 WARN: S lookup min: -1.148460 WARN: S explicit min: 0.000000 vertex = 1140 #-------------------------------------------- #@# ASeg Stats Wed May 22 14:05:50 JST 2013 INFO: mri_segstats will not calculate Supratentorial due to missing ribbon.mgz file /home/yamamoto/freesurfer/5.3.0/dist/subjects/test mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /usr/local/freesurfer/5.3.0/dist/ASegStatsLUT.txt --subject test $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /usr/local/freesurfer/5.3.0/dist/ASegStatsLUT.txt --subject test sysname Linux hostname dhcp006.tkl.iis.u-tokyo.ac.jp machine x86_64 user yamamoto UseRobust 0 atlas_icv (eTIV) = 1629767 mm^3 (det: 1.195328 ) mghRead(/home/yamamoto/freesurfer/5.3.0/dist/subjects/test/mri/ribbon.mgz, -1): could not open file Computing euler number orig.nofix lheno = -54, rheno = -56 orig.nofix lhholes = 28, rhholes = 29 Loading mri/aseg.mgz Getting Brain Volume Statistics Linux dhcp006.tkl.iis.u-tokyo.ac.jp 2.6.32-358.6.2.el6.x86_64 #1 SMP Thu May 16 20:59:36 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s test exited with ERRORS at Wed May 22 14:05:56 JST 2013 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting