Fri Nov 23 16:46:06 CST 2018 /home/liuzb/work/tutorial_data/practice_with_data/Subj004 /usr/local/freesurfer/bin/recon-all -all -i nii-004/ADNI_004_3D_FLAIR.nii.gz -s Subj004 -itkthreads 4 subjid Subj004 setenv SUBJECTS_DIR /home/liuzb/work/tutorial_data/practice_with_data FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-linux-centos6_x86_64-dev-20181116-bbf4668 Linux liuzb-System-Product-Name 4.15.0-39-generic #42~16.04.1-Ubuntu SMP Wed Oct 24 17:09:54 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 63653 maxlocks unlimited maxsignal 63653 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 16365104 957712 14373996 68556 1033396 14966852 Swap: 15999996 0 15999996 ######################################## program versions used $Id: recon-all,v 1.601 2017/02/08 21:17:33 greve Exp $ $Id: lta_convert.cpp,v 1.10 2016/08/09 02:11:11 zkaufman Exp $ ProgramName: lta_convert ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:06-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: lta_convert.cpp,v 1.10 2016/08/09 02:11:11 zkaufman Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:06-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_annotation2label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:06-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mri_annotation2label.c,v 1.32 2016/08/02 21:20:27 nicks Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_aparc2aseg ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:06-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mri_aparc2aseg.c,v 1.54 2016/12/26 15:29:30 fischl Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_aparc2wmseg ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:06-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mri_aparc2wmseg.c,v 1.6 2011/03/02 00:04:13 nicks Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_binarize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:06-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:06-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mri_ca_label.c,v 1.115 2016/10/22 17:31:36 fischl Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:06-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mri_ca_normalize.c,v 1.69 2016/10/22 17:30:57 fischl Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:06-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mri_ca_register.c,v 1.99 2016/10/22 17:31:24 fischl Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_cc ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:06-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mri_cc.c,v 1.39 2015/12/04 13:59:56 fischl Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_compute_overlap ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:06-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mri_compute_overlap.c,v 1.19 2015/10/20 20:07:19 fischl Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_compute_seg_overlap ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:06-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mri_compute_seg_overlap.c,v 1.18 2015/08/28 18:05:30 greve Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_concat ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:06-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mri_concat.c,v 1.67 2017/02/16 19:49:35 greve Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:06-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:06-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_diff ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:06-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mri_diff.c,v 1.37 2017/01/11 18:15:33 greve Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_edit_wm_with_aseg ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:06-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mri_edit_wm_with_aseg.c,v 1.25 2012/03/29 13:17:38 fischl Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:06-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mri_em_register.c,v 1.106 2016/10/22 17:31:12 fischl Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:06-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:06-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mri_fuse_segmentations.cpp,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_fwhm ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:06-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mri_fwhm.c,v 1.35 2016/11/01 20:25:24 greve Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:06-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_info ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:06-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mri_info.c,v 1.87 2014/11/20 23:46:54 greve Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:06-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mri_label2label.c,v 1.50 2016/12/10 22:57:43 fischl Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_label2vol ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:06-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mri_label2vol.c,v 1.46 2014/12/08 21:11:54 greve Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_log_likelihood ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:06-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mri_log_likelihood.c,v 1.4 2011/03/02 00:04:22 nicks Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_mask ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:06-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mri_mask.c,v 1.24 2016/11/28 20:30:57 fischl Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_matrix_multiply ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:06-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mri_matrix_multiply.c,v 1.13 2011/03/02 00:04:23 nicks Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:06-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mri_normalize.c,v 1.92 2017/01/27 22:31:34 ah221 Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:06-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:06-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:06-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_relabel_nonwm_hypos ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:06-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mri_relabel_nonwm_hypos.c,v 1.2 2014/04/17 18:03:22 greve Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_remove_neck ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:06-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mri_remove_neck.c,v 1.10 2011/03/02 00:04:24 nicks Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:06-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:06-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:06-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:06-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:06-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mris_calc.c,v 1.55 2016/09/27 18:50:16 greve Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_convert ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:06-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id$ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:06-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:06-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_diff ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:06-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mris_diff.c,v 1.20 2014/03/21 23:57:48 greve Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_divide_parcellation ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:06-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mris_divide_parcellation.c,v 1.12 2012/10/24 19:50:06 maritza Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:06-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mri_segment.c,v 1.44 2016/10/22 17:29:37 fischl Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:06-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mri_segstats.c,v 1.122 2017/01/23 18:23:14 greve Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:07-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:07-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mris_fix_topology.c,v 1.51 2016/10/27 19:43:58 fischl Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:07-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_jacobian ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:07-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mris_jacobian.c,v 1.11 2015/02/05 23:34:40 zkaufman Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_label2annot ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:07-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_left_right_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:07-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mris_left_right_register.c,v 1.2 2011/12/16 20:49:37 greve Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:07-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mris_make_surfaces.c,v 1.172 2017/02/16 19:42:36 fischl Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:07-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:07-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mris_register.c,v 1.64 2017/02/07 19:04:44 fischl Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:07-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:07-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mris_sphere.c,v 1.62 2017/02/07 19:04:37 fischl Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_surface_stats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:07-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mris_surface_stats.c,v 1.10 2011/03/02 00:04:34 nicks Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_stats2seg ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:07-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mri_stats2seg.c,v 1.9 2011/03/02 00:04:24 nicks Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_thickness ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:07-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mris_thickness.c,v 1.28 2012/11/27 17:41:26 fischl Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_thickness_diff ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:07-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mris_thickness_diff.c,v 1.16 2011/03/02 00:04:34 nicks Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:07-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_surf2surf ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:07-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_surf2vol ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:07-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mri_surf2vol.c,v 1.28 2014/12/08 19:49:02 greve Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_surfcluster ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:07-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mri_surfcluster.c,v 1.60 2016/11/01 19:49:22 greve Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mris_volmask ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:07-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mris_volmask.cpp,v 1.28 2016/11/18 19:19:29 fischl Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:07-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mri_tessellate.c,v 1.39 2016/07/20 21:05:04 zkaufman Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_vol2surf ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:07-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mri_vol2surf.c,v 1.68 2014/05/30 20:58:47 greve Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_vol2vol ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:07-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mri_vol2vol.c,v 1.89 2016/06/22 22:33:40 fischl Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_voldiff ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:07-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mri_voldiff.c,v 1.6 2011/03/02 00:04:25 nicks Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:07-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 ProgramName: tkregister2_cmdl ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:07-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: tkregister2.c,v 1.133 2016/08/02 21:17:11 greve Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/11/23-08:46:07-GMT BuildTimeStamp: Nov 16 2018 02:40:28 Id: $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ User: liuzb Machine: liuzb-System-Product-Name Platform: Linux PlatformVersion: 4.15.0-39-generic CompilerName: GCC CompilerVersion: 40800 FLIRT version 6.0 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ####################################### GCADIR /usr/local/freesurfer/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /usr/local/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /home/liuzb/work/tutorial_data/practice_with_data/Subj004 mri_convert /home/liuzb/work/tutorial_data/practice_with_data/nii-004/ADNI_004_3D_FLAIR.nii.gz /home/liuzb/work/tutorial_data/practice_with_data/Subj004/mri/orig/001.mgz mri_convert /home/liuzb/work/tutorial_data/practice_with_data/nii-004/ADNI_004_3D_FLAIR.nii.gz /home/liuzb/work/tutorial_data/practice_with_data/Subj004/mri/orig/001.mgz INFO: using NIfTI-1 qform $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ reading from /home/liuzb/work/tutorial_data/practice_with_data/nii-004/ADNI_004_3D_FLAIR.nii.gz... INFO: this is an unsiged short. I'll try to read it, but it might not work if there are values over 32k TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to /home/liuzb/work/tutorial_data/practice_with_data/Subj004/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Fri Nov 23 16:46:09 CST 2018 Found 1 runs /home/liuzb/work/tutorial_data/practice_with_data/Subj004/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... Only one run found so motion correction will not be performed. I'll copy the run to rawavg and continue. cp /home/liuzb/work/tutorial_data/practice_with_data/Subj004/mri/orig/001.mgz /home/liuzb/work/tutorial_data/practice_with_data/Subj004/mri/rawavg.mgz /home/liuzb/work/tutorial_data/practice_with_data/Subj004 mri_convert /home/liuzb/work/tutorial_data/practice_with_data/Subj004/mri/rawavg.mgz /home/liuzb/work/tutorial_data/practice_with_data/Subj004/mri/orig.mgz --conform mri_convert /home/liuzb/work/tutorial_data/practice_with_data/Subj004/mri/rawavg.mgz /home/liuzb/work/tutorial_data/practice_with_data/Subj004/mri/orig.mgz --conform $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ reading from /home/liuzb/work/tutorial_data/practice_with_data/Subj004/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram 0 820 1000, flo=0, fhi=0.999, dest_type=0 Reslicing using trilinear interpolation writing to /home/liuzb/work/tutorial_data/practice_with_data/Subj004/mri/orig.mgz... mri_add_xform_to_header -c /home/liuzb/work/tutorial_data/practice_with_data/Subj004/mri/transforms/talairach.xfm /home/liuzb/work/tutorial_data/practice_with_data/Subj004/mri/orig.mgz /home/liuzb/work/tutorial_data/practice_with_data/Subj004/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Fri Nov 23 16:46:17 CST 2018 /home/liuzb/work/tutorial_data/practice_with_data/Subj004/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /home/liuzb/work/tutorial_data/practice_with_data/Subj004/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 nIters 1 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux liuzb-System-Product-Name 4.15.0-39-generic #42~16.04.1-Ubuntu SMP Wed Oct 24 17:09:54 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux Fri Nov 23 16:46:17 CST 2018 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 /usr/bin/bc Found /dev/shm , will use for temp dir tmpdir is /dev/shm/tmp.mri_nu_correct.mni.3305 /home/liuzb/work/tutorial_data/practice_with_data/Subj004/mri mri_convert orig.mgz /dev/shm/tmp.mri_nu_correct.mni.3305/nu0.mnc -odt float mri_convert orig.mgz /dev/shm/tmp.mri_nu_correct.mni.3305/nu0.mnc -odt float $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to /dev/shm/tmp.mri_nu_correct.mni.3305/nu0.mnc... -------------------------------------------------------- Iteration 1 Fri Nov 23 16:46:18 CST 2018 nu_correct -clobber /dev/shm/tmp.mri_nu_correct.mni.3305/nu0.mnc /dev/shm/tmp.mri_nu_correct.mni.3305/nu1.mnc -tmpdir /dev/shm/tmp.mri_nu_correct.mni.3305/0/ -iterations 1000 -distance 50 [liuzb@liuzb-System-Product-Name:/home/liuzb/work/tutorial_data/practice_with_data/Subj004/mri/] [2018-11-23 16:46:18] running: /usr/local/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir /dev/shm/tmp.mri_nu_correct.mni.3305/0/ /dev/shm/tmp.mri_nu_correct.mni.3305/nu0.mnc /dev/shm/tmp.mri_nu_correct.mni.3305/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 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 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 Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 81 CV of field change: 0.000970562 mri_convert /dev/shm/tmp.mri_nu_correct.mni.3305/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert /dev/shm/tmp.mri_nu_correct.mni.3305/nu1.mnc orig_nu.mgz --like orig.mgz --conform $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ reading from /dev/shm/tmp.mri_nu_correct.mni.3305/nu1.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 changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram 0 431.084 1000, flo=0, fhi=0.999, dest_type=0 writing to orig_nu.mgz... Fri Nov 23 16:47:21 CST 2018 mri_nu_correct.mni done talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... Started at Fri Nov 23 16:47:21 CST 2018 Ended at Fri Nov 23 16:47:45 CST 2018 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Fri Nov 23 16:47:47 CST 2018 /home/liuzb/work/tutorial_data/practice_with_data/Subj004/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7468, pval=0.6675 >= threshold=0.0050) awk -f /usr/local/freesurfer/bin/extract_talairach_avi_QA.awk /home/liuzb/work/tutorial_data/practice_with_data/Subj004/mri/transforms/talairach_avi.log tal_QC_AZS /home/liuzb/work/tutorial_data/practice_with_data/Subj004/mri/transforms/talairach_avi.log TalAviQA: 0.95401 z-score: -5 #-------------------------------------------- #@# Nu Intensity Correction Fri Nov 23 16:47:47 CST 2018 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /home/liuzb/work/tutorial_data/practice_with_data/Subj004/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux liuzb-System-Product-Name 4.15.0-39-generic #42~16.04.1-Ubuntu SMP Wed Oct 24 17:09:54 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux Fri Nov 23 16:47:47 CST 2018 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 /usr/bin/bc Found /dev/shm , will use for temp dir tmpdir is /dev/shm/tmp.mri_nu_correct.mni.4556 /home/liuzb/work/tutorial_data/practice_with_data/Subj004/mri mri_convert orig.mgz /dev/shm/tmp.mri_nu_correct.mni.4556/nu0.mnc -odt float mri_convert orig.mgz /dev/shm/tmp.mri_nu_correct.mni.4556/nu0.mnc -odt float $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to /dev/shm/tmp.mri_nu_correct.mni.4556/nu0.mnc... -------------------------------------------------------- Iteration 1 Fri Nov 23 16:47:49 CST 2018 nu_correct -clobber /dev/shm/tmp.mri_nu_correct.mni.4556/nu0.mnc /dev/shm/tmp.mri_nu_correct.mni.4556/nu1.mnc -tmpdir /dev/shm/tmp.mri_nu_correct.mni.4556/0/ [liuzb@liuzb-System-Product-Name:/home/liuzb/work/tutorial_data/practice_with_data/Subj004/mri/] [2018-11-23 16:47:49] running: /usr/local/freesurfer/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 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /dev/shm/tmp.mri_nu_correct.mni.4556/0/ /dev/shm/tmp.mri_nu_correct.mni.4556/nu0.mnc /dev/shm/tmp.mri_nu_correct.mni.4556/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 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 Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 50 CV of field change: 0.00166077 -------------------------------------------------------- Iteration 2 Fri Nov 23 16:48:24 CST 2018 nu_correct -clobber /dev/shm/tmp.mri_nu_correct.mni.4556/nu1.mnc /dev/shm/tmp.mri_nu_correct.mni.4556/nu2.mnc -tmpdir /dev/shm/tmp.mri_nu_correct.mni.4556/1/ [liuzb@liuzb-System-Product-Name:/home/liuzb/work/tutorial_data/practice_with_data/Subj004/mri/] [2018-11-23 16:48:24] running: /usr/local/freesurfer/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 1.0e-7 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir /dev/shm/tmp.mri_nu_correct.mni.4556/1/ /dev/shm/tmp.mri_nu_correct.mni.4556/nu1.mnc /dev/shm/tmp.mri_nu_correct.mni.4556/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 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 Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 50 CV of field change: 0.00101448 mri_binarize --i /dev/shm/tmp.mri_nu_correct.mni.4556/nu2.mnc --min -1 --o /dev/shm/tmp.mri_nu_correct.mni.4556/ones.mgz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /home/liuzb/work/tutorial_data/practice_with_data/Subj004/mri cmdline mri_binarize --i /dev/shm/tmp.mri_nu_correct.mni.4556/nu2.mnc --min -1 --o /dev/shm/tmp.mri_nu_correct.mni.4556/ones.mgz sysname Linux hostname liuzb-System-Product-Name machine x86_64 user liuzb input /dev/shm/tmp.mri_nu_correct.mni.4556/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output /dev/shm/tmp.mri_nu_correct.mni.4556/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 16777216 values in range Counting number of voxels in first frame Found 16777215 voxels in final mask Count: 16777215 16777215.000000 16777216 99.999994 mri_binarize done mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.4556/ones.mgz --i orig.mgz --sum /dev/shm/tmp.mri_nu_correct.mni.4556/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.4556/input.mean.dat $Id: mri_segstats.c,v 1.122 2017/01/23 18:23:14 greve Exp $ cwd cmdline mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.4556/ones.mgz --i orig.mgz --sum /dev/shm/tmp.mri_nu_correct.mni.4556/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.4556/input.mean.dat sysname Linux hostname liuzb-System-Product-Name machine x86_64 user liuzb whitesurfname white UseRobust 0 Loading /dev/shm/tmp.mri_nu_correct.mni.4556/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to /dev/shm/tmp.mri_nu_correct.mni.4556/input.mean.dat mri_segstats done mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.4556/ones.mgz --i /dev/shm/tmp.mri_nu_correct.mni.4556/nu2.mnc --sum /dev/shm/tmp.mri_nu_correct.mni.4556/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.4556/output.mean.dat $Id: mri_segstats.c,v 1.122 2017/01/23 18:23:14 greve Exp $ cwd cmdline mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.4556/ones.mgz --i /dev/shm/tmp.mri_nu_correct.mni.4556/nu2.mnc --sum /dev/shm/tmp.mri_nu_correct.mni.4556/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.4556/output.mean.dat sysname Linux hostname liuzb-System-Product-Name machine x86_64 user liuzb whitesurfname white UseRobust 0 Loading /dev/shm/tmp.mri_nu_correct.mni.4556/ones.mgz Loading /dev/shm/tmp.mri_nu_correct.mni.4556/nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation Reporting on 1 segmentations Using PrintSegStat Computing spatial average of each frame 0 Writing to /dev/shm/tmp.mri_nu_correct.mni.4556/output.mean.dat mri_segstats done mris_calc -o /dev/shm/tmp.mri_nu_correct.mni.4556/nu2.mnc /dev/shm/tmp.mri_nu_correct.mni.4556/nu2.mnc mul 1.04092288419956584926 Saving result to '/dev/shm/tmp.mri_nu_correct.mni.4556/nu2.mnc' (type = MINC ) [ ok ] mri_convert /dev/shm/tmp.mri_nu_correct.mni.4556/nu2.mnc nu.mgz --like orig.mgz mri_convert /dev/shm/tmp.mri_nu_correct.mni.4556/nu2.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.227 2017/02/16 19:15:42 greve Exp $ reading from /dev/shm/tmp.mri_nu_correct.mni.4556/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 ( 5, 158) to ( 3, 110) Fri Nov 23 16:49:21 CST 2018 mri_nu_correct.mni done mri_add_xform_to_header -c /home/liuzb/work/tutorial_data/practice_with_data/Subj004/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Fri Nov 23 16:49:22 CST 2018 /home/liuzb/work/tutorial_data/practice_with_data/Subj004/mri mri_normalize -g 1 -seed 1234 -mprage nu.mgz T1.mgz using max gradient = 1.000 setting seed for random number genererator to 1234 assuming input volume is MGH (Van der Kouwe) MP-RAGE reading from nu.mgz... normalizing image... talairach transform 1.01741 0.04700 -0.01864 -202.33369; -0.06283 1.06951 0.09716 -359.51270; 0.04270 -0.06693 1.12100 -604.89435; 0.00000 0.00000 0.00000 1.00000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 14 Starting OpenSpline(): npoints = 14 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 78 (78), valley at 62 (62) csf peak at 39, setting threshold to 65 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 67 (67), valley at 36 (36) csf peak at 34, setting threshold to 56 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 1 minutes and 37 seconds. #-------------------------------------------- #@# Skull Stripping Fri Nov 23 16:50:59 CST 2018 /home/liuzb/work/tutorial_data/practice_with_data/Subj004/mri mri_em_register -rusage /home/liuzb/work/tutorial_data/practice_with_data/Subj004/touch/rusage.mri_em_register.skull.dat -skull nu.mgz /usr/local/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 == Number of threads available to mri_em_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach_with_skull.log reading '/usr/local/freesurfer/average/RB_all_withskull_2016-05-10.vc700.gca'... GCAread took 0 minutes and 1 seconds. average std = 22.9 using min determinant for regularization = 52.6 0 singular and 9002 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 8.7 or > 569.1 total sample mean = 77.6 (1399 zeros) ************************************************ spacing=8, using 3243 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3243, passno 0, spacing 8 resetting wm mean[0]: 100 --> 108 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=6.0 skull bounding box = (51, 16, 35) --> (203, 255, 240) finding center of left hemi white matter using (102, 96, 138) as brain centroid of Right_Cerebral_White_Matter... mean wm in atlas = 108, using box (83,66,113) --> (120, 125,163) to find MRI wm before smoothing, mri peak at 80 robust fit to distribution - 80 +- 7.1 after smoothing, mri peak at 80, scaling input intensities by 1.350 scaling channel 0 by 1.35 initial log_p = -4.747 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.689455 @ (-10.526, 31.579, -10.526) max log p = -4.563197 @ (5.263, -5.263, -5.263) max log p = -4.550458 @ (2.632, 2.632, -2.632) max log p = -4.515568 @ (-1.316, -1.316, 3.947) max log p = -4.515568 @ (0.000, 0.000, 0.000) max log p = -4.514416 @ (-0.329, -0.987, 0.329) max log p = -4.514416 @ (0.000, 0.000, 0.000) max log p = -4.514416 @ (0.000, 0.000, 0.000) Found translation: (-4.3, 26.6, -14.1): log p = -4.514 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.467, old_max_log_p =-4.514 (thresh=-4.5) 1.07500 0.00000 0.00000 -13.96270; 0.00000 1.22567 0.16136 -12.10856; 0.00000 -0.15011 1.14016 -14.33289; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 18 seconds. **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.467, old_max_log_p =-4.467 (thresh=-4.5) 1.07500 0.00000 0.00000 -13.96270; 0.00000 1.22567 0.16136 -12.10856; 0.00000 -0.15011 1.14016 -14.33289; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 iteration took 1 minutes and 15 seconds. **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.399, old_max_log_p =-4.467 (thresh=-4.5) 1.01474 0.00345 -0.03537 -0.40701; 0.00000 1.20695 0.12026 -6.70525; 0.03449 -0.10927 1.12185 -17.16788; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 11 seconds. **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.393, old_max_log_p =-4.399 (thresh=-4.4) 1.03325 -0.03682 -0.03880 0.25747; 0.03147 1.18667 0.08075 -3.66937; 0.03382 -0.06841 1.10409 -17.60373; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 12 seconds. **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.393, old_max_log_p =-4.393 (thresh=-4.4) 1.03325 -0.03682 -0.03880 0.25747; 0.03147 1.18667 0.08075 -3.66937; 0.03382 -0.06841 1.10409 -17.60373; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 iteration took 1 minutes and 12 seconds. **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.385, old_max_log_p =-4.393 (thresh=-4.4) 1.03125 -0.03785 -0.02068 -1.53181; 0.03140 1.18389 0.08056 -2.39005; 0.01695 -0.06796 1.10716 -16.78148; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 10 seconds. **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.385, old_max_log_p =-4.385 (thresh=-4.4) 1.03125 -0.03785 -0.02068 -1.53181; 0.03140 1.18389 0.08056 -2.39005; 0.01695 -0.06796 1.10716 -16.78148; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3243 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.03125 -0.03785 -0.02068 -1.53181; 0.03140 1.18389 0.08056 -2.39005; 0.01695 -0.06796 1.10716 -16.78148; 0.00000 0.00000 0.00000 1.00000; nsamples 3243 Quasinewton: input matrix 1.03125 -0.03785 -0.02068 -1.53181; 0.03140 1.18389 0.08056 -2.39005; 0.01695 -0.06796 1.10716 -16.78148; 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) = -0.0 tol 0.000010 Resulting transform: 1.03125 -0.03785 -0.02068 -1.53181; 0.03140 1.18389 0.08056 -2.39005; 0.01695 -0.06796 1.10716 -16.78148; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -4.385 (old=-4.747) transform before final EM align: 1.03125 -0.03785 -0.02068 -1.53181; 0.03140 1.18389 0.08056 -2.39005; 0.01695 -0.06796 1.10716 -16.78148; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 364799 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.03125 -0.03785 -0.02068 -1.53181; 0.03140 1.18389 0.08056 -2.39005; 0.01695 -0.06796 1.10716 -16.78148; 0.00000 0.00000 0.00000 1.00000; nsamples 364799 Quasinewton: input matrix 1.03125 -0.03785 -0.02068 -1.53181; 0.03140 1.18389 0.08056 -2.39005; 0.01695 -0.06796 1.10716 -16.78148; 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: 011: -log(p) = 4.7 tol 0.000000 final transform: 1.03125 -0.03785 -0.02068 -1.53181; 0.03140 1.18389 0.08056 -2.39005; 0.01695 -0.06796 1.10716 -16.78148; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... #VMPC# mri_em_register VmPeak 839280 FSRUNTIME@ mri_ca_register 0.1573 hours 1 threads registration took 9 minutes and 26 seconds. mri_watershed -rusage /home/liuzb/work/tutorial_data/practice_with_data/Subj004/touch/rusage.mri_watershed.dat -T1 -brain_atlas /usr/local/freesurfer/average/RB_all_withskull_2016-05-10.vc700.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=130 y=87 z=118 r=91 first estimation of the main basin volume: 3214154 voxels Looking for seedpoints 2 found in the cerebellum 18 found in the rest of the brain global maximum in x=156, y=88, z=75, Imax=255 CSF=16, 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=9273935686 voxels, voxel volume =1.000 = 9273935686 mmm3 = 9273935.872 cm3 done. PostAnalyze...Basin Prior 492 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=92, z=114, r=8854 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=56 , nb = 44820 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=28 , nb = 3168 LEFT_CER CSF_MIN=0, CSF_intensity=5, CSF_MAX=29 , nb = 2772 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=50 , nb = 19458 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=62 , nb = 18972 OTHER CSF_MIN=0, CSF_intensity=24, CSF_MAX=55 , nb = 450 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 56, 74, 80, 95 after analyzing : 56, 78, 80, 82 RIGHT_CER before analyzing : 28, 58, 78, 95 after analyzing : 28, 71, 78, 77 LEFT_CER before analyzing : 29, 60, 80, 95 after analyzing : 29, 73, 80, 78 RIGHT_BRAIN before analyzing : 50, 71, 80, 95 after analyzing : 50, 77, 80, 81 LEFT_BRAIN before analyzing : 62, 76, 80, 95 after analyzing : 62, 78, 80, 82 OTHER before analyzing : 55, 71, 80, 95 after analyzing : 55, 77, 80, 81 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...62 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.013 curvature mean = 66.427, std = 6.955 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 4.31, sigma = 5.75 after rotation: sse = 4.31, sigma = 5.75 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 5.03, its var is 7.03 before Erosion-Dilatation 2.36% of inacurate vertices after Erosion-Dilatation 2.02% 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...46 iterations mri_strip_skull: done peeling brain Brain Size = 1454813 voxels, voxel volume = 1.000 mm3 = 1454813 mmm3 = 1454.813 cm3 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 16.076213 mri_watershed stimesec 0.219948 mri_watershed ru_maxrss 866724 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 219361 mri_watershed ru_majflt 9 mri_watershed ru_nswap 0 mri_watershed ru_inblock 9496 mri_watershed ru_oublock 2424 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 44 mri_watershed ru_nivcsw 23 mri_watershed done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Fri Nov 23 17:00:43 CST 2018 /home/liuzb/work/tutorial_data/practice_with_data/Subj004/mri mri_em_register -rusage /home/liuzb/work/tutorial_data/practice_with_data/Subj004/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... == Number of threads available to mri_em_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach.log reading '/usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca'... GCAread took 0 minutes and 1 seconds. average std = 7.3 using min determinant for regularization = 5.3 0 singular and 841 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 6.3 or > 503.7 total sample mean = 78.8 (1011 zeros) ************************************************ spacing=8, using 2830 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2830, passno 0, spacing 8 resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=32.4 skull bounding box = (61, 34, 39) --> (195, 149, 200) finding center of left hemi white matter using (106, 72, 120) as brain centroid of Right_Cerebral_White_Matter... mean wm in atlas = 107, using box (90,58,100) --> (122, 86,139) to find MRI wm before smoothing, mri peak at 81 robust fit to distribution - 80 +- 6.0 after smoothing, mri peak at 80, scaling input intensities by 1.337 scaling channel 0 by 1.3375 initial log_p = -4.679 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.298451 @ (-10.526, 31.579, -10.526) max log p = -4.110013 @ (5.263, -5.263, -5.263) max log p = -4.077231 @ (2.632, -2.632, 2.632) max log p = -4.066107 @ (1.316, 1.316, 1.316) max log p = -4.021470 @ (-0.658, -0.658, 0.658) max log p = -4.021470 @ (0.000, 0.000, 0.000) max log p = -4.021470 @ (0.000, 0.000, 0.000) max log p = -4.021470 @ (0.000, 0.000, 0.000) Found translation: (-2.0, 24.3, -11.2): log p = -4.021 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.015, old_max_log_p =-4.021 (thresh=-4.0) 1.00000 0.00000 0.00000 -1.97369; 0.00000 1.07500 0.00000 17.22101; 0.00000 0.00000 1.07500 -19.93136; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 9 seconds. **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.015, old_max_log_p =-4.015 (thresh=-4.0) 1.00000 0.00000 0.00000 -1.97369; 0.00000 1.07500 0.00000 17.22101; 0.00000 0.00000 1.07500 -19.93136; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 iteration took 1 minutes and 7 seconds. **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.914, old_max_log_p =-4.015 (thresh=-4.0) 1.01602 -0.03490 -0.07282 5.76168; 0.03326 1.13499 0.03615 6.84299; 0.06540 -0.03378 1.07221 -22.81888; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 3 seconds. **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.914, old_max_log_p =-3.914 (thresh=-3.9) 1.01602 -0.03490 -0.07282 5.76168; 0.03326 1.13499 0.03615 6.84299; 0.06540 -0.03378 1.07221 -22.81888; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 iteration took 1 minutes and 3 seconds. **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.888, old_max_log_p =-3.914 (thresh=-3.9) 1.01635 0.00105 -0.05301 0.62584; 0.00170 1.13572 0.06427 8.14749; 0.04785 -0.06114 1.07331 -19.08662; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 1 seconds. **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.886, old_max_log_p =-3.888 (thresh=-3.9) 1.01516 0.00105 -0.05295 0.77399; 0.00170 1.13572 0.06427 8.14749; 0.04785 -0.06114 1.07331 -19.08662; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2830 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.01516 0.00105 -0.05295 0.77399; 0.00170 1.13572 0.06427 8.14749; 0.04785 -0.06114 1.07331 -19.08662; 0.00000 0.00000 0.00000 1.00000; nsamples 2830 Quasinewton: input matrix 1.01516 0.00105 -0.05295 0.77399; 0.00170 1.13572 0.06427 8.14749; 0.04785 -0.06114 1.07331 -19.08662; 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: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.01516 0.00105 -0.05295 0.77399; 0.00170 1.13572 0.06427 8.14749; 0.04785 -0.06114 1.07331 -19.08662; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.886 (old=-4.679) transform before final EM align: 1.01516 0.00105 -0.05295 0.77399; 0.00170 1.13572 0.06427 8.14749; 0.04785 -0.06114 1.07331 -19.08662; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 315557 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.01516 0.00105 -0.05295 0.77399; 0.00170 1.13572 0.06427 8.14749; 0.04785 -0.06114 1.07331 -19.08662; 0.00000 0.00000 0.00000 1.00000; nsamples 315557 Quasinewton: input matrix 1.01516 0.00105 -0.05295 0.77399; 0.00170 1.13572 0.06427 8.14749; 0.04785 -0.06114 1.07331 -19.08662; 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: 010: -log(p) = 4.4 tol 0.000000 final transform: 1.01516 0.00105 -0.05295 0.77399; 0.00170 1.13572 0.06427 8.14749; 0.04785 -0.06114 1.07331 -19.08662; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... #VMPC# mri_em_register VmPeak 828832 FSRUNTIME@ mri_ca_register 0.1186 hours 1 threads registration took 7 minutes and 7 seconds. #-------------------------------------- #@# CA Normalize Fri Nov 23 17:07:50 CST 2018 /home/liuzb/work/tutorial_data/practice_with_data/Subj004/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.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/average/RB_all_2016-05-10.vc700.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=32.4 skull bounding box = (61, 34, 39) --> (195, 149, 200) finding center of left hemi white matter using (106, 72, 120) as brain centroid of Right_Cerebral_White_Matter... mean wm in atlas = 107, using box (90,58,100) --> (122, 86,139) to find MRI wm before smoothing, mri peak at 81 robust fit to distribution - 80 +- 6.0 after smoothing, mri peak at 80, scaling input intensities by 1.337 scaling channel 0 by 1.3375 using 246344 sample points... INFO: compute sample coordinates transform 1.01516 0.00105 -0.05295 0.77399; 0.00170 1.13572 0.06427 8.14749; 0.04785 -0.06114 1.07331 -19.08662; 0.00000 0.00000 0.00000 1.00000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (126, 32, 41) --> (194, 136, 198) Left_Cerebral_White_Matter: limiting intensities to 93.0 --> 132.0 0 of 169 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (66, 33, 43) --> (133, 136, 199) Right_Cerebral_White_Matter: limiting intensities to 90.0 --> 132.0 0 of 110 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (129, 109, 63) --> (177, 147, 114) Left_Cerebellum_White_Matter: limiting intensities to 113.0 --> 132.0 0 of 7 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (85, 109, 63) --> (128, 146, 117) Right_Cerebellum_White_Matter: limiting intensities to 97.0 --> 132.0 0 of 29 (0.0%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (114, 101, 97) --> (147, 163, 126) Brain_Stem: limiting intensities to 101.0 --> 132.0 0 of 8 (0.0%) samples deleted using 323 total control points for intensity normalization... bias field = 0.934 +- 0.085 0 of 323 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (126, 32, 41) --> (194, 136, 198) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 114.0 4 of 272 (1.5%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (66, 33, 43) --> (133, 136, 199) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 0 of 171 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (129, 109, 63) --> (177, 147, 114) Left_Cerebellum_White_Matter: limiting intensities to 115.0 --> 132.0 46 of 51 (90.2%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (85, 109, 63) --> (128, 146, 117) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 18 of 71 (25.4%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (114, 101, 97) --> (147, 163, 126) Brain_Stem: limiting intensities to 111.0 --> 132.0 53 of 57 (93.0%) samples deleted using 622 total control points for intensity normalization... bias field = 1.007 +- 0.083 4 of 494 control points discarded finding control points in Left_Cerebral_White_Matter.... found 39915 control points for structure... bounding box (126, 32, 41) --> (194, 136, 198) Left_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 7 of 409 (1.7%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39557 control points for structure... bounding box (66, 33, 43) --> (133, 136, 199) Right_Cerebral_White_Matter: limiting intensities to 88.0 --> 132.0 11 of 292 (3.8%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3059 control points for structure... bounding box (129, 109, 63) --> (177, 147, 114) Left_Cerebellum_White_Matter: limiting intensities to 100.0 --> 132.0 85 of 98 (86.7%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2705 control points for structure... bounding box (85, 109, 63) --> (128, 146, 117) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 37 of 61 (60.7%) samples deleted finding control points in Brain_Stem.... found 3518 control points for structure... bounding box (114, 101, 97) --> (147, 163, 126) Brain_Stem: limiting intensities to 88.0 --> 132.0 65 of 112 (58.0%) samples deleted using 972 total control points for intensity normalization... bias field = 1.003 +- 0.091 0 of 756 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 1 seconds. #-------------------------------------- #@# CA Reg Fri Nov 23 17:08:50 CST 2018 /home/liuzb/work/tutorial_data/practice_with_data/Subj004/mri mri_ca_register -rusage /home/liuzb/work/tutorial_data/practice_with_data/Subj004/touch/rusage.mri_ca_register.dat -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.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... == Number of threads available to mri_ca_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach.log reading input volume 'norm.mgz'... reading GCA '/usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.24 (predicted orig area = 6.4) label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.156 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=1.475, neg=0, invalid=762 0001: dt=8.092000, rms=1.473 (0.102%), neg=0, invalid=762 0002: dt=0.054187, rms=1.473 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=1.475, neg=0, invalid=762 0003: dt=0.000000, rms=1.473 (0.098%), neg=0, invalid=762 0004: dt=0.000000, rms=1.473 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.615 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=1.475, neg=0, invalid=762 0005: dt=145.152000, rms=1.436 (2.667%), neg=0, invalid=762 0006: dt=145.152000, rms=1.415 (1.461%), neg=0, invalid=762 0007: dt=36.288000, rms=1.414 (0.049%), neg=0, invalid=762 0008: dt=36.288000, rms=1.414 (0.012%), neg=0, invalid=762 0009: dt=36.288000, rms=1.412 (0.122%), neg=0, invalid=762 0010: dt=36.288000, rms=1.408 (0.288%), neg=0, invalid=762 0011: dt=36.288000, rms=1.406 (0.152%), neg=0, invalid=762 0012: dt=36.288000, rms=1.402 (0.273%), neg=0, invalid=762 0013: dt=36.288000, rms=1.396 (0.435%), neg=0, invalid=762 0014: dt=36.288000, rms=1.389 (0.498%), neg=0, invalid=762 0015: dt=36.288000, rms=1.383 (0.420%), neg=0, invalid=762 0016: dt=36.288000, rms=1.383 (-0.050%), neg=0, invalid=762 0017: dt=0.000000, rms=1.383 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=1.384, neg=0, invalid=762 0018: dt=0.000000, rms=1.383 (0.073%), neg=0, invalid=762 0019: dt=0.000000, rms=1.383 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 2.353 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=1.468, neg=0, invalid=762 0020: dt=8.000000, rms=1.462 (0.385%), neg=0, invalid=762 0021: dt=11.200000, rms=1.458 (0.299%), neg=0, invalid=762 0022: dt=25.600000, rms=1.452 (0.447%), neg=0, invalid=762 0023: dt=44.800000, rms=1.434 (1.195%), neg=0, invalid=762 0024: dt=0.125000, rms=1.434 (0.006%), neg=0, invalid=762 0025: dt=0.125000, rms=1.434 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=1.435, neg=0, invalid=762 0026: dt=0.000000, rms=1.434 (0.063%), neg=0, invalid=762 0027: dt=0.000000, rms=1.434 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 8.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=1.549, neg=0, invalid=762 0028: dt=0.673913, rms=1.547 (0.095%), neg=0, invalid=762 0029: dt=0.252000, rms=1.547 (0.006%), neg=0, invalid=762 0030: dt=0.252000, rms=1.547 (0.004%), neg=0, invalid=762 0031: dt=0.252000, rms=1.547 (-0.011%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=1.548, neg=0, invalid=762 0032: dt=0.000000, rms=1.547 (0.056%), neg=0, invalid=762 0033: dt=0.000000, rms=1.547 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 20.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=1.746, neg=0, invalid=762 0034: dt=1.024000, rms=1.736 (0.602%), neg=0, invalid=762 0035: dt=0.535294, rms=1.727 (0.492%), neg=0, invalid=762 0036: dt=0.448000, rms=1.723 (0.270%), neg=0, invalid=762 0037: dt=0.384000, rms=1.719 (0.239%), neg=0, invalid=762 0038: dt=0.384000, rms=1.714 (0.243%), neg=0, invalid=762 0039: dt=0.384000, rms=1.707 (0.425%), neg=0, invalid=762 0040: dt=0.384000, rms=1.699 (0.482%), neg=0, invalid=762 0041: dt=0.384000, rms=1.687 (0.690%), neg=0, invalid=762 0042: dt=0.384000, rms=1.675 (0.690%), neg=0, invalid=762 0043: dt=0.384000, rms=1.662 (0.805%), neg=0, invalid=762 0044: dt=0.384000, rms=1.649 (0.771%), neg=0, invalid=762 0045: dt=0.384000, rms=1.635 (0.865%), neg=0, invalid=762 0046: dt=0.384000, rms=1.622 (0.807%), neg=0, invalid=762 0047: dt=0.384000, rms=1.609 (0.795%), neg=0, invalid=762 0048: dt=0.384000, rms=1.597 (0.752%), neg=0, invalid=762 0049: dt=0.384000, rms=1.585 (0.721%), neg=0, invalid=762 0050: dt=0.384000, rms=1.575 (0.634%), neg=0, invalid=762 0051: dt=0.384000, rms=1.566 (0.551%), neg=0, invalid=762 0052: dt=0.384000, rms=1.559 (0.506%), neg=0, invalid=762 0053: dt=0.384000, rms=1.551 (0.466%), neg=0, invalid=762 0054: dt=0.384000, rms=1.545 (0.400%), neg=0, invalid=762 0055: dt=0.384000, rms=1.540 (0.341%), neg=0, invalid=762 0056: dt=0.384000, rms=1.535 (0.315%), neg=0, invalid=762 0057: dt=0.384000, rms=1.530 (0.295%), neg=0, invalid=762 0058: dt=0.384000, rms=1.527 (0.253%), neg=0, invalid=762 0059: dt=0.384000, rms=1.523 (0.260%), neg=0, invalid=762 0060: dt=0.384000, rms=1.519 (0.239%), neg=0, invalid=762 0061: dt=0.384000, rms=1.515 (0.269%), neg=0, invalid=762 0062: dt=0.384000, rms=1.511 (0.260%), neg=0, invalid=762 0063: dt=0.384000, rms=1.506 (0.303%), neg=0, invalid=762 0064: dt=0.384000, rms=1.502 (0.300%), neg=0, invalid=762 0065: dt=0.384000, rms=1.498 (0.282%), neg=0, invalid=762 0066: dt=0.384000, rms=1.494 (0.270%), neg=0, invalid=762 0067: dt=0.384000, rms=1.490 (0.246%), neg=0, invalid=762 0068: dt=0.384000, rms=1.487 (0.221%), neg=0, invalid=762 0069: dt=0.384000, rms=1.484 (0.198%), neg=0, invalid=762 0070: dt=0.384000, rms=1.481 (0.178%), neg=0, invalid=762 0071: dt=0.384000, rms=1.479 (0.160%), neg=0, invalid=762 0072: dt=0.384000, rms=1.477 (0.142%), neg=0, invalid=762 0073: dt=0.384000, rms=1.475 (0.122%), neg=0, invalid=762 0074: dt=0.384000, rms=1.473 (0.104%), neg=0, invalid=762 0075: dt=0.256000, rms=1.473 (0.004%), neg=0, invalid=762 0076: dt=0.256000, rms=1.473 (0.001%), neg=0, invalid=762 0077: dt=0.256000, rms=1.473 (-0.001%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=1.474, neg=0, invalid=762 0078: dt=0.384000, rms=1.473 (0.109%), neg=0, invalid=762 0079: dt=0.000000, rms=1.473 (0.001%), neg=0, invalid=762 0080: dt=0.100000, rms=1.473 (-0.021%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 40.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=1.465, neg=0, invalid=762 0081: dt=0.388636, rms=1.450 (0.991%), neg=0, invalid=762 0082: dt=0.028000, rms=1.450 (0.015%), neg=0, invalid=762 0083: dt=0.028000, rms=1.450 (-0.010%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=1.451, neg=0, invalid=762 0084: dt=0.028000, rms=1.450 (0.093%), neg=0, invalid=762 0085: dt=0.000750, rms=1.450 (-0.000%), neg=0, invalid=762 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10027 (20) mri peak = 0.22210 ( 9) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (925 voxels, overlap=0.018) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (925 voxels, peak = 8), gca=8.0 gca peak = 0.15565 (16) mri peak = 0.22603 (10) Right_Lateral_Ventricle (43): linear fit = 0.57 x + 0.0 (647 voxels, overlap=0.042) Right_Lateral_Ventricle (43): linear fit = 0.57 x + 0.0 (647 voxels, peak = 9), gca=9.2 gca peak = 0.26829 (96) mri peak = 0.12179 (75) Right_Pallidum (52): linear fit = 0.79 x + 0.0 (680 voxels, overlap=0.021) Right_Pallidum (52): linear fit = 0.79 x + 0.0 (680 voxels, peak = 75), gca=75.4 gca peak = 0.20183 (93) mri peak = 0.06897 (76) Left_Pallidum: unreasonable value (74.9/76.0), not in range [75, 135] - rejecting gca peak = 0.21683 (55) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.30730 (58) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.11430 (101) mri peak = 0.05913 (103) Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (54041 voxels, overlap=0.809) Right_Cerebral_White_Matter (41): linear fit = 1.04 x + 0.0 (54041 voxels, peak = 106), gca=105.5 gca peak = 0.12076 (102) mri peak = 0.06740 (104) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (55689 voxels, overlap=0.768) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (55689 voxels, peak = 107), gca=106.6 gca peak = 0.14995 (59) mri peak = 0.12376 (94) Left_Cerebral_Cortex (3): linear fit = 1.57 x + 0.0 (11210 voxels, overlap=0.000) Left_Cerebral_Cortex (3): linear fit = 1.57 x + 0.0 (11210 voxels, peak = 92), gca=92.3 gca peak = 0.15082 (58) mri peak = 0.13589 (95) Right_Cerebral_Cortex (42): linear fit = 1.57 x + 0.0 (10159 voxels, overlap=0.000) Right_Cerebral_Cortex (42): linear fit = 1.57 x + 0.0 (10159 voxels, peak = 91), gca=90.8 gca peak = 0.14161 (67) mri peak = 0.50000 (99) Right_Caudate: unreasonable value (102.2/99.0), not in range [50, 100] - rejecting gca peak = 0.15243 (71) mri peak = 0.27644 (99) Left_Caudate (11): linear fit = 1.33 x + 0.0 (705 voxels, overlap=0.011) Left_Caudate (11): linear fit = 1.33 x + 0.0 (705 voxels, peak = 94), gca=94.1 gca peak = 0.13336 (57) mri peak = 0.02870 (109) Left_Cerebellum_Cortex (8): linear fit = 1.88 x + 0.0 (12202 voxels, overlap=0.001) Left_Cerebellum_Cortex (8): linear fit = 1.88 x + 0.0 (12202 voxels, peak = 107), gca=107.4 gca peak = 0.13252 (56) mri peak = 0.02439 (95) Right_Cerebellum_Cortex (47): linear fit = 1.93 x + 0.0 (14773 voxels, overlap=0.000) Right_Cerebellum_Cortex (47): linear fit = 1.93 x + 0.0 (14773 voxels, peak = 108), gca=108.4 gca peak = 0.18181 (84) mri peak = 0.04595 (78) Left_Cerebellum_White_Matter (7): linear fit = 0.93 x + 0.0 (6635 voxels, overlap=0.986) Left_Cerebellum_White_Matter (7): linear fit = 0.93 x + 0.0 (6635 voxels, peak = 78), gca=77.7 gca peak = 0.20573 (83) mri peak = 0.04776 (81) Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (5878 voxels, overlap=0.976) Right_Cerebellum_White_Matter (46): linear fit = 1.01 x + 0.0 (5878 voxels, peak = 84), gca=84.2 gca peak = 0.21969 (57) mri peak = 1.00000 (89) Left_Amygdala (18): linear fit = 1.54 x + 0.0 (299 voxels, overlap=1.938) Left_Amygdala (18): linear fit = 1.54 x + 0.0 (299 voxels, peak = 88), gca=88.1 gca peak = 0.39313 (56) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.14181 (85) mri peak = 0.06185 (101) Left_Thalamus (10): linear fit = 1.21 x + 0.0 (3863 voxels, overlap=0.011) Left_Thalamus (10): linear fit = 1.21 x + 0.0 (3863 voxels, peak = 102), gca=102.4 gca peak = 0.11978 (83) mri peak = 0.06025 (105) Right_Thalamus (49): linear fit = 1.26 x + 0.0 (1861 voxels, overlap=0.009) Right_Thalamus (49): linear fit = 1.26 x + 0.0 (1861 voxels, peak = 105), gca=105.0 gca peak = 0.13399 (79) mri peak = 0.08309 (103) Left_Putamen (12): linear fit = 1.29 x + 0.0 (1319 voxels, overlap=0.011) Left_Putamen (12): linear fit = 1.29 x + 0.0 (1319 voxels, peak = 102), gca=102.3 gca peak = 0.14159 (79) mri peak = 0.06368 (97) Right_Putamen (51): linear fit = 1.28 x + 0.0 (1525 voxels, overlap=0.014) Right_Putamen (51): linear fit = 1.28 x + 0.0 (1525 voxels, peak = 102), gca=101.5 gca peak = 0.10025 (80) mri peak = 0.08865 (80) Brain_Stem (16): linear fit = 1.10 x + 0.0 (7822 voxels, overlap=0.402) Brain_Stem (16): linear fit = 1.10 x + 0.0 (7822 voxels, peak = 88), gca=87.6 gca peak = 0.13281 (86) mri peak = 0.06122 (102) Right_VentralDC (60): linear fit = 1.14 x + 0.0 (420 voxels, overlap=0.335) Right_VentralDC (60): linear fit = 1.14 x + 0.0 (420 voxels, peak = 98), gca=98.5 gca peak = 0.12801 (89) mri peak = 0.05852 (97) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (619 voxels, overlap=0.683) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (619 voxels, peak = 97), gca=97.5 gca peak = 0.20494 (23) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.15061 (21) mri peak = 0.10435 (13) Fourth_Ventricle (15): linear fit = 0.44 x + 0.0 (201 voxels, overlap=0.646) Fourth_Ventricle (15): linear fit = 0.44 x + 0.0 (201 voxels, peak = 9), gca=9.1 gca peak Unknown = 0.94835 ( 0) gca peak Left_Cerebral_Cortex = 0.14995 (59) gca peak Left_Inf_Lat_Vent = 0.18056 (32) gca peak Left_Cerebellum_Cortex = 0.13336 (57) gca peak = 0.64095 (94) gca peak Left_Pallidum = 0.20183 (93) gca peak Third_Ventricle = 0.20494 (23) gca peak Fourth_Ventricle = 0.15061 (21) gca peak Left_Hippocampus = 0.30730 (58) gca peak Left_Amygdala = 0.21969 (57) gca peak CSF = 0.20999 (34) gca peak Left_Accumbens_area = 0.39030 (62) gca peak Left_undetermined = 0.95280 (25) gca peak Left_vessel = 0.67734 (53) gca peak Left_choroid_plexus = 0.09433 (44) gca peak Right_Cerebral_Cortex = 0.15082 (58) gca peak Right_Inf_Lat_Vent = 0.23544 (26) gca peak Right_Cerebellum_Cortex = 0.13252 (56) gca peak Right_Caudate = 0.14161 (67) gca peak Right_Hippocampus = 0.21683 (55) gca peak Right_Amygdala = 0.39313 (56) gca peak Right_Accumbens_area = 0.30312 (64) gca peak Right_vessel = 0.46315 (51) gca peak Right_choroid_plexus = 0.14086 (44) gca peak Fifth_Ventricle = 0.51669 (36) gca peak WM_hypointensities = 0.09722 (76) gca peak non_WM_hypointensities = 0.11899 (47) gca peak Optic_Chiasm = 0.39033 (72) label assignment complete, 0 changed (0.00%) not using caudate to estimate GM means setting label Right_Caudate based on Left_Caudate = 1.33 x + 0: 94 setting label Left_Pallidum based on Right_Pallidum = 0.79 x + 0: 75 estimating mean gm scale to be 1.00 x + 0.0 estimating mean wm scale to be 1.04 x + 0.0 estimating mean csf scale to be 0.49 x + 0.0 setting left cbm cortex = 1.00 x + 0.00 setting right cbm cortex = 1.00 x + 0.00 Left_Putamen too bright - rescaling by 0.933 (from 1.295) to 95.5 (was 102.3) Right_Putamen too bright - rescaling by 0.940 (from 1.285) to 95.5 (was 101.5) saving intensity scales to talairach.label_intensities.txt **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=1.440, neg=0, invalid=762 0086: dt=-0.003906, rms=1.439 (0.075%), neg=0, invalid=762 0087: dt=0.000000, rms=1.439 (0.000%), neg=0, invalid=762 0088: dt=0.850000, rms=1.439 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=1.440, neg=0, invalid=762 0089: dt=0.000000, rms=1.439 (0.075%), neg=0, invalid=762 0090: dt=0.000000, rms=1.439 (0.000%), neg=0, invalid=762 0091: dt=0.850000, rms=1.439 (-0.008%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=1.440, neg=0, invalid=762 0092: dt=134.981818, rms=1.409 (2.108%), neg=0, invalid=762 0093: dt=145.152000, rms=1.370 (2.813%), neg=0, invalid=762 0094: dt=36.288000, rms=1.365 (0.322%), neg=0, invalid=762 0095: dt=36.288000, rms=1.360 (0.392%), neg=0, invalid=762 0096: dt=36.288000, rms=1.355 (0.365%), neg=0, invalid=762 0097: dt=9.072000, rms=1.354 (0.090%), neg=0, invalid=762 0098: dt=9.072000, rms=1.353 (0.079%), neg=0, invalid=762 0099: dt=0.567000, rms=1.353 (0.010%), neg=0, invalid=762 0100: dt=0.070875, rms=1.352 (0.001%), neg=0, invalid=762 0101: dt=0.008859, rms=1.353 (-0.002%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=1.353, neg=0, invalid=762 0102: dt=0.000000, rms=1.353 (0.069%), neg=0, invalid=762 0103: dt=0.000000, rms=1.353 (0.000%), neg=0, invalid=762 0104: dt=0.450000, rms=1.353 (-0.005%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=1.356, neg=0, invalid=762 0105: dt=2.800000, rms=1.350 (0.472%), neg=0, invalid=762 0106: dt=2.800000, rms=1.345 (0.394%), neg=0, invalid=762 0107: dt=0.500000, rms=1.344 (0.073%), neg=0, invalid=762 0108: dt=0.031250, rms=1.343 (0.005%), neg=0, invalid=762 0109: dt=0.001953, rms=1.343 (0.000%), neg=0, invalid=762 0110: dt=0.000244, rms=1.343 (0.000%), neg=0, invalid=762 0111: dt=0.000122, rms=1.343 (0.000%), neg=0, invalid=762 0112: dt=0.000000, rms=1.343 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=1.344, neg=0, invalid=762 0113: dt=0.000000, rms=1.343 (0.075%), neg=0, invalid=762 0114: dt=0.000000, rms=1.343 (0.000%), neg=0, invalid=762 0115: dt=0.000061, rms=1.343 (0.000%), neg=0, invalid=762 0116: dt=0.000031, rms=1.343 (0.000%), neg=0, invalid=762 0117: dt=0.000008, rms=1.343 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=1.354, neg=0, invalid=762 0118: dt=0.000000, rms=1.353 (0.074%), neg=0, invalid=762 0119: dt=0.000000, rms=1.353 (0.000%), neg=0, invalid=762 0120: dt=0.150000, rms=1.352 (0.096%), neg=0, invalid=762 0121: dt=0.150000, rms=1.349 (0.184%), neg=0, invalid=762 0122: dt=0.150000, rms=1.346 (0.257%), neg=0, invalid=762 0123: dt=0.150000, rms=1.341 (0.337%), neg=0, invalid=762 0124: dt=0.150000, rms=1.336 (0.409%), neg=0, invalid=762 0125: dt=0.150000, rms=1.329 (0.465%), neg=0, invalid=762 0126: dt=0.150000, rms=1.328 (0.096%), neg=0, invalid=762 0127: dt=0.150000, rms=1.326 (0.182%), neg=0, invalid=762 0128: dt=0.150000, rms=1.322 (0.259%), neg=0, invalid=762 0129: dt=0.150000, rms=1.318 (0.326%), neg=0, invalid=762 0130: dt=0.150000, rms=1.313 (0.402%), neg=0, invalid=762 0131: dt=0.150000, rms=1.307 (0.455%), neg=0, invalid=762 0132: dt=0.150000, rms=1.300 (0.505%), neg=0, invalid=762 0133: dt=0.150000, rms=1.299 (0.090%), neg=0, invalid=762 0134: dt=0.150000, rms=1.297 (0.169%), neg=0, invalid=762 0135: dt=0.150000, rms=1.294 (0.240%), neg=0, invalid=762 0136: dt=0.150000, rms=1.290 (0.308%), neg=0, invalid=762 0137: dt=0.150000, rms=1.289 (0.088%), neg=0, invalid=762 0138: dt=0.150000, rms=1.286 (0.164%), neg=0, invalid=762 0139: dt=0.150000, rms=1.285 (0.085%), neg=0, invalid=762 0140: dt=0.150000, rms=1.284 (0.087%), neg=0, invalid=762 0141: dt=0.018750, rms=1.284 (0.011%), neg=0, invalid=762 0142: dt=0.004688, rms=1.284 (0.003%), neg=0, invalid=762 0143: dt=0.000984, rms=1.284 (0.001%), neg=0, invalid=762 0144: dt=0.000246, rms=1.284 (0.000%), neg=0, invalid=762 0145: dt=0.000123, rms=1.284 (0.000%), neg=0, invalid=762 0146: dt=0.000015, rms=1.284 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=1.285, neg=0, invalid=762 0147: dt=4.032000, rms=1.272 (1.050%), neg=0, invalid=762 0148: dt=4.032000, rms=1.261 (0.831%), neg=0, invalid=762 0149: dt=4.032000, rms=1.252 (0.688%), neg=0, invalid=762 0150: dt=4.032000, rms=1.245 (0.585%), neg=0, invalid=762 0151: dt=2.880000, rms=1.240 (0.364%), neg=0, invalid=762 0152: dt=1.008000, rms=1.239 (0.112%), neg=0, invalid=762 0153: dt=0.015750, rms=1.239 (0.001%), neg=0, invalid=762 0154: dt=0.015750, rms=1.239 (0.002%), neg=0, invalid=762 0155: dt=0.000123, rms=1.239 (0.000%), neg=0, invalid=762 0156: dt=0.000031, rms=1.239 (0.000%), neg=0, invalid=762 0157: dt=0.000000, rms=1.239 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=1.266, neg=0, invalid=762 0158: dt=1.792000, rms=1.252 (1.076%), neg=0, invalid=762 0159: dt=1.536000, rms=1.239 (1.021%), neg=0, invalid=762 0160: dt=1.536000, rms=1.231 (0.680%), neg=0, invalid=762 0161: dt=1.536000, rms=1.224 (0.539%), neg=0, invalid=762 0162: dt=1.536000, rms=1.220 (0.332%), neg=0, invalid=762 0163: dt=1.536000, rms=1.217 (0.272%), neg=0, invalid=762 0164: dt=1.536000, rms=1.215 (0.170%), neg=0, invalid=762 0165: dt=1.536000, rms=1.213 (0.161%), neg=0, invalid=762 0166: dt=1.536000, rms=1.212 (0.092%), neg=0, invalid=762 0167: dt=1.536000, rms=1.210 (0.112%), neg=0, invalid=762 0168: dt=1.792000, rms=1.210 (0.064%), neg=0, invalid=762 0169: dt=1.792000, rms=1.208 (0.092%), neg=0, invalid=762 0170: dt=1.792000, rms=1.208 (0.029%), neg=0, invalid=762 0171: dt=1.792000, rms=1.207 (0.077%), neg=0, invalid=762 0172: dt=1.792000, rms=1.206 (0.092%), neg=0, invalid=762 0173: dt=1.792000, rms=1.205 (0.115%), neg=0, invalid=762 0174: dt=1.792000, rms=1.205 (0.014%), neg=0, invalid=762 0175: dt=1.792000, rms=1.204 (0.018%), neg=0, invalid=762 0176: dt=1.792000, rms=1.204 (0.053%), neg=0, invalid=762 0177: dt=1.792000, rms=1.202 (0.113%), neg=0, invalid=762 0178: dt=1.792000, rms=1.202 (0.006%), neg=0, invalid=762 0179: dt=1.792000, rms=1.202 (0.010%), neg=0, invalid=762 0180: dt=1.792000, rms=1.202 (0.048%), neg=0, invalid=762 0181: dt=1.792000, rms=1.201 (0.068%), neg=0, invalid=762 0182: dt=1.792000, rms=1.201 (-0.009%), neg=0, invalid=762 0183: dt=0.384000, rms=1.201 (0.001%), neg=0, invalid=762 0184: dt=1.536000, rms=1.201 (0.008%), neg=0, invalid=762 0185: dt=1.024000, rms=1.201 (0.006%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=1.202, neg=0, invalid=762 0186: dt=0.000000, rms=1.201 (0.083%), neg=0, invalid=762 0187: dt=0.000000, rms=1.201 (0.000%), neg=0, invalid=762 0188: dt=0.100000, rms=1.201 (-0.002%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=1.156, neg=0, invalid=762 0189: dt=0.112000, rms=1.145 (0.997%), neg=0, invalid=762 0190: dt=0.112000, rms=1.135 (0.828%), neg=0, invalid=762 0191: dt=0.112000, rms=1.127 (0.769%), neg=0, invalid=762 0192: dt=0.112000, rms=1.119 (0.686%), neg=0, invalid=762 0193: dt=0.112000, rms=1.112 (0.623%), neg=0, invalid=762 0194: dt=0.112000, rms=1.106 (0.560%), neg=0, invalid=762 0195: dt=0.112000, rms=1.100 (0.508%), neg=0, invalid=762 0196: dt=0.112000, rms=1.095 (0.454%), neg=0, invalid=762 0197: dt=0.112000, rms=1.090 (0.417%), neg=0, invalid=762 0198: dt=0.112000, rms=1.086 (0.367%), neg=0, invalid=762 0199: dt=0.112000, rms=1.083 (0.336%), neg=0, invalid=762 0200: dt=0.112000, rms=1.080 (0.302%), neg=0, invalid=762 0201: dt=0.112000, rms=1.077 (0.274%), neg=0, invalid=762 0202: dt=0.112000, rms=1.074 (0.246%), neg=0, invalid=762 0203: dt=0.258929, rms=1.069 (0.502%), neg=0, invalid=762 0204: dt=0.148438, rms=1.066 (0.227%), neg=0, invalid=762 0205: dt=0.171875, rms=1.064 (0.240%), neg=0, invalid=762 0206: dt=0.112000, rms=1.062 (0.126%), neg=0, invalid=762 0207: dt=0.112000, rms=1.061 (0.138%), neg=0, invalid=762 0208: dt=0.112000, rms=1.060 (0.116%), neg=0, invalid=762 0209: dt=0.112000, rms=1.058 (0.099%), neg=0, invalid=762 0210: dt=0.112000, rms=1.058 (0.091%), neg=0, invalid=762 0211: dt=0.112000, rms=1.057 (0.078%), neg=0, invalid=762 0212: dt=0.112000, rms=1.056 (0.078%), neg=0, invalid=762 0213: dt=0.112000, rms=1.055 (0.064%), neg=0, invalid=762 0214: dt=0.112000, rms=1.054 (0.067%), neg=0, invalid=762 0215: dt=0.112000, rms=1.054 (0.056%), neg=0, invalid=762 0216: dt=0.112000, rms=1.053 (0.057%), neg=0, invalid=762 0217: dt=0.112000, rms=1.053 (0.051%), neg=0, invalid=762 0218: dt=0.112000, rms=1.052 (0.051%), neg=0, invalid=762 0219: dt=0.112000, rms=1.052 (0.042%), neg=0, invalid=762 0220: dt=0.112000, rms=1.051 (0.045%), neg=0, invalid=762 0221: dt=0.112000, rms=1.050 (0.077%), neg=0, invalid=762 0222: dt=0.112000, rms=1.049 (0.109%), neg=0, invalid=762 0223: dt=0.112000, rms=1.048 (0.128%), neg=0, invalid=762 0224: dt=0.112000, rms=1.047 (0.137%), neg=0, invalid=762 0225: dt=0.112000, rms=1.045 (0.134%), neg=0, invalid=762 0226: dt=0.112000, rms=1.044 (0.129%), neg=0, invalid=762 0227: dt=0.112000, rms=1.043 (0.111%), neg=0, invalid=762 0228: dt=0.112000, rms=1.042 (0.098%), neg=0, invalid=762 0229: dt=0.112000, rms=1.041 (0.077%), neg=0, invalid=762 0230: dt=0.112000, rms=1.040 (0.054%), neg=0, invalid=762 0231: dt=0.112000, rms=1.040 (0.039%), neg=0, invalid=762 0232: dt=0.112000, rms=1.040 (0.025%), neg=0, invalid=762 0233: dt=0.112000, rms=1.040 (0.008%), neg=0, invalid=762 0234: dt=0.112000, rms=1.039 (-0.003%), neg=0, invalid=762 0235: dt=0.000000, rms=1.039 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=1.041, neg=0, invalid=762 0236: dt=0.112000, rms=1.035 (0.511%), neg=0, invalid=762 0237: dt=0.112000, rms=1.032 (0.334%), neg=0, invalid=762 0238: dt=0.112000, rms=1.029 (0.269%), neg=0, invalid=762 0239: dt=0.112000, rms=1.027 (0.215%), neg=0, invalid=762 0240: dt=0.138889, rms=1.025 (0.212%), neg=0, invalid=762 0241: dt=0.112000, rms=1.023 (0.129%), neg=0, invalid=762 0242: dt=0.112000, rms=1.022 (0.104%), neg=0, invalid=762 0243: dt=0.112000, rms=1.021 (0.078%), neg=0, invalid=762 0244: dt=0.112000, rms=1.021 (0.059%), neg=0, invalid=762 0245: dt=0.112000, rms=1.020 (0.046%), neg=0, invalid=762 0246: dt=0.112000, rms=1.020 (0.030%), neg=0, invalid=762 0247: dt=0.112000, rms=1.020 (0.046%), neg=0, invalid=762 0248: dt=0.112000, rms=1.019 (0.038%), neg=0, invalid=762 0249: dt=0.112000, rms=1.019 (0.003%), neg=0, invalid=762 0250: dt=0.112000, rms=1.019 (-0.058%), neg=0, invalid=762 0251: dt=0.000000, rms=1.019 (-0.000%), neg=0, invalid=762 label assignment complete, 0 changed (0.00%) ********************* ALLOWING NEGATIVE NODES IN DEFORMATION******************************** **************** pass 1 of 1 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=1.013, neg=0, invalid=762 0252: dt=0.000000, rms=1.012 (0.110%), neg=0, invalid=762 0253: dt=0.000000, rms=1.012 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=1.013, neg=0, invalid=762 0254: dt=0.000000, rms=1.012 (0.110%), neg=0, invalid=762 0255: dt=0.000000, rms=1.012 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=1.013, neg=0, invalid=762 0256: dt=0.000000, rms=1.012 (0.110%), neg=0, invalid=762 0257: dt=0.000000, rms=1.012 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=1.013, neg=0, invalid=762 0258: dt=0.000000, rms=1.012 (0.110%), neg=0, invalid=762 0259: dt=0.000000, rms=1.012 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=1.014, neg=0, invalid=762 iter 0, gcam->neg = 152 after 22 iterations, nbhd size=1, neg = 0 0260: dt=18.758621, rms=1.003 (1.086%), neg=0, invalid=762 0261: dt=0.000000, rms=1.003 (-0.004%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0262: dt=0.250000, rms=1.003 (-0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=1.004, neg=0, invalid=762 0263: dt=6.400000, rms=1.002 (0.208%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 8 iterations, nbhd size=1, neg = 0 0264: dt=8.000000, rms=1.001 (0.063%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 11 iterations, nbhd size=1, neg = 0 0265: dt=8.000000, rms=1.000 (0.104%), neg=0, invalid=762 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0266: dt=8.000000, rms=0.999 (0.146%), neg=0, invalid=762 iter 0, gcam->neg = 7 after 1 iterations, nbhd size=0, neg = 0 0267: dt=8.000000, rms=0.997 (0.164%), neg=0, invalid=762 iter 0, gcam->neg = 24 after 9 iterations, nbhd size=1, neg = 0 0268: dt=8.000000, rms=0.995 (0.204%), neg=0, invalid=762 iter 0, gcam->neg = 45 after 10 iterations, nbhd size=1, neg = 0 0269: dt=8.000000, rms=0.993 (0.209%), neg=0, invalid=762 iter 0, gcam->neg = 107 after 15 iterations, nbhd size=1, neg = 0 0270: dt=8.000000, rms=0.991 (0.149%), neg=0, invalid=762 iter 0, gcam->neg = 124 after 15 iterations, nbhd size=1, neg = 0 0271: dt=8.000000, rms=0.991 (0.018%), neg=0, invalid=762 iter 0, gcam->neg = 137 after 20 iterations, nbhd size=1, neg = 0 0272: dt=8.000000, rms=0.991 (-0.016%), neg=0, invalid=762 iter 0, gcam->neg = 11 after 9 iterations, nbhd size=0, neg = 0 0273: dt=11.200000, rms=0.991 (0.027%), neg=0, invalid=762 iter 0, gcam->neg = 25 after 10 iterations, nbhd size=1, neg = 0 0274: dt=19.200000, rms=0.991 (0.025%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.996, neg=0, invalid=762 iter 0, gcam->neg = 2967 after 24 iterations, nbhd size=1, neg = 0 0275: dt=13.254054, rms=0.986 (0.932%), neg=0, invalid=762 iter 0, gcam->neg = 702 after 21 iterations, nbhd size=1, neg = 0 0276: dt=7.034483, rms=0.985 (0.159%), neg=0, invalid=762 iter 0, gcam->neg = 506 after 20 iterations, nbhd size=1, neg = 0 0277: dt=7.034483, rms=0.984 (0.073%), neg=0, invalid=762 iter 0, gcam->neg = 1657 after 27 iterations, nbhd size=1, neg = 0 0278: dt=7.034483, rms=0.984 (-0.582%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.985, neg=0, invalid=762 iter 0, gcam->neg = 7 after 9 iterations, nbhd size=1, neg = 0 0279: dt=1.008000, rms=0.984 (0.133%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 3 iterations, nbhd size=0, neg = 0 0280: dt=1.008000, rms=0.984 (0.008%), neg=0, invalid=762 iter 0, gcam->neg = 3 after 1 iterations, nbhd size=0, neg = 0 0281: dt=1.008000, rms=0.984 (0.007%), neg=0, invalid=762 iter 0, gcam->neg = 6 after 9 iterations, nbhd size=1, neg = 0 0282: dt=1.008000, rms=0.984 (-0.015%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.999, neg=0, invalid=762 0283: dt=0.000000, rms=0.998 (0.112%), neg=0, invalid=762 0284: dt=0.000000, rms=0.998 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.999, neg=0, invalid=762 0285: dt=0.000030, rms=0.998 (0.112%), neg=0, invalid=762 0286: dt=0.000000, rms=0.998 (0.000%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.976, neg=0, invalid=762 iter 0, gcam->neg = 7651 after 22 iterations, nbhd size=1, neg = 0 0287: dt=0.864399, rms=0.966 (1.026%), neg=0, invalid=762 iter 0, gcam->neg = 12 after 3 iterations, nbhd size=0, neg = 0 0288: dt=0.256000, rms=0.963 (0.245%), neg=0, invalid=762 iter 0, gcam->neg = 5 after 1 iterations, nbhd size=0, neg = 0 0289: dt=0.256000, rms=0.959 (0.498%), neg=0, invalid=762 iter 0, gcam->neg = 75 after 11 iterations, nbhd size=1, neg = 0 0290: dt=0.256000, rms=0.952 (0.719%), neg=0, invalid=762 iter 0, gcam->neg = 700 after 20 iterations, nbhd size=1, neg = 0 0291: dt=0.256000, rms=0.951 (0.121%), neg=0, invalid=762 iter 0, gcam->neg = 333 after 18 iterations, nbhd size=1, neg = 0 0292: dt=0.256000, rms=0.946 (0.516%), neg=0, invalid=762 iter 0, gcam->neg = 574 after 20 iterations, nbhd size=1, neg = 0 0293: dt=0.256000, rms=0.946 (-0.078%), neg=0, invalid=762 0294: dt=0.112000, rms=0.945 (0.069%), neg=0, invalid=762 0295: dt=0.112000, rms=0.945 (0.039%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.946, neg=0, invalid=762 iter 0, gcam->neg = 6879 after 22 iterations, nbhd size=1, neg = 0 0296: dt=1.177492, rms=0.932 (1.427%), neg=0, invalid=762 0297: dt=0.007000, rms=0.932 (-0.002%), neg=0, invalid=762 0298: dt=0.007000, rms=0.932 (0.000%), neg=0, invalid=762 0299: dt=0.007000, rms=0.932 (-0.002%), neg=0, invalid=762 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 ************************ enabling zero nodes setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.924, neg=0, invalid=762 0300: dt=0.000000, rms=0.924 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.924, neg=0, invalid=762 0301: dt=0.000000, rms=0.924 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.924, neg=0, invalid=762 0302: dt=0.000000, rms=0.924 (0.000%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.924, neg=0, invalid=762 0303: dt=0.000000, rms=0.924 (0.000%), neg=0, invalid=762 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.925, neg=0, invalid=762 iter 0, gcam->neg = 265 after 20 iterations, nbhd size=1, neg = 0 0304: dt=6.400000, rms=0.925 (-0.061%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.925, neg=0, invalid=762 iter 0, gcam->neg = 54 after 14 iterations, nbhd size=1, neg = 0 0305: dt=8.000000, rms=0.924 (0.032%), neg=0, invalid=762 iter 0, gcam->neg = 116 after 20 iterations, nbhd size=1, neg = 0 0306: dt=11.200000, rms=0.924 (-0.004%), neg=0, invalid=762 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.926, neg=0, invalid=762 iter 0, gcam->neg = 5713 after 32 iterations, nbhd size=1, neg = 0 0307: dt=12.963015, rms=0.926 (-1.260%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.926, neg=0, invalid=762 iter 0, gcam->neg = 2425 after 25 iterations, nbhd size=1, neg = 0 0308: dt=17.974895, rms=0.921 (0.517%), neg=0, invalid=762 iter 0, gcam->neg = 677 after 21 iterations, nbhd size=1, neg = 0 0309: dt=10.370803, rms=0.917 (0.458%), neg=0, invalid=762 iter 0, gcam->neg = 503 after 20 iterations, nbhd size=1, neg = 0 0310: dt=9.216000, rms=0.915 (0.167%), neg=0, invalid=762 iter 0, gcam->neg = 468 after 20 iterations, nbhd size=1, neg = 0 0311: dt=9.216000, rms=0.913 (0.215%), neg=0, invalid=762 iter 0, gcam->neg = 744 after 24 iterations, nbhd size=1, neg = 0 0312: dt=9.216000, rms=0.912 (0.139%), neg=0, invalid=762 iter 0, gcam->neg = 1596 after 33 iterations, nbhd size=1, neg = 0 0313: dt=9.216000, rms=0.912 (-0.259%), neg=0, invalid=762 iter 0, gcam->neg = 286 after 22 iterations, nbhd size=1, neg = 0 0314: dt=7.478261, rms=0.911 (0.051%), neg=0, invalid=762 iter 0, gcam->neg = 533 after 29 iterations, nbhd size=1, neg = 0 0315: dt=9.808696, rms=0.911 (0.062%), neg=0, invalid=762 iter 0, gcam->neg = 261 after 17 iterations, nbhd size=1, neg = 0 0316: dt=7.157895, rms=0.910 (0.126%), neg=0, invalid=762 iter 0, gcam->neg = 305 after 22 iterations, nbhd size=1, neg = 0 0317: dt=7.731092, rms=0.909 (0.077%), neg=0, invalid=762 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.916, neg=0, invalid=762 iter 0, gcam->neg = 8 after 3 iterations, nbhd size=0, neg = 0 0318: dt=0.448000, rms=0.915 (0.041%), neg=0, invalid=762 iter 0, gcam->neg = 14 after 11 iterations, nbhd size=1, neg = 0 0319: dt=0.768000, rms=0.915 (0.040%), neg=0, invalid=762 iter 0, gcam->neg = 14 after 3 iterations, nbhd size=0, neg = 0 0320: dt=0.768000, rms=0.914 (0.041%), neg=0, invalid=762 iter 0, gcam->neg = 30 after 4 iterations, nbhd size=0, neg = 0 0321: dt=0.768000, rms=0.914 (0.006%), neg=0, invalid=762 iter 0, gcam->neg = 66 after 18 iterations, nbhd size=1, neg = 0 0322: dt=0.768000, rms=0.914 (-0.190%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.914, neg=0, invalid=762 iter 0, gcam->neg = 54 after 16 iterations, nbhd size=1, neg = 0 0323: dt=2.218750, rms=0.911 (0.378%), neg=0, invalid=762 iter 0, gcam->neg = 2422 after 21 iterations, nbhd size=1, neg = 0 0324: dt=4.288184, rms=0.910 (0.133%), neg=0, invalid=762 iter 0, gcam->neg = 2818 after 26 iterations, nbhd size=1, neg = 0 0325: dt=4.288184, rms=0.910 (-1.975%), neg=0, invalid=762 resetting metric properties... setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.903, neg=0, invalid=762 iter 0, gcam->neg = 4937 after 31 iterations, nbhd size=1, neg = 0 0326: dt=0.842222, rms=0.903 (-0.280%), neg=0, invalid=762 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.903, neg=0, invalid=762 iter 0, gcam->neg = 9931 after 23 iterations, nbhd size=1, neg = 0 0327: dt=1.060346, rms=0.903 (-0.956%), neg=0, invalid=762 writing output transformation to transforms/talairach.m3z... GCAMwrite mri_ca_register took 1 hours, 7 minutes and 31 seconds. #VMPC# mri_ca_register VmPeak 2037736 FSRUNTIME@ mri_ca_register 1.1252 hours 1 threads #-------------------------------------- #@# SubCort Seg Fri Nov 23 18:16:21 CST 2018 mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz sysname Linux hostname liuzb-System-Product-Name machine x86_64 setenv SUBJECTS_DIR /home/liuzb/work/tutorial_data/practice_with_data cd /home/liuzb/work/tutorial_data/practice_with_data/Subj004/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz == Number of threads available to mri_ca_label for OpenMP = 1 == relabeling unlikely voxels with window_size = 9 and prior threshold 0.30 using Gibbs prior factor = 0.500 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/average/RB_all_2016-05-10.vc700.gca reading input volume from norm.mgz average std[0] = 7.3 reading transform from transforms/talairach.m3z setting orig areas to linear transform determinant scaled 6.43 Atlas used for the 3D morph was /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca average std = 7.3 using min determinant for regularization = 5.3 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.16259 (20) mri peak = 0.13571 ( 9) Left_Lateral_Ventricle (4): linear fit = 0.44 x + 0.0 (1686 voxels, overlap=0.015) Left_Lateral_Ventricle (4): linear fit = 0.44 x + 0.0 (1686 voxels, peak = 9), gca=8.9 gca peak = 0.17677 (13) mri peak = 0.16386 (10) Right_Lateral_Ventricle (43): linear fit = 0.62 x + 0.0 (2128 voxels, overlap=0.092) Right_Lateral_Ventricle (43): linear fit = 0.62 x + 0.0 (2128 voxels, peak = 8), gca=8.1 gca peak = 0.28129 (95) mri peak = 0.11404 (92) Right_Pallidum (52): linear fit = 0.94 x + 0.0 (136 voxels, overlap=0.244) Right_Pallidum (52): linear fit = 0.94 x + 0.0 (136 voxels, peak = 90), gca=89.8 gca peak = 0.16930 (96) mri peak = 0.09007 (76) Left_Pallidum (13): linear fit = 0.81 x + 0.0 (494 voxels, overlap=0.027) Left_Pallidum (13): linear fit = 0.81 x + 0.0 (494 voxels, peak = 78), gca=78.2 gca peak = 0.24553 (55) mri peak = 0.10624 (87) gca peak = 0.30264 (59) mri peak = 0.12662 (86) Left_Hippocampus (17): linear fit = 1.51 x + 0.0 (126 voxels, overlap=0.022) Left_Hippocampus (17): linear fit = 1.51 x + 0.0 (126 voxels, peak = 89), gca=89.4 gca peak = 0.07580 (103) mri peak = 0.05924 (103) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (32186 voxels, overlap=0.737) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (32186 voxels, peak = 107), gca=106.6 gca peak = 0.07714 (104) mri peak = 0.07409 (104) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (30984 voxels, overlap=0.704) Left_Cerebral_White_Matter (2): linear fit = 1.02 x + 0.0 (30984 voxels, peak = 107), gca=106.6 gca peak = 0.09712 (58) mri peak = 0.13265 (95) Left_Cerebral_Cortex (3): linear fit = 1.50 x + 0.0 (17478 voxels, overlap=0.000) Left_Cerebral_Cortex (3): linear fit = 1.50 x + 0.0 (17478 voxels, peak = 87), gca=86.7 gca peak = 0.11620 (58) mri peak = 0.14632 (95) Right_Cerebral_Cortex (42): linear fit = 1.57 x + 0.0 (15172 voxels, overlap=0.000) Right_Cerebral_Cortex (42): linear fit = 1.57 x + 0.0 (15172 voxels, peak = 91), gca=90.8 gca peak = 0.30970 (66) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.15280 (69) mri peak = 0.50000 (98) Left_Caudate (11): linear fit = 1.40 x + 0.0 (156 voxels, overlap=1.384) Left_Caudate (11): linear fit = 1.40 x + 0.0 (156 voxels, peak = 97), gca=96.9 gca peak = 0.13902 (56) mri peak = 0.03689 (101) Left_Cerebellum_Cortex (8): linear fit = 1.75 x + 0.0 (5245 voxels, overlap=0.001) Left_Cerebellum_Cortex (8): linear fit = 1.75 x + 0.0 (5245 voxels, peak = 98), gca=98.3 gca peak = 0.14777 (55) mri peak = 0.02167 (101) Right_Cerebellum_Cortex (47): linear fit = 1.93 x + 0.0 (7983 voxels, overlap=0.000) Right_Cerebellum_Cortex (47): linear fit = 1.93 x + 0.0 (7983 voxels, peak = 106), gca=106.4 gca peak = 0.16765 (84) mri peak = 0.05094 (93) Left_Cerebellum_White_Matter (7): linear fit = 1.11 x + 0.0 (2996 voxels, overlap=0.730) Left_Cerebellum_White_Matter (7): linear fit = 1.11 x + 0.0 (2996 voxels, peak = 93), gca=92.8 gca peak = 0.18739 (84) mri peak = 0.04914 (90) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (1885 voxels, overlap=0.837) Right_Cerebellum_White_Matter (46): linear fit = 1.07 x + 0.0 (1885 voxels, peak = 89), gca=89.5 gca peak = 0.29869 (57) mri peak = 0.19092 (90) Left_Amygdala (18): linear fit = 1.50 x + 0.0 (293 voxels, overlap=0.032) Left_Amygdala (18): linear fit = 1.50 x + 0.0 (293 voxels, peak = 86), gca=85.8 gca peak = 0.33601 (57) mri peak = 1.00000 (68) gca peak = 0.11131 (90) mri peak = 0.06596 (108) Left_Thalamus (10): linear fit = 1.24 x + 0.0 (2296 voxels, overlap=0.010) Left_Thalamus (10): linear fit = 1.24 x + 0.0 (2296 voxels, peak = 111), gca=111.2 gca peak = 0.11793 (83) mri peak = 0.06042 (107) Right_Thalamus (49): linear fit = 1.28 x + 0.0 (862 voxels, overlap=0.012) Right_Thalamus (49): linear fit = 1.28 x + 0.0 (862 voxels, peak = 107), gca=106.7 gca peak = 0.08324 (81) mri peak = 0.07003 (103) Left_Putamen (12): linear fit = 1.25 x + 0.0 (786 voxels, overlap=0.067) Left_Putamen (12): linear fit = 1.25 x + 0.0 (786 voxels, peak = 102), gca=101.7 gca peak = 0.10360 (77) mri peak = 0.05534 (93) Right_Putamen (51): linear fit = 1.26 x + 0.0 (138 voxels, overlap=0.142) Right_Putamen (51): linear fit = 1.26 x + 0.0 (138 voxels, peak = 97), gca=97.4 gca peak = 0.08424 (78) mri peak = 0.08079 (81) Brain_Stem (16): linear fit = 1.12 x + 0.0 (3258 voxels, overlap=0.476) Brain_Stem (16): linear fit = 1.12 x + 0.0 (3258 voxels, peak = 88), gca=87.8 gca peak = 0.12631 (89) mri peak = 0.05362 (93) Right_VentralDC (60): linear fit = 1.18 x + 0.0 (249 voxels, overlap=0.258) Right_VentralDC (60): linear fit = 1.18 x + 0.0 (249 voxels, peak = 105), gca=105.5 gca peak = 0.14500 (87) mri peak = 0.06319 (97) Left_VentralDC (28): linear fit = 1.13 x + 0.0 (497 voxels, overlap=0.448) Left_VentralDC (28): linear fit = 1.13 x + 0.0 (497 voxels, peak = 99), gca=98.7 gca peak = 0.14975 (24) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.19357 (14) uniform distribution in MR - rejecting arbitrary fit gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.16825 (27) gca peak Left_Cerebellum_Cortex = 0.13902 (56) gca peak = 1.00000 (94) gca peak Third_Ventricle = 0.14975 (24) gca peak Fourth_Ventricle = 0.19357 (14) gca peak Left_Hippocampus = 0.30264 (59) gca peak Left_Amygdala = 0.29869 (57) gca peak CSF = 0.23379 (36) gca peak Left_Accumbens_area = 0.70037 (62) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.75997 (52) gca peak Left_choroid_plexus = 0.12089 (35) gca peak Right_Cerebral_Cortex = 0.11620 (58) gca peak Right_Inf_Lat_Vent = 0.24655 (23) gca peak Right_Cerebellum_Cortex = 0.14777 (55) gca peak Right_Caudate = 0.30970 (66) gca peak Right_Hippocampus = 0.24553 (55) gca peak Right_Amygdala = 0.33601 (57) gca peak Right_Accumbens_area = 0.45042 (65) gca peak Right_vessel = 0.82168 (52) gca peak Right_choroid_plexus = 0.14516 (37) gca peak Fifth_Ventricle = 0.65475 (32) gca peak WM_hypointensities = 0.07854 (76) gca peak non_WM_hypointensities = 0.08491 (43) gca peak Optic_Chiasm = 0.71127 (75) not using caudate to estimate GM means setting label Right_Cerebral_Cortex based on Left_Cerebral_Cortex = 1.50 x + 0: 87 setting label Right_Caudate based on Left_Caudate = 1.40 x + 0: 97 estimating mean gm scale to be 1.50 x + 0.0 estimating mean wm scale to be 1.03 x + 0.0 estimating mean csf scale to be 0.53 x + 0.0 setting left cbm cortex = 1.50 x + 0.00 setting right cbm cortex = 1.50 x + 0.00 Left_Putamen too bright - rescaling by 0.944 (from 1.255) to 95.9 (was 101.7) Right_Putamen too bright - rescaling by 0.985 (from 1.265) to 95.9 (was 97.4) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.29482 ( 9) mri peak = 0.13571 ( 9) Left_Lateral_Ventricle (4): linear fit = 1.05 x + 0.0 (1686 voxels, overlap=0.831) Left_Lateral_Ventricle (4): linear fit = 1.05 x + 0.0 (1686 voxels, peak = 9), gca=9.5 gca peak = 0.26213 ( 8) mri peak = 0.16386 (10) Right_Lateral_Ventricle (43): linear fit = 1.05 x + 0.0 (2128 voxels, overlap=0.613) Right_Lateral_Ventricle (43): linear fit = 1.05 x + 0.0 (2128 voxels, peak = 8), gca=8.4 gca peak = 0.23259 (89) mri peak = 0.11404 (92) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (136 voxels, overlap=0.619) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (136 voxels, peak = 89), gca=88.6 gca peak = 0.19245 (79) mri peak = 0.09007 (76) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (494 voxels, overlap=0.933) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (494 voxels, peak = 79), gca=78.6 gca peak = 0.22814 (83) mri peak = 0.10624 (87) gca peak = 0.24888 (84) mri peak = 0.12662 (86) Left_Hippocampus (17): linear fit = 1.01 x + 0.0 (126 voxels, overlap=0.942) Left_Hippocampus (17): linear fit = 1.01 x + 0.0 (126 voxels, peak = 85), gca=85.3 gca peak = 0.07474 (107) mri peak = 0.05924 (103) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (32186 voxels, overlap=0.842) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (32186 voxels, peak = 106), gca=106.5 gca peak = 0.07666 (107) mri peak = 0.07409 (104) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (30984 voxels, overlap=0.809) Left_Cerebral_White_Matter (2): linear fit = 1.01 x + 0.0 (30984 voxels, peak = 109), gca=108.6 gca peak = 0.06500 (86) mri peak = 0.13265 (95) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (17478 voxels, overlap=0.848) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (17478 voxels, peak = 86), gca=86.4 gca peak = 0.08093 (87) mri peak = 0.14632 (95) Right_Cerebral_Cortex (42): linear fit = 1.04 x + 0.0 (15172 voxels, overlap=0.666) Right_Cerebral_Cortex (42): linear fit = 1.04 x + 0.0 (15172 voxels, peak = 91), gca=90.9 gca peak = 0.22769 (93) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.11773 (108) mri peak = 0.50000 (98) Left_Caudate: unreasonable value (109.6/98.0), not in range [50, 100] - rejecting gca peak = 0.09569 (84) mri peak = 0.03689 (101) Left_Cerebellum_Cortex (8): linear fit = 1.18 x + 0.0 (5245 voxels, overlap=0.034) Left_Cerebellum_Cortex (8): linear fit = 1.18 x + 0.0 (5245 voxels, peak = 100), gca=99.5 gca peak = 0.10199 (82) mri peak = 0.02167 (101) Right_Cerebellum_Cortex (47): linear fit = 1.24 x + 0.0 (7983 voxels, overlap=0.000) Right_Cerebellum_Cortex (47): linear fit = 1.24 x + 0.0 (7983 voxels, peak = 101), gca=101.3 gca peak = 0.14458 (93) mri peak = 0.05094 (93) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (2996 voxels, overlap=0.992) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (2996 voxels, peak = 93), gca=92.5 gca peak = 0.17701 (90) mri peak = 0.04914 (90) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (1885 voxels, overlap=0.995) Right_Cerebellum_White_Matter (46): linear fit = 0.99 x + 0.0 (1885 voxels, peak = 89), gca=88.7 gca peak = 0.29153 (85) mri peak = 0.19092 (90) Left_Amygdala (18): linear fit = 1.01 x + 0.0 (293 voxels, overlap=0.955) Left_Amygdala (18): linear fit = 1.01 x + 0.0 (293 voxels, peak = 86), gca=86.3 gca peak = 0.32753 (85) mri peak = 1.00000 (68) gca peak = 0.10250 (109) mri peak = 0.06596 (108) Left_Thalamus (10): linear fit = 1.00 x + 0.0 (2296 voxels, overlap=0.868) Left_Thalamus (10): linear fit = 1.00 x + 0.0 (2296 voxels, peak = 109), gca=109.0 gca peak = 0.08982 (107) mri peak = 0.06042 (107) Right_Thalamus (49): linear fit = 1.01 x + 0.0 (862 voxels, overlap=0.868) Right_Thalamus (49): linear fit = 1.01 x + 0.0 (862 voxels, peak = 109), gca=108.6 gca peak = 0.08048 (90) mri peak = 0.07003 (103) Left_Putamen (12): linear fit = 1.07 x + 0.0 (786 voxels, overlap=0.572) Left_Putamen (12): linear fit = 1.07 x + 0.0 (786 voxels, peak = 96), gca=95.9 gca peak = 0.09091 (94) mri peak = 0.05534 (93) Right_Putamen (51): linear fit = 1.02 x + 0.0 (138 voxels, overlap=0.683) Right_Putamen (51): linear fit = 1.02 x + 0.0 (138 voxels, peak = 96), gca=96.3 gca peak = 0.08369 (88) mri peak = 0.08079 (81) Brain_Stem (16): linear fit = 0.99 x + 0.0 (3258 voxels, overlap=0.750) Brain_Stem (16): linear fit = 0.99 x + 0.0 (3258 voxels, peak = 87), gca=86.7 gca peak = 0.09675 (105) mri peak = 0.05362 (93) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (249 voxels, overlap=0.789) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (249 voxels, peak = 106), gca=105.5 gca peak = 0.15146 (97) mri peak = 0.06319 (97) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (497 voxels, overlap=0.934) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (497 voxels, peak = 97), gca=97.5 gca peak = 0.24453 (14) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.27948 ( 8) uniform distribution in MR - rejecting arbitrary fit gca peak Unknown = 0.94835 ( 0) gca peak Left_Inf_Lat_Vent = 0.22964 (18) gca peak = 0.72551 (141) gca peak Left_Caudate = 0.11773 (108) gca peak Third_Ventricle = 0.24453 (14) gca peak Fourth_Ventricle = 0.27948 ( 8) gca peak CSF = 0.25283 (19) gca peak Left_Accumbens_area = 0.57330 (87) gca peak Left_undetermined = 1.00000 (26) gca peak Left_vessel = 0.50590 (52) gca peak Left_choroid_plexus = 0.12089 (35) gca peak Right_Inf_Lat_Vent = 0.25886 (15) gca peak Right_Caudate = 0.22769 (93) gca peak Right_Hippocampus = 0.22814 (83) gca peak Right_Amygdala = 0.32753 (85) gca peak Right_Accumbens_area = 0.23971 (92) gca peak Right_vessel = 0.49073 (51) gca peak Right_choroid_plexus = 0.14516 (37) gca peak Fifth_Ventricle = 0.89470 (17) gca peak WM_hypointensities = 0.07121 (79) gca peak non_WM_hypointensities = 0.11678 (56) gca peak Optic_Chiasm = 0.53404 (76) not using caudate to estimate GM means setting label Right_Hippocampus based on Left_Hippocampus = 1.01 x + 0: 85 setting label Right_Amygdala based on Left_Amygdala = 1.01 x + 0: 86 estimating mean gm scale to be 1.02 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.05 x + 0.0 Left_Putamen too bright - rescaling by 1.010 (from 1.065) to 96.8 (was 95.9) Right_Putamen too bright - rescaling by 1.004 (from 1.025) to 96.8 (was 96.3) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 120538 voxels changed in iteration 0 of unlikely voxel relabeling 376 voxels changed in iteration 1 of unlikely voxel relabeling 23 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 239371 gm and wm labels changed (% 9 to gray, %91 to white out of all changed labels) 541 hippocampal voxels changed. 8 amygdala voxels changed. pass 1: 113597 changed. image ll: -2.863, PF=0.500 pass 2: 30944 changed. image ll: -2.855, PF=0.500 pass 3: 10899 changed. pass 4: 4690 changed. 113618 voxels changed in iteration 0 of unlikely voxel relabeling 641 voxels changed in iteration 1 of unlikely voxel relabeling 16 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 12747 voxels changed in iteration 0 of unlikely voxel relabeling 335 voxels changed in iteration 1 of unlikely voxel relabeling 13 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 10701 voxels changed in iteration 0 of unlikely voxel relabeling 114 voxels changed in iteration 1 of unlikely voxel relabeling 0 voxels changed in iteration 2 of unlikely voxel relabeling 9726 voxels changed in iteration 0 of unlikely voxel relabeling 80 voxels changed in iteration 1 of unlikely voxel relabeling 9 voxels changed in iteration 2 of unlikely voxel relabeling 2 voxels changed in iteration 3 of unlikely voxel relabeling 0 voxels changed in iteration 4 of unlikely voxel relabeling !!!!!!!!! ventricle segment 3 with volume 9710 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 3 with volume 9375 above threshold 100 - not erasing !!!!!!!!!! MRItoUCHAR: min=0, max=85 MRItoUCHAR: converting to UCHAR writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 3260.613201 mri_ca_label stimesec 1.004001 mri_ca_label ru_maxrss 2212692 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 1140178 mri_ca_label ru_majflt 11 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 2216 mri_ca_label ru_oublock 448 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 11 mri_ca_label ru_nivcsw 5608 auto-labeling took 54 minutes and 22 seconds. #-------------------------------------- #@# CC Seg Fri Nov 23 19:10:43 CST 2018 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /home/liuzb/work/tutorial_data/practice_with_data/Subj004/mri/transforms/cc_up.lta Subj004 will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /home/liuzb/work/tutorial_data/practice_with_data/Subj004/mri/transforms/cc_up.lta reading aseg from /home/liuzb/work/tutorial_data/practice_with_data/Subj004/mri/aseg.auto_noCCseg.mgz reading norm from /home/liuzb/work/tutorial_data/practice_with_data/Subj004/mri/norm.mgz 70917 voxels in left wm, 67565 in right wm, xrange [123, 138] searching rotation angles z=[-7 7], y=[-9 5] searching scale 1 Z rot -6.5 searching scale 1 Z rot -6.3 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 searching scale 1 Z rot 7.7 global minimum found at slice 130.0, rotations (-2.73, 0.98) final transformation (x=130.0, yr=-2.726, zr=0.975): 0.99872 -0.01702 -0.04755 5.12184; 0.01701 0.99986 -0.00081 46.89628; 0.04756 0.00000 0.99887 3.95105; 0.00000 0.00000 0.00000 1.00000; updating x range to be [124, 135] in xformed coordinates best xformed slice 127 cc center is found at 127 79 118 eigenvectors: 0.00603 0.02106 0.99976; 0.44212 -0.89681 0.01623; 0.89694 0.44192 -0.01471; writing aseg with callosum to /home/liuzb/work/tutorial_data/practice_with_data/Subj004/mri/aseg.auto.mgz... corpus callosum segmentation took 1.2 minutes #-------------------------------------- #@# Merge ASeg Fri Nov 23 19:11:53 CST 2018 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Fri Nov 23 19:11:53 CST 2018 /home/liuzb/work/tutorial_data/practice_with_data/Subj004/mri mri_normalize -seed 1234 -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz setting seed for random number genererator to 1234 assuming input volume is MGH (Van der Kouwe) MP-RAGE using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading from norm.mgz... Reading aseg aseg.presurf.mgz normalizing image... processing with aseg removing outliers in the aseg WM... 1442 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 110 white matter peak found at 103 gm peak at 78 (78), valley at 56 (56) csf peak at 39, setting threshold to 65 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 77 (77), valley at 0 (0) csf peak at 38, setting threshold to 64 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 2 minutes and 36 seconds. #-------------------------------------------- #@# Mask BFS Fri Nov 23 19:14:30 CST 2018 /home/liuzb/work/tutorial_data/practice_with_data/Subj004/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1412451 voxels in mask (pct= 8.42) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Fri Nov 23 19:14:31 CST 2018 mri_segment -mprage brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... setting bottom of white matter range to 77.1 setting top of gray matter range to 93.2 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... 9513 sparsely connected voxels removed... thickening thin strands.... 20 segments, 1234 filled 13266 bright non-wm voxels segmented. 19178 diagonally connected voxels added... white matter segmentation took 1.4 minutes writing output to wm.seg.mgz... assuming input volume is MGH (Van der Kouwe) MP-RAGE CCS WM (109.0): 109.6 +- 6.9 [79.0 --> 125.0] CCS GM (63.0) : 61.0 +- 16.1 [30.0 --> 95.0] mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.39 minutes reading wm segmentation from wm.seg.mgz... 784 voxels added to wm to prevent paths from MTL structures to cortex 12781 additional wm voxels added 0 additional wm voxels added SEG EDIT: 65665 voxels turned on, 50659 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 0 new 0 115,126,128 old 0 new 0 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 164 found - 164 modified | TOTAL: 164 pass 2 (xy+): 0 found - 164 modified | TOTAL: 164 pass 1 (xy-): 173 found - 173 modified | TOTAL: 337 pass 2 (xy-): 0 found - 173 modified | TOTAL: 337 pass 1 (yz+): 202 found - 202 modified | TOTAL: 539 pass 2 (yz+): 0 found - 202 modified | TOTAL: 539 pass 1 (yz-): 216 found - 216 modified | TOTAL: 755 pass 2 (yz-): 0 found - 216 modified | TOTAL: 755 pass 1 (xz+): 211 found - 211 modified | TOTAL: 966 pass 2 (xz+): 0 found - 211 modified | TOTAL: 966 pass 1 (xz-): 211 found - 211 modified | TOTAL: 1177 pass 2 (xz-): 0 found - 211 modified | TOTAL: 1177 Iteration Number : 1 pass 1 (+++): 408 found - 408 modified | TOTAL: 408 pass 2 (+++): 0 found - 408 modified | TOTAL: 408 pass 1 (+++): 579 found - 579 modified | TOTAL: 987 pass 2 (+++): 0 found - 579 modified | TOTAL: 987 pass 1 (+++): 336 found - 336 modified | TOTAL: 1323 pass 2 (+++): 0 found - 336 modified | TOTAL: 1323 pass 1 (+++): 717 found - 717 modified | TOTAL: 2040 pass 2 (+++): 0 found - 717 modified | TOTAL: 2040 Iteration Number : 1 pass 1 (++): 518 found - 518 modified | TOTAL: 518 pass 2 (++): 0 found - 518 modified | TOTAL: 518 pass 1 (+-): 527 found - 527 modified | TOTAL: 1045 pass 2 (+-): 1 found - 528 modified | TOTAL: 1046 pass 3 (+-): 0 found - 528 modified | TOTAL: 1046 pass 1 (--): 474 found - 474 modified | TOTAL: 1520 pass 2 (--): 4 found - 478 modified | TOTAL: 1524 pass 3 (--): 0 found - 478 modified | TOTAL: 1524 pass 1 (-+): 517 found - 517 modified | TOTAL: 2041 pass 2 (-+): 0 found - 517 modified | TOTAL: 2041 Iteration Number : 2 pass 1 (xy+): 146 found - 146 modified | TOTAL: 146 pass 2 (xy+): 0 found - 146 modified | TOTAL: 146 pass 1 (xy-): 135 found - 135 modified | TOTAL: 281 pass 2 (xy-): 0 found - 135 modified | TOTAL: 281 pass 1 (yz+): 110 found - 110 modified | TOTAL: 391 pass 2 (yz+): 0 found - 110 modified | TOTAL: 391 pass 1 (yz-): 132 found - 132 modified | TOTAL: 523 pass 2 (yz-): 0 found - 132 modified | TOTAL: 523 pass 1 (xz+): 120 found - 120 modified | TOTAL: 643 pass 2 (xz+): 0 found - 120 modified | TOTAL: 643 pass 1 (xz-): 127 found - 127 modified | TOTAL: 770 pass 2 (xz-): 0 found - 127 modified | TOTAL: 770 Iteration Number : 2 pass 1 (+++): 20 found - 20 modified | TOTAL: 20 pass 2 (+++): 0 found - 20 modified | TOTAL: 20 pass 1 (+++): 20 found - 20 modified | TOTAL: 40 pass 2 (+++): 0 found - 20 modified | TOTAL: 40 pass 1 (+++): 20 found - 20 modified | TOTAL: 60 pass 2 (+++): 0 found - 20 modified | TOTAL: 60 pass 1 (+++): 22 found - 22 modified | TOTAL: 82 pass 2 (+++): 0 found - 22 modified | TOTAL: 82 Iteration Number : 2 pass 1 (++): 65 found - 65 modified | TOTAL: 65 pass 2 (++): 0 found - 65 modified | TOTAL: 65 pass 1 (+-): 58 found - 58 modified | TOTAL: 123 pass 2 (+-): 0 found - 58 modified | TOTAL: 123 pass 1 (--): 54 found - 54 modified | TOTAL: 177 pass 2 (--): 1 found - 55 modified | TOTAL: 178 pass 3 (--): 0 found - 55 modified | TOTAL: 178 pass 1 (-+): 48 found - 48 modified | TOTAL: 226 pass 2 (-+): 0 found - 48 modified | TOTAL: 226 Iteration Number : 3 pass 1 (xy+): 12 found - 12 modified | TOTAL: 12 pass 2 (xy+): 0 found - 12 modified | TOTAL: 12 pass 1 (xy-): 12 found - 12 modified | TOTAL: 24 pass 2 (xy-): 0 found - 12 modified | TOTAL: 24 pass 1 (yz+): 10 found - 10 modified | TOTAL: 34 pass 2 (yz+): 0 found - 10 modified | TOTAL: 34 pass 1 (yz-): 13 found - 13 modified | TOTAL: 47 pass 2 (yz-): 0 found - 13 modified | TOTAL: 47 pass 1 (xz+): 11 found - 11 modified | TOTAL: 58 pass 2 (xz+): 0 found - 11 modified | TOTAL: 58 pass 1 (xz-): 8 found - 8 modified | TOTAL: 66 pass 2 (xz-): 0 found - 8 modified | TOTAL: 66 Iteration Number : 3 pass 1 (+++): 4 found - 4 modified | TOTAL: 4 pass 2 (+++): 0 found - 4 modified | TOTAL: 4 pass 1 (+++): 2 found - 2 modified | TOTAL: 6 pass 2 (+++): 0 found - 2 modified | TOTAL: 6 pass 1 (+++): 0 found - 0 modified | TOTAL: 6 pass 1 (+++): 2 found - 2 modified | TOTAL: 8 pass 2 (+++): 0 found - 2 modified | TOTAL: 8 Iteration Number : 3 pass 1 (++): 4 found - 4 modified | TOTAL: 4 pass 2 (++): 0 found - 4 modified | TOTAL: 4 pass 1 (+-): 6 found - 6 modified | TOTAL: 10 pass 2 (+-): 0 found - 6 modified | TOTAL: 10 pass 1 (--): 4 found - 4 modified | TOTAL: 14 pass 2 (--): 0 found - 4 modified | TOTAL: 14 pass 1 (-+): 6 found - 6 modified | TOTAL: 20 pass 2 (-+): 0 found - 6 modified | TOTAL: 20 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 1 found - 1 modified | TOTAL: 1 pass 2 (xy-): 0 found - 1 modified | TOTAL: 1 pass 1 (yz+): 1 found - 1 modified | TOTAL: 2 pass 2 (yz+): 0 found - 1 modified | TOTAL: 2 pass 1 (yz-): 2 found - 2 modified | TOTAL: 4 pass 2 (yz-): 0 found - 2 modified | TOTAL: 4 pass 1 (xz+): 1 found - 1 modified | TOTAL: 5 pass 2 (xz+): 0 found - 1 modified | TOTAL: 5 pass 1 (xz-): 0 found - 0 modified | TOTAL: 5 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 1 found - 1 modified | TOTAL: 1 pass 2 (+++): 0 found - 1 modified | TOTAL: 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 1 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 1 found - 1 modified | TOTAL: 1 pass 2 (--): 0 found - 1 modified | TOTAL: 1 pass 1 (-+): 0 found - 0 modified | TOTAL: 1 Iteration Number : 5 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+): 1 found - 1 modified | TOTAL: 2 pass 2 (xz+): 0 found - 1 modified | TOTAL: 2 pass 1 (xz-): 0 found - 0 modified | TOTAL: 2 Iteration Number : 5 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 : 5 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 : 6 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 : 6 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 : 6 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 = 6439 (out of 772768: 0.833238) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Fri Nov 23 19:16:23 CST 2018 /home/liuzb/work/tutorial_data/practice_with_data/Subj004/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.presurf.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.presurf.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.01516 0.00105 -0.05295 0.77399; 0.00170 1.13572 0.06427 8.14746; 0.04785 -0.06114 1.07331 -19.08664; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.01516 0.00105 -0.05295 0.77399; 0.00170 1.13572 0.06427 8.14746; 0.04785 -0.06114 1.07331 -19.08664; 0.00000 0.00000 0.00000 1.00000; reading segmented volume aseg.presurf.mgz removing CC from segmentation Looking for area (min, max) = (350, 1400) area[0] = 3396 (min = 350, max = 1400), aspect = 0.72 (min = 0.10, max = 0.75) need search nearby using seed (126, 140, 106), TAL = (2.0, -22.0, -12.0) talairach voxel to voxel transform 0.98278 0.00169 0.04838 0.14897; 0.00100 0.87767 -0.05251 -8.15386; -0.04376 0.04992 0.92655 17.31190; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (126, 140, 106) --> (2.0, -22.0, -12.0) done. writing output to filled.mgz... filling took 1.0 minutes talairach cc position changed to (2.00, -22.00, -12.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, -22.00, -12.00) SRC: (111.66, 109.26, 117.79) search lh wm seed point around talairach space (-16.00, -22.00, -12.00), SRC: (147.04, 109.30, 116.21) 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 Fri Nov 23 19:17:25 CST 2018 /home/liuzb/work/tutorial_data/practice_with_data/Subj004/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 32 found - 32 modified | TOTAL: 32 pass 2 (xy+): 0 found - 32 modified | TOTAL: 32 pass 1 (xy-): 19 found - 19 modified | TOTAL: 51 pass 2 (xy-): 0 found - 19 modified | TOTAL: 51 pass 1 (yz+): 27 found - 27 modified | TOTAL: 78 pass 2 (yz+): 0 found - 27 modified | TOTAL: 78 pass 1 (yz-): 20 found - 20 modified | TOTAL: 98 pass 2 (yz-): 0 found - 20 modified | TOTAL: 98 pass 1 (xz+): 16 found - 16 modified | TOTAL: 114 pass 2 (xz+): 0 found - 16 modified | TOTAL: 114 pass 1 (xz-): 11 found - 11 modified | TOTAL: 125 pass 2 (xz-): 0 found - 11 modified | TOTAL: 125 Iteration Number : 1 pass 1 (+++): 5 found - 5 modified | TOTAL: 5 pass 2 (+++): 0 found - 5 modified | TOTAL: 5 pass 1 (+++): 2 found - 2 modified | TOTAL: 7 pass 2 (+++): 0 found - 2 modified | TOTAL: 7 pass 1 (+++): 6 found - 6 modified | TOTAL: 13 pass 2 (+++): 0 found - 6 modified | TOTAL: 13 pass 1 (+++): 0 found - 0 modified | TOTAL: 13 Iteration Number : 1 pass 1 (++): 7 found - 7 modified | TOTAL: 7 pass 2 (++): 0 found - 7 modified | TOTAL: 7 pass 1 (+-): 15 found - 15 modified | TOTAL: 22 pass 2 (+-): 0 found - 15 modified | TOTAL: 22 pass 1 (--): 16 found - 16 modified | TOTAL: 38 pass 2 (--): 0 found - 16 modified | TOTAL: 38 pass 1 (-+): 10 found - 10 modified | TOTAL: 48 pass 2 (-+): 0 found - 10 modified | TOTAL: 48 Iteration Number : 2 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 2 found - 2 modified | TOTAL: 3 pass 2 (xy-): 0 found - 2 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+): 0 found - 0 modified | TOTAL: 4 pass 1 (xz-): 0 found - 0 modified | TOTAL: 4 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 (--): 1 found - 1 modified | TOTAL: 1 pass 2 (--): 0 found - 1 modified | TOTAL: 1 pass 1 (-+): 1 found - 1 modified | TOTAL: 2 pass 2 (-+): 0 found - 1 modified | TOTAL: 2 Iteration Number : 3 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+): 0 found - 0 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 193 (out of 385878: 0.050016) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix $Id: mri_tessellate.c,v 1.39 2016/07/20 21:05:04 zkaufman Exp $ $Id$ slice 40: 293 vertices, 347 faces slice 50: 4055 vertices, 4265 faces slice 60: 14146 vertices, 14660 faces slice 70: 31420 vertices, 32247 faces slice 80: 52336 vertices, 53354 faces slice 90: 72228 vertices, 73402 faces slice 100: 91735 vertices, 93003 faces slice 110: 110208 vertices, 111558 faces slice 120: 126452 vertices, 127863 faces slice 130: 142809 vertices, 144294 faces slice 140: 161405 vertices, 163096 faces slice 150: 179233 vertices, 180942 faces slice 160: 195436 vertices, 197205 faces slice 170: 209019 vertices, 210828 faces slice 180: 219992 vertices, 221698 faces slice 190: 227358 vertices, 228970 faces slice 200: 230423 vertices, 231810 faces slice 210: 230432 vertices, 231814 faces slice 220: 230432 vertices, 231814 faces slice 230: 230432 vertices, 231814 faces slice 240: 230432 vertices, 231814 faces slice 250: 230432 vertices, 231814 faces using the conformed surface RAS to save vertex points... writing ../surf/lh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 230432 voxel in cpt #1: X=-1382 [v=230432,e=695442,f=463628] located at (-28.616386, -13.744615, 39.650177) For the whole surface: X=-1382 [v=230432,e=695442,f=463628] One single component has been found nothing to do done #-------------------------------------------- #@# Tessellate rh Fri Nov 23 19:17:31 CST 2018 /home/liuzb/work/tutorial_data/practice_with_data/Subj004/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 33 found - 33 modified | TOTAL: 33 pass 2 (xy+): 0 found - 33 modified | TOTAL: 33 pass 1 (xy-): 34 found - 34 modified | TOTAL: 67 pass 2 (xy-): 0 found - 34 modified | TOTAL: 67 pass 1 (yz+): 25 found - 25 modified | TOTAL: 92 pass 2 (yz+): 0 found - 25 modified | TOTAL: 92 pass 1 (yz-): 21 found - 21 modified | TOTAL: 113 pass 2 (yz-): 0 found - 21 modified | TOTAL: 113 pass 1 (xz+): 23 found - 23 modified | TOTAL: 136 pass 2 (xz+): 0 found - 23 modified | TOTAL: 136 pass 1 (xz-): 29 found - 29 modified | TOTAL: 165 pass 2 (xz-): 0 found - 29 modified | TOTAL: 165 Iteration Number : 1 pass 1 (+++): 4 found - 4 modified | TOTAL: 4 pass 2 (+++): 0 found - 4 modified | TOTAL: 4 pass 1 (+++): 4 found - 4 modified | TOTAL: 8 pass 2 (+++): 0 found - 4 modified | TOTAL: 8 pass 1 (+++): 12 found - 12 modified | TOTAL: 20 pass 2 (+++): 0 found - 12 modified | TOTAL: 20 pass 1 (+++): 6 found - 6 modified | TOTAL: 26 pass 2 (+++): 0 found - 6 modified | TOTAL: 26 Iteration Number : 1 pass 1 (++): 14 found - 14 modified | TOTAL: 14 pass 2 (++): 0 found - 14 modified | TOTAL: 14 pass 1 (+-): 15 found - 15 modified | TOTAL: 29 pass 2 (+-): 1 found - 16 modified | TOTAL: 30 pass 3 (+-): 0 found - 16 modified | TOTAL: 30 pass 1 (--): 15 found - 15 modified | TOTAL: 45 pass 2 (--): 0 found - 15 modified | TOTAL: 45 pass 1 (-+): 17 found - 17 modified | TOTAL: 62 pass 2 (-+): 0 found - 17 modified | TOTAL: 62 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 3 found - 3 modified | TOTAL: 3 pass 2 (xy-): 0 found - 3 modified | TOTAL: 3 pass 1 (yz+): 3 found - 3 modified | TOTAL: 6 pass 2 (yz+): 0 found - 3 modified | TOTAL: 6 pass 1 (yz-): 2 found - 2 modified | TOTAL: 8 pass 2 (yz-): 0 found - 2 modified | TOTAL: 8 pass 1 (xz+): 3 found - 3 modified | TOTAL: 11 pass 2 (xz+): 0 found - 3 modified | TOTAL: 11 pass 1 (xz-): 0 found - 0 modified | TOTAL: 11 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 (++): 2 found - 2 modified | TOTAL: 2 pass 2 (++): 0 found - 2 modified | TOTAL: 2 pass 1 (+-): 4 found - 4 modified | TOTAL: 6 pass 2 (+-): 0 found - 4 modified | TOTAL: 6 pass 1 (--): 1 found - 1 modified | TOTAL: 7 pass 2 (--): 0 found - 1 modified | TOTAL: 7 pass 1 (-+): 3 found - 3 modified | TOTAL: 10 pass 2 (-+): 0 found - 3 modified | TOTAL: 10 Iteration Number : 3 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+): 0 found - 0 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 4 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 275 (out of 389486: 0.070606) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.39 2016/07/20 21:05:04 zkaufman Exp $ $Id$ slice 50: 2231 vertices, 2363 faces slice 60: 9669 vertices, 10088 faces slice 70: 23949 vertices, 24612 faces slice 80: 42820 vertices, 43783 faces slice 90: 62204 vertices, 63246 faces slice 100: 80893 vertices, 82032 faces slice 110: 99572 vertices, 100839 faces slice 120: 119156 vertices, 120619 faces slice 130: 138701 vertices, 140303 faces slice 140: 158114 vertices, 159851 faces slice 150: 177316 vertices, 179178 faces slice 160: 195322 vertices, 197200 faces slice 170: 210060 vertices, 211920 faces slice 180: 222967 vertices, 224849 faces slice 190: 232443 vertices, 234212 faces slice 200: 237119 vertices, 238671 faces slice 210: 237396 vertices, 238888 faces slice 220: 237396 vertices, 238888 faces slice 230: 237396 vertices, 238888 faces slice 240: 237396 vertices, 238888 faces slice 250: 237396 vertices, 238888 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 237396 voxel in cpt #1: X=-1492 [v=237396,e=716664,f=477776] located at (25.589790, -8.784457, 36.943966) For the whole surface: X=-1492 [v=237396,e=716664,f=477776] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Fri Nov 23 19:17:36 CST 2018 /home/liuzb/work/tutorial_data/practice_with_data/Subj004/scripts mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Smooth1 rh Fri Nov 23 19:17:41 CST 2018 /home/liuzb/work/tutorial_data/practice_with_data/Subj004/scripts mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 lh Fri Nov 23 19:17:46 CST 2018 /home/liuzb/work/tutorial_data/practice_with_data/Subj004/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 46.0 mm, total surface area = 112911 mm^2 step 000: RMS=0.216 (target=0.015) step 005: RMS=0.176 (target=0.015) step 010: RMS=0.157 (target=0.015) step 015: RMS=0.150 (target=0.015) step 020: RMS=0.145 (target=0.015) step 025: RMS=0.140 (target=0.015) step 030: RMS=0.136 (target=0.015) step 035: RMS=0.134 (target=0.015) step 040: RMS=0.132 (target=0.015) step 045: RMS=0.131 (target=0.015) step 050: RMS=0.130 (target=0.015) step 055: RMS=0.131 (target=0.015) step 060: RMS=0.133 (target=0.015) writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.8 minutes inflation complete. Not saving sulc mris_inflate utimesec 49.976224 mris_inflate stimesec 0.288024 mris_inflate ru_maxrss 335020 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 301503 mris_inflate ru_majflt 21 mris_inflate ru_nswap 0 mris_inflate ru_inblock 4664 mris_inflate ru_oublock 16272 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 21 mris_inflate ru_nivcsw 85 #-------------------------------------------- #@# Inflation1 rh Fri Nov 23 19:18:37 CST 2018 /home/liuzb/work/tutorial_data/practice_with_data/Subj004/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 45.6 mm, total surface area = 114369 mm^2 step 000: RMS=0.219 (target=0.015) step 005: RMS=0.178 (target=0.015) step 010: RMS=0.159 (target=0.015) step 015: RMS=0.153 (target=0.015) step 020: RMS=0.148 (target=0.015) step 025: RMS=0.145 (target=0.015) step 030: RMS=0.143 (target=0.015) step 035: RMS=0.141 (target=0.015) step 040: RMS=0.140 (target=0.015) step 045: RMS=0.139 (target=0.015) step 050: RMS=0.139 (target=0.015) step 055: RMS=0.140 (target=0.015) step 060: RMS=0.141 (target=0.015) writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.9 minutes inflation complete. Not saving sulc mris_inflate utimesec 52.019034 mris_inflate stimesec 0.275994 mris_inflate ru_maxrss 345124 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 310832 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 16768 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 0 mris_inflate ru_nivcsw 98 #-------------------------------------------- #@# QSphere lh Fri Nov 23 19:19:29 CST 2018 /home/liuzb/work/tutorial_data/practice_with_data/Subj004/scripts mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. limitting unfolding to 6 passes using n_averages = 128 setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.62 2017/02/07 19:04:37 fischl Exp $ $Id$ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.91 +- 0.77 (0.00-->10.93) (max @ vno 120846 --> 122405) face area 0.02 +- 0.07 (-1.12-->1.59) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.318... Entering MRISinflateToSphere() inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.376, avgs=0 005/300: dt: 0.9000, rms radial error=177.126, avgs=0 010/300: dt: 0.9000, rms radial error=176.591, avgs=0 015/300: dt: 0.9000, rms radial error=175.889, avgs=0 020/300: dt: 0.9000, rms radial error=175.088, avgs=0 025/300: dt: 0.9000, rms radial error=174.233, avgs=0 030/300: dt: 0.9000, rms radial error=173.346, avgs=0 035/300: dt: 0.9000, rms radial error=172.444, avgs=0 040/300: dt: 0.9000, rms radial error=171.534, avgs=0 045/300: dt: 0.9000, rms radial error=170.623, avgs=0 050/300: dt: 0.9000, rms radial error=169.713, avgs=0 055/300: dt: 0.9000, rms radial error=168.805, avgs=0 060/300: dt: 0.9000, rms radial error=167.901, avgs=0 065/300: dt: 0.9000, rms radial error=167.001, avgs=0 070/300: dt: 0.9000, rms radial error=166.107, avgs=0 075/300: dt: 0.9000, rms radial error=165.217, avgs=0 080/300: dt: 0.9000, rms radial error=164.332, avgs=0 085/300: dt: 0.9000, rms radial error=163.452, avgs=0 090/300: dt: 0.9000, rms radial error=162.576, avgs=0 095/300: dt: 0.9000, rms radial error=161.706, avgs=0 100/300: dt: 0.9000, rms radial error=160.842, avgs=0 105/300: dt: 0.9000, rms radial error=159.983, avgs=0 110/300: dt: 0.9000, rms radial error=159.129, avgs=0 115/300: dt: 0.9000, rms radial error=158.279, avgs=0 120/300: dt: 0.9000, rms radial error=157.435, avgs=0 125/300: dt: 0.9000, rms radial error=156.595, avgs=0 130/300: dt: 0.9000, rms radial error=155.759, avgs=0 135/300: dt: 0.9000, rms radial error=154.928, avgs=0 140/300: dt: 0.9000, rms radial error=154.102, avgs=0 145/300: dt: 0.9000, rms radial error=153.281, avgs=0 150/300: dt: 0.9000, rms radial error=152.464, avgs=0 155/300: dt: 0.9000, rms radial error=151.652, avgs=0 160/300: dt: 0.9000, rms radial error=150.844, avgs=0 165/300: dt: 0.9000, rms radial error=150.041, avgs=0 170/300: dt: 0.9000, rms radial error=149.242, avgs=0 175/300: dt: 0.9000, rms radial error=148.447, avgs=0 180/300: dt: 0.9000, rms radial error=147.657, avgs=0 185/300: dt: 0.9000, rms radial error=146.872, avgs=0 190/300: dt: 0.9000, rms radial error=146.090, avgs=0 195/300: dt: 0.9000, rms radial error=145.313, avgs=0 200/300: dt: 0.9000, rms radial error=144.541, avgs=0 205/300: dt: 0.9000, rms radial error=143.772, avgs=0 210/300: dt: 0.9000, rms radial error=143.008, avgs=0 215/300: dt: 0.9000, rms radial error=142.249, avgs=0 220/300: dt: 0.9000, rms radial error=141.493, avgs=0 225/300: dt: 0.9000, rms radial error=140.742, avgs=0 230/300: dt: 0.9000, rms radial error=139.995, avgs=0 235/300: dt: 0.9000, rms radial error=139.253, avgs=0 240/300: dt: 0.9000, rms radial error=138.514, avgs=0 245/300: dt: 0.9000, rms radial error=137.780, avgs=0 250/300: dt: 0.9000, rms radial error=137.050, avgs=0 255/300: dt: 0.9000, rms radial error=136.323, avgs=0 260/300: dt: 0.9000, rms radial error=135.601, avgs=0 265/300: dt: 0.9000, rms radial error=134.883, avgs=0 270/300: dt: 0.9000, rms radial error=134.169, avgs=0 275/300: dt: 0.9000, rms radial error=133.459, avgs=0 280/300: dt: 0.9000, rms radial error=132.753, avgs=0 285/300: dt: 0.9000, rms radial error=132.051, avgs=0 290/300: dt: 0.9000, rms radial error=131.353, avgs=0 295/300: dt: 0.9000, rms radial error=130.659, avgs=0 300/300: dt: 0.9000, rms radial error=129.969, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 28766.03 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/13 = 0.00076 epoch 2 (K=40.0), pass 1, starting sse = 6612.77 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.04/13 = 0.00297 epoch 3 (K=160.0), pass 1, starting sse = 2086.09 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.13/15 = 0.00850 epoch 4 (K=640.0), pass 1, starting sse = 1096.73 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.18/18 = 0.00976 final distance error %44.65 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.0823 hours mris_sphere utimesec 295.701747 mris_sphere stimesec 0.447996 mris_sphere ru_maxrss 334904 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 377874 mris_sphere ru_majflt 10 mris_sphere ru_nswap 0 mris_sphere ru_inblock 1616 mris_sphere ru_oublock 16272 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 10 mris_sphere ru_nivcsw 1680 FSRUNTIME@ mris_sphere 0.0823 hours 1 threads #-------------------------------------------- #@# QSphere rh Fri Nov 23 19:24:25 CST 2018 /home/liuzb/work/tutorial_data/practice_with_data/Subj004/scripts mris_sphere -q -p 6 -a 128 -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. limitting unfolding to 6 passes using n_averages = 128 setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.62 2017/02/07 19:04:37 fischl Exp $ $Id$ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 0.91 +- 0.76 (0.00-->16.84) (max @ vno 129588 --> 129589) face area 0.02 +- 0.06 (-1.21-->1.75) == Number of threads available to mris_sphere for OpenMP = 1 == scaling brain by 0.318... Entering MRISinflateToSphere() inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.595, avgs=0 005/300: dt: 0.9000, rms radial error=177.343, avgs=0 010/300: dt: 0.9000, rms radial error=176.801, avgs=0 015/300: dt: 0.9000, rms radial error=176.088, avgs=0 020/300: dt: 0.9000, rms radial error=175.276, avgs=0 025/300: dt: 0.9000, rms radial error=174.408, avgs=0 030/300: dt: 0.9000, rms radial error=173.508, avgs=0 035/300: dt: 0.9000, rms radial error=172.592, avgs=0 040/300: dt: 0.9000, rms radial error=171.668, avgs=0 045/300: dt: 0.9000, rms radial error=170.742, avgs=0 050/300: dt: 0.9000, rms radial error=169.817, avgs=0 055/300: dt: 0.9000, rms radial error=168.896, avgs=0 060/300: dt: 0.9000, rms radial error=167.978, avgs=0 065/300: dt: 0.9000, rms radial error=167.065, avgs=0 070/300: dt: 0.9000, rms radial error=166.156, avgs=0 075/300: dt: 0.9000, rms radial error=165.253, avgs=0 080/300: dt: 0.9000, rms radial error=164.354, avgs=0 085/300: dt: 0.9000, rms radial error=163.461, avgs=0 090/300: dt: 0.9000, rms radial error=162.572, avgs=0 095/300: dt: 0.9000, rms radial error=161.689, avgs=0 100/300: dt: 0.9000, rms radial error=160.810, avgs=0 105/300: dt: 0.9000, rms radial error=159.937, avgs=0 110/300: dt: 0.9000, rms radial error=159.069, avgs=0 115/300: dt: 0.9000, rms radial error=158.207, avgs=0 120/300: dt: 0.9000, rms radial error=157.349, avgs=0 125/300: dt: 0.9000, rms radial error=156.496, avgs=0 130/300: dt: 0.9000, rms radial error=155.648, avgs=0 135/300: dt: 0.9000, rms radial error=154.805, avgs=0 140/300: dt: 0.9000, rms radial error=153.966, avgs=0 145/300: dt: 0.9000, rms radial error=153.132, avgs=0 150/300: dt: 0.9000, rms radial error=152.304, avgs=0 155/300: dt: 0.9000, rms radial error=151.481, avgs=0 160/300: dt: 0.9000, rms radial error=150.662, avgs=0 165/300: dt: 0.9000, rms radial error=149.848, avgs=0 170/300: dt: 0.9000, rms radial error=149.039, avgs=0 175/300: dt: 0.9000, rms radial error=148.234, avgs=0 180/300: dt: 0.9000, rms radial error=147.433, avgs=0 185/300: dt: 0.9000, rms radial error=146.637, avgs=0 190/300: dt: 0.9000, rms radial error=145.845, avgs=0 195/300: dt: 0.9000, rms radial error=145.058, avgs=0 200/300: dt: 0.9000, rms radial error=144.275, avgs=0 205/300: dt: 0.9000, rms radial error=143.496, avgs=0 210/300: dt: 0.9000, rms radial error=142.722, avgs=0 215/300: dt: 0.9000, rms radial error=141.952, avgs=0 220/300: dt: 0.9000, rms radial error=141.187, avgs=0 225/300: dt: 0.9000, rms radial error=140.425, avgs=0 230/300: dt: 0.9000, rms radial error=139.668, avgs=0 235/300: dt: 0.9000, rms radial error=138.916, avgs=0 240/300: dt: 0.9000, rms radial error=138.167, avgs=0 245/300: dt: 0.9000, rms radial error=137.422, avgs=0 250/300: dt: 0.9000, rms radial error=136.682, avgs=0 255/300: dt: 0.9000, rms radial error=135.946, avgs=0 260/300: dt: 0.9000, rms radial error=135.214, avgs=0 265/300: dt: 0.9000, rms radial error=134.486, avgs=0 270/300: dt: 0.9000, rms radial error=133.762, avgs=0 275/300: dt: 0.9000, rms radial error=133.042, avgs=0 280/300: dt: 0.9000, rms radial error=132.326, avgs=0 285/300: dt: 0.9000, rms radial error=131.614, avgs=0 290/300: dt: 0.9000, rms radial error=130.906, avgs=0 295/300: dt: 0.9000, rms radial error=130.203, avgs=0 300/300: dt: 0.9000, rms radial error=129.503, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 29496.78 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/13 = 0.00079 epoch 2 (K=40.0), pass 1, starting sse = 6525.84 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.02/13 = 0.00176 epoch 3 (K=160.0), pass 1, starting sse = 2012.55 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.10/14 = 0.00693 epoch 4 (K=640.0), pass 1, starting sse = 1098.66 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.13/16 = 0.00804 final distance error %42.71 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.0816 hours mris_sphere utimesec 293.481873 mris_sphere stimesec 0.455996 mris_sphere ru_maxrss 345628 mris_sphere ru_ixrss 0 mris_sphere ru_idrss 0 mris_sphere ru_isrss 0 mris_sphere ru_minflt 376014 mris_sphere ru_majflt 0 mris_sphere ru_nswap 0 mris_sphere ru_inblock 0 mris_sphere ru_oublock 16768 mris_sphere ru_msgsnd 0 mris_sphere ru_msgrcv 0 mris_sphere ru_nsignals 0 mris_sphere ru_nvcsw 0 mris_sphere ru_nivcsw 384 FSRUNTIME@ mris_sphere 0.0816 hours 1 threads #@# Fix Topology lh Fri Nov 23 19:29:19 CST 2018 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig -ga -seed 1234 Subj004 lh reading spherical homeomorphism from 'qsphere.nofix' reading inflated coordinates from 'inflated.nofix' reading original coordinates from 'orig.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 writing corrected surface to 'orig' $Id: mris_fix_topology.c,v 1.51 2016/10/27 19:43:58 fischl Exp $ $Id$ before topology correction, eno=-1382 (nv=230432, nf=463628, ne=695442, g=692) 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 14 iterations marking ambiguous vertices... 283973 ambiguous faces found in tessellation segmenting defects... 86 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 5 into 0 -merging segment 11 into 0 -merging segment 12 into 0 -merging segment 17 into 0 -merging segment 21 into 0 -merging segment 27 into 0 -merging segment 30 into 0 -merging segment 31 into 0 -merging segment 35 into 0 -merging segment 42 into 0 -merging segment 45 into 0 -merging segment 65 into 0 -merging segment 66 into 0 -merging segment 26 into 0 -merging segment 46 into 0 -merging segment 33 into 29 -merging segment 51 into 48 -merging segment 0 into 67 -merging segment 77 into 74 67 defects to be corrected 0 vertices coincident reading input surface /home/liuzb/work/tutorial_data/practice_with_data/Subj004/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Reading original properties of orig.nofix Reading vertex positions of inflated.nofix Computing Initial Surface Statistics -face loglikelihood: -9.6172 (-4.8086) -vertex loglikelihood: -8.1039 (-4.0520) -normal dot loglikelihood: -3.4307 (-3.4307) -quad curv loglikelihood: -6.0054 (-3.0027) Total Loglikelihood : -27.1572 CORRECTING DEFECT 0 (vertices=94, convex hull=63, v0=2314) After retessellation of defect 0 (v0=2314), euler #=52 (81991,233617,151678) : difference with theory (-64) = -116 CORRECTING DEFECT 1 (vertices=145, convex hull=136, v0=2522) After retessellation of defect 1 (v0=2522), euler #=53 (82057,233878,151874) : difference with theory (-63) = -116 CORRECTING DEFECT 2 (vertices=69, convex hull=69, v0=3552) After retessellation of defect 2 (v0=3552), euler #=54 (82077,233967,151944) : difference with theory (-62) = -116 CORRECTING DEFECT 3 (vertices=32, convex hull=70, v0=3558) After retessellation of defect 3 (v0=3558), euler #=55 (82090,234031,151996) : difference with theory (-61) = -116 CORRECTING DEFECT 4 (vertices=9, convex hull=23, v0=11315) After retessellation of defect 4 (v0=11315), euler #=56 (82090,234035,152001) : difference with theory (-60) = -116 CORRECTING DEFECT 5 (vertices=23, convex hull=28, v0=11773) After retessellation of defect 5 (v0=11773), euler #=57 (82091,234045,152011) : difference with theory (-59) = -116 CORRECTING DEFECT 6 (vertices=51, convex hull=28, v0=12301) After retessellation of defect 6 (v0=12301), euler #=58 (82096,234070,152032) : difference with theory (-58) = -116 CORRECTING DEFECT 7 (vertices=42, convex hull=90, v0=14074) After retessellation of defect 7 (v0=14074), euler #=59 (82118,234174,152115) : difference with theory (-57) = -116 CORRECTING DEFECT 8 (vertices=21, convex hull=48, v0=14119) After retessellation of defect 8 (v0=14119), euler #=60 (82123,234205,152142) : difference with theory (-56) = -116 CORRECTING DEFECT 9 (vertices=5, convex hull=13, v0=25237) After retessellation of defect 9 (v0=25237), euler #=61 (82123,234209,152147) : difference with theory (-55) = -116 CORRECTING DEFECT 10 (vertices=19, convex hull=45, v0=25316) After retessellation of defect 10 (v0=25316), euler #=62 (82133,234256,152185) : difference with theory (-54) = -116 CORRECTING DEFECT 11 (vertices=9, convex hull=17, v0=27265) After retessellation of defect 11 (v0=27265), euler #=63 (82134,234262,152191) : difference with theory (-53) = -116 CORRECTING DEFECT 12 (vertices=31, convex hull=43, v0=36509) After retessellation of defect 12 (v0=36509), euler #=64 (82136,234288,152216) : difference with theory (-52) = -116 CORRECTING DEFECT 13 (vertices=67, convex hull=34, v0=43472) After retessellation of defect 13 (v0=43472), euler #=65 (82141,234317,152241) : difference with theory (-51) = -116 CORRECTING DEFECT 14 (vertices=72, convex hull=93, v0=44159) After retessellation of defect 14 (v0=44159), euler #=66 (82167,234436,152335) : difference with theory (-50) = -116 CORRECTING DEFECT 15 (vertices=58, convex hull=24, v0=45224) After retessellation of defect 15 (v0=45224), euler #=67 (82169,234455,152353) : difference with theory (-49) = -116 CORRECTING DEFECT 16 (vertices=63, convex hull=46, v0=50961) After retessellation of defect 16 (v0=50961), euler #=68 (82188,234531,152411) : difference with theory (-48) = -116 CORRECTING DEFECT 17 (vertices=23, convex hull=31, v0=52226) After retessellation of defect 17 (v0=52226), euler #=69 (82191,234554,152432) : difference with theory (-47) = -116 CORRECTING DEFECT 18 (vertices=93, convex hull=30, v0=52264) After retessellation of defect 18 (v0=52264), euler #=70 (82200,234588,152458) : difference with theory (-46) = -116 CORRECTING DEFECT 19 (vertices=110, convex hull=66, v0=54755) After retessellation of defect 19 (v0=54755), euler #=71 (82236,234724,152559) : difference with theory (-45) = -116 CORRECTING DEFECT 20 (vertices=87, convex hull=40, v0=58192) After retessellation of defect 20 (v0=58192), euler #=72 (82245,234767,152594) : difference with theory (-44) = -116 CORRECTING DEFECT 21 (vertices=170, convex hull=151, v0=60854) After retessellation of defect 21 (v0=60854), euler #=74 (82299,235008,152783) : difference with theory (-43) = -117 CORRECTING DEFECT 22 (vertices=42, convex hull=73, v0=66552) After retessellation of defect 22 (v0=66552), euler #=75 (82311,235070,152834) : difference with theory (-42) = -117 CORRECTING DEFECT 23 (vertices=100, convex hull=118, v0=67276) After retessellation of defect 23 (v0=67276), euler #=76 (82365,235281,152992) : difference with theory (-41) = -117 CORRECTING DEFECT 24 (vertices=23, convex hull=46, v0=68717) After retessellation of defect 24 (v0=68717), euler #=77 (82370,235313,153020) : difference with theory (-40) = -117 CORRECTING DEFECT 25 (vertices=467, convex hull=168, v0=74999) After retessellation of defect 25 (v0=74999), euler #=78 (82518,235847,153407) : difference with theory (-39) = -117 CORRECTING DEFECT 26 (vertices=20, convex hull=44, v0=82314) After retessellation of defect 26 (v0=82314), euler #=79 (82528,235897,153448) : difference with theory (-38) = -117 CORRECTING DEFECT 27 (vertices=233, convex hull=111, v0=82860) After retessellation of defect 27 (v0=82860), euler #=80 (82562,236057,153575) : difference with theory (-37) = -117 CORRECTING DEFECT 28 (vertices=32, convex hull=77, v0=84075) After retessellation of defect 28 (v0=84075), euler #=81 (82573,236123,153631) : difference with theory (-36) = -117 CORRECTING DEFECT 29 (vertices=8, convex hull=34, v0=84263) After retessellation of defect 29 (v0=84263), euler #=82 (82577,236143,153648) : difference with theory (-35) = -117 CORRECTING DEFECT 30 (vertices=211, convex hull=44, v0=87286) After retessellation of defect 30 (v0=87286), euler #=83 (82594,236215,153704) : difference with theory (-34) = -117 CORRECTING DEFECT 31 (vertices=545, convex hull=343, v0=88249) After retessellation of defect 31 (v0=88249), euler #=82 (82783,236956,154255) : difference with theory (-33) = -115 CORRECTING DEFECT 32 (vertices=35, convex hull=17, v0=90499) After retessellation of defect 32 (v0=90499), euler #=83 (82786,236969,154266) : difference with theory (-32) = -115 CORRECTING DEFECT 33 (vertices=909, convex hull=174, v0=91893) After retessellation of defect 33 (v0=91893), euler #=85 (82807,237108,154386) : difference with theory (-31) = -116 CORRECTING DEFECT 34 (vertices=73, convex hull=41, v0=94067) After retessellation of defect 34 (v0=94067), euler #=86 (82817,237154,154423) : difference with theory (-30) = -116 CORRECTING DEFECT 35 (vertices=82, convex hull=100, v0=105112) After retessellation of defect 35 (v0=105112), euler #=87 (82842,237272,154517) : difference with theory (-29) = -116 CORRECTING DEFECT 36 (vertices=44, convex hull=83, v0=106227) After retessellation of defect 36 (v0=106227), euler #=88 (82869,237386,154605) : difference with theory (-28) = -116 CORRECTING DEFECT 37 (vertices=80, convex hull=38, v0=108735) After retessellation of defect 37 (v0=108735), euler #=89 (82878,237426,154637) : difference with theory (-27) = -116 CORRECTING DEFECT 38 (vertices=19, convex hull=49, v0=108988) After retessellation of defect 38 (v0=108988), euler #=90 (82887,237472,154675) : difference with theory (-26) = -116 CORRECTING DEFECT 39 (vertices=36, convex hull=65, v0=118440) After retessellation of defect 39 (v0=118440), euler #=91 (82904,237551,154738) : difference with theory (-25) = -116 CORRECTING DEFECT 40 (vertices=78, convex hull=101, v0=120245) After retessellation of defect 40 (v0=120245), euler #=92 (82951,237743,154884) : difference with theory (-24) = -116 CORRECTING DEFECT 41 (vertices=25, convex hull=66, v0=124012) After retessellation of defect 41 (v0=124012), euler #=93 (82966,237811,154938) : difference with theory (-23) = -116 CORRECTING DEFECT 42 (vertices=39, convex hull=46, v0=130054) After retessellation of defect 42 (v0=130054), euler #=93 (82986,237893,155000) : difference with theory (-22) = -115 CORRECTING DEFECT 43 (vertices=83, convex hull=100, v0=130131) After retessellation of defect 43 (v0=130131), euler #=94 (83013,238016,155097) : difference with theory (-21) = -115 CORRECTING DEFECT 44 (vertices=900, convex hull=118, v0=133135) normal vector of length zero at vertex 87213 with 4 faces After retessellation of defect 44 (v0=133135), euler #=95 (83057,238212,155250) : difference with theory (-20) = -115 CORRECTING DEFECT 45 (vertices=24, convex hull=53, v0=135114) After retessellation of defect 45 (v0=135114), euler #=96 (83072,238273,155297) : difference with theory (-19) = -115 CORRECTING DEFECT 46 (vertices=97, convex hull=30, v0=136402) After retessellation of defect 46 (v0=136402), euler #=97 (83078,238301,155320) : difference with theory (-18) = -115 CORRECTING DEFECT 47 (vertices=74, convex hull=24, v0=138982) After retessellation of defect 47 (v0=138982), euler #=98 (83088,238338,155348) : difference with theory (-17) = -115 CORRECTING DEFECT 48 (vertices=83, convex hull=55, v0=139717) After retessellation of defect 48 (v0=139717), euler #=99 (83098,238391,155392) : difference with theory (-16) = -115 CORRECTING DEFECT 49 (vertices=141431, convex hull=17606, v0=149662)