Thu Jul 23 06:00:06 EDT 2020 cd /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert setenv SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running /usr/local/freesurfer/dev/bin/recon-all -all -s bert -i /space/freesurfer/subjects/testsets/bert/raw/003.mgz -i /space/freesurfer/subjects/testsets/bert/raw/002.mgz -i /space/freesurfer/subjects/testsets/bert/raw/001.mgz subjid bert setenv SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos7_x86_64/dev build-stamp.txt: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 Linux nike 3.10.0-1062.7.1.el7.x86_64 #1 SMP Mon Dec 2 17:33:29 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse 7340032 kbytes descriptors 32768 memorylocked unlimited maxproc 2062766 maxlocks unlimited maxsignal 2062766 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 503G 8.3G 35G 3.6G 459G 490G Swap: 23G 3.2G 20G pbsjob 667167.nike.nmr.mgh.harvard.edu ######################################## program versions used dev (freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95) dev ProgramName: lta_convert ProgramArguments: lta_convert -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:06-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_and ProgramArguments: mri_and -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:06-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_annotation2label ProgramArguments: mri_annotation2label -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:06-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_aparc2aseg ProgramArguments: mri_aparc2aseg -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:06-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surf2volseg ProgramArguments: mri_surf2volseg -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:06-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_binarize ProgramArguments: mri_binarize -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:06-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_ca_label ProgramArguments: mri_ca_label -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:06-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_ca_normalize ProgramArguments: mri_ca_normalize -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:06-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_ca_register ProgramArguments: mri_ca_register -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:06-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_cc ProgramArguments: mri_cc -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:06-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_compute_overlap ProgramArguments: mri_compute_overlap -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:06-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_compute_seg_overlap ProgramArguments: mri_compute_seg_overlap -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:06-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_concat ProgramArguments: mri_concat -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:06-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_concatenate_lta ProgramArguments: mri_concatenate_lta -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:06-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:06-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_diff ProgramArguments: mri_diff -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:06-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_edit_wm_with_aseg ProgramArguments: mri_edit_wm_with_aseg -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:07-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_em_register ProgramArguments: mri_em_register -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:07-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_fill ProgramArguments: mri_fill -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:07-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_fuse_segmentations ProgramArguments: mri_fuse_segmentations -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:07-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_fwhm ProgramArguments: mri_fwhm -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:07-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_gcut ProgramArguments: mri_gcut -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:07-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_info ProgramArguments: mri_info -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:07-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_label2label ProgramArguments: mri_label2label -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:07-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_label2vol ProgramArguments: mri_label2vol -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:07-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_log_likelihood ProgramArguments: mri_log_likelihood -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:07-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_mask ProgramArguments: mri_mask -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:07-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_matrix_multiply ProgramArguments: mri_matrix_multiply -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:07-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_normalize ProgramArguments: mri_normalize -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:07-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_normalize_tp2 ProgramArguments: mri_normalize_tp2 -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:07-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_or ProgramArguments: mri_or -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:07-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_relabel_hypointensities ProgramArguments: mri_relabel_hypointensities -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:07-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_relabel_nonwm_hypos ProgramArguments: mri_relabel_nonwm_hypos -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:07-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_remove_neck ProgramArguments: mri_remove_neck -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:07-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 dev ProgramName: mri_robust_register ProgramArguments: mri_robust_register -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:07-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 dev ProgramName: mri_robust_template ProgramArguments: mri_robust_template -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:08-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_anatomical_stats ProgramArguments: mris_anatomical_stats -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:08-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_ca_label ProgramArguments: mris_ca_label -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:08-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_calc ProgramArguments: mris_calc -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:08-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_convert ProgramArguments: mris_convert -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:08-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_curvature ProgramArguments: mris_curvature -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:08-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_curvature_stats ProgramArguments: mris_curvature_stats -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:08-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_diff ProgramArguments: mris_diff -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:08-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_divide_parcellation ProgramArguments: mris_divide_parcellation -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:08-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_segment ProgramArguments: mri_segment -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:08-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_segstats ProgramArguments: mri_segstats -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:08-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_euler_number ProgramArguments: mris_euler_number -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:08-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_fix_topology ProgramArguments: mris_fix_topology -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:08-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:08-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_jacobian ProgramArguments: mris_jacobian -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:08-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_label2annot ProgramArguments: mris_label2annot -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:08-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_left_right_register ProgramArguments: mris_left_right_register -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:08-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_place_surface ProgramArguments: mris_place_surface -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:09-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mrisp_paint ProgramArguments: mrisp_paint -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:09-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_register ProgramArguments: mris_register -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:09-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_smooth ProgramArguments: mris_smooth -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:09-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_sphere ProgramArguments: mris_sphere -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:09-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_surface_stats ProgramArguments: mris_surface_stats -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:09-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_stats2seg ProgramArguments: mri_stats2seg -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:09-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_thickness ProgramArguments: mris_thickness -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:09-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_thickness_diff ProgramArguments: mris_thickness_diff -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:09-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:09-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surf2surf ProgramArguments: mri_surf2surf -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:09-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surf2vol ProgramArguments: mri_surf2vol -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:09-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surfcluster ProgramArguments: mri_surfcluster -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:09-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_volmask ProgramArguments: mris_volmask -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:09-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_tessellate ProgramArguments: mri_tessellate -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:09-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_vol2surf ProgramArguments: mri_vol2surf -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:09-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_vol2vol ProgramArguments: mri_vol2vol -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:09-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_voldiff ProgramArguments: mri_voldiff -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:09-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_watershed ProgramArguments: mri_watershed -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:09-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: tkregister2 ProgramArguments: tkregister2_cmdl -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:09-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 mri_motion_correct.fsl dev mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: dev TimeStamp: 2020/07/23-10:00:10-GMT BuildTime: Jul 23 2020 00:05:05 BuildStamp: freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 User: ah221 Machine: nike Platform: Linux PlatformVersion: 3.10.0-1062.7.1.el7.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 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/dev/average GCA RB_all_2020-01-02.gca GCASkull RB_all_withskull_2020_01_02.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /usr/local/freesurfer/dev/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert mri_convert /autofs/cluster/fssubjects/testsets/bert/raw/003.mgz /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/orig/001.mgz mri_convert /autofs/cluster/fssubjects/testsets/bert/raw/003.mgz /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/orig/001.mgz reading from /autofs/cluster/fssubjects/testsets/bert/raw/003.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) writing to /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/orig/001.mgz... @#@FSTIME 2020:07:23:06:00:10 mri_convert N 2 e 4.27 S 0.06 U 4.09 P 97% M 69280 F 1 R 28335 W 0 c 3 w 511 I 19712 O 17984 L 1.11 1.08 1.05 @#@FSLOADPOST 2020:07:23:06:00:14 mri_convert N 2 1.18 1.10 1.06 /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert mri_convert /autofs/cluster/fssubjects/testsets/bert/raw/002.mgz /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/orig/002.mgz mri_convert /autofs/cluster/fssubjects/testsets/bert/raw/002.mgz /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/orig/002.mgz reading from /autofs/cluster/fssubjects/testsets/bert/raw/002.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) writing to /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/orig/002.mgz... @#@FSTIME 2020:07:23:06:00:15 mri_convert N 2 e 4.26 S 0.07 U 4.07 P 97% M 69276 F 0 R 28292 W 0 c 2 w 520 I 17968 O 17968 L 1.25 1.11 1.06 @#@FSLOADPOST 2020:07:23:06:00:19 mri_convert N 2 1.25 1.11 1.06 /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert mri_convert /autofs/cluster/fssubjects/testsets/bert/raw/001.mgz /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/orig/003.mgz mri_convert /autofs/cluster/fssubjects/testsets/bert/raw/001.mgz /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/orig/003.mgz reading from /autofs/cluster/fssubjects/testsets/bert/raw/001.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) writing to /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/orig/003.mgz... @#@FSTIME 2020:07:23:06:00:20 mri_convert N 2 e 4.24 S 0.07 U 4.05 P 97% M 69276 F 0 R 28229 W 0 c 3 w 375 I 17744 O 17744 L 1.23 1.11 1.06 @#@FSLOADPOST 2020:07:23:06:00:24 mri_convert N 2 1.23 1.11 1.06 #-------------------------------------------- #@# MotionCor Thu Jul 23 06:00:25 EDT 2020 Found 3 runs /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/orig/001.mgz /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/orig/002.mgz /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/orig/003.mgz Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert mri_robust_template --mov /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/orig/001.mgz /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/orig/002.mgz /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/orig/003.mgz --average 1 --template /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --iscaleout /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/orig/001-iscale.txt /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/orig/002-iscale.txt /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/orig/003-iscale.txt --subsample 200 --lta /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/orig/001.lta /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/orig/002.lta /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/orig/003.lta dev --mov: Using /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/orig/001.mgz as movable/source volume. --mov: Using /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/orig/002.mgz as movable/source volume. --mov: Using /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/orig/003.mgz as movable/source volume. Total: 3 input volumes --average: Using method 1 for template computation. --template: Using /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/rawavg.mgz as template output volume. --satit: Will estimate SAT iteratively! --inittp: Using TP 1 as target for initialization --fixtp: Will map everything to init TP! --noit: Will output only first template (no iterations)! --iscale: Enabling intensity scaling! --iscaleout: Will perform intensity scaling and output results --subsample: Will subsample if size is larger than 200 on all axes! --lta: Will output LTA transforms Setting iscale ... reading source '/autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/orig/001.mgz'... converting source '/autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/orig/001.mgz' to bspline ... MRItoBSpline degree 3 reading source '/autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/orig/002.mgz'... converting source '/autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/orig/002.mgz' to bspline ... MRItoBSpline degree 3 reading source '/autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/orig/003.mgz'... converting source '/autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/orig/003.mgz' to bspline ... MRItoBSpline degree 3 MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) : [init] ========================= TP 2 to TP 1 ============================== Register TP 2 ( /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/orig/002.mgz ) to TP 1 ( /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/orig/001.mgz ) - Max Resolution used: 2 -- gpS ( 64 , 64 , 64 ) -- gpT ( 64 , 64 , 64 ) - running loop to estimate saturation parameter: [init] ========================= TP 3 to TP 1 ============================== Register TP 3 ( /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/orig/003.mgz ) to TP 1 ( /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/orig/001.mgz ) - Max Resolution used: 2 -- gpS ( 64 , 64 , 64 ) -- gpT ( 64 , 64 , 64 ) - running loop to estimate saturation parameter: * WARNING: TP 2 to 1 did not converge !! mapping movs and creating initial template... allow intensity scaling using median -- Template : (1, 1, 1)mm and (256, 256, 256) voxels. Writing final template: /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/rawavg.mgz Writing final transforms (warps etc.)... Determinant( lta[ 0 ]) : 1 Determinant( lta[ 1 ]) : 1 Determinant( lta[ 2 ]) : 1 registration took 1 minutes and 46 seconds. Thank you for using RobustTemplate! If you find it useful and use it for a publication, please cite: Within-Subject Template Estimation for Unbiased Longitudinal Image Analysis M. Reuter, N.J. Schmansky, H.D. Rosas, B. Fischl. NeuroImage 2012. http://dx.doi.org/10.1016/j.neuroimage.2012.02.084 http://reuter.mit.edu/papers/reuter-long12.pdf @#@FSTIME 2020:07:23:06:00:26 mri_robust_template N 24 e 106.22 S 7.26 U 98.86 P 99% M 1525152 F 0 R 4260052 W 0 c 34 w 481 I 0 O 89120 L 1.29 1.12 1.07 @#@FSLOADPOST 2020:07:23:06:02:12 mri_robust_template N 24 2.02 1.43 1.18 /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert mri_convert /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/rawavg.mgz /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/orig.mgz --conform mri_convert /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/rawavg.mgz /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/orig.mgz --conform reading from /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/rawavg.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 float to uchar (noscale = 0)... MRIchangeType: Building histogram 0 265.402 1000, flo=0, fhi=0.999, dest_type=0 writing to /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/orig.mgz... @#@FSTIME 2020:07:23:06:02:12 mri_convert N 3 e 5.84 S 0.13 U 5.65 P 99% M 85900 F 0 R 58968 W 0 c 13 w 356 I 0 O 12472 L 2.02 1.43 1.18 @#@FSLOADPOST 2020:07:23:06:02:18 mri_convert N 3 2.02 1.44 1.19 mri_add_xform_to_header -c /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/transforms/talairach.xfm /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/orig.mgz /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/orig.mgz INFO: extension is mgz @#@FSTIME 2020:07:23:06:02:18 mri_add_xform_to_header N 4 e 1.18 S 0.02 U 1.02 P 88% M 19684 F 5 R 5037 W 0 c 8 w 503 I 5736 O 12472 L 2.02 1.44 1.19 @#@FSLOADPOST 2020:07:23:06:02:19 mri_add_xform_to_header N 4 2.02 1.44 1.19 #-------------------------------------------- #@# Talairach Thu Jul 23 06:02:19 EDT 2020 /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50 /usr/bin/bc /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri /usr/local/freesurfer/dev/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50 nIters 1 mri_nu_correct.mni dev Linux nike 3.10.0-1062.7.1.el7.x86_64 #1 SMP Mon Dec 2 17:33:29 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux Thu Jul 23 06:02:19 EDT 2020 Found /dev/shm , will use for temp dir tmpdir is /dev/shm/tmp.mri_nu_correct.mni.25651 cd /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o /dev/shm/tmp.mri_nu_correct.mni.25651/nu0.mgz Using shrink factor: 4 mri_convert /dev/shm/tmp.mri_nu_correct.mni.25651/nu0.mgz orig_nu.mgz --like orig.mgz --conform mri_convert /dev/shm/tmp.mri_nu_correct.mni.25651/nu0.mgz orig_nu.mgz --like orig.mgz --conform reading from /dev/shm/tmp.mri_nu_correct.mni.25651/nu0.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) INFO: transform src into the like-volume: orig.mgz writing to orig_nu.mgz... Thu Jul 23 06:05:19 EDT 2020 mri_nu_correct.mni done @#@FSTIME 2020:07:23:06:02:19 mri_nu_correct.mni N 12 e 179.73 S 0.36 U 179.20 P 99% M 486240 F 6 R 211950 W 0 c 118 w 679 I 6536 O 11968 L 2.02 1.44 1.19 @#@FSLOADPOST 2020:07:23:06:05:19 mri_nu_correct.mni N 12 2.01 1.71 1.34 talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... Started at Thu Jul 23 06:05:19 EDT 2020 Ended at Thu Jul 23 06:05:45 EDT 2020 talairach_avi done @#@FSTIME 2020:07:23:06:05:19 talairach_avi N 4 e 25.73 S 1.50 U 15.38 P 65% M 253964 F 6 R 508229 W 0 c 69 w 11607 I 270760 O 296008 L 2.01 1.71 1.34 @#@FSLOADPOST 2020:07:23:06:05:45 talairach_avi N 4 2.01 1.73 1.36 cp transforms/talairach.auto.xfm transforms/talairach.xfm lta_convert --src orig.mgz --trg /usr/local/freesurfer/dev/average/mni305.cor.mgz --inxfm transforms/talairach.xfm --outlta transforms/talairach.xfm.lta --subject fsaverage --ltavox2vox dev --src: orig.mgz src image (geometry). --trg: /usr/local/freesurfer/dev/average/mni305.cor.mgz trg image (geometry). --inmni: transforms/talairach.xfm input MNI/XFM transform. --outlta: transforms/talairach.xfm.lta output LTA. --s: fsaverage subject name --ltavox2vox: output LTA as VOX_TO_VOX transform. LTA read, type : 1 1.12196 -0.01197 0.04185 -6.33839; 0.02483 1.00998 0.15933 -23.73698; -0.04063 -0.15312 1.10653 -3.03511; 0.00000 0.00000 0.00000 1.00000; setting subject to fsaverage Writing LTA to file transforms/talairach.xfm.lta... lta_convert successful. #-------------------------------------------- #@# Talairach Failure Detection Thu Jul 23 06:05:47 EDT 2020 /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7826, pval=0.8469 >= threshold=0.0050) @#@FSTIME 2020:07:23:06:05:47 talairach_afd N 4 e 0.08 S 0.00 U 0.00 P 8% M 2160 F 4 R 639 W 0 c 1 w 23 I 4296 O 8 L 1.93 1.72 1.35 @#@FSLOADPOST 2020:07:23:06:05:47 talairach_afd N 4 1.93 1.72 1.35 awk -f /usr/local/freesurfer/dev/bin/extract_talairach_avi_QA.awk /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/transforms/talairach_avi.log tal_QC_AZS /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/transforms/talairach_avi.log TalAviQA: 0.97389 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Thu Jul 23 06:05:47 EDT 2020 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4 /usr/bin/bc /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri /usr/local/freesurfer/dev/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4 nIters 2 mri_nu_correct.mni dev Linux nike 3.10.0-1062.7.1.el7.x86_64 #1 SMP Mon Dec 2 17:33:29 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux Thu Jul 23 06:05:47 EDT 2020 Found /dev/shm , will use for temp dir tmpdir is /dev/shm/tmp.mri_nu_correct.mni.26856 cd /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o /dev/shm/tmp.mri_nu_correct.mni.26856/nu0.mgz Using shrink factor: 4 mri_binarize --i /dev/shm/tmp.mri_nu_correct.mni.26856/nu0.mgz --min -1 --o /dev/shm/tmp.mri_nu_correct.mni.26856/ones.mgz dev cwd /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri cmdline mri_binarize --i /dev/shm/tmp.mri_nu_correct.mni.26856/nu0.mgz --min -1 --o /dev/shm/tmp.mri_nu_correct.mni.26856/ones.mgz sysname Linux hostname nike machine x86_64 user ah221 input /dev/shm/tmp.mri_nu_correct.mni.26856/nu0.mgz frame 0 nErode3d 0 nErode2d 0 output /dev/shm/tmp.mri_nu_correct.mni.26856/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.26856/ones.mgz --i orig.mgz --sum /dev/shm/tmp.mri_nu_correct.mni.26856/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.26856/input.mean.dat dev cwd cmdline mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.26856/ones.mgz --i orig.mgz --sum /dev/shm/tmp.mri_nu_correct.mni.26856/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.26856/input.mean.dat sysname Linux hostname nike machine x86_64 user ah221 whitesurfname white UseRobust 0 Loading /dev/shm/tmp.mri_nu_correct.mni.26856/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.26856/input.mean.dat mri_segstats done mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.26856/ones.mgz --i /dev/shm/tmp.mri_nu_correct.mni.26856/nu0.mgz --sum /dev/shm/tmp.mri_nu_correct.mni.26856/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.26856/output.mean.dat dev cwd cmdline mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.26856/ones.mgz --i /dev/shm/tmp.mri_nu_correct.mni.26856/nu0.mgz --sum /dev/shm/tmp.mri_nu_correct.mni.26856/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.26856/output.mean.dat sysname Linux hostname nike machine x86_64 user ah221 whitesurfname white UseRobust 0 Loading /dev/shm/tmp.mri_nu_correct.mni.26856/ones.mgz Loading /dev/shm/tmp.mri_nu_correct.mni.26856/nu0.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.26856/output.mean.dat mri_segstats done mris_calc -o /dev/shm/tmp.mri_nu_correct.mni.26856/nu0.mgz /dev/shm/tmp.mri_nu_correct.mni.26856/nu0.mgz mul 1.16495328252684911009 Saving result to '/dev/shm/tmp.mri_nu_correct.mni.26856/nu0.mgz' (type = MGH ) [ ok ] mri_convert /dev/shm/tmp.mri_nu_correct.mni.26856/nu0.mgz nu.mgz --like orig.mgz mri_convert /dev/shm/tmp.mri_nu_correct.mni.26856/nu0.mgz nu.mgz --like orig.mgz reading from /dev/shm/tmp.mri_nu_correct.mni.26856/nu0.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) 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 ( 8, 167) to ( 3, 110) Thu Jul 23 06:09:11 EDT 2020 mri_nu_correct.mni done @#@FSTIME 2020:07:23:06:05:47 mri_nu_correct.mni N 9 e 203.51 S 1.21 U 201.94 P 99% M 610284 F 8 R 701622 W 0 c 113 w 1139 I 27288 O 27400 L 1.93 1.72 1.35 @#@FSLOADPOST 2020:07:23:06:09:11 mri_nu_correct.mni N 9 2.11 1.90 1.50 mri_add_xform_to_header -c /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz @#@FSTIME 2020:07:23:06:09:11 mri_add_xform_to_header N 4 e 0.73 S 0.02 U 0.65 P 92% M 19760 F 0 R 5062 W 0 c 2 w 283 I 0 O 8888 L 2.11 1.90 1.50 @#@FSLOADPOST 2020:07:23:06:09:12 mri_add_xform_to_header N 4 2.11 1.90 1.50 #-------------------------------------------- #@# Intensity Normalization Thu Jul 23 06:09:12 EDT 2020 /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/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 mri_src from nu.mgz... normalizing image... talairach transform 1.12196 -0.01197 0.04185 -6.33839; 0.02483 1.00998 0.15933 -23.73698; -0.04063 -0.15312 1.10653 -3.03511; 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 = 20 Starting OpenSpline(): npoints = 20 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 110 white matter peak found at 110 gm peak at 80 (80), valley at 21 (21) csf peak at 40, setting threshold to 66 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 79 (79), valley at 22 (22) csf peak at 40, setting threshold to 66 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 1 minutes and 49 seconds. @#@FSTIME 2020:07:23:06:09:12 mri_normalize N 7 e 109.75 S 0.63 U 109.06 P 99% M 578756 F 2 R 490041 W 0 c 32 w 327 I 1728 O 8608 L 2.11 1.90 1.50 @#@FSLOADPOST 2020:07:23:06:11:01 mri_normalize N 7 2.11 1.96 1.56 #-------------------------------------------- #@# Skull Stripping Thu Jul 23 06:11:02 EDT 2020 /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri mri_em_register -skull nu.mgz /usr/local/freesurfer/dev/average/RB_all_withskull_2020_01_02.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/dev/average/RB_all_withskull_2020_01_02.gca'... GCAread took 0 minutes and 1 seconds. average std = 23.0 using min determinant for regularization = 52.8 0 singular and 9205 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 8.9 or > 556.0 total sample mean = 77.3 (1403 zeros) ************************************************ spacing=8, using 3292 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3292, 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=7.0 skull bounding box = (49, 45, 10) --> (204, 255, 206) finding center of left hemi white matter using (101, 115, 108) as brain centroid of Right_Cerebral_White_Matter... MRImask(): AllowDiffGeom = 1 mean wm in atlas = 108, using box (82,89,84) --> (120, 140,132) to find MRI wm before smoothing, mri peak at 109 robust fit to distribution - 109 +- 3.5 after smoothing, mri peak at 109, scaling input intensities by 0.991 scaling channel 0 by 0.990826 initial log_p = -4.259 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.238800 @ (0.000, 0.000, 0.000) max log p = -4.238800 @ (0.000, 0.000, 0.000) max log p = -4.238800 @ (0.000, 0.000, 0.000) max log p = -4.203619 @ (-1.316, 1.316, -3.947) max log p = -4.201626 @ (0.658, 0.658, 1.974) max log p = -4.199538 @ (-1.645, -2.961, -2.303) max log p = -4.199538 @ (0.000, 0.000, 0.000) max log p = -4.199538 @ (0.000, 0.000, 0.000) Found translation: (-2.3, -1.0, -4.3): log p = -4.200 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.126, old_max_log_p =-4.200 (thresh=-4.2) 1.06375 0.00000 0.00000 -10.42470; 0.00000 0.99317 0.41138 -47.50136; 0.00000 -0.38268 0.92388 51.77216; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 25 seconds. **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.092, old_max_log_p =-4.126 (thresh=-4.1) 1.06375 0.00000 0.00000 -10.42470; 0.00000 1.05837 0.15825 -25.66788; 0.00000 -0.11259 0.99887 12.22094; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 24 seconds. **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.092, old_max_log_p =-4.092 (thresh=-4.1) 1.06375 0.00000 0.00000 -10.42470; 0.00000 1.05837 0.15825 -25.66788; 0.00000 -0.11259 0.99887 12.22094; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 iteration took 1 minutes and 24 seconds. **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.038, old_max_log_p =-4.092 (thresh=-4.1) 1.08311 0.03670 0.00442 -18.46219; -0.03415 1.07980 0.13008 -19.30501; 0.00000 -0.07238 0.96627 12.28473; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 23 seconds. **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.038, old_max_log_p =-4.038 (thresh=-4.0) 1.08311 0.03670 0.00442 -18.46219; -0.03415 1.07980 0.13008 -19.30501; 0.00000 -0.07238 0.96627 12.28473; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 iteration took 1 minutes and 23 seconds. **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.019, old_max_log_p =-4.038 (thresh=-4.0) 1.08565 0.03679 0.00443 -18.79867; -0.03415 1.07980 0.13008 -19.77376; 0.00000 -0.07221 0.96401 12.51649; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 22 seconds. **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.019, old_max_log_p =-4.019 (thresh=-4.0) 1.08565 0.03679 0.00443 -18.79867; -0.03415 1.07980 0.13008 -19.77376; 0.00000 -0.07221 0.96401 12.51649; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 3292 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.08565 0.03679 0.00443 -18.79867; -0.03415 1.07980 0.13008 -19.77376; 0.00000 -0.07221 0.96401 12.51649; 0.00000 0.00000 0.00000 1.00000; nsamples 3292 Quasinewton: input matrix 1.08565 0.03679 0.00443 -18.79867; -0.03415 1.07980 0.13008 -19.77376; 0.00000 -0.07221 0.96401 12.51649; 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: 1.08565 0.03679 0.00443 -18.79867; -0.03415 1.07980 0.13008 -19.77376; 0.00000 -0.07221 0.96401 12.51649; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -4.019 (old=-4.259) transform before final EM align: 1.08565 0.03679 0.00443 -18.79867; -0.03415 1.07980 0.13008 -19.77376; 0.00000 -0.07221 0.96401 12.51649; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 364986 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.08565 0.03679 0.00443 -18.79867; -0.03415 1.07980 0.13008 -19.77376; 0.00000 -0.07221 0.96401 12.51649; 0.00000 0.00000 0.00000 1.00000; nsamples 364986 Quasinewton: input matrix 1.08565 0.03679 0.00443 -18.79867; -0.03415 1.07980 0.13008 -19.77376; 0.00000 -0.07221 0.96401 12.51649; 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) = 4.4 tol 0.000000 final transform: 1.08565 0.03679 0.00443 -18.79867; -0.03415 1.07980 0.13008 -19.77376; 0.00000 -0.07221 0.96401 12.51649; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach_with_skull.lta... #VMPC# mri_em_register VmPeak 904304 FSRUNTIME@ mri_em_register 0.1822 hours 1 threads registration took 10 minutes and 56 seconds. @#@FSTIME 2020:07:23:06:11:02 mri_em_register N 4 e 656.09 S 1.93 U 654.10 P 99% M 625292 F 2 R 957322 W 0 c 174 w 46 I 151640 O 32 L 2.11 1.96 1.56 @#@FSLOADPOST 2020:07:23:06:21:58 mri_em_register N 4 2.17 2.10 1.84 mri_watershed -T1 -brain_atlas /usr/local/freesurfer/dev/average/RB_all_withskull_2020_01_02.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=129 y=116 z=112 r=86 first estimation of the main basin volume: 2707500 voxels Looking for seedpoints 2 found in the cerebellum 18 found in the rest of the brain global maximum in x=157, y=108, z=70, Imax=255 CSF=14, 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=9817693645 voxels, voxel volume =1.000 = 9817693645 mmm3 = 9817693.184 cm3 done. PostAnalyze...Basin Prior 44 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=127,y=120, z=106, r=10158 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=16 , nb = 43560 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=28 , nb = 2556 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=19 , nb = 2448 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=17 , nb = 19332 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=14 , nb = 18684 OTHER CSF_MIN=1, CSF_intensity=2, CSF_MAX=6 , nb = 540 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 16, 32, 58, 79 after analyzing : 16, 49, 58, 56 RIGHT_CER before analyzing : 28, 36, 49, 90 after analyzing : 28, 44, 49, 55 LEFT_CER before analyzing : 19, 37, 64, 88 after analyzing : 19, 55, 64, 63 RIGHT_BRAIN before analyzing : 17, 33, 57, 79 after analyzing : 17, 49, 57, 56 LEFT_BRAIN before analyzing : 14, 30, 59, 79 after analyzing : 14, 49, 59, 56 OTHER before analyzing : 6, 9, 21, 33 after analyzing : 6, 19, 25, 22 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...69 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.009 curvature mean = 71.899, std = 8.821 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 2.67, sigma = 4.18 after rotation: sse = 2.67, sigma = 4.18 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 2.68, its var is 3.37 before Erosion-Dilatation 0.12% of inacurate vertices after Erosion-Dilatation 0.00% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...47 iterations mri_strip_skull: done peeling brain Brain Size = 1805432 voxels, voxel volume = 1.000 mm3 = 1805432 mmm3 = 1805.432 cm3 MRImask(): AllowDiffGeom = 1 ****************************** Saving brainmask.auto.mgz done mri_watershed utimesec 14.901963 mri_watershed stimesec 0.487998 mri_watershed ru_maxrss 811068 mri_watershed ru_ixrss 0 mri_watershed ru_idrss 0 mri_watershed ru_isrss 0 mri_watershed ru_minflt 367240 mri_watershed ru_majflt 3 mri_watershed ru_nswap 0 mri_watershed ru_inblock 10120 mri_watershed ru_oublock 2744 mri_watershed ru_msgsnd 0 mri_watershed ru_msgrcv 0 mri_watershed ru_nsignals 0 mri_watershed ru_nvcsw 143 mri_watershed ru_nivcsw 5 mri_watershed done @#@FSTIME 2020:07:23:06:21:58 mri_watershed N 6 e 15.75 S 0.55 U 14.90 P 98% M 811068 F 3 R 367266 W 0 c 5 w 145 I 10120 O 2744 L 2.17 2.10 1.84 @#@FSLOADPOST 2020:07:23:06:22:14 mri_watershed N 6 2.13 2.10 1.84 cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Thu Jul 23 06:22:15 EDT 2020 /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /usr/local/freesurfer/dev/average/RB_all_2020-01-02.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/dev/average/RB_all_2020-01-02.gca'... GCAread took 0 minutes and 1 seconds. average std = 7.2 using min determinant for regularization = 5.2 0 singular and 884 ill-conditioned covariance matrices regularized reading 'nu.mgz'... MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 freeing gibbs priors...done. accounting for voxel sizes in initial transform bounding unknown intensity as < 5.9 or > 519.0 total sample mean = 79.1 (1017 zeros) ************************************************ spacing=8, using 2841 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2841, 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=21.0 skull bounding box = (65, 59, 26) --> (191, 180, 206) finding center of left hemi white matter using (107, 99, 116) as brain centroid of Right_Cerebral_White_Matter... MRImask(): AllowDiffGeom = 1 mean wm in atlas = 107, using box (92,84,94) --> (122, 113,138) to find MRI wm before smoothing, mri peak at 109 robust fit to distribution - 108 +- 3.5 after smoothing, mri peak at 108, scaling input intensities by 0.991 scaling channel 0 by 0.990741 initial log_p = -3.861 ************************************************ First Search limited to translation only. ************************************************ max log p = -3.829435 @ (0.000, 0.000, 0.000) max log p = -3.829435 @ (0.000, 0.000, 0.000) max log p = -3.787157 @ (-2.632, -2.632, -2.632) max log p = -3.761957 @ (-1.316, 3.947, 1.316) max log p = -3.746438 @ (0.658, 0.658, -1.974) max log p = -3.728484 @ (-0.987, -0.329, -0.987) max log p = -3.728484 @ (0.000, 0.000, 0.000) max log p = -3.728484 @ (0.000, 0.000, 0.000) Found translation: (-4.3, 1.6, -4.3): log p = -3.728 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.651, old_max_log_p =-3.728 (thresh=-3.7) 1.06375 0.00000 0.00000 -12.63257; 0.00000 1.06580 0.11927 -19.18014; 0.00000 -0.14032 0.90593 22.55010; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 15 seconds. **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.651, old_max_log_p =-3.651 (thresh=-3.6) 1.06375 0.00000 0.00000 -12.63257; 0.00000 1.06580 0.11927 -19.18014; 0.00000 -0.14032 0.90593 22.55010; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.2500 iteration took 1 minutes and 14 seconds. **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.488, old_max_log_p =-3.651 (thresh=-3.6) 1.10364 0.00000 0.00000 -14.11138; 0.00000 1.03383 0.17480 -23.45563; 0.00000 -0.20579 0.87939 35.03963; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 14 seconds. **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.478, old_max_log_p =-3.488 (thresh=-3.5) 1.10305 0.03383 0.00572 -18.70644; -0.03543 1.01391 0.17143 -16.18003; 0.00000 -0.20193 0.86290 38.23428; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 14 seconds. **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.475, old_max_log_p =-3.478 (thresh=-3.5) 1.10305 0.03383 0.00572 -18.70644; -0.03543 1.01391 0.17143 -16.18003; 0.00000 -0.20572 0.87908 36.97453; 0.00000 0.00000 0.00000 1.00000; reducing scale to 0.0625 iteration took 1 minutes and 14 seconds. **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.456, old_max_log_p =-3.475 (thresh=-3.5) 1.10305 0.03383 0.00572 -18.70644; -0.03552 1.01628 0.17183 -16.49754; 0.00000 -0.20524 0.87702 37.13496; 0.00000 0.00000 0.00000 1.00000; iteration took 1 minutes and 13 seconds. **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.456, old_max_log_p =-3.456 (thresh=-3.5) 1.10305 0.03383 0.00572 -18.70644; -0.03552 1.01628 0.17183 -16.49754; 0.00000 -0.20524 0.87702 37.13496; 0.00000 0.00000 0.00000 1.00000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2841 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.10305 0.03383 0.00572 -18.70644; -0.03552 1.01628 0.17183 -16.49754; 0.00000 -0.20524 0.87702 37.13496; 0.00000 0.00000 0.00000 1.00000; nsamples 2841 Quasinewton: input matrix 1.10305 0.03383 0.00572 -18.70644; -0.03552 1.01628 0.17183 -16.49754; 0.00000 -0.20524 0.87702 37.13496; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 4 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.10305 0.03383 0.00572 -18.70644; -0.03552 1.01628 0.17183 -16.49754; 0.00000 -0.20524 0.87702 37.13496; 0.00000 0.00000 0.00000 1.00000; pass 1, spacing 8: log(p) = -3.456 (old=-3.861) transform before final EM align: 1.10305 0.03383 0.00572 -18.70644; -0.03552 1.01628 0.17183 -16.49754; 0.00000 -0.20524 0.87702 37.13496; 0.00000 0.00000 0.00000 1.00000; ************************************************** EM alignment process ... Computing final MAP estimate using 315638 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.10305 0.03383 0.00572 -18.70644; -0.03552 1.01628 0.17183 -16.49754; 0.00000 -0.20524 0.87702 37.13496; 0.00000 0.00000 0.00000 1.00000; nsamples 315638 Quasinewton: input matrix 1.10305 0.03383 0.00572 -18.70644; -0.03552 1.01628 0.17183 -16.49754; 0.00000 -0.20524 0.87702 37.13496; 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) = 3.9 tol 0.000000 final transform: 1.10305 0.03383 0.00572 -18.70644; -0.03552 1.01628 0.17183 -16.49754; 0.00000 -0.20524 0.87702 37.13496; 0.00000 0.00000 0.00000 1.00000; writing output transformation to transforms/talairach.lta... #VMPC# mri_em_register VmPeak 891752 FSRUNTIME@ mri_em_register 0.1583 hours 1 threads registration took 9 minutes and 30 seconds. @#@FSTIME 2020:07:23:06:22:15 mri_em_register N 7 e 569.84 S 1.87 U 567.95 P 99% M 612588 F 0 R 980145 W 0 c 147 w 57 I 139952 O 24 L 2.13 2.10 1.84 @#@FSLOADPOST 2020:07:23:06:31:45 mri_em_register N 7 2.11 2.09 1.95 #-------------------------------------- #@# CA Normalize Thu Jul 23 06:31:45 EDT 2020 /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /usr/local/freesurfer/dev/average/RB_all_2020-01-02.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/dev/average/RB_all_2020-01-02.gca'... reading transform from 'transforms/talairach.lta'... reading input volume from nu.mgz... MRImask(): AllowDiffGeom = 1 resetting wm mean[0]: 98 --> 107 resetting gm mean[0]: 61 --> 61 input volume #1 is the most T1-like using real data threshold=16.0 skull bounding box = (65, 58, 25) --> (191, 181, 206) finding center of left hemi white matter using (107, 99, 116) as brain centroid of Right_Cerebral_White_Matter... MRImask(): AllowDiffGeom = 1 mean wm in atlas = 107, using box (92,84,94) --> (122, 114,138) to find MRI wm before smoothing, mri peak at 109 robust fit to distribution - 108 +- 3.5 after smoothing, mri peak at 108, scaling input intensities by 0.991 scaling channel 0 by 0.990741 using 246437 sample points... INFO: compute sample coordinates transform 1.10305 0.03383 0.00572 -18.70644; -0.03552 1.01628 0.17183 -16.49754; 0.00000 -0.20524 0.87702 37.13496; 0.00000 0.00000 0.00000 1.00000; INFO: transform used finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (126, 56, 20) --> (187, 166, 206) Left_Cerebral_White_Matter: limiting intensities to 98.0 --> 132.0 6 of 8241 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (68, 57, 19) --> (129, 166, 206) Right_Cerebral_White_Matter: limiting intensities to 98.0 --> 132.0 6 of 8374 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (128, 140, 52) --> (171, 186, 113) Left_Cerebellum_White_Matter: limiting intensities to 98.0 --> 132.0 0 of 104 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (86, 139, 49) --> (127, 182, 113) Right_Cerebellum_White_Matter: limiting intensities to 97.0 --> 132.0 1 of 34 (2.9%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (111, 131, 93) --> (143, 198, 125) Brain_Stem: limiting intensities to 93.0 --> 132.0 0 of 690 (0.0%) samples deleted using 17443 total control points for intensity normalization... bias field = 0.973 +- 0.054 238 of 17430 control points discarded finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (126, 56, 20) --> (187, 166, 206) Left_Cerebral_White_Matter: limiting intensities to 93.0 --> 132.0 7 of 8459 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (68, 57, 19) --> (129, 166, 206) Right_Cerebral_White_Matter: limiting intensities to 92.0 --> 132.0 5 of 8549 (0.1%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (128, 140, 52) --> (171, 186, 113) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 19 of 149 (12.8%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (86, 139, 49) --> (127, 182, 113) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 24 of 74 (32.4%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (111, 131, 93) --> (143, 198, 125) Brain_Stem: limiting intensities to 88.0 --> 132.0 2 of 744 (0.3%) samples deleted using 17975 total control points for intensity normalization... bias field = 1.029 +- 0.048 185 of 17830 control points discarded finding control points in Left_Cerebral_White_Matter.... found 40230 control points for structure... bounding box (126, 56, 20) --> (187, 166, 206) Left_Cerebral_White_Matter: limiting intensities to 93.0 --> 132.0 5 of 8442 (0.1%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 39478 control points for structure... bounding box (68, 57, 19) --> (129, 166, 206) Right_Cerebral_White_Matter: limiting intensities to 92.0 --> 132.0 17 of 8514 (0.2%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3105 control points for structure... bounding box (128, 140, 52) --> (171, 186, 113) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 58 of 184 (31.5%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2710 control points for structure... bounding box (86, 139, 49) --> (127, 182, 113) Right_Cerebellum_White_Matter: limiting intensities to 88.0 --> 132.0 56 of 107 (52.3%) samples deleted finding control points in Brain_Stem.... found 3475 control points for structure... bounding box (111, 131, 93) --> (143, 198, 125) Brain_Stem: limiting intensities to 88.0 --> 132.0 9 of 773 (1.2%) samples deleted using 18020 total control points for intensity normalization... bias field = 1.023 +- 0.042 139 of 17778 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 5 seconds. @#@FSTIME 2020:07:23:06:31:45 mri_ca_normalize N 8 e 64.70 S 0.86 U 63.79 P 99% M 711364 F 2 R 720297 W 0 c 28 w 111 I 1712 O 4216 L 2.11 2.09 1.95 @#@FSLOADPOST 2020:07:23:06:32:49 mri_ca_normalize N 8 2.07 2.08 1.96 #-------------------------------------- #@# CA Reg Thu Jul 23 06:32:49 EDT 2020 /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /usr/local/freesurfer/dev/average/RB_all_2020-01-02.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'... MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 reading GCA '/usr/local/freesurfer/dev/average/RB_all_2020-01-02.gca'... label assignment complete, 0 changed (0.00%) freeing gibbs priors...done. average std[0] = 5.0 Starting GCAMregister() label assignment complete, 0 changed (0.00%) npasses = 1, nlevels = 6 #pass# 1 of 1 ************************ enabling zero nodes setting smoothness cost coefficient to 0.156 #GCAMreg# pass 0 level1 5 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.16 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.889548 #FOTS# QuadFit found better minimum quadopt=(dt=293.409,rms=0.797055) vs oldopt=(dt=369.92,rms=0.803243) #GCMRL# 0 dt 293.408907 rms 0.797 10.398% neg 0 invalid 762 tFOTS 14.1870 tGradient 7.5430 tsec 22.7130 #FOTS# QuadFit found better minimum quadopt=(dt=202.131,rms=0.776834) vs oldopt=(dt=92.48,rms=0.7832) #GCMRL# 1 dt 202.131274 rms 0.777 2.537% neg 0 invalid 762 tFOTS 14.1350 tGradient 8.0080 tsec 23.1840 #FOTS# QuadFit found better minimum quadopt=(dt=221.952,rms=0.767913) vs oldopt=(dt=369.92,rms=0.76985) #GCMRL# 2 dt 221.952000 rms 0.768 1.148% neg 0 invalid 762 tFOTS 13.2270 tGradient 7.9180 tsec 22.1340 #FOTS# QuadFit found better minimum quadopt=(dt=152.523,rms=0.762769) vs oldopt=(dt=92.48,rms=0.763861) #GCMRL# 3 dt 152.523364 rms 0.763 0.670% neg 0 invalid 762 tFOTS 14.1270 tGradient 7.8420 tsec 22.9500 #FOTS# QuadFit found better minimum quadopt=(dt=295.936,rms=0.758727) vs oldopt=(dt=369.92,rms=0.759253) #GCMRL# 4 dt 295.936000 rms 0.759 0.530% neg 0 invalid 762 tFOTS 14.0860 tGradient 7.6960 tsec 22.7680 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.75519) vs oldopt=(dt=92.48,rms=0.755453) #GCMRL# 5 dt 129.472000 rms 0.755 0.466% neg 0 invalid 762 tFOTS 14.0650 tGradient 7.7080 tsec 22.7590 #FOTS# QuadFit found better minimum quadopt=(dt=295.936,rms=0.752683) vs oldopt=(dt=369.92,rms=0.752914) #GCMRL# 6 dt 295.936000 rms 0.753 0.332% neg 0 invalid 762 tFOTS 14.1210 tGradient 8.1140 tsec 23.2230 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.750634) vs oldopt=(dt=92.48,rms=0.750784) #GCMRL# 7 dt 129.472000 rms 0.751 0.272% neg 0 invalid 762 tFOTS 14.9100 tGradient 7.9390 tsec 23.8350 #FOTS# QuadFit found better minimum quadopt=(dt=295.936,rms=0.748842) vs oldopt=(dt=369.92,rms=0.748922) #GCMRL# 8 dt 295.936000 rms 0.749 0.000% neg 0 invalid 762 tFOTS 14.0820 tGradient 7.6390 tsec 22.7290 #GCAMreg# pass 0 level1 5 level2 1 tsec 220.084 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.16 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.749471 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.74515) vs oldopt=(dt=92.48,rms=0.745875) #GCMRL# 10 dt 129.472000 rms 0.745 0.577% neg 0 invalid 762 tFOTS 14.1450 tGradient 7.6340 tsec 22.7760 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.741108) vs oldopt=(dt=369.92,rms=0.74187) #GCMRL# 11 dt 517.888000 rms 0.741 0.542% neg 0 invalid 762 tFOTS 14.0500 tGradient 7.7260 tsec 22.7660 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.740266) vs oldopt=(dt=92.48,rms=0.740381) #GCMRL# 12 dt 129.472000 rms 0.740 0.000% neg 0 invalid 762 tFOTS 14.0890 tGradient 7.9150 tsec 23.0130 #GCMRL# 13 dt 129.472000 rms 0.740 0.055% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7220 tsec 8.7070 #GCMRL# 14 dt 129.472000 rms 0.739 0.119% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7950 tsec 8.7790 #GCMRL# 15 dt 129.472000 rms 0.738 0.164% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.8630 tsec 8.8470 #GCMRL# 16 dt 129.472000 rms 0.736 0.210% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.9120 tsec 8.9000 #GCMRL# 17 dt 129.472000 rms 0.735 0.231% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7420 tsec 8.7250 #GCMRL# 18 dt 129.472000 rms 0.733 0.240% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.5970 tsec 8.5810 #GCMRL# 19 dt 129.472000 rms 0.731 0.229% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7350 tsec 8.7200 #GCMRL# 20 dt 129.472000 rms 0.730 0.210% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.6270 tsec 8.6270 #GCMRL# 21 dt 129.472000 rms 0.728 0.195% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.9230 tsec 8.9660 #GCMRL# 22 dt 129.472000 rms 0.727 0.186% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.6820 tsec 8.6670 #GCMRL# 23 dt 129.472000 rms 0.725 0.176% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.8470 tsec 8.8310 #GCMRL# 24 dt 129.472000 rms 0.724 0.153% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.6640 tsec 8.6480 #GCMRL# 25 dt 129.472000 rms 0.723 0.137% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.5790 tsec 8.5650 #GCMRL# 26 dt 129.472000 rms 0.722 0.137% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.6760 tsec 8.6600 #GCMRL# 27 dt 129.472000 rms 0.721 0.136% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7050 tsec 8.6940 #GCMRL# 28 dt 129.472000 rms 0.720 0.144% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7480 tsec 8.7440 #GCMRL# 29 dt 129.472000 rms 0.719 0.132% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7260 tsec 8.7100 #GCMRL# 30 dt 129.472000 rms 0.719 0.120% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7150 tsec 8.6990 #GCMRL# 31 dt 129.472000 rms 0.718 0.104% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7380 tsec 8.7460 #FOTS# QuadFit found better minimum quadopt=(dt=73.984,rms=0.717796) vs oldopt=(dt=92.48,rms=0.717797) setting smoothness cost coefficient to 0.615 #GCAMreg# pass 0 level1 4 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.62 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.732704 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.730769) vs oldopt=(dt=25.92,rms=0.73091) #GCMRL# 33 dt 36.288000 rms 0.731 0.264% neg 0 invalid 762 tFOTS 14.0850 tGradient 4.7520 tsec 19.8250 #FOTS# QuadFit found better minimum quadopt=(dt=77.2571,rms=0.729068) vs oldopt=(dt=103.68,rms=0.729238) #GCMRL# 34 dt 77.257143 rms 0.729 0.000% neg 0 invalid 762 tFOTS 14.1230 tGradient 4.6400 tsec 19.7730 #GCMRL# 35 dt 77.257143 rms 0.725 0.519% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.7800 tsec 5.7650 #GCMRL# 36 dt 77.257143 rms 0.721 0.601% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.8460 tsec 5.8290 #GCMRL# 37 dt 77.257143 rms 0.718 0.471% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.8290 tsec 5.8160 #GCMRL# 38 dt 77.257143 rms 0.714 0.457% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.9410 tsec 5.9260 #GCMRL# 39 dt 77.257143 rms 0.710 0.554% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6680 tsec 5.6530 #GCMRL# 40 dt 77.257143 rms 0.706 0.560% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.7610 tsec 5.7470 #GCMRL# 41 dt 77.257143 rms 0.704 0.394% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.6830 tsec 5.6680 #GCMRL# 42 dt 77.257143 rms 0.702 0.187% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.7500 tsec 5.7350 #GCMRL# 43 dt 77.257143 rms 0.702 0.098% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.8280 tsec 5.8170 #GCMRL# 44 dt 77.257143 rms 0.701 0.068% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.7450 tsec 5.7540 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.700104) vs oldopt=(dt=103.68,rms=0.700209) #GCMRL# 45 dt 145.152000 rms 0.700 0.135% neg 0 invalid 762 tFOTS 14.1320 tGradient 4.7770 tsec 19.8930 #FOTS# QuadFit found better minimum quadopt=(dt=82.944,rms=0.699638) vs oldopt=(dt=103.68,rms=0.699651) #GCMRL# 46 dt 82.944000 rms 0.700 0.000% neg 0 invalid 762 tFOTS 14.0890 tGradient 4.5530 tsec 19.6510 #GCAMreg# pass 0 level1 4 level2 1 tsec 147.715 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.62 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.700401 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.698848) vs oldopt=(dt=25.92,rms=0.698982) #GCMRL# 48 dt 36.288000 rms 0.699 0.222% neg 0 invalid 762 tFOTS 13.2690 tGradient 4.8060 tsec 19.0620 setting smoothness cost coefficient to 2.353 #GCAMreg# pass 0 level1 3 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.35 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.745686 #FOTS# QuadFit found better minimum quadopt=(dt=2.8,rms=0.743242) vs oldopt=(dt=2,rms=0.74358) #GCMRL# 50 dt 2.800000 rms 0.743 0.328% neg 0 invalid 762 tFOTS 13.2630 tGradient 4.0930 tsec 18.3400 #FOTS# QuadFit found better minimum quadopt=(dt=2.8,rms=0.742711) vs oldopt=(dt=2,rms=0.742763) #GCMRL# 51 dt 2.800000 rms 0.743 0.000% neg 0 invalid 762 tFOTS 13.2640 tGradient 4.0700 tsec 18.3430 #GCAMreg# pass 0 level1 3 level2 1 tsec 46.827 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.35 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.743421 #FOTS# QuadFit found better minimum quadopt=(dt=1.6,rms=0.742577) vs oldopt=(dt=2,rms=0.742592) #GCMRL# 53 dt 1.600000 rms 0.743 0.114% neg 0 invalid 762 tFOTS 13.3050 tGradient 4.0880 tsec 18.3770 #FOTS# QuadFit found better minimum quadopt=(dt=0.175,rms=0.742586) vs oldopt=(dt=0.125,rms=0.742586) setting smoothness cost coefficient to 8.000 #GCAMreg# pass 0 level1 2 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=8.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.839154 #FOTS# QuadFit found better minimum quadopt=(dt=2.73116,rms=0.813217) vs oldopt=(dt=2.88,rms=0.813293) #GCMRL# 55 dt 2.731159 rms 0.813 3.091% neg 0 invalid 762 tFOTS 13.2640 tGradient 3.8690 tsec 18.1180 #FOTS# QuadFit found better minimum quadopt=(dt=2.9038,rms=0.806091) vs oldopt=(dt=2.88,rms=0.806091) #GCMRL# 56 dt 2.903803 rms 0.806 0.876% neg 0 invalid 762 tFOTS 13.2510 tGradient 3.8410 tsec 18.0790 #FOTS# QuadFit found better minimum quadopt=(dt=2.77733,rms=0.802489) vs oldopt=(dt=2.88,rms=0.802493) #GCMRL# 57 dt 2.777328 rms 0.802 0.447% neg 0 invalid 762 tFOTS 13.2950 tGradient 3.9990 tsec 18.2760 #FOTS# QuadFit found better minimum quadopt=(dt=1.96407,rms=0.801228) vs oldopt=(dt=2.88,rms=0.801493) #GCMRL# 58 dt 1.964072 rms 0.801 0.000% neg 0 invalid 762 tFOTS 13.2570 tGradient 3.8340 tsec 18.0990 #GCMRL# 59 dt 1.964072 rms 0.800 0.134% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7470 tsec 4.7320 #GCMRL# 60 dt 1.964072 rms 0.800 0.066% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.9070 tsec 4.8920 #GCMRL# 61 dt 1.964072 rms 0.800 -0.085% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7450 tsec 5.6560 #FOTS# QuadFit found better minimum quadopt=(dt=1.008,rms=0.799556) vs oldopt=(dt=0.72,rms=0.799569) #GCMRL# 62 dt 1.008000 rms 0.800 0.011% neg 0 invalid 762 tFOTS 14.0710 tGradient 3.7620 tsec 18.8170 #FOTS# QuadFit found better minimum quadopt=(dt=2.304,rms=0.799462) vs oldopt=(dt=2.88,rms=0.799473) #GCMRL# 63 dt 2.304000 rms 0.799 0.012% neg 0 invalid 762 tFOTS 14.1670 tGradient 3.9710 tsec 19.1190 #GCAMreg# pass 0 level1 2 level2 1 tsec 148.786 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=8.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.799985 #GCMRL# 65 dt 0.000000 rms 0.799 0.075% neg 0 invalid 762 tFOTS 12.4140 tGradient 3.8520 tsec 17.2490 setting smoothness cost coefficient to 20.000 #GCAMreg# pass 0 level1 1 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=20.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.846008 #GCMRL# 67 dt 0.000000 rms 0.845 0.067% neg 0 invalid 762 tFOTS 12.4760 tGradient 3.7310 tsec 17.1910 #GCAMreg# pass 0 level1 1 level2 1 tsec 39.423 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=20.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.846008 #GCMRL# 69 dt 0.000000 rms 0.845 0.067% neg 0 invalid 762 tFOTS 12.4290 tGradient 3.7090 tsec 17.1230 resetting metric properties... setting smoothness cost coefficient to 40.000 #GCAMreg# pass 0 level1 0 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=40.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.767772 #FOTS# QuadFit found better minimum quadopt=(dt=0.203061,rms=0.763114) vs oldopt=(dt=0.32,rms=0.764118) #GCMRL# 71 dt 0.203061 rms 0.763 0.607% neg 0 invalid 762 tFOTS 13.2680 tGradient 3.1840 tsec 17.4350 #GCMRL# 72 dt 0.020000 rms 0.763 0.000% neg 0 invalid 762 tFOTS 13.2610 tGradient 3.1050 tsec 17.3730 #GCAMreg# pass 0 level1 0 level2 1 tsec 44.054 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=40.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.763539 #FOTS# QuadFit found better minimum quadopt=(dt=0.007,rms=0.762846) vs oldopt=(dt=0.005,rms=0.762853) #GCMRL# 74 dt 0.007000 rms 0.763 0.091% neg 0 invalid 762 tFOTS 13.2640 tGradient 3.1850 tsec 17.4320 #GCMRL# 75 dt 0.005000 rms 0.763 0.000% neg 0 invalid 762 tFOTS 13.3060 tGradient 3.2050 tsec 17.5190 GCAMregister done in 18.5572 min Starting GCAmapRenormalizeWithAlignment() without scales renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.10253 (16) mri peak = 0.25687 (27) Left_Lateral_Ventricle (4): linear fit = 1.53 x + 0.0 (1653 voxels, overlap=0.309) Left_Lateral_Ventricle (4): linear fit = 1.50 x + 0.0 (1653 voxels, peak = 25), gca=24.0 gca peak = 0.17690 (16) mri peak = 0.16433 (31) Right_Lateral_Ventricle (43): linear fit = 1.85 x + 0.0 (1344 voxels, overlap=0.100) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (1344 voxels, peak = 30), gca=24.0 gca peak = 0.28275 (96) mri peak = 0.11876 (98) Right_Pallidum (52): linear fit = 1.03 x + 0.0 (1161 voxels, overlap=0.997) Right_Pallidum (52): linear fit = 1.03 x + 0.0 (1161 voxels, peak = 99), gca=99.4 gca peak = 0.18948 (93) mri peak = 0.17025 (101) Left_Pallidum (13): linear fit = 1.04 x + 0.0 (1022 voxels, overlap=0.681) Left_Pallidum (13): linear fit = 1.04 x + 0.0 (1022 voxels, peak = 97), gca=97.2 gca peak = 0.20755 (55) mri peak = 0.05781 (75) Right_Hippocampus (53): linear fit = 1.33 x + 0.0 (1200 voxels, overlap=0.025) Right_Hippocampus (53): linear fit = 1.33 x + 0.0 (1200 voxels, peak = 73), gca=72.9 gca peak = 0.31831 (58) mri peak = 0.06689 (75) Left_Hippocampus (17): linear fit = 1.30 x + 0.0 (1165 voxels, overlap=0.014) Left_Hippocampus (17): linear fit = 1.30 x + 0.0 (1165 voxels, peak = 76), gca=75.7 gca peak = 0.11957 (102) mri peak = 0.17878 (104) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (84442 voxels, overlap=0.576) Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (84442 voxels, peak = 105), gca=104.5 gca peak = 0.11429 (102) mri peak = 0.18288 (105) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (87350 voxels, overlap=0.521) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (87350 voxels, peak = 106), gca=105.6 gca peak = 0.14521 (59) mri peak = 0.05257 (79) Left_Cerebral_Cortex (3): linear fit = 1.35 x + 0.0 (35111 voxels, overlap=0.000) Left_Cerebral_Cortex (3): linear fit = 1.35 x + 0.0 (35111 voxels, peak = 79), gca=79.4 gca peak = 0.14336 (58) mri peak = 0.05520 (79) Right_Cerebral_Cortex (42): linear fit = 1.35 x + 0.0 (34322 voxels, overlap=0.000) Right_Cerebral_Cortex (42): linear fit = 1.35 x + 0.0 (34322 voxels, peak = 78), gca=78.0 gca peak = 0.13305 (70) mri peak = 0.10659 (79) Right_Caudate (50): linear fit = 1.22 x + 0.0 (971 voxels, overlap=0.019) Right_Caudate (50): linear fit = 1.22 x + 0.0 (971 voxels, peak = 85), gca=85.1 gca peak = 0.15761 (71) mri peak = 0.12636 (79) Left_Caudate (11): linear fit = 1.11 x + 0.0 (1307 voxels, overlap=0.470) Left_Caudate (11): linear fit = 1.11 x + 0.0 (1307 voxels, peak = 78), gca=78.5 gca peak = 0.13537 (57) mri peak = 0.03984 (93) Left_Cerebellum_Cortex (8): linear fit = 1.47 x + 0.0 (21745 voxels, overlap=0.001) Left_Cerebellum_Cortex (8): linear fit = 1.47 x + 0.0 (21745 voxels, peak = 84), gca=83.5 gca peak = 0.13487 (56) mri peak = 0.04555 (94) Right_Cerebellum_Cortex (47): linear fit = 1.63 x + 0.0 (22609 voxels, overlap=0.001) Right_Cerebellum_Cortex (47): linear fit = 1.63 x + 0.0 (22609 voxels, peak = 92), gca=91.6 gca peak = 0.19040 (84) mri peak = 0.05749 (91) Left_Cerebellum_White_Matter (7): linear fit = 1.11 x + 0.0 (10849 voxels, overlap=0.977) Left_Cerebellum_White_Matter (7): linear fit = 1.11 x + 0.0 (10849 voxels, peak = 93), gca=92.8 gca peak = 0.18871 (83) mri peak = 0.05570 (82) Right_Cerebellum_White_Matter (46): linear fit = 0.96 x + 0.0 (8025 voxels, overlap=0.982) Right_Cerebellum_White_Matter (46): linear fit = 0.96 x + 0.0 (8025 voxels, peak = 80), gca=80.1 gca peak = 0.24248 (57) mri peak = 0.08945 (77) Left_Amygdala (18): linear fit = 1.33 x + 0.0 (570 voxels, overlap=0.065) Left_Amygdala (18): linear fit = 1.33 x + 0.0 (570 voxels, peak = 76), gca=75.5 gca peak = 0.35833 (56) mri peak = 0.12379 (77) Right_Amygdala (54): linear fit = 1.32 x + 0.0 (648 voxels, overlap=0.047) Right_Amygdala (54): linear fit = 1.32 x + 0.0 (648 voxels, peak = 74), gca=73.6 gca peak = 0.12897 (85) mri peak = 0.09510 (96) Left_Thalamus (10): linear fit = 1.09 x + 0.0 (6447 voxels, overlap=0.590) Left_Thalamus (10): linear fit = 1.09 x + 0.0 (6447 voxels, peak = 92), gca=92.2 gca peak = 0.13127 (83) mri peak = 0.10786 (95) Right_Thalamus (49): linear fit = 1.12 x + 0.0 (5836 voxels, overlap=0.364) Right_Thalamus (49): linear fit = 1.12 x + 0.0 (5836 voxels, peak = 93), gca=92.5 gca peak = 0.12974 (78) mri peak = 0.10494 (89) Left_Putamen (12): linear fit = 1.15 x + 0.0 (2953 voxels, overlap=0.169) Left_Putamen (12): linear fit = 1.15 x + 0.0 (2953 voxels, peak = 90), gca=90.1 gca peak = 0.17796 (79) mri peak = 0.08899 (89) Right_Putamen (51): linear fit = 1.14 x + 0.0 (3118 voxels, overlap=0.493) Right_Putamen (51): linear fit = 1.14 x + 0.0 (3118 voxels, peak = 90), gca=90.5 gca peak = 0.10999 (80) mri peak = 0.16896 (91) Brain_Stem (16): linear fit = 1.15 x + 0.0 (11672 voxels, overlap=0.006) Brain_Stem (16): linear fit = 1.15 x + 0.0 (11672 voxels, peak = 92), gca=92.4 gca peak = 0.13215 (88) mri peak = 0.16223 (95) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1591 voxels, overlap=0.031) Right_VentralDC (60): linear fit = 1.09 x + 0.0 (1591 voxels, peak = 95), gca=95.5 gca peak = 0.11941 (89) mri peak = 0.16129 (97) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1686 voxels, overlap=0.073) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (1686 voxels, peak = 97), gca=97.5 gca peak = 0.20775 (25) mri peak = 0.20059 (37) gca peak = 0.13297 (21) mri peak = 0.12664 (25) Fourth_Ventricle (15): linear fit = 1.51 x + 0.0 (788 voxels, overlap=0.512) Fourth_Ventricle (15): linear fit = 1.51 x + 0.0 (788 voxels, peak = 32), gca=31.8 gca peak Unknown = 0.94777 ( 0) gca peak Left_Inf_Lat_Vent = 0.19087 (28) gca peak Third_Ventricle = 0.20775 (25) gca peak Fourth_Ventricle = 0.13297 (21) gca peak CSF = 0.16821 (33) gca peak Left_Accumbens_area = 0.32850 (63) gca peak Left_undetermined = 0.98480 (28) gca peak Left_vessel = 0.40887 (53) gca peak Left_choroid_plexus = 0.10898 (46) gca peak Right_Inf_Lat_Vent = 0.17798 (26) gca peak Right_Cerebellum_Cortex = 0.13487 (56) gca peak Right_Accumbens_area = 0.30137 (64) gca peak Right_vessel = 0.47828 (52) gca peak Right_choroid_plexus = 0.11612 (45) gca peak Fifth_Ventricle = 0.59466 (35) gca peak WM_hypointensities = 0.10053 (78) gca peak non_WM_hypointensities = 0.07253 (60) gca peak Optic_Chiasm = 0.25330 (73) not using caudate to estimate GM means setting label Right_Cerebellum_Cortex based on Left_Cerebellum_Cortex = 1.47 x + 0: 84 estimating mean gm scale to be 1.33 x + 0.0 estimating mean wm scale to be 1.03 x + 0.0 estimating mean csf scale to be 1.50 x + 0.0 saving intensity scales to talairach.label_intensities.txt GCAmapRenormalizeWithAlignment() took 3.1809 min noneg pre Starting GCAMregister() label assignment complete, 0 changed (0.00%) npasses = 1, nlevels = 6 #pass# 1 of 1 ************************ enabling zero nodes setting smoothness cost coefficient to 0.008 #GCAMreg# pass 0 level1 5 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.01 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.780777 #FOTS# QuadFit found better minimum quadopt=(dt=161.952,rms=0.711894) vs oldopt=(dt=92.48,rms=0.725343) #GCMRL# 77 dt 161.951773 rms 0.712 8.822% neg 0 invalid 762 tFOTS 14.1070 tGradient 7.6780 tsec 22.7720 #GCMRL# 78 dt 369.920000 rms 0.688 3.422% neg 0 invalid 762 tFOTS 14.1210 tGradient 7.6740 tsec 22.7800 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.681109) vs oldopt=(dt=92.48,rms=0.68172) #GCMRL# 79 dt 129.472000 rms 0.681 0.934% neg 0 invalid 762 tFOTS 14.0650 tGradient 7.6690 tsec 22.7180 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.670587) vs oldopt=(dt=369.92,rms=0.672605) #GCMRL# 80 dt 517.888000 rms 0.671 1.545% neg 0 invalid 762 tFOTS 14.0900 tGradient 7.6060 tsec 22.6810 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.667743) vs oldopt=(dt=92.48,rms=0.668007) #GCMRL# 81 dt 129.472000 rms 0.668 0.424% neg 0 invalid 762 tFOTS 14.9600 tGradient 7.6980 tsec 23.6430 #FOTS# QuadFit found better minimum quadopt=(dt=295.936,rms=0.665351) vs oldopt=(dt=369.92,rms=0.665598) #GCMRL# 82 dt 295.936000 rms 0.665 0.358% neg 0 invalid 762 tFOTS 14.0700 tGradient 7.6560 tsec 22.7100 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.66311) vs oldopt=(dt=92.48,rms=0.663234) #GCMRL# 83 dt 129.472000 rms 0.663 0.337% neg 0 invalid 762 tFOTS 14.9210 tGradient 7.6240 tsec 23.5320 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.661892) vs oldopt=(dt=92.48,rms=0.662131) #GCMRL# 84 dt 129.472000 rms 0.662 0.184% neg 0 invalid 762 tFOTS 14.1850 tGradient 7.7080 tsec 22.8790 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.659071) vs oldopt=(dt=369.92,rms=0.659495) #GCMRL# 85 dt 517.888000 rms 0.659 0.426% neg 0 invalid 762 tFOTS 14.0750 tGradient 7.5920 tsec 22.6520 #GCMRL# 86 dt 92.480000 rms 0.658 0.215% neg 0 invalid 762 tFOTS 14.9150 tGradient 7.6040 tsec 23.5060 #FOTS# QuadFit found better minimum quadopt=(dt=2071.55,rms=0.650815) vs oldopt=(dt=1479.68,rms=0.651845) #GCMRL# 87 dt 2071.552000 rms 0.651 1.040% neg 0 invalid 762 tFOTS 14.1260 tGradient 7.6410 tsec 22.7520 #GCMRL# 88 dt 92.480000 rms 0.649 0.203% neg 0 invalid 762 tFOTS 14.9210 tGradient 7.8360 tsec 23.7420 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.648816) vs oldopt=(dt=369.92,rms=0.648951) #GCMRL# 89 dt 517.888000 rms 0.649 0.105% neg 0 invalid 762 tFOTS 14.9030 tGradient 7.6430 tsec 23.5330 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.64844) vs oldopt=(dt=92.48,rms=0.648503) #GCMRL# 90 dt 129.472000 rms 0.648 0.058% neg 0 invalid 762 tFOTS 14.9710 tGradient 7.6350 tsec 23.5900 #FOTS# QuadFit found better minimum quadopt=(dt=517.888,rms=0.647752) vs oldopt=(dt=369.92,rms=0.647812) #GCMRL# 91 dt 517.888000 rms 0.648 0.106% neg 0 invalid 762 tFOTS 14.9180 tGradient 7.6660 tsec 23.5680 #GCMRL# 92 dt 92.480000 rms 0.647 0.065% neg 0 invalid 762 tFOTS 14.0660 tGradient 7.5180 tsec 22.5690 #FOTS# QuadFit found better minimum quadopt=(dt=2071.55,rms=0.645114) vs oldopt=(dt=1479.68,rms=0.645544) #GCMRL# 93 dt 2071.552000 rms 0.645 0.343% neg 0 invalid 762 tFOTS 14.9660 tGradient 7.5780 tsec 23.5280 #FOTS# QuadFit found better minimum quadopt=(dt=110.976,rms=0.644438) vs oldopt=(dt=92.48,rms=0.644454) #GCMRL# 94 dt 110.976000 rms 0.644 0.105% neg 0 invalid 762 tFOTS 14.0820 tGradient 7.7830 tsec 22.8500 #GCMRL# 95 dt 369.920000 rms 0.644 0.079% neg 0 invalid 762 tFOTS 14.9090 tGradient 7.5190 tsec 23.4140 #GCMRL# 96 dt 92.480000 rms 0.644 0.000% neg 0 invalid 762 tFOTS 14.1380 tGradient 7.7200 tsec 22.8670 #GCMRL# 97 dt 92.480000 rms 0.644 0.019% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.5250 tsec 8.5120 #GCMRL# 98 dt 92.480000 rms 0.643 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.5340 tsec 8.5770 #GCMRL# 99 dt 92.480000 rms 0.643 0.041% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.6680 tsec 8.6530 #GCMRL# 100 dt 92.480000 rms 0.643 0.052% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.5700 tsec 8.5530 #GCMRL# 101 dt 92.480000 rms 0.642 0.063% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.5140 tsec 8.4980 #GCMRL# 102 dt 92.480000 rms 0.642 0.075% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.6610 tsec 8.6530 #GCMRL# 103 dt 92.480000 rms 0.641 0.084% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.6860 tsec 8.6810 #GCMRL# 104 dt 92.480000 rms 0.641 0.088% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.6320 tsec 8.6200 #GCMRL# 105 dt 92.480000 rms 0.640 0.094% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.6390 tsec 8.6760 #GCMRL# 106 dt 92.480000 rms 0.640 0.094% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.8170 tsec 8.8020 #GCMRL# 107 dt 92.480000 rms 0.639 0.099% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7450 tsec 8.7300 #GCMRL# 108 dt 92.480000 rms 0.638 0.108% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.6250 tsec 8.6100 #GCMRL# 109 dt 92.480000 rms 0.637 0.116% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.5950 tsec 8.5810 #GCMRL# 110 dt 92.480000 rms 0.637 0.117% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7280 tsec 8.7160 #GCMRL# 111 dt 92.480000 rms 0.636 0.109% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.6360 tsec 8.6330 #GCMRL# 112 dt 92.480000 rms 0.635 0.108% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.6650 tsec 8.6510 #GCMRL# 113 dt 92.480000 rms 0.635 0.107% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.6690 tsec 8.6560 #GCMRL# 114 dt 92.480000 rms 0.634 0.106% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7290 tsec 8.7140 #GCMRL# 115 dt 92.480000 rms 0.633 0.098% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.6520 tsec 8.6380 #GCMRL# 116 dt 92.480000 rms 0.633 0.094% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7220 tsec 8.7060 #GCMRL# 117 dt 92.480000 rms 0.632 0.089% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.6800 tsec 8.6660 #GCMRL# 118 dt 92.480000 rms 0.632 0.089% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.6560 tsec 8.6440 #GCMRL# 119 dt 92.480000 rms 0.631 0.087% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.6680 tsec 8.6550 #GCMRL# 120 dt 92.480000 rms 0.631 0.084% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.5810 tsec 8.5750 #GCMRL# 121 dt 92.480000 rms 0.630 0.075% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7110 tsec 8.6970 #GCMRL# 122 dt 92.480000 rms 0.630 0.072% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.5930 tsec 8.5790 #GCMRL# 123 dt 92.480000 rms 0.629 0.071% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.6120 tsec 8.5970 #GCMRL# 124 dt 92.480000 rms 0.629 0.068% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.6120 tsec 8.5980 #GCMRL# 125 dt 92.480000 rms 0.628 0.067% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.5940 tsec 8.5760 #GCMRL# 126 dt 92.480000 rms 0.628 0.065% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.6590 tsec 8.6430 #GCMRL# 127 dt 92.480000 rms 0.628 0.056% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.5690 tsec 8.5590 #GCMRL# 128 dt 92.480000 rms 0.627 0.050% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.6100 tsec 8.6070 #GCMRL# 129 dt 92.480000 rms 0.627 0.056% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7220 tsec 8.7070 #GCMRL# 130 dt 92.480000 rms 0.627 0.059% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.6300 tsec 8.6160 #GCMRL# 131 dt 92.480000 rms 0.626 0.047% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.6220 tsec 8.6060 #GCMRL# 132 dt 92.480000 rms 0.626 0.045% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.5350 tsec 8.5200 #GCMRL# 133 dt 92.480000 rms 0.626 0.042% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.5880 tsec 8.5740 #GCMRL# 134 dt 92.480000 rms 0.625 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.6760 tsec 8.6610 #GCMRL# 135 dt 92.480000 rms 0.625 0.044% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.6210 tsec 8.6150 #GCMRL# 136 dt 92.480000 rms 0.625 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.5270 tsec 8.5130 #GCMRL# 137 dt 92.480000 rms 0.625 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.5470 tsec 8.5300 #GCMRL# 138 dt 92.480000 rms 0.624 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.6320 tsec 8.6150 #GCMRL# 139 dt 92.480000 rms 0.624 0.047% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.5910 tsec 8.5780 #GCMRL# 140 dt 92.480000 rms 0.624 0.042% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7360 tsec 8.7200 #GCMRL# 141 dt 92.480000 rms 0.624 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7420 tsec 8.7290 #GCMRL# 142 dt 92.480000 rms 0.623 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.6810 tsec 8.6680 #GCMRL# 143 dt 92.480000 rms 0.623 0.038% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.6820 tsec 8.6670 #GCMRL# 144 dt 92.480000 rms 0.623 0.041% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.8130 tsec 8.7980 #GCMRL# 145 dt 92.480000 rms 0.623 0.039% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.8680 tsec 8.8630 #GCMRL# 146 dt 92.480000 rms 0.622 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.6160 tsec 8.6010 #GCMRL# 147 dt 92.480000 rms 0.622 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.6010 tsec 8.5850 #GCMRL# 148 dt 92.480000 rms 0.622 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.8170 tsec 8.8080 #GCMRL# 149 dt 92.480000 rms 0.622 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.6500 tsec 8.6360 #GCMRL# 150 dt 92.480000 rms 0.622 0.036% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.7120 tsec 8.6990 #GCMRL# 151 dt 92.480000 rms 0.621 0.033% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.6810 tsec 8.6690 #GCMRL# 152 dt 92.480000 rms 0.621 0.025% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.5420 tsec 8.5330 #GCMRL# 153 dt 92.480000 rms 0.621 0.023% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.6890 tsec 8.7120 #FOTS# QuadFit found better minimum quadopt=(dt=1183.74,rms=0.620798) vs oldopt=(dt=1479.68,rms=0.620834) #GCMRL# 154 dt 1183.744000 rms 0.621 0.047% neg 0 invalid 762 tFOTS 15.0090 tGradient 7.6170 tsec 23.6120 #FOTS# QuadFit found better minimum quadopt=(dt=32.368,rms=0.620755) vs oldopt=(dt=23.12,rms=0.620765) #GCMRL# 155 dt 32.368000 rms 0.621 0.000% neg 0 invalid 762 tFOTS 14.9210 tGradient 7.7030 tsec 23.6340 #GCMRL# 156 dt 32.368000 rms 0.621 0.003% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.6320 tsec 8.6160 #GCAMreg# pass 0 level1 5 level2 1 tsec 1024.37 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.01 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.620929 #GCMRL# 158 dt 369.920000 rms 0.620 0.197% neg 0 invalid 762 tFOTS 14.9850 tGradient 7.6570 tsec 23.6270 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.619375) vs oldopt=(dt=92.48,rms=0.619413) #GCMRL# 159 dt 129.472000 rms 0.619 0.054% neg 0 invalid 762 tFOTS 14.0790 tGradient 7.6390 tsec 22.7050 #FOTS# QuadFit found better minimum quadopt=(dt=443.904,rms=0.619196) vs oldopt=(dt=369.92,rms=0.619201) #GCMRL# 160 dt 443.904000 rms 0.619 0.000% neg 0 invalid 762 tFOTS 14.9060 tGradient 7.6330 tsec 23.5490 #GCMRL# 161 dt 443.904000 rms 0.619 0.004% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.6160 tsec 8.6100 setting smoothness cost coefficient to 0.031 #GCAMreg# pass 0 level1 4 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.03 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.621044 #FOTS# QuadFit found better minimum quadopt=(dt=90.0485,rms=0.618016) vs oldopt=(dt=103.68,rms=0.618086) #GCMRL# 163 dt 90.048518 rms 0.618 0.488% neg 0 invalid 762 tFOTS 14.1490 tGradient 4.6550 tsec 19.7890 #FOTS# QuadFit found better minimum quadopt=(dt=209.611,rms=0.612049) vs oldopt=(dt=103.68,rms=0.613372) #GCMRL# 164 dt 209.610738 rms 0.612 0.966% neg 0 invalid 762 tFOTS 14.0970 tGradient 4.5340 tsec 19.6160 #FOTS# QuadFit found better minimum quadopt=(dt=70.4,rms=0.608587) vs oldopt=(dt=25.92,rms=0.609544) #GCMRL# 165 dt 70.400000 rms 0.609 0.566% neg 0 invalid 762 tFOTS 14.0940 tGradient 4.4400 tsec 19.5220 #FOTS# QuadFit found better minimum quadopt=(dt=162.83,rms=0.604817) vs oldopt=(dt=103.68,rms=0.605231) #GCMRL# 166 dt 162.829932 rms 0.605 0.619% neg 0 invalid 762 tFOTS 15.0210 tGradient 4.5510 tsec 20.5600 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.602891) vs oldopt=(dt=25.92,rms=0.603269) #GCMRL# 167 dt 36.288000 rms 0.603 0.318% neg 0 invalid 762 tFOTS 14.0820 tGradient 4.4410 tsec 19.5100 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.600745) vs oldopt=(dt=103.68,rms=0.601105) #GCMRL# 168 dt 145.152000 rms 0.601 0.356% neg 0 invalid 762 tFOTS 13.2480 tGradient 4.3960 tsec 18.6290 #FOTS# QuadFit found better minimum quadopt=(dt=115.978,rms=0.598356) vs oldopt=(dt=103.68,rms=0.598372) #GCMRL# 169 dt 115.977901 rms 0.598 0.398% neg 0 invalid 762 tFOTS 14.0910 tGradient 4.5120 tsec 19.5880 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.597306) vs oldopt=(dt=25.92,rms=0.597524) #GCMRL# 170 dt 36.288000 rms 0.597 0.175% neg 0 invalid 762 tFOTS 13.2970 tGradient 4.4900 tsec 18.7700 #FOTS# QuadFit found better minimum quadopt=(dt=248.832,rms=0.595073) vs oldopt=(dt=414.72,rms=0.595471) #GCMRL# 171 dt 248.832000 rms 0.595 0.374% neg 0 invalid 762 tFOTS 13.2620 tGradient 4.3950 tsec 18.6410 #FOTS# QuadFit found better minimum quadopt=(dt=70.6513,rms=0.592693) vs oldopt=(dt=103.68,rms=0.593132) #GCMRL# 172 dt 70.651270 rms 0.593 0.400% neg 0 invalid 762 tFOTS 14.0870 tGradient 4.4200 tsec 19.4890 #GCMRL# 173 dt 103.680000 rms 0.592 0.156% neg 0 invalid 762 tFOTS 13.3330 tGradient 4.4310 tsec 18.7490 #GCMRL# 174 dt 103.680000 rms 0.590 0.260% neg 0 invalid 762 tFOTS 14.1270 tGradient 4.3890 tsec 19.5050 #FOTS# QuadFit found better minimum quadopt=(dt=68.987,rms=0.589418) vs oldopt=(dt=103.68,rms=0.589596) #GCMRL# 175 dt 68.987013 rms 0.589 0.137% neg 0 invalid 762 tFOTS 14.0690 tGradient 4.3700 tsec 19.4250 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.587933) vs oldopt=(dt=103.68,rms=0.588222) #GCMRL# 176 dt 145.152000 rms 0.588 0.252% neg 0 invalid 762 tFOTS 14.0830 tGradient 4.3870 tsec 19.4680 #FOTS# QuadFit found better minimum quadopt=(dt=82.944,rms=0.5872) vs oldopt=(dt=103.68,rms=0.5873) #GCMRL# 177 dt 82.944000 rms 0.587 0.125% neg 0 invalid 762 tFOTS 14.1340 tGradient 4.4430 tsec 19.5630 #FOTS# QuadFit found better minimum quadopt=(dt=124.416,rms=0.58607) vs oldopt=(dt=103.68,rms=0.5861) #GCMRL# 178 dt 124.416000 rms 0.586 0.192% neg 0 invalid 762 tFOTS 14.1060 tGradient 4.4310 tsec 19.5220 #FOTS# QuadFit found better minimum quadopt=(dt=63.2289,rms=0.585285) vs oldopt=(dt=103.68,rms=0.585527) #GCMRL# 179 dt 63.228916 rms 0.585 0.134% neg 0 invalid 762 tFOTS 14.9090 tGradient 4.3600 tsec 20.2520 #FOTS# QuadFit found better minimum quadopt=(dt=248.832,rms=0.583795) vs oldopt=(dt=414.72,rms=0.584157) #GCMRL# 180 dt 248.832000 rms 0.584 0.255% neg 0 invalid 762 tFOTS 14.0920 tGradient 4.3890 tsec 19.4680 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.582914) vs oldopt=(dt=25.92,rms=0.583072) #GCMRL# 181 dt 36.288000 rms 0.583 0.151% neg 0 invalid 762 tFOTS 14.1910 tGradient 4.4040 tsec 19.5810 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.58201) vs oldopt=(dt=103.68,rms=0.582185) #GCMRL# 182 dt 145.152000 rms 0.582 0.155% neg 0 invalid 762 tFOTS 14.0860 tGradient 4.3750 tsec 19.4450 #GCMRL# 183 dt 103.680000 rms 0.581 0.123% neg 0 invalid 762 tFOTS 14.0870 tGradient 4.4110 tsec 19.4850 #FOTS# QuadFit found better minimum quadopt=(dt=62.208,rms=0.580744) vs oldopt=(dt=103.68,rms=0.580886) #GCMRL# 184 dt 62.208000 rms 0.581 0.095% neg 0 invalid 762 tFOTS 14.1490 tGradient 4.5350 tsec 19.6690 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.579941) vs oldopt=(dt=103.68,rms=0.58009) #GCMRL# 185 dt 145.152000 rms 0.580 0.138% neg 0 invalid 762 tFOTS 14.1400 tGradient 4.3890 tsec 19.5140 #FOTS# QuadFit found better minimum quadopt=(dt=82.944,rms=0.579401) vs oldopt=(dt=103.68,rms=0.579445) #GCMRL# 186 dt 82.944000 rms 0.579 0.093% neg 0 invalid 762 tFOTS 14.0800 tGradient 4.4930 tsec 19.5580 #GCMRL# 187 dt 103.680000 rms 0.579 0.097% neg 0 invalid 762 tFOTS 14.0950 tGradient 4.3650 tsec 19.4450 #FOTS# QuadFit found better minimum quadopt=(dt=82.944,rms=0.578277) vs oldopt=(dt=103.68,rms=0.578322) #GCMRL# 188 dt 82.944000 rms 0.578 0.097% neg 0 invalid 762 tFOTS 14.1360 tGradient 4.4100 tsec 19.5310 #GCMRL# 189 dt 103.680000 rms 0.578 0.091% neg 0 invalid 762 tFOTS 14.1390 tGradient 4.3620 tsec 19.4860 #FOTS# QuadFit found better minimum quadopt=(dt=82.944,rms=0.57725) vs oldopt=(dt=103.68,rms=0.577314) #GCMRL# 190 dt 82.944000 rms 0.577 0.086% neg 0 invalid 762 tFOTS 14.0680 tGradient 4.4070 tsec 19.4590 #GCMRL# 191 dt 103.680000 rms 0.577 0.089% neg 0 invalid 762 tFOTS 14.0950 tGradient 4.3920 tsec 19.4720 #FOTS# QuadFit found better minimum quadopt=(dt=82.944,rms=0.576204) vs oldopt=(dt=103.68,rms=0.576227) #GCMRL# 192 dt 82.944000 rms 0.576 0.092% neg 0 invalid 762 tFOTS 14.1300 tGradient 4.4710 tsec 19.6450 #GCMRL# 193 dt 103.680000 rms 0.576 0.081% neg 0 invalid 762 tFOTS 14.0900 tGradient 4.4050 tsec 19.4790 #FOTS# QuadFit found better minimum quadopt=(dt=82.944,rms=0.575321) vs oldopt=(dt=103.68,rms=0.575359) #GCMRL# 194 dt 82.944000 rms 0.575 0.073% neg 0 invalid 762 tFOTS 14.0830 tGradient 4.4290 tsec 19.5010 #GCMRL# 195 dt 103.680000 rms 0.575 0.081% neg 0 invalid 762 tFOTS 14.0810 tGradient 4.4670 tsec 19.5570 #FOTS# QuadFit found better minimum quadopt=(dt=62.208,rms=0.574473) vs oldopt=(dt=103.68,rms=0.574562) #GCMRL# 196 dt 62.208000 rms 0.574 0.066% neg 0 invalid 762 tFOTS 14.1390 tGradient 4.4630 tsec 19.5870 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.573809) vs oldopt=(dt=103.68,rms=0.573942) #GCMRL# 197 dt 145.152000 rms 0.574 0.116% neg 0 invalid 762 tFOTS 14.0940 tGradient 4.4380 tsec 19.5190 #FOTS# QuadFit found better minimum quadopt=(dt=62.208,rms=0.57354) vs oldopt=(dt=103.68,rms=0.57362) #GCMRL# 198 dt 62.208000 rms 0.574 0.000% neg 0 invalid 762 tFOTS 14.0880 tGradient 4.4190 tsec 19.5160 #GCMRL# 199 dt 62.208000 rms 0.573 0.053% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3630 tsec 5.3570 #GCMRL# 200 dt 62.208000 rms 0.573 0.091% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3870 tsec 5.3730 #GCMRL# 201 dt 62.208000 rms 0.572 0.116% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4670 tsec 5.4540 #GCMRL# 202 dt 62.208000 rms 0.571 0.129% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3560 tsec 5.3410 #GCMRL# 203 dt 62.208000 rms 0.570 0.172% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3490 tsec 5.3910 #GCMRL# 204 dt 62.208000 rms 0.569 0.190% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3630 tsec 5.3470 #GCMRL# 205 dt 62.208000 rms 0.568 0.180% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3700 tsec 5.3580 #GCMRL# 206 dt 62.208000 rms 0.567 0.186% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3710 tsec 5.3590 #GCMRL# 207 dt 62.208000 rms 0.566 0.184% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3630 tsec 5.3500 #GCMRL# 208 dt 62.208000 rms 0.565 0.187% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3680 tsec 5.3530 #GCMRL# 209 dt 62.208000 rms 0.564 0.178% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3660 tsec 5.3510 #GCMRL# 210 dt 62.208000 rms 0.563 0.171% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3610 tsec 5.3510 #GCMRL# 211 dt 62.208000 rms 0.562 0.162% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3650 tsec 5.3500 #GCMRL# 212 dt 62.208000 rms 0.561 0.151% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4450 tsec 5.4330 #GCMRL# 213 dt 62.208000 rms 0.561 0.145% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4510 tsec 5.4350 #GCMRL# 214 dt 62.208000 rms 0.560 0.133% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3680 tsec 5.3530 #GCMRL# 215 dt 62.208000 rms 0.559 0.128% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4780 tsec 5.4630 #GCMRL# 216 dt 62.208000 rms 0.558 0.122% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4410 tsec 5.4270 #GCMRL# 217 dt 62.208000 rms 0.558 0.105% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4650 tsec 5.4500 #GCMRL# 218 dt 62.208000 rms 0.557 0.110% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4490 tsec 5.4320 #GCMRL# 219 dt 62.208000 rms 0.557 0.114% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4080 tsec 5.3980 #GCMRL# 220 dt 62.208000 rms 0.556 0.100% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3770 tsec 5.3610 #GCMRL# 221 dt 62.208000 rms 0.555 0.100% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3780 tsec 5.3660 #GCMRL# 222 dt 62.208000 rms 0.555 0.086% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3420 tsec 5.3300 #GCMRL# 223 dt 62.208000 rms 0.554 0.093% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3800 tsec 5.3630 #GCMRL# 224 dt 62.208000 rms 0.554 0.082% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3970 tsec 5.3840 #GCMRL# 225 dt 62.208000 rms 0.554 0.074% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3590 tsec 5.3440 #GCMRL# 226 dt 62.208000 rms 0.553 0.095% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3740 tsec 5.3670 #GCMRL# 227 dt 62.208000 rms 0.553 0.091% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3650 tsec 5.3500 #GCMRL# 228 dt 62.208000 rms 0.552 0.073% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4130 tsec 5.3990 #GCMRL# 229 dt 62.208000 rms 0.552 0.056% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3740 tsec 5.3610 #GCMRL# 230 dt 62.208000 rms 0.552 0.052% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4190 tsec 5.4050 #GCMRL# 231 dt 62.208000 rms 0.551 0.071% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3510 tsec 5.3350 #GCMRL# 232 dt 62.208000 rms 0.551 0.067% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4490 tsec 5.4350 #GCMRL# 233 dt 62.208000 rms 0.550 0.072% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4080 tsec 5.3940 #GCMRL# 234 dt 62.208000 rms 0.550 0.058% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3680 tsec 5.3570 #GCMRL# 235 dt 62.208000 rms 0.550 0.050% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3780 tsec 5.3610 #GCMRL# 236 dt 62.208000 rms 0.549 0.066% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3550 tsec 5.3400 #GCMRL# 237 dt 62.208000 rms 0.549 0.076% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3470 tsec 5.3360 #GCMRL# 238 dt 62.208000 rms 0.549 0.056% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3790 tsec 5.3630 #GCMRL# 239 dt 62.208000 rms 0.548 0.036% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3450 tsec 5.3420 #GCMRL# 240 dt 62.208000 rms 0.548 0.045% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3410 tsec 5.3270 #GCMRL# 241 dt 62.208000 rms 0.548 0.069% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3480 tsec 5.3330 #GCMRL# 242 dt 62.208000 rms 0.548 0.066% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4170 tsec 5.4020 #GCMRL# 243 dt 62.208000 rms 0.547 0.044% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3540 tsec 5.3390 #GCMRL# 244 dt 62.208000 rms 0.547 0.022% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3970 tsec 5.3840 #GCMRL# 245 dt 62.208000 rms 0.547 0.042% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3680 tsec 5.3560 #GCMRL# 246 dt 62.208000 rms 0.547 0.066% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3940 tsec 5.3790 #GCMRL# 247 dt 62.208000 rms 0.546 0.043% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3400 tsec 5.3260 #GCMRL# 248 dt 62.208000 rms 0.546 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3510 tsec 5.3350 #GCMRL# 249 dt 62.208000 rms 0.546 0.019% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3260 tsec 5.3110 #GCMRL# 250 dt 62.208000 rms 0.546 0.040% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3730 tsec 5.3570 #GCMRL# 251 dt 62.208000 rms 0.546 0.044% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4010 tsec 5.3870 #GCMRL# 252 dt 62.208000 rms 0.545 0.025% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3390 tsec 5.3260 #GCMRL# 253 dt 62.208000 rms 0.545 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3780 tsec 5.3710 #GCMRL# 254 dt 62.208000 rms 0.545 0.038% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3710 tsec 5.3570 #GCMRL# 255 dt 62.208000 rms 0.545 0.048% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4200 tsec 5.4090 #GCMRL# 256 dt 62.208000 rms 0.545 0.029% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3440 tsec 5.3290 #GCMRL# 257 dt 62.208000 rms 0.545 0.019% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4170 tsec 5.4050 #GCMRL# 258 dt 62.208000 rms 0.544 0.019% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3630 tsec 5.3470 #GCMRL# 259 dt 62.208000 rms 0.544 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4180 tsec 5.4080 #GCMRL# 260 dt 62.208000 rms 0.544 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4290 tsec 5.4170 #GCMRL# 261 dt 62.208000 rms 0.544 0.020% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4220 tsec 5.4070 #GCMRL# 262 dt 62.208000 rms 0.544 0.023% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4170 tsec 5.4020 #GCMRL# 263 dt 62.208000 rms 0.544 0.029% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4220 tsec 5.4060 #GCMRL# 264 dt 62.208000 rms 0.544 0.024% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4610 tsec 5.4520 #GCMRL# 265 dt 62.208000 rms 0.544 0.016% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4500 tsec 5.4580 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.54335) vs oldopt=(dt=103.68,rms=0.543373) #GCMRL# 266 dt 145.152000 rms 0.543 0.035% neg 0 invalid 762 tFOTS 14.1510 tGradient 4.4280 tsec 19.5670 #FOTS# QuadFit found better minimum quadopt=(dt=5.184,rms=0.543356) vs oldopt=(dt=6.48,rms=0.543356) #GCAMreg# pass 0 level1 4 level2 1 tsec 1106.79 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.03 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.543618 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.5412) vs oldopt=(dt=103.68,rms=0.541466) #GCMRL# 268 dt 145.152000 rms 0.541 0.445% neg 0 invalid 762 tFOTS 14.0900 tGradient 4.4740 tsec 19.5500 #FOTS# QuadFit found better minimum quadopt=(dt=82.944,rms=0.540605) vs oldopt=(dt=103.68,rms=0.540693) #GCMRL# 269 dt 82.944000 rms 0.541 0.110% neg 0 invalid 762 tFOTS 14.1010 tGradient 4.4450 tsec 19.5310 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.540018) vs oldopt=(dt=103.68,rms=0.540054) #GCMRL# 270 dt 145.152000 rms 0.540 0.109% neg 0 invalid 762 tFOTS 14.2050 tGradient 4.4450 tsec 19.6340 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.539752) vs oldopt=(dt=25.92,rms=0.539799) #GCMRL# 271 dt 36.288000 rms 0.540 0.000% neg 0 invalid 762 tFOTS 14.9260 tGradient 4.4110 tsec 20.3450 #GCMRL# 272 dt 36.288000 rms 0.540 0.021% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3890 tsec 5.3760 #GCMRL# 273 dt 36.288000 rms 0.539 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4080 tsec 5.3940 #GCMRL# 274 dt 36.288000 rms 0.539 0.041% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4350 tsec 5.4270 #GCMRL# 275 dt 36.288000 rms 0.539 0.052% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3730 tsec 5.3610 #GCMRL# 276 dt 36.288000 rms 0.539 0.051% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3700 tsec 5.3650 #GCMRL# 277 dt 36.288000 rms 0.538 0.040% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4080 tsec 5.3930 #GCMRL# 278 dt 36.288000 rms 0.538 0.042% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3710 tsec 5.4120 #GCMRL# 279 dt 36.288000 rms 0.538 0.036% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3950 tsec 5.3810 #GCMRL# 280 dt 36.288000 rms 0.538 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3760 tsec 5.3640 #GCMRL# 281 dt 36.288000 rms 0.538 0.029% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4370 tsec 5.4290 #GCMRL# 282 dt 36.288000 rms 0.538 0.026% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3070 tsec 5.2920 #GCMRL# 283 dt 36.288000 rms 0.537 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4020 tsec 5.3860 #GCMRL# 284 dt 36.288000 rms 0.537 0.040% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3630 tsec 5.3500 #GCMRL# 285 dt 36.288000 rms 0.537 0.035% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3330 tsec 5.3210 #GCMRL# 286 dt 36.288000 rms 0.537 0.027% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3760 tsec 5.3620 #GCMRL# 287 dt 36.288000 rms 0.537 0.028% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3570 tsec 5.3520 #GCMRL# 288 dt 36.288000 rms 0.537 0.028% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3840 tsec 5.3690 #GCMRL# 289 dt 36.288000 rms 0.536 0.038% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3660 tsec 5.3530 #GCMRL# 290 dt 36.288000 rms 0.536 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3900 tsec 5.3770 #GCMRL# 291 dt 36.288000 rms 0.536 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3690 tsec 5.3530 #GCMRL# 292 dt 36.288000 rms 0.536 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4240 tsec 5.4090 #GCMRL# 293 dt 36.288000 rms 0.536 0.025% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3670 tsec 5.3520 #GCMRL# 294 dt 36.288000 rms 0.536 0.024% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4280 tsec 5.4380 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.535395) vs oldopt=(dt=103.68,rms=0.535415) #GCMRL# 295 dt 145.152000 rms 0.535 0.025% neg 0 invalid 762 tFOTS 14.0920 tGradient 4.3710 tsec 19.4470 setting smoothness cost coefficient to 0.118 #GCAMreg# pass 0 level1 3 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.12 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.548568 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.547865) vs oldopt=(dt=8,rms=0.547951) #GCMRL# 297 dt 11.200000 rms 0.548 0.128% neg 0 invalid 762 tFOTS 14.1440 tGradient 3.7430 tsec 18.8720 #FOTS# QuadFit found better minimum quadopt=(dt=19.2,rms=0.547429) vs oldopt=(dt=32,rms=0.547542) #GCMRL# 298 dt 19.200000 rms 0.547 0.080% neg 0 invalid 762 tFOTS 14.1390 tGradient 3.7580 tsec 18.8950 #FOTS# QuadFit found better minimum quadopt=(dt=38.4,rms=0.546738) vs oldopt=(dt=32,rms=0.546764) #GCMRL# 299 dt 38.400000 rms 0.547 0.126% neg 0 invalid 762 tFOTS 14.0800 tGradient 3.7590 tsec 18.8240 #FOTS# QuadFit found better minimum quadopt=(dt=140.172,rms=0.543827) vs oldopt=(dt=128,rms=0.543831) #GCMRL# 300 dt 140.171779 rms 0.544 0.532% neg 0 invalid 762 tFOTS 14.0960 tGradient 3.6790 tsec 18.7590 #FOTS# QuadFit found better minimum quadopt=(dt=79.3425,rms=0.541197) vs oldopt=(dt=32,rms=0.541913) #GCMRL# 301 dt 79.342466 rms 0.541 0.484% neg 0 invalid 762 tFOTS 14.1400 tGradient 3.8100 tsec 18.9350 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.538262) vs oldopt=(dt=32,rms=0.538552) #GCMRL# 302 dt 44.800000 rms 0.538 0.542% neg 0 invalid 762 tFOTS 14.0900 tGradient 3.8490 tsec 18.9230 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.537424) vs oldopt=(dt=32,rms=0.537485) #GCMRL# 303 dt 44.800000 rms 0.537 0.156% neg 0 invalid 762 tFOTS 14.0850 tGradient 3.7340 tsec 18.8060 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.536123) vs oldopt=(dt=32,rms=0.53638) #GCMRL# 304 dt 44.800000 rms 0.536 0.242% neg 0 invalid 762 tFOTS 14.0960 tGradient 3.7470 tsec 18.8280 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.535474) vs oldopt=(dt=32,rms=0.535543) #GCMRL# 305 dt 44.800000 rms 0.535 0.121% neg 0 invalid 762 tFOTS 14.1380 tGradient 3.7740 tsec 18.8990 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.534324) vs oldopt=(dt=32,rms=0.534523) #GCMRL# 306 dt 44.800000 rms 0.534 0.215% neg 0 invalid 762 tFOTS 14.0880 tGradient 3.8520 tsec 18.9250 #GCMRL# 307 dt 32.000000 rms 0.534 0.081% neg 0 invalid 762 tFOTS 14.0840 tGradient 3.8130 tsec 18.8890 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.533035) vs oldopt=(dt=32,rms=0.533198) #GCMRL# 308 dt 44.800000 rms 0.533 0.160% neg 0 invalid 762 tFOTS 13.2640 tGradient 3.7700 tsec 18.0200 #FOTS# QuadFit found better minimum quadopt=(dt=38.4,rms=0.532627) vs oldopt=(dt=32,rms=0.532629) #GCMRL# 309 dt 38.400000 rms 0.533 0.077% neg 0 invalid 762 tFOTS 14.1990 tGradient 3.7250 tsec 18.9110 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.531893) vs oldopt=(dt=32,rms=0.531955) #GCMRL# 310 dt 44.800000 rms 0.532 0.138% neg 0 invalid 762 tFOTS 14.0880 tGradient 3.6810 tsec 18.7540 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.531487) vs oldopt=(dt=32,rms=0.531494) #GCMRL# 311 dt 25.600000 rms 0.531 0.076% neg 0 invalid 762 tFOTS 14.0830 tGradient 3.7400 tsec 18.8090 #FOTS# QuadFit found better minimum quadopt=(dt=102.4,rms=0.530489) vs oldopt=(dt=128,rms=0.530507) #GCMRL# 312 dt 102.400000 rms 0.530 0.188% neg 0 invalid 762 tFOTS 13.2610 tGradient 3.7480 tsec 17.9950 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.529978) vs oldopt=(dt=32,rms=0.530018) #GCMRL# 313 dt 25.600000 rms 0.530 0.096% neg 0 invalid 762 tFOTS 14.1450 tGradient 3.8100 tsec 18.9400 #GCMRL# 314 dt 128.000000 rms 0.529 0.206% neg 0 invalid 762 tFOTS 13.2700 tGradient 3.7350 tsec 17.9890 #FOTS# QuadFit found better minimum quadopt=(dt=25.6,rms=0.528445) vs oldopt=(dt=32,rms=0.528504) #GCMRL# 315 dt 25.600000 rms 0.528 0.083% neg 0 invalid 762 tFOTS 13.2650 tGradient 3.7720 tsec 18.0210 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.527898) vs oldopt=(dt=32,rms=0.527954) #GCMRL# 316 dt 44.800000 rms 0.528 0.104% neg 0 invalid 762 tFOTS 13.2690 tGradient 3.7250 tsec 17.9790 #GCMRL# 317 dt 32.000000 rms 0.528 0.000% neg 0 invalid 762 tFOTS 14.1400 tGradient 3.7810 tsec 18.9330 #GCMRL# 318 dt 32.000000 rms 0.527 0.065% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7350 tsec 4.7210 #GCMRL# 319 dt 32.000000 rms 0.527 0.090% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7470 tsec 4.7350 #GCMRL# 320 dt 32.000000 rms 0.526 0.117% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7690 tsec 4.7530 #GCMRL# 321 dt 32.000000 rms 0.525 0.151% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.8210 tsec 4.8050 #GCMRL# 322 dt 32.000000 rms 0.524 0.188% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7940 tsec 4.7810 #GCMRL# 323 dt 32.000000 rms 0.524 0.176% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7640 tsec 4.7500 #GCMRL# 324 dt 32.000000 rms 0.523 0.175% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7220 tsec 4.7120 #GCMRL# 325 dt 32.000000 rms 0.521 0.211% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7920 tsec 4.7770 #GCMRL# 326 dt 32.000000 rms 0.520 0.203% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7130 tsec 4.6980 #GCMRL# 327 dt 32.000000 rms 0.520 0.167% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7690 tsec 4.7540 #GCMRL# 328 dt 32.000000 rms 0.519 0.159% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7380 tsec 4.7220 #GCMRL# 329 dt 32.000000 rms 0.518 0.171% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7930 tsec 4.7800 #GCMRL# 330 dt 32.000000 rms 0.518 0.003% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7940 tsec 5.1400 #GCMRL# 331 dt 32.000000 rms 0.518 0.005% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7140 tsec 4.7030 #GCMRL# 332 dt 32.000000 rms 0.518 0.032% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.8250 tsec 4.8110 #GCMRL# 333 dt 32.000000 rms 0.518 0.012% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7640 tsec 5.1100 #GCMRL# 334 dt 32.000000 rms 0.518 0.013% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.8620 tsec 4.8470 #GCMRL# 335 dt 32.000000 rms 0.517 0.028% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.0150 tsec 5.0030 #GCMRL# 336 dt 32.000000 rms 0.517 0.022% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.8200 tsec 4.8050 #GCMRL# 337 dt 32.000000 rms 0.517 0.023% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7930 tsec 4.7810 #GCMRL# 338 dt 32.000000 rms 0.517 0.047% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7360 tsec 4.7210 #GCMRL# 339 dt 32.000000 rms 0.517 0.065% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7450 tsec 4.7360 #GCMRL# 340 dt 32.000000 rms 0.516 0.084% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7390 tsec 4.7260 #GCMRL# 341 dt 32.000000 rms 0.516 0.067% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7620 tsec 4.7470 #GCMRL# 342 dt 32.000000 rms 0.516 0.038% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7650 tsec 4.7520 #GCMRL# 343 dt 32.000000 rms 0.515 0.070% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7870 tsec 4.7740 #GCMRL# 344 dt 32.000000 rms 0.515 0.077% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.8490 tsec 4.8410 #GCMRL# 345 dt 32.000000 rms 0.515 0.044% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7710 tsec 4.7560 #GCMRL# 346 dt 32.000000 rms 0.514 0.051% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7360 tsec 4.7260 #GCMRL# 347 dt 32.000000 rms 0.514 0.089% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.8230 tsec 4.8120 #GCMRL# 348 dt 16.000000 rms 0.514 0.012% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.8220 tsec 5.5040 #GCMRL# 349 dt 2.000000 rms 0.514 0.002% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.8390 tsec 6.2310 #FOTS# QuadFit found better minimum quadopt=(dt=0.7,rms=0.513802) vs oldopt=(dt=0.5,rms=0.513804) #GCAMreg# pass 0 level1 3 level2 1 tsec 568.113 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.12 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.514065 #FOTS# QuadFit found better minimum quadopt=(dt=72.8511,rms=0.510863) vs oldopt=(dt=32,rms=0.51144) #GCMRL# 351 dt 72.851064 rms 0.511 0.623% neg 0 invalid 762 tFOTS 14.0890 tGradient 3.8400 tsec 18.9150 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.510521) vs oldopt=(dt=8,rms=0.510595) #GCMRL# 352 dt 11.200000 rms 0.511 0.067% neg 0 invalid 762 tFOTS 14.1900 tGradient 3.7250 tsec 18.9000 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.510361) vs oldopt=(dt=8,rms=0.510387) #GCMRL# 353 dt 11.200000 rms 0.510 0.000% neg 0 invalid 762 tFOTS 14.0970 tGradient 3.7680 tsec 18.8750 #GCMRL# 354 dt 11.200000 rms 0.510 0.017% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7140 tsec 4.7000 #GCMRL# 355 dt 11.200000 rms 0.510 0.023% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7110 tsec 4.6950 #GCMRL# 356 dt 11.200000 rms 0.510 0.018% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7400 tsec 4.7250 #GCMRL# 357 dt 11.200000 rms 0.510 0.028% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7140 tsec 4.7070 #GCMRL# 358 dt 11.200000 rms 0.510 0.039% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7220 tsec 4.7080 #GCMRL# 359 dt 11.200000 rms 0.510 0.042% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7390 tsec 4.7260 #GCMRL# 360 dt 11.200000 rms 0.509 0.045% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7360 tsec 4.7210 #GCMRL# 361 dt 11.200000 rms 0.509 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7400 tsec 4.7300 #GCMRL# 362 dt 11.200000 rms 0.509 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7730 tsec 4.7600 #GCMRL# 363 dt 11.200000 rms 0.509 0.016% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.6610 tsec 4.6480 #GCMRL# 364 dt 11.200000 rms 0.509 0.016% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7160 tsec 4.7020 #GCMRL# 365 dt 11.200000 rms 0.509 0.024% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7720 tsec 4.7590 #GCMRL# 366 dt 11.200000 rms 0.509 0.021% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7120 tsec 4.7150 #FOTS# QuadFit found better minimum quadopt=(dt=102.4,rms=0.507972) vs oldopt=(dt=128,rms=0.508023) #GCMRL# 367 dt 102.400000 rms 0.508 0.115% neg 0 invalid 762 tFOTS 14.0780 tGradient 3.7480 tsec 18.8110 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.507883) vs oldopt=(dt=8,rms=0.507909) #GCMRL# 368 dt 11.200000 rms 0.508 0.000% neg 0 invalid 762 tFOTS 14.0830 tGradient 3.7430 tsec 18.8350 #GCMRL# 369 dt 11.200000 rms 0.508 0.015% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7120 tsec 4.6990 #GCMRL# 370 dt 11.200000 rms 0.508 0.002% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7170 tsec 4.7050 setting smoothness cost coefficient to 0.400 #GCAMreg# pass 0 level1 2 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.40 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.53298 #GCMRL# 372 dt 0.000000 rms 0.533 0.041% neg 0 invalid 762 tFOTS 13.3260 tGradient 3.4320 tsec 17.7430 #GCAMreg# pass 0 level1 2 level2 1 tsec 40.517 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.40 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.53298 #GCMRL# 374 dt 0.000000 rms 0.533 0.041% neg 0 invalid 762 tFOTS 13.2890 tGradient 3.4290 tsec 17.7060 setting smoothness cost coefficient to 1.000 #GCAMreg# pass 0 level1 1 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=1.00 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.58247 #FOTS# QuadFit found better minimum quadopt=(dt=1.79574,rms=0.575782) vs oldopt=(dt=1.28,rms=0.57649) #GCMRL# 376 dt 1.795745 rms 0.576 1.148% neg 0 invalid 762 tFOTS 13.2710 tGradient 3.2800 tsec 17.5380 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.575554) vs oldopt=(dt=0.32,rms=0.575589) #GCMRL# 377 dt 0.448000 rms 0.576 0.000% neg 0 invalid 762 tFOTS 13.2580 tGradient 3.5860 tsec 17.8610 #GCMRL# 378 dt 0.448000 rms 0.576 0.002% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.5050 tsec 4.4920 #GCAMreg# pass 0 level1 1 level2 1 tsec 49.407 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=1.00 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.575753 #FOTS# QuadFit found better minimum quadopt=(dt=1.024,rms=0.574905) vs oldopt=(dt=1.28,rms=0.574931) #GCMRL# 380 dt 1.024000 rms 0.575 0.147% neg 0 invalid 762 tFOTS 13.3060 tGradient 3.4020 tsec 17.6950 #GCMRL# 381 dt 0.320000 rms 0.575 0.000% neg 0 invalid 762 tFOTS 13.3230 tGradient 3.3650 tsec 17.7030 resetting metric properties... setting smoothness cost coefficient to 2.000 #GCAMreg# pass 0 level1 0 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.00 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=2.0,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.525417 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.512007) vs oldopt=(dt=0.32,rms=0.515593) #GCMRL# 383 dt 0.448000 rms 0.512 2.552% neg 0 invalid 762 tFOTS 12.4320 tGradient 2.7920 tsec 16.2100 #FOTS# QuadFit found better minimum quadopt=(dt=1.536,rms=0.500625) vs oldopt=(dt=1.28,rms=0.502344) #GCMRL# 384 dt 1.536000 rms 0.501 2.223% neg 0 invalid 762 tFOTS 13.2780 tGradient 2.8340 tsec 17.0980 #GCMRL# 385 dt 0.050000 rms 0.501 0.000% neg 0 invalid 762 tFOTS 11.6640 tGradient 2.8100 tsec 16.4410 #GCAMreg# pass 0 level1 0 level2 1 tsec 58.6 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.00 tol=5.00e-02, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=0.5,type=2, relabel=0, neg=no blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.500892 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.497983) vs oldopt=(dt=0.32,rms=0.498612) #GCMRL# 387 dt 0.448000 rms 0.498 0.581% neg 0 invalid 762 tFOTS 12.4440 tGradient 2.8010 tsec 16.2330 #FOTS# QuadFit found better minimum quadopt=(dt=0.448,rms=0.497757) vs oldopt=(dt=0.32,rms=0.497806) #GCMRL# 388 dt 0.448000 rms 0.498 0.000% neg 0 invalid 762 tFOTS 12.4420 tGradient 2.8250 tsec 16.2800 #GCMRL# 389 dt 0.448000 rms 0.497 0.089% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7800 tsec 3.7650 #GCMRL# 390 dt 0.448000 rms 0.497 0.120% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7450 tsec 3.7320 #GCMRL# 391 dt 0.448000 rms 0.496 0.128% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7990 tsec 3.7830 #GCMRL# 392 dt 0.448000 rms 0.495 0.119% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7720 tsec 3.7570 #GCMRL# 393 dt 0.448000 rms 0.495 0.130% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7700 tsec 3.7660 #GCMRL# 394 dt 0.448000 rms 0.494 0.146% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.8290 tsec 3.8140 #GCMRL# 395 dt 0.448000 rms 0.493 0.143% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7720 tsec 3.7580 #GCMRL# 396 dt 0.448000 rms 0.493 0.098% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.7720 tsec 3.7580 #GCMRL# 397 dt 0.448000 rms 0.493 0.042% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.8060 tsec 3.7920 #GCMRL# 398 dt 0.448000 rms 0.493 -0.014% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.8280 tsec 4.7380 GCAMregister done in 58.8972 min ********************* ALLOWING NEGATIVE NODES IN DEFORMATION******************************** noneg post Starting GCAMregister() label assignment complete, 0 changed (0.00%) npasses = 1, nlevels = 6 #pass# 1 of 1 ************************ enabling zero nodes setting smoothness cost coefficient to 0.008 #GCAMreg# pass 0 level1 5 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.01 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.490356 #GCMRL# 400 dt 0.000000 rms 0.490 0.055% neg 0 invalid 762 tFOTS 14.9480 tGradient 7.5060 tsec 23.4390 #GCAMreg# pass 0 level1 5 level2 1 tsec 52.073 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.01 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.490356 #FOTS# QuadFit found better minimum quadopt=(dt=73.984,rms=0.490006) vs oldopt=(dt=92.48,rms=0.490008) #GCMRL# 402 dt 73.984000 rms 0.490 0.071% neg 0 invalid 762 tFOTS 14.9150 tGradient 7.5340 tsec 23.4330 #FOTS# QuadFit found better minimum quadopt=(dt=295.936,rms=0.489794) vs oldopt=(dt=369.92,rms=0.489815) #GCMRL# 403 dt 295.936000 rms 0.490 0.000% neg 0 invalid 762 tFOTS 14.9300 tGradient 7.4460 tsec 23.3850 #GCMRL# 404 dt 295.936000 rms 0.489 0.064% neg 0 invalid 762 tFOTS 0.0000 tGradient 7.5950 tsec 8.5830 setting smoothness cost coefficient to 0.031 #GCAMreg# pass 0 level1 4 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.03 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.489792 #FOTS# QuadFit found better minimum quadopt=(dt=20.736,rms=0.489402) vs oldopt=(dt=25.92,rms=0.489413) #GCMRL# 406 dt 20.736000 rms 0.489 0.080% neg 0 invalid 762 tFOTS 14.9520 tGradient 4.3550 tsec 20.2940 #FOTS# QuadFit found better minimum quadopt=(dt=15.552,rms=0.489345) vs oldopt=(dt=25.92,rms=0.489355) #GCMRL# 407 dt 15.552000 rms 0.489 0.000% neg 0 invalid 762 tFOTS 14.9510 tGradient 4.3590 tsec 20.3190 #GCMRL# 408 dt 15.552000 rms 0.489 0.009% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3430 tsec 5.3380 #GCAMreg# pass 0 level1 4 level2 1 tsec 56.436 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.03 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.489584 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.48648) vs oldopt=(dt=103.68,rms=0.48689) #GCMRL# 410 dt 145.152000 rms 0.486 0.634% neg 0 invalid 762 tFOTS 15.0000 tGradient 4.4140 tsec 20.3990 #FOTS# QuadFit found better minimum quadopt=(dt=31.104,rms=0.486205) vs oldopt=(dt=25.92,rms=0.486216) #GCMRL# 411 dt 31.104000 rms 0.486 0.000% neg 0 invalid 762 tFOTS 14.9520 tGradient 4.3130 tsec 20.2750 #GCMRL# 412 dt 31.104000 rms 0.486 0.034% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3650 tsec 5.3540 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 413 dt 31.104000 rms 0.486 0.049% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3290 tsec 6.5920 #GCMRL# 414 dt 31.104000 rms 0.485 0.077% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3580 tsec 5.3410 #GCMRL# 415 dt 31.104000 rms 0.485 0.120% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.4120 tsec 5.4080 #GCMRL# 416 dt 31.104000 rms 0.484 0.150% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3490 tsec 5.3340 #GCMRL# 417 dt 31.104000 rms 0.483 0.146% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3500 tsec 5.3950 #GCMRL# 418 dt 31.104000 rms 0.483 0.132% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.2940 tsec 5.2800 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 #GCMRL# 419 dt 31.104000 rms 0.482 0.106% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3130 tsec 9.3470 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 #GCMRL# 420 dt 31.104000 rms 0.482 0.094% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3820 tsec 9.3990 #FOTS# QuadFit found better minimum quadopt=(dt=82.944,rms=0.481623) vs oldopt=(dt=103.68,rms=0.481624) #GCMRL# 421 dt 82.944000 rms 0.482 0.000% neg 0 invalid 762 tFOTS 14.9120 tGradient 4.3540 tsec 20.2730 #GCMRL# 422 dt 82.944000 rms 0.482 0.006% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3520 tsec 5.3460 #GCMRL# 423 dt 82.944000 rms 0.481 0.083% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3610 tsec 5.3480 #GCMRL# 424 dt 82.944000 rms 0.481 0.097% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3700 tsec 5.3610 #GCMRL# 425 dt 82.944000 rms 0.480 0.070% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3770 tsec 5.3610 #GCMRL# 426 dt 82.944000 rms 0.480 0.114% neg 0 invalid 762 tFOTS 0.0000 tGradient 4.3730 tsec 5.3580 setting smoothness cost coefficient to 0.118 #GCAMreg# pass 0 level1 3 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.12 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.480188 #FOTS# QuadFit found better minimum quadopt=(dt=23.8933,rms=0.478917) vs oldopt=(dt=32,rms=0.479087) iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 428 dt 23.893333 rms 0.479 0.265% neg 0 invalid 762 tFOTS 15.7800 tGradient 3.7770 tsec 21.8180 #FOTS# QuadFit found better minimum quadopt=(dt=73.4815,rms=0.477322) vs oldopt=(dt=32,rms=0.477578) iter 0, gcam->neg = 1 after 7 iterations, nbhd size=1, neg = 0 #GCMRL# 429 dt 73.481481 rms 0.477 0.326% neg 0 invalid 762 tFOTS 15.7730 tGradient 3.6640 tsec 24.8760 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.4759) vs oldopt=(dt=32,rms=0.475994) #GCMRL# 430 dt 44.800000 rms 0.476 0.305% neg 0 invalid 762 tFOTS 15.8480 tGradient 3.7910 tsec 20.6250 #FOTS# QuadFit found better minimum quadopt=(dt=38.4,rms=0.47405) vs oldopt=(dt=32,rms=0.474084) iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 431 dt 38.400000 rms 0.474 0.389% neg 0 invalid 762 tFOTS 15.8160 tGradient 3.6930 tsec 21.7760 #FOTS# QuadFit found better minimum quadopt=(dt=19.2,rms=0.473516) vs oldopt=(dt=32,rms=0.47363) iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 #GCMRL# 432 dt 19.200000 rms 0.474 0.000% neg 0 invalid 762 tFOTS 15.7610 tGradient 3.6940 tsec 24.4630 iter 0, gcam->neg = 1 after 6 iterations, nbhd size=1, neg = 0 #GCMRL# 433 dt 19.200000 rms 0.473 0.109% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.6480 tsec 8.6290 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 434 dt 19.200000 rms 0.472 0.145% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.6510 tsec 5.9170 #GCMRL# 435 dt 19.200000 rms 0.472 0.181% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7270 tsec 4.7120 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 436 dt 19.200000 rms 0.471 0.192% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7210 tsec 5.9740 #GCMRL# 437 dt 19.200000 rms 0.470 0.187% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.6430 tsec 4.6280 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 #GCMRL# 438 dt 19.200000 rms 0.469 0.176% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7810 tsec 6.5510 #GCMRL# 439 dt 19.200000 rms 0.468 0.167% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.6770 tsec 4.6650 #GCMRL# 440 dt 19.200000 rms 0.467 0.155% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7230 tsec 4.7040 iter 0, gcam->neg = 2 after 2 iterations, nbhd size=0, neg = 0 #GCMRL# 441 dt 19.200000 rms 0.467 0.152% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7880 tsec 6.9330 #GCMRL# 442 dt 19.200000 rms 0.466 0.139% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7270 tsec 4.7130 #GCMRL# 443 dt 19.200000 rms 0.465 0.118% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7180 tsec 4.7010 iter 0, gcam->neg = 2 after 3 iterations, nbhd size=0, neg = 0 #GCMRL# 444 dt 19.200000 rms 0.465 0.095% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7710 tsec 7.4130 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.464777) vs oldopt=(dt=32,rms=0.464819) #GCMRL# 445 dt 44.800000 rms 0.465 0.000% neg 0 invalid 762 tFOTS 14.9230 tGradient 3.7610 tsec 19.6920 #GCAMreg# pass 0 level1 3 level2 1 tsec 212.655 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.12 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.464986 #FOTS# QuadFit found better minimum quadopt=(dt=71.5,rms=0.460588) vs oldopt=(dt=32,rms=0.461563) iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 447 dt 71.500000 rms 0.461 0.946% neg 0 invalid 762 tFOTS 15.8180 tGradient 3.7470 tsec 21.8340 #FOTS# QuadFit found better minimum quadopt=(dt=25.4031,rms=0.459257) vs oldopt=(dt=32,rms=0.459406) #GCMRL# 448 dt 25.403077 rms 0.459 0.289% neg 0 invalid 762 tFOTS 15.7730 tGradient 3.7730 tsec 20.5330 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.458546) vs oldopt=(dt=32,rms=0.458633) #GCMRL# 449 dt 44.800000 rms 0.459 0.000% neg 0 invalid 762 tFOTS 15.7750 tGradient 3.8020 tsec 20.5850 #GCMRL# 450 dt 44.800000 rms 0.458 0.074% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7340 tsec 4.7180 #GCMRL# 451 dt 44.800000 rms 0.457 0.183% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.8600 tsec 4.8500 #GCMRL# 452 dt 44.800000 rms 0.457 0.112% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7810 tsec 4.7660 #GCMRL# 453 dt 44.800000 rms 0.457 0.010% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.8020 tsec 4.8120 #FOTS# QuadFit found better minimum quadopt=(dt=38.4,rms=0.456472) vs oldopt=(dt=32,rms=0.456474) #GCMRL# 454 dt 38.400000 rms 0.456 0.074% neg 0 invalid 762 tFOTS 15.7690 tGradient 3.6900 tsec 20.4450 #FOTS# QuadFit found better minimum quadopt=(dt=11.2,rms=0.456393) vs oldopt=(dt=8,rms=0.456412) #GCMRL# 455 dt 11.200000 rms 0.456 0.000% neg 0 invalid 762 tFOTS 15.7570 tGradient 3.7490 tsec 20.5160 #GCMRL# 456 dt 11.200000 rms 0.456 0.020% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7310 tsec 4.7140 #GCMRL# 457 dt 11.200000 rms 0.456 0.014% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7350 tsec 4.7270 #GCMRL# 458 dt 11.200000 rms 0.456 0.020% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.6670 tsec 4.6550 #GCMRL# 459 dt 11.200000 rms 0.456 0.025% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.6920 tsec 4.7350 #GCMRL# 460 dt 11.200000 rms 0.456 0.031% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.6900 tsec 4.6780 setting smoothness cost coefficient to 0.400 #GCAMreg# pass 0 level1 2 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.40 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.462154 #GCMRL# 462 dt 0.000000 rms 0.462 0.061% neg 0 invalid 762 tFOTS 14.9710 tGradient 3.4700 tsec 19.4260 #GCAMreg# pass 0 level1 2 level2 1 tsec 44.039 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=0.40 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.462154 #FOTS# QuadFit found better minimum quadopt=(dt=1.008,rms=0.461834) vs oldopt=(dt=0.72,rms=0.461842) #GCMRL# 464 dt 1.008000 rms 0.462 0.069% neg 0 invalid 762 tFOTS 15.8530 tGradient 3.4820 tsec 20.3200 #FOTS# QuadFit found better minimum quadopt=(dt=1.008,rms=0.461827) vs oldopt=(dt=0.72,rms=0.46183) #GCMRL# 465 dt 1.008000 rms 0.462 0.000% neg 0 invalid 762 tFOTS 15.8560 tGradient 3.4740 tsec 20.3410 #GCMRL# 466 dt 1.008000 rms 0.462 0.004% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.4170 tsec 4.4050 setting smoothness cost coefficient to 1.000 #GCAMreg# pass 0 level1 1 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=1.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.473471 #FOTS# QuadFit found better minimum quadopt=(dt=0.768,rms=0.472704) vs oldopt=(dt=1.28,rms=0.472802) #GCMRL# 468 dt 0.768000 rms 0.473 0.162% neg 0 invalid 762 tFOTS 15.8040 tGradient 3.3190 tsec 20.1110 #GCMRL# 469 dt 0.320000 rms 0.473 0.000% neg 0 invalid 762 tFOTS 15.8500 tGradient 3.3460 tsec 20.2060 #GCAMreg# pass 0 level1 1 level2 1 tsec 49.697 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=1.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.472936 #FOTS# QuadFit found better minimum quadopt=(dt=1.536,rms=0.471696) vs oldopt=(dt=1.28,rms=0.471729) #GCMRL# 471 dt 1.536000 rms 0.472 0.262% neg 0 invalid 762 tFOTS 15.8130 tGradient 3.2870 tsec 20.0860 #FOTS# QuadFit found better minimum quadopt=(dt=0.768,rms=0.471577) vs oldopt=(dt=1.28,rms=0.471613) #GCMRL# 472 dt 0.768000 rms 0.472 0.000% neg 0 invalid 762 tFOTS 15.7990 tGradient 3.3200 tsec 20.1300 resetting metric properties... setting smoothness cost coefficient to 2.000 #GCAMreg# pass 0 level1 0 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.461351 #FOTS# QuadFit found better minimum quadopt=(dt=2.1381,rms=0.432816) vs oldopt=(dt=1.28,rms=0.437541) iter 0, gcam->neg = 504 after 14 iterations, nbhd size=1, neg = 0 #GCMRL# 474 dt 2.138098 rms 0.435 5.661% neg 0 invalid 762 tFOTS 15.9130 tGradient 2.7260 tsec 27.3220 #GCMRL# 475 dt 0.080000 rms 0.435 0.000% neg 0 invalid 762 tFOTS 15.8320 tGradient 2.7810 tsec 19.6220 #GCAMreg# pass 0 level1 0 level2 1 tsec 55.761 sigma 0.5 l_jacobian=1.00 l_label=1.00 l_log_likelihood=0.20 l_smoothness=2.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.435321 #GCMRL# 477 dt 0.080000 rms 0.435 0.129% neg 0 invalid 762 tFOTS 15.8330 tGradient 2.7890 tsec 19.6100 #FOTS# QuadFit found better minimum quadopt=(dt=0.007,rms=0.434753) vs oldopt=(dt=0.005,rms=0.434754) #GCMRL# 478 dt 0.007000 rms 0.435 0.000% neg 0 invalid 762 tFOTS 15.9290 tGradient 2.7600 tsec 19.7020 label assignment complete, 0 changed (0.00%) GCAMregister done in 16.605 min Starting GCAMcomputeMaxPriorLabels() Morphing with label term set to 0 ******************************* Starting GCAMregister() label assignment complete, 0 changed (0.00%) npasses = 1, nlevels = 6 #pass# 1 of 1 ************************ enabling zero nodes setting smoothness cost coefficient to 0.008 #GCAMreg# pass 0 level1 5 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.01 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.421533 #GCAMreg# pass 0 level1 5 level2 1 tsec 27.371 sigma 0.5 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.01 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=256, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.421533 #FOTS# QuadFit found better minimum quadopt=(dt=73.984,rms=0.421504) vs oldopt=(dt=92.48,rms=0.421507) #GCMRL# 481 dt 73.984000 rms 0.422 0.007% neg 0 invalid 762 tFOTS 14.6680 tGradient 6.7820 tsec 22.4170 #FOTS# QuadFit found better minimum quadopt=(dt=129.472,rms=0.421487) vs oldopt=(dt=92.48,rms=0.42149) #GCMRL# 482 dt 129.472000 rms 0.421 0.000% neg 0 invalid 762 tFOTS 14.6490 tGradient 6.7800 tsec 22.4200 #GCMRL# 483 dt 129.472000 rms 0.421 0.004% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.7880 tsec 7.7550 #GCMRL# 484 dt 129.472000 rms 0.421 0.005% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.7750 tsec 7.7420 #GCMRL# 485 dt 129.472000 rms 0.421 0.002% neg 0 invalid 762 tFOTS 0.0000 tGradient 6.7730 tsec 7.7400 setting smoothness cost coefficient to 0.031 #GCAMreg# pass 0 level1 4 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.03 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.4216 #GCAMreg# pass 0 level1 4 level2 1 tsec 24.318 sigma 0.5 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.03 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=64, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.4216 #FOTS# QuadFit found better minimum quadopt=(dt=145.152,rms=0.42112) vs oldopt=(dt=103.68,rms=0.421215) #GCMRL# 488 dt 145.152000 rms 0.421 0.114% neg 0 invalid 762 tFOTS 14.6090 tGradient 3.7290 tsec 19.3070 #FOTS# QuadFit found better minimum quadopt=(dt=124.416,rms=0.420964) vs oldopt=(dt=103.68,rms=0.42097) #GCMRL# 489 dt 124.416000 rms 0.421 0.000% neg 0 invalid 762 tFOTS 14.5880 tGradient 3.6570 tsec 19.2420 #GCMRL# 490 dt 124.416000 rms 0.421 0.054% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.6700 tsec 4.6360 #GCMRL# 491 dt 124.416000 rms 0.421 0.018% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.6590 tsec 4.6280 #GCMRL# 492 dt 124.416000 rms 0.420 0.131% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.6660 tsec 4.6430 #GCMRL# 493 dt 124.416000 rms 0.420 0.037% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.6700 tsec 4.6410 #GCMRL# 494 dt 124.416000 rms 0.420 0.030% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.6630 tsec 4.6570 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.41968) vs oldopt=(dt=25.92,rms=0.419711) #GCMRL# 495 dt 36.288000 rms 0.420 0.036% neg 0 invalid 762 tFOTS 15.4580 tGradient 3.6660 tsec 20.1480 #GCMRL# 496 dt 414.720000 rms 0.420 0.040% neg 0 invalid 762 tFOTS 14.5960 tGradient 3.6710 tsec 19.2330 #FOTS# QuadFit found better minimum quadopt=(dt=36.288,rms=0.419421) vs oldopt=(dt=25.92,rms=0.419437) #GCMRL# 497 dt 36.288000 rms 0.419 0.000% neg 0 invalid 762 tFOTS 15.4080 tGradient 3.6560 tsec 20.0570 #GCMRL# 498 dt 36.288000 rms 0.419 0.006% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.6800 tsec 4.6540 #GCMRL# 499 dt 36.288000 rms 0.419 0.007% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.6670 tsec 4.6330 #GCMRL# 500 dt 36.288000 rms 0.419 0.008% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7170 tsec 4.6840 #GCMRL# 501 dt 36.288000 rms 0.419 0.009% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.6540 tsec 4.6230 #GCMRL# 502 dt 36.288000 rms 0.419 0.010% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.6580 tsec 4.6280 #GCMRL# 503 dt 36.288000 rms 0.419 0.010% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.7270 tsec 4.6960 #GCMRL# 504 dt 36.288000 rms 0.419 0.011% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.6560 tsec 4.6240 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 505 dt 36.288000 rms 0.419 0.013% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.6630 tsec 5.9130 #GCMRL# 506 dt 36.288000 rms 0.419 0.015% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.6590 tsec 4.6290 setting smoothness cost coefficient to 0.118 #GCAMreg# pass 0 level1 3 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.12 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.419749 #FOTS# QuadFit found better minimum quadopt=(dt=2.8,rms=0.419723) vs oldopt=(dt=2,rms=0.419728) #GCMRL# 508 dt 2.800000 rms 0.420 0.006% neg 0 invalid 762 tFOTS 15.4370 tGradient 3.0370 tsec 19.4440 #GCMRL# 509 dt 2.000000 rms 0.420 0.000% neg 0 invalid 762 tFOTS 15.4890 tGradient 3.0520 tsec 19.5350 #GCAMreg# pass 0 level1 3 level2 1 tsec 47.984 sigma 0.5 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.12 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=16, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.419718 #FOTS# QuadFit found better minimum quadopt=(dt=179.2,rms=0.41577) vs oldopt=(dt=128,rms=0.416061) iter 0, gcam->neg = 4 after 9 iterations, nbhd size=1, neg = 0 #GCMRL# 511 dt 179.200000 rms 0.416 0.912% neg 0 invalid 762 tFOTS 15.4340 tGradient 3.0350 tsec 24.7940 #FOTS# QuadFit found better minimum quadopt=(dt=25.1852,rms=0.414931) vs oldopt=(dt=32,rms=0.415049) #GCMRL# 512 dt 25.185185 rms 0.415 0.000% neg 0 invalid 762 tFOTS 15.4300 tGradient 3.0350 tsec 19.4560 #GCMRL# 513 dt 25.185185 rms 0.415 0.069% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0490 tsec 4.0260 #GCMRL# 514 dt 25.185185 rms 0.414 0.065% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0440 tsec 4.0120 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 #GCMRL# 515 dt 25.185185 rms 0.414 0.073% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0380 tsec 5.7270 iter 0, gcam->neg = 1 after 2 iterations, nbhd size=0, neg = 0 #GCMRL# 516 dt 25.185185 rms 0.414 0.107% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0930 tsec 6.2370 iter 0, gcam->neg = 3 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 517 dt 25.185185 rms 0.413 0.155% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0360 tsec 5.2690 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 518 dt 25.185185 rms 0.412 0.176% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0960 tsec 5.3330 iter 0, gcam->neg = 2 after 0 iterations, nbhd size=0, neg = 0 #GCMRL# 519 dt 25.185185 rms 0.412 0.160% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0370 tsec 5.2720 iter 0, gcam->neg = 1 after 7 iterations, nbhd size=1, neg = 0 #GCMRL# 520 dt 25.185185 rms 0.411 0.128% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0480 tsec 8.4620 iter 0, gcam->neg = 2 after 1 iterations, nbhd size=0, neg = 0 #GCMRL# 521 dt 25.185185 rms 0.411 0.107% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0390 tsec 5.7250 #GCMRL# 522 dt 25.185185 rms 0.410 0.100% neg 0 invalid 762 tFOTS 0.0000 tGradient 3.0360 tsec 4.0290 #FOTS# QuadFit found better minimum quadopt=(dt=44.8,rms=0.410076) vs oldopt=(dt=32,rms=0.410103) #GCMRL# 523 dt 44.800000 rms 0.410 0.000% neg 0 invalid 762 tFOTS 14.6000 tGradient 3.0360 tsec 18.6280 setting smoothness cost coefficient to 0.400 #GCAMreg# pass 0 level1 2 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.40 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.414324 #GCMRL# 525 dt 0.000176 rms 0.414 0.000% neg 0 invalid 762 tFOTS 19.5950 tGradient 2.8110 tsec 23.4020 #GCAMreg# pass 0 level1 2 level2 1 tsec 32.184 sigma 0.5 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=0.40 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=4, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.414324 #FOTS# QuadFit found better minimum quadopt=(dt=4.88889,rms=0.414142) vs oldopt=(dt=2.88,rms=0.414173) #GCMRL# 527 dt 4.888889 rms 0.414 0.044% neg 0 invalid 762 tFOTS 15.4420 tGradient 2.8100 tsec 19.2180 #FOTS# QuadFit found better minimum quadopt=(dt=4.032,rms=0.414082) vs oldopt=(dt=2.88,rms=0.414086) #GCMRL# 528 dt 4.032000 rms 0.414 0.000% neg 0 invalid 762 tFOTS 15.4430 tGradient 2.8100 tsec 19.2470 #GCMRL# 529 dt 4.032000 rms 0.414 0.007% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.8240 tsec 3.7920 setting smoothness cost coefficient to 1.000 #GCAMreg# pass 0 level1 1 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=1.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.421098 #GCAMreg# pass 0 level1 1 level2 1 tsec 23.329 sigma 0.5 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=1.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=1, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.421098 resetting metric properties... setting smoothness cost coefficient to 2.000 #GCAMreg# pass 0 level1 0 level2 0 tsec 0 sigma 2 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=2.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=2.0,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=2.000... GCAMRegisterLevel(): init RMS 0.409286 #FOTS# QuadFit found better minimum quadopt=(dt=1.30145,rms=0.399569) vs oldopt=(dt=1.28,rms=0.399582) iter 0, gcam->neg = 359 after 14 iterations, nbhd size=1, neg = 0 #GCMRL# 533 dt 1.301453 rms 0.402 1.863% neg 0 invalid 762 tFOTS 15.4580 tGradient 2.0910 tsec 26.2780 #FOTS# QuadFit found better minimum quadopt=(dt=2.34375e-05,rms=0.401661) vs oldopt=(dt=1.95313e-05,rms=0.401661) #GCMRL# 534 dt 0.000023 rms 0.402 0.000% neg 0 invalid 762 tFOTS 19.5640 tGradient 2.0970 tsec 22.6550 #GCAMreg# pass 0 level1 0 level2 1 tsec 56.995 sigma 0.5 l_jacobian=1.00 l_log_likelihood=0.20 l_smoothness=2.00 tol=2.50e-01, dt=5.00e-02, exp_k=20.0, momentum=0.90, levels=6, niter=500, lbl_dist=10.00, avgs=0, sigma=0.5,type=2, relabel=0, neg=yes blurring input image with Gaussian with sigma=0.500... GCAMRegisterLevel(): init RMS 0.401661 #FOTS# QuadFit found better minimum quadopt=(dt=0.112,rms=0.401375) vs oldopt=(dt=0.08,rms=0.401411) #GCMRL# 536 dt 0.112000 rms 0.401 0.071% neg 0 invalid 762 tFOTS 15.4650 tGradient 2.0880 tsec 18.5200 #FOTS# QuadFit found better minimum quadopt=(dt=0.096,rms=0.401283) vs oldopt=(dt=0.08,rms=0.401284) #GCMRL# 537 dt 0.096000 rms 0.401 0.000% neg 0 invalid 762 tFOTS 15.4720 tGradient 2.0970 tsec 18.5600 #GCMRL# 538 dt 0.096000 rms 0.401 0.011% neg 0 invalid 762 tFOTS 0.0000 tGradient 2.1530 tsec 3.1260 GCAMregister done in 11.816 min writing output transformation to transforms/talairach.m3z... GCAMwrite Calls to gcamLogLikelihoodEnergy 4274 tmin = 13.3955 Calls to gcamLabelEnergy 3730 tmin = 1.12803 Calls to gcamJacobianEnergy 4274 tmin = 15.5375 Calls to gcamSmoothnessEnergy 4274 tmin = 13.1793 Calls to gcamLogLikelihoodTerm 540 tmin = 4.02353 Calls to gcamLabelTerm 480 tmin = 6.23477 Calls to gcamJacobianTerm 540 tmin = 10.0376 Calls to gcamSmoothnessTerm 540 tmin = 2.94175 Calls to gcamComputeGradient 540 tmin = 43.1831 Calls to gcamComputeMetricProperties 5771 tmin = 11.7383 mri_ca_register took 1 hours, 49 minutes and 19 seconds. #VMPC# mri_ca_register VmPeak 2085280 FSRUNTIME@ mri_ca_register 1.8220 hours 1 threads @#@FSTIME 2020:07:23:06:32:49 mri_ca_register N 9 e 6559.28 S 11.85 U 6547.88 P 100% M 1319624 F 2 R 19123485 W 0 c 1697 w 1083 I 2368 O 63016 L 2.07 2.08 1.96 @#@FSLOADPOST 2020:07:23:08:22:09 mri_ca_register N 9 2.04 2.08 2.07 #-------------------------------------- #@# SubCort Seg Thu Jul 23 08:22:09 EDT 2020 mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/dev/average/RB_all_2020-01-02.gca aseg.auto_noCCseg.mgz sysname Linux hostname nike machine x86_64 setenv SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running cd /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /usr/local/freesurfer/dev/average/RB_all_2020-01-02.gca aseg.auto_noCCseg.mgz 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 == Number of threads available to for OpenMP = 1 == reading 1 input volumes reading classifier array from /usr/local/freesurfer/dev/average/RB_all_2020-01-02.gca reading input volume from norm.mgz average std[0] = 7.2 reading transform from transforms/talairach.m3z setting orig areas to linear transform determinant scaled 7.82 Atlas used for the 3D morph was /usr/local/freesurfer/dev/average/RB_all_2020-01-02.gca average std = 7.2 using min determinant for regularization = 5.2 0 singular and 0 ill-conditioned covariance matrices regularized labeling volume... renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15521 (20) mri peak = 0.23561 (27) Left_Lateral_Ventricle (4): linear fit = 1.30 x + 0.0 (1496 voxels, overlap=0.176) Left_Lateral_Ventricle (4): linear fit = 1.30 x + 0.0 (1496 voxels, peak = 26), gca=26.1 gca peak = 0.20380 (13) mri peak = 0.16851 (31) Right_Lateral_Ventricle (43): linear fit = 2.08 x + 0.0 (1127 voxels, overlap=0.141) Right_Lateral_Ventricle (43): linear fit = 1.50 x + 0.0 (1127 voxels, peak = 27), gca=19.5 gca peak = 0.26283 (96) mri peak = 0.18928 (100) Right_Pallidum (52): linear fit = 1.03 x + 0.0 (788 voxels, overlap=0.937) Right_Pallidum (52): linear fit = 1.03 x + 0.0 (788 voxels, peak = 99), gca=99.4 gca peak = 0.15814 (97) mri peak = 0.28889 (101) Left_Pallidum (13): linear fit = 1.04 x + 0.0 (804 voxels, overlap=0.487) Left_Pallidum (13): linear fit = 1.04 x + 0.0 (804 voxels, peak = 101), gca=101.4 gca peak = 0.27624 (56) mri peak = 0.11246 (74) Right_Hippocampus (53): linear fit = 1.29 x + 0.0 (1240 voxels, overlap=0.022) Right_Hippocampus (53): linear fit = 1.29 x + 0.0 (1240 voxels, peak = 73), gca=72.5 gca peak = 0.28723 (59) mri peak = 0.11317 (75) Left_Hippocampus (17): linear fit = 1.29 x + 0.0 (1144 voxels, overlap=0.021) Left_Hippocampus (17): linear fit = 1.29 x + 0.0 (1144 voxels, peak = 76), gca=76.4 gca peak = 0.07623 (103) mri peak = 0.19174 (104) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (53493 voxels, overlap=0.567) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (53493 voxels, peak = 104), gca=103.5 gca peak = 0.07837 (105) mri peak = 0.20132 (105) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (52971 voxels, overlap=0.525) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (52971 voxels, peak = 106), gca=105.5 gca peak = 0.10165 (58) mri peak = 0.05997 (77) Left_Cerebral_Cortex (3): linear fit = 1.33 x + 0.0 (36365 voxels, overlap=0.001) Left_Cerebral_Cortex (3): linear fit = 1.33 x + 0.0 (36365 voxels, peak = 77), gca=76.9 gca peak = 0.11113 (58) mri peak = 0.06320 (79) Right_Cerebral_Cortex (42): linear fit = 1.35 x + 0.0 (32499 voxels, overlap=0.000) Right_Cerebral_Cortex (42): linear fit = 1.35 x + 0.0 (32499 voxels, peak = 78), gca=78.0 gca peak = 0.27796 (67) mri peak = 0.12702 (82) Right_Caudate (50): linear fit = 1.22 x + 0.0 (866 voxels, overlap=0.018) Right_Caudate (50): linear fit = 1.22 x + 0.0 (866 voxels, peak = 81), gca=81.4 gca peak = 0.14473 (69) mri peak = 0.14985 (79) Left_Caudate (11): linear fit = 1.12 x + 0.0 (844 voxels, overlap=0.423) Left_Caudate (11): linear fit = 1.12 x + 0.0 (844 voxels, peak = 78), gca=77.6 gca peak = 0.14301 (56) mri peak = 0.06791 (79) Left_Cerebellum_Cortex (8): linear fit = 1.42 x + 0.0 (31116 voxels, overlap=0.001) Left_Cerebellum_Cortex (8): linear fit = 1.42 x + 0.0 (31116 voxels, peak = 80), gca=79.8 gca peak = 0.14610 (55) mri peak = 0.06623 (80) Right_Cerebellum_Cortex (47): linear fit = 1.40 x + 0.0 (30968 voxels, overlap=0.001) Right_Cerebellum_Cortex (47): linear fit = 1.40 x + 0.0 (30968 voxels, peak = 77), gca=77.3 gca peak = 0.16309 (85) mri peak = 0.19231 (93) Left_Cerebellum_White_Matter (7): linear fit = 1.10 x + 0.0 (6218 voxels, overlap=0.002) Left_Cerebellum_White_Matter (7): linear fit = 1.10 x + 0.0 (6218 voxels, peak = 93), gca=93.1 gca peak = 0.15172 (84) mri peak = 0.13533 (92) Right_Cerebellum_White_Matter (46): linear fit = 1.10 x + 0.0 (6887 voxels, overlap=0.214) Right_Cerebellum_White_Matter (46): linear fit = 1.10 x + 0.0 (6887 voxels, peak = 92), gca=92.0 gca peak = 0.30461 (58) mri peak = 0.12144 (79) Left_Amygdala (18): linear fit = 1.35 x + 0.0 (532 voxels, overlap=0.057) Left_Amygdala (18): linear fit = 1.35 x + 0.0 (532 voxels, peak = 78), gca=78.0 gca peak = 0.32293 (57) mri peak = 0.16907 (77) Right_Amygdala (54): linear fit = 1.37 x + 0.0 (485 voxels, overlap=0.036) Right_Amygdala (54): linear fit = 1.37 x + 0.0 (485 voxels, peak = 78), gca=77.8 gca peak = 0.11083 (90) mri peak = 0.10377 (96) Left_Thalamus (10): linear fit = 1.05 x + 0.0 (5045 voxels, overlap=0.675) Left_Thalamus (10): linear fit = 1.05 x + 0.0 (5045 voxels, peak = 95), gca=94.9 gca peak = 0.11393 (83) mri peak = 0.11451 (95) Right_Thalamus (49): linear fit = 1.11 x + 0.0 (5207 voxels, overlap=0.323) Right_Thalamus (49): linear fit = 1.11 x + 0.0 (5207 voxels, peak = 92), gca=91.7 gca peak = 0.08575 (81) mri peak = 0.10927 (89) Left_Putamen (12): linear fit = 1.12 x + 0.0 (2233 voxels, overlap=0.358) Left_Putamen (12): linear fit = 1.12 x + 0.0 (2233 voxels, peak = 91), gca=91.1 gca peak = 0.08618 (78) mri peak = 0.10287 (89) Right_Putamen (51): linear fit = 1.12 x + 0.0 (2325 voxels, overlap=0.475) Right_Putamen (51): linear fit = 1.12 x + 0.0 (2325 voxels, peak = 88), gca=87.8 gca peak = 0.08005 (78) mri peak = 0.13771 (91) Brain_Stem (16): linear fit = 1.13 x + 0.0 (15248 voxels, overlap=0.099) Brain_Stem (16): linear fit = 1.13 x + 0.0 (15248 voxels, peak = 89), gca=88.5 gca peak = 0.12854 (88) mri peak = 0.16433 (97) Right_VentralDC (60): linear fit = 1.11 x + 0.0 (2023 voxels, overlap=0.124) Right_VentralDC (60): linear fit = 1.11 x + 0.0 (2023 voxels, peak = 97), gca=97.2 gca peak = 0.15703 (87) mri peak = 0.16394 (97) Left_VentralDC (28): linear fit = 1.11 x + 0.0 (1976 voxels, overlap=0.084) Left_VentralDC (28): linear fit = 1.11 x + 0.0 (1976 voxels, peak = 96), gca=96.1 gca peak = 0.17522 (25) mri peak = 0.38095 (27) gca peak = 0.17113 (14) mri peak = 0.19293 (27) Fourth_Ventricle (15): linear fit = 1.85 x + 0.0 (203 voxels, overlap=0.163) Fourth_Ventricle (15): linear fit = 1.85 x + 0.0 (203 voxels, peak = 26), gca=25.8 gca peak Unknown = 0.94777 ( 0) gca peak Left_Inf_Lat_Vent = 0.16627 (28) gca peak Third_Ventricle = 0.17522 (25) gca peak Fourth_Ventricle = 0.17113 (14) gca peak CSF = 0.20346 (36) gca peak Left_Accumbens_area = 0.70646 (62) gca peak Left_undetermined = 1.00000 (28) gca peak Left_vessel = 0.89917 (53) gca peak Left_choroid_plexus = 0.11689 (35) gca peak Right_Inf_Lat_Vent = 0.25504 (23) gca peak Right_Accumbens_area = 0.31650 (65) gca peak Right_vessel = 0.77268 (52) gca peak Right_choroid_plexus = 0.13275 (38) gca peak Fifth_Ventricle = 0.60973 (33) gca peak WM_hypointensities = 0.11013 (77) gca peak non_WM_hypointensities = 0.11354 (41) gca peak Optic_Chiasm = 0.51646 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.33 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.40 x + 0.0 Left_Pallidum too bright - rescaling by 1.000 (from 1.045) to 101.4 (was 101.4) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.15330 (24) mri peak = 0.23561 (27) Left_Lateral_Ventricle (4): linear fit = 1.08 x + 0.0 (1496 voxels, overlap=0.653) Left_Lateral_Ventricle (4): linear fit = 1.08 x + 0.0 (1496 voxels, peak = 26), gca=25.8 gca peak = 0.17030 (19) mri peak = 0.16851 (31) Right_Lateral_Ventricle (43): linear fit = 1.40 x + 0.0 (1127 voxels, overlap=0.321) Right_Lateral_Ventricle (43): linear fit = 1.40 x + 0.0 (1127 voxels, peak = 27), gca=26.7 gca peak = 0.20739 (99) mri peak = 0.18928 (100) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (788 voxels, overlap=0.999) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (788 voxels, peak = 99), gca=99.5 gca peak = 0.17574 (99) mri peak = 0.28889 (101) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (804 voxels, overlap=0.969) Left_Pallidum (13): linear fit = 1.00 x + 0.0 (804 voxels, peak = 99), gca=98.5 gca peak = 0.24427 (72) mri peak = 0.11246 (74) Right_Hippocampus (53): linear fit = 1.01 x + 0.0 (1240 voxels, overlap=1.002) Right_Hippocampus (53): linear fit = 1.01 x + 0.0 (1240 voxels, peak = 73), gca=73.1 gca peak = 0.29189 (73) mri peak = 0.11317 (75) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (1144 voxels, overlap=1.004) Left_Hippocampus (17): linear fit = 1.00 x + 0.0 (1144 voxels, peak = 73), gca=73.0 gca peak = 0.07891 (104) mri peak = 0.19174 (104) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (53493 voxels, overlap=0.584) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (53493 voxels, peak = 104), gca=104.0 gca peak = 0.07990 (105) mri peak = 0.20132 (105) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (52971 voxels, overlap=0.548) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (52971 voxels, peak = 106), gca=105.5 gca peak = 0.07661 (77) mri peak = 0.05997 (77) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (36365 voxels, overlap=0.941) Left_Cerebral_Cortex (3): linear fit = 0.99 x + 0.0 (36365 voxels, peak = 76), gca=75.8 gca peak = 0.08459 (78) mri peak = 0.06320 (79) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (32499 voxels, overlap=0.870) Right_Cerebral_Cortex (42): linear fit = 0.99 x + 0.0 (32499 voxels, peak = 77), gca=76.8 gca peak = 0.21188 (81) mri peak = 0.12702 (82) Right_Caudate (50): linear fit = 1.00 x + 0.0 (866 voxels, overlap=0.999) Right_Caudate (50): linear fit = 1.00 x + 0.0 (866 voxels, peak = 81), gca=81.0 gca peak = 0.14149 (77) mri peak = 0.14985 (79) Left_Caudate (11): linear fit = 0.96 x + 0.0 (844 voxels, overlap=0.769) Left_Caudate (11): linear fit = 0.96 x + 0.0 (844 voxels, peak = 74), gca=74.3 gca peak = 0.09803 (79) mri peak = 0.06791 (79) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (31116 voxels, overlap=0.942) Left_Cerebellum_Cortex (8): linear fit = 1.00 x + 0.0 (31116 voxels, peak = 79), gca=79.0 gca peak = 0.10915 (78) mri peak = 0.06623 (80) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (30968 voxels, overlap=0.939) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (30968 voxels, peak = 78), gca=77.6 gca peak = 0.14913 (93) mri peak = 0.19231 (93) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6218 voxels, overlap=0.798) Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (6218 voxels, peak = 93), gca=92.5 gca peak = 0.13809 (93) mri peak = 0.13533 (92) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6887 voxels, overlap=0.890) Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (6887 voxels, peak = 93), gca=92.5 gca peak = 0.29098 (78) mri peak = 0.12144 (79) Left_Amygdala (18): linear fit = 0.99 x + 0.0 (532 voxels, overlap=1.012) Left_Amygdala (18): linear fit = 0.99 x + 0.0 (532 voxels, peak = 77), gca=76.8 gca peak = 0.21637 (79) mri peak = 0.16907 (77) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (485 voxels, overlap=0.996) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (485 voxels, peak = 79), gca=79.0 gca peak = 0.10934 (93) mri peak = 0.10377 (96) Left_Thalamus (10): linear fit = 1.01 x + 0.0 (5045 voxels, overlap=0.896) Left_Thalamus (10): linear fit = 1.01 x + 0.0 (5045 voxels, peak = 94), gca=94.4 gca peak = 0.10165 (89) mri peak = 0.11451 (95) Right_Thalamus (49): linear fit = 1.02 x + 0.0 (5207 voxels, overlap=0.884) Right_Thalamus (49): linear fit = 1.02 x + 0.0 (5207 voxels, peak = 91), gca=91.2 gca peak = 0.08343 (86) mri peak = 0.10927 (89) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2233 voxels, overlap=0.863) Left_Putamen (12): linear fit = 1.00 x + 0.0 (2233 voxels, peak = 86), gca=85.6 gca peak = 0.09510 (87) mri peak = 0.10287 (89) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2325 voxels, overlap=0.929) Right_Putamen (51): linear fit = 1.00 x + 0.0 (2325 voxels, peak = 87), gca=87.0 gca peak = 0.08055 (89) mri peak = 0.13771 (91) Brain_Stem (16): linear fit = 0.99 x + 0.0 (15248 voxels, overlap=0.646) Brain_Stem (16): linear fit = 0.99 x + 0.0 (15248 voxels, peak = 88), gca=87.7 gca peak = 0.11716 (98) mri peak = 0.16433 (97) Right_VentralDC (60): linear fit = 1.01 x + 0.0 (2023 voxels, overlap=0.787) Right_VentralDC (60): linear fit = 1.01 x + 0.0 (2023 voxels, peak = 99), gca=99.5 gca peak = 0.15559 (96) mri peak = 0.16394 (97) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1976 voxels, overlap=0.846) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (1976 voxels, peak = 96), gca=96.0 gca peak = 0.17118 (35) mri peak = 0.38095 (27) gca peak = 0.15172 (20) mri peak = 0.19293 (27) Fourth_Ventricle (15): linear fit = 1.27 x + 0.0 (203 voxels, overlap=0.306) Fourth_Ventricle (15): linear fit = 1.27 x + 0.0 (203 voxels, peak = 26), gca=25.5 gca peak Unknown = 0.94777 ( 0) gca peak Left_Inf_Lat_Vent = 0.14083 (36) gca peak Third_Ventricle = 0.17118 (35) gca peak CSF = 0.16012 (51) gca peak Left_Accumbens_area = 0.60176 (70) gca peak Left_undetermined = 0.99358 (30) gca peak Left_vessel = 0.63642 (53) gca peak Left_choroid_plexus = 0.11176 (35) gca peak Right_Inf_Lat_Vent = 0.22774 (30) gca peak Right_Accumbens_area = 0.37515 (79) gca peak Right_vessel = 0.77268 (52) gca peak Right_choroid_plexus = 0.13291 (38) gca peak Fifth_Ventricle = 0.59466 (44) gca peak WM_hypointensities = 0.10800 (77) gca peak non_WM_hypointensities = 0.14722 (41) gca peak Optic_Chiasm = 0.61570 (76) not using caudate to estimate GM means estimating mean gm scale to be 1.00 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.25 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 63676 voxels changed in iteration 0 of unlikely voxel relabeling 266 voxels changed in iteration 1 of unlikely voxel relabeling 4 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 69047 gm and wm labels changed (%32 to gray, %68 to white out of all changed labels) 436 hippocampal voxels changed. 0 amygdala voxels changed. Reclassifying using Gibbs Priors pass 1: 70886 changed. image ll: -2.207, PF=0.500 pass 2: 19637 changed. image ll: -2.206, PF=0.500 pass 3: 6189 changed. pass 4: 2376 changed. 60384 voxels changed in iteration 0 of unlikely voxel relabeling 457 voxels changed in iteration 1 of unlikely voxel relabeling 25 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 6929 voxels changed in iteration 0 of unlikely voxel relabeling 148 voxels changed in iteration 1 of unlikely voxel relabeling 30 voxels changed in iteration 2 of unlikely voxel relabeling 18 voxels changed in iteration 3 of unlikely voxel relabeling 6 voxels changed in iteration 4 of unlikely voxel relabeling 6369 voxels changed in iteration 0 of unlikely voxel relabeling 76 voxels changed in iteration 1 of unlikely voxel relabeling 4 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling 5334 voxels changed in iteration 0 of unlikely voxel relabeling 36 voxels changed in iteration 1 of unlikely voxel relabeling 2 voxels changed in iteration 2 of unlikely voxel relabeling 0 voxels changed in iteration 3 of unlikely voxel relabeling !!!!!!!!! ventricle segment 0 with volume 366 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 1 with volume 6636 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 4 with volume 130 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 0 with volume 128 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 1 with volume 6597 above threshold 100 - not erasing !!!!!!!!!! !!!!!!!!! ventricle segment 1 with volume 211 above threshold 100 - not erasing !!!!!!!!!! writing labeled volume to aseg.auto_noCCseg.mgz mri_ca_label utimesec 2788.930266 mri_ca_label stimesec 6.541624 mri_ca_label ru_maxrss 2116932 mri_ca_label ru_ixrss 0 mri_ca_label ru_idrss 0 mri_ca_label ru_isrss 0 mri_ca_label ru_minflt 8243790 mri_ca_label ru_majflt 3 mri_ca_label ru_nswap 0 mri_ca_label ru_inblock 2408 mri_ca_label ru_oublock 688 mri_ca_label ru_msgsnd 0 mri_ca_label ru_msgrcv 0 mri_ca_label ru_nsignals 0 mri_ca_label ru_nvcsw 114 mri_ca_label ru_nivcsw 728 auto-labeling took 46 minutes and 35 seconds. @#@FSTIME 2020:07:23:08:22:09 mri_ca_label N 10 e 2795.41 S 6.70 U 2788.93 P 100% M 2116932 F 3 R 8243811 W 0 c 728 w 116 I 2408 O 688 L 2.04 2.08 2.07 @#@FSLOADPOST 2020:07:23:09:08:44 mri_ca_label N 10 2.09 2.09 2.10 #-------------------------------------- #@# CC Seg Thu Jul 23 09:08:44 EDT 2020 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/transforms/cc_up.lta bert will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/transforms/cc_up.lta reading aseg from /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/aseg.auto_noCCseg.mgz reading norm from /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/norm.mgz 40017 voxels in left wm, 50578 in right wm, xrange [124, 133] searching rotation angles z=[-10 4], y=[-7 7] searching scale 1 Z rot -10.1 searching scale 1 Z rot -9.9 searching scale 1 Z rot -9.6 searching scale 1 Z rot -9.4 searching scale 1 Z rot -9.1 searching scale 1 Z rot -8.9 searching scale 1 Z rot -8.6 searching scale 1 Z rot -8.4 searching scale 1 Z rot -8.1 searching scale 1 Z rot -7.9 searching scale 1 Z rot -7.6 searching scale 1 Z rot -7.4 searching scale 1 Z rot -7.1 searching scale 1 Z rot -6.9 searching scale 1 Z rot -6.6 searching scale 1 Z rot -6.4 searching scale 1 Z rot -6.1 searching scale 1 Z rot -5.9 searching scale 1 Z rot -5.6 searching scale 1 Z rot -5.4 searching scale 1 Z rot -5.1 searching scale 1 Z rot -4.9 searching scale 1 Z rot -4.6 searching scale 1 Z rot -4.4 searching scale 1 Z rot -4.1 searching scale 1 Z rot -3.9 searching scale 1 Z rot -3.6 searching scale 1 Z rot -3.4 searching scale 1 Z rot -3.1 searching scale 1 Z rot -2.9 searching scale 1 Z rot -2.6 searching scale 1 Z rot -2.4 searching scale 1 Z rot -2.1 searching scale 1 Z rot -1.9 searching scale 1 Z rot -1.6 searching scale 1 Z rot -1.4 searching scale 1 Z rot -1.1 searching scale 1 Z rot -0.9 searching scale 1 Z rot -0.6 searching scale 1 Z rot -0.4 searching scale 1 Z rot -0.1 searching scale 1 Z rot 0.1 searching scale 1 Z rot 0.4 searching scale 1 Z rot 0.6 searching scale 1 Z rot 0.9 searching scale 1 Z rot 1.1 searching scale 1 Z rot 1.4 searching scale 1 Z rot 1.6 searching scale 1 Z rot 1.9 searching scale 1 Z rot 2.1 searching scale 1 Z rot 2.4 searching scale 1 Z rot 2.6 searching scale 1 Z rot 2.9 searching scale 1 Z rot 3.1 searching scale 1 Z rot 3.4 searching scale 1 Z rot 3.6 global minimum found at slice 128.5, rotations (0.50, -3.12) final transformation (x=128.5, yr=0.496, zr=-3.123): 0.99848 0.05447 0.00865 -6.65447; -0.05447 0.99852 -0.00047 36.19880; -0.00866 0.00000 0.99996 17.11703; 0.00000 0.00000 0.00000 1.00000; updating x range to be [126, 131] in xformed coordinates best xformed slice 128 min_x_fornix = 140 min_x_fornix = 142 WARNING: min_x_fornix not set min_x_fornix = 149 min_x_fornix = 143 cc center is found at 128 99 112 eigenvectors: 0.00191 -0.00854 0.99996; -0.01031 -0.99991 -0.00852; 0.99994 -0.01030 -0.00200; writing aseg with callosum to /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/aseg.auto.mgz... corpus callosum segmentation took 0.7 minutes #VMPC# mri_cc VmPeak 554168 mri_cc done @#@FSTIME 2020:07:23:09:08:44 mri_cc N 7 e 42.80 S 0.51 U 42.27 P 99% M 340504 F 2 R 340120 W 0 c 55 w 52 I 1632 O 680 L 2.09 2.09 2.10 @#@FSLOADPOST 2020:07:23:09:09:27 mri_cc N 7 2.04 2.08 2.09 #-------------------------------------- #@# Merge ASeg Thu Jul 23 09:09:27 EDT 2020 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Thu Jul 23 09:09:27 EDT 2020 /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/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 mri_src from norm.mgz... MRImask(): AllowDiffGeom = 1 Reading aseg aseg.presurf.mgz normalizing image... processing with aseg removing outliers in the aseg WM... 351 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 109 gm peak at 84 (84), valley at 58 (58) csf peak at 43, setting threshold to 70 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 85 (85), valley at 21 (21) csf peak at 43, setting threshold to 71 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 2 minutes and 39 seconds. @#@FSTIME 2020:07:23:09:09:27 mri_normalize N 9 e 160.14 S 1.72 U 158.41 P 99% M 1200272 F 0 R 1051834 W 0 c 43 w 89 I 0 O 2760 L 2.04 2.08 2.09 @#@FSLOADPOST 2020:07:23:09:12:07 mri_normalize N 9 2.09 2.08 2.09 #-------------------------------------------- #@# Mask BFS Thu Jul 23 09:12:07 EDT 2020 /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1720190 voxels in mask (pct= 10.25) MRImask(): AllowDiffGeom = 1 Writing masked volume to brain.finalsurfs.mgz...done. @#@FSTIME 2020:07:23:09:12:07 mri_mask N 5 e 1.08 S 0.04 U 1.02 P 97% M 70576 F 1 R 17757 W 0 c 1 w 120 I 1576 O 2656 L 2.09 2.08 2.09 @#@FSLOADPOST 2020:07:23:09:12:09 mri_mask N 5 2.09 2.08 2.09 #-------------------------------------------- #@# WM Segmentation Thu Jul 23 09:12:09 EDT 2020 AntsDenoiseImageFs -i brain.mgz -o antsdn.brain.mgz @#@FSTIME 2020:07:23:09:12:09 AntsDenoiseImageFs N 4 e 39.61 S 0.25 U 39.33 P 99% M 347524 F 6 R 227728 W 0 c 11 w 117 I 6352 O 2728 L 2.09 2.08 2.09 @#@FSLOADPOST 2020:07:23:09:12:48 AntsDenoiseImageFs N 4 2.09 2.09 2.09 mri_segment -wsizemm 13 -mprage antsdn.brain.mgz wm.seg.mgz wsizemm = 13, voxres = 1, wsize = 13 WHITE_MATTER_MEAN 110 wsize 13 assuming input volume is MGH (Van der Kouwe) MP-RAGE wm_low 79 wm_hi 125 gray_low 30 gray_hi 99 Doing initial trinary intensity segmentation Using local statistics to label ambiguous voxels Autodetecting stats Computing class statistics for intensity windows... CCS WM (103.0): 103.4 +- 5.1 [79.0 --> 125.0] CCS GM (83.0) : 79.5 +- 12.4 [30.0 --> 95.0] white_mean 103.409 white_sigma 5.12096 gray_mean 79.5308 gray_sigma 12.4342 setting bottom of white matter range wm_low to 92.0 setting top of gray matter range gray_hi to 102.4 wm_low 91.965 wm_hi 125 gray_low 30 gray_hi 102.409 Redoing initial intensity segmentation... Recomputing local statistics to label ambiguous voxels... wm_low 91.965 wm_hi 125 gray_low 30 gray_hi 102.409 using local geometry to label remaining ambiguous voxels... polvwsize = 5, polvlen = 3, gray_hi = 102.409, wm_low = 91.965 MRIcpolvMedianCurveSegment(): wsize=5, len=3, gmhi=102.409, wmlow=91.965 160530 voxels processed (0.96%) 74539 voxels white (0.44%) 85991 voxels non-white (0.51%) Reclassifying voxels using Gaussian border classifier niter=1 MRIreclassify(): wm_low=86.965, gray_hi=102.409, wsize=13 367255 voxels tested (2.19%) 55194 voxels changed (0.33%) 51201 multi-scale searches (0.31%) Recovering bright white MRIrecoverBrightWhite() wm_low 91.965 wm_hi 125 slack 5.12096 pct_thresh 0.33 intensity_thresh 130.121 nvox_thresh 8.58 1227 voxels tested (0.01%) 663 voxels changed (0.00%) removing voxels with positive offset direction... MRIremoveWrongDirection() wsize=3, lowthr=86.965, hithr=102.409 smoothing input volume with sigma = 0.250 150412 voxels tested (0.90%) 16054 voxels changed (0.10%) thicken = 1 removing 1-dimensional structures... MRIremove1dStructures(): max_iter=10000, thresh=2, WM_MIN_VAL=5 4006 sparsely connected voxels removed in 1 iterations thickening thin strands.... thickness 4 nsegments 20 wm_hi 125 1718 diagonally connected voxels added... MRIthickenThinWMStrands(): thickness=4, nsegments=20 20 segments, 3795 filled MRIfindBrightNonWM(): 7804 bright non-wm voxels segmented. MRIfilterMorphology() WM_MIN_VAL=5, DIAGONAL_FILL=230 white matter segmentation took 1.4 minutes writing output to wm.seg.mgz... @#@FSTIME 2020:07:23:09:12:48 mri_segment N 5 e 86.65 S 0.54 U 86.09 P 99% M 143188 F 2 R 340133 W 0 c 70 w 45 I 1616 O 792 L 2.09 2.09 2.09 @#@FSLOADPOST 2020:07:23:09:14:15 mri_segment N 5 2.06 2.08 2.09 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 0.47 minutes reading wm segmentation from wm.seg.mgz... 0 voxels added to wm to prevent paths from MTL structures to cortex 4166 additional wm voxels added 0 additional wm voxels added SEG EDIT: 45346 voxels turned on, 55920 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 110 new 110 115,126,128 old 110 new 110 writing edited volume to wm.asegedit.mgz.... @#@FSTIME 2020:07:23:09:14:15 mri_edit_wm_with_aseg N 5 e 28.06 S 0.33 U 27.71 P 99% M 473524 F 2 R 312880 W 0 c 14 w 75 I 1496 O 712 L 2.06 2.08 2.09 @#@FSLOADPOST 2020:07:23:09:14:43 mri_edit_wm_with_aseg N 5 2.03 2.07 2.09 mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 11 found - 11 modified | TOTAL: 11 pass 2 (xy+): 0 found - 11 modified | TOTAL: 11 pass 1 (xy-): 9 found - 9 modified | TOTAL: 20 pass 2 (xy-): 0 found - 9 modified | TOTAL: 20 pass 1 (yz+): 21 found - 21 modified | TOTAL: 41 pass 2 (yz+): 0 found - 21 modified | TOTAL: 41 pass 1 (yz-): 29 found - 29 modified | TOTAL: 70 pass 2 (yz-): 0 found - 29 modified | TOTAL: 70 pass 1 (xz+): 15 found - 15 modified | TOTAL: 85 pass 2 (xz+): 0 found - 15 modified | TOTAL: 85 pass 1 (xz-): 14 found - 14 modified | TOTAL: 99 pass 2 (xz-): 0 found - 14 modified | TOTAL: 99 Iteration Number : 1 pass 1 (+++): 8 found - 8 modified | TOTAL: 8 pass 2 (+++): 0 found - 8 modified | TOTAL: 8 pass 1 (+++): 8 found - 8 modified | TOTAL: 16 pass 2 (+++): 0 found - 8 modified | TOTAL: 16 pass 1 (+++): 5 found - 5 modified | TOTAL: 21 pass 2 (+++): 0 found - 5 modified | TOTAL: 21 pass 1 (+++): 8 found - 8 modified | TOTAL: 29 pass 2 (+++): 0 found - 8 modified | TOTAL: 29 Iteration Number : 1 pass 1 (++): 27 found - 27 modified | TOTAL: 27 pass 2 (++): 0 found - 27 modified | TOTAL: 27 pass 1 (+-): 41 found - 41 modified | TOTAL: 68 pass 2 (+-): 0 found - 41 modified | TOTAL: 68 pass 1 (--): 35 found - 35 modified | TOTAL: 103 pass 2 (--): 0 found - 35 modified | TOTAL: 103 pass 1 (-+): 24 found - 24 modified | TOTAL: 127 pass 2 (-+): 0 found - 24 modified | TOTAL: 127 Iteration Number : 2 pass 1 (xy+): 2 found - 2 modified | TOTAL: 2 pass 2 (xy+): 0 found - 2 modified | TOTAL: 2 pass 1 (xy-): 0 found - 0 modified | TOTAL: 2 pass 1 (yz+): 5 found - 5 modified | TOTAL: 7 pass 2 (yz+): 0 found - 5 modified | TOTAL: 7 pass 1 (yz-): 2 found - 2 modified | TOTAL: 9 pass 2 (yz-): 0 found - 2 modified | TOTAL: 9 pass 1 (xz+): 0 found - 0 modified | TOTAL: 9 pass 1 (xz-): 0 found - 0 modified | TOTAL: 9 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 (+-): 2 found - 2 modified | TOTAL: 2 pass 2 (+-): 0 found - 2 modified | TOTAL: 2 pass 1 (--): 0 found - 0 modified | TOTAL: 2 pass 1 (-+): 3 found - 3 modified | TOTAL: 5 pass 2 (-+): 0 found - 3 modified | TOTAL: 5 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 1 found - 1 modified | TOTAL: 1 pass 2 (yz-): 0 found - 1 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 = 270 (out of 583566: 0.046267) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done @#@FSTIME 2020:07:23:09:14:43 mri_pretess N 4 e 2.80 S 0.03 U 2.73 P 99% M 53524 F 5 R 22103 W 0 c 3 w 72 I 5768 O 704 L 2.03 2.07 2.09 @#@FSLOADPOST 2020:07:23:09:14:46 mri_pretess N 4 2.03 2.07 2.09 #-------------------------------------------- #@# Fill Thu Jul 23 09:14:46 EDT 2020 /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/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 1.10305 0.03383 0.00572 -18.70644; -0.03552 1.01628 0.17183 -16.49753; 0.00000 -0.20524 0.87702 37.13496; 0.00000 0.00000 0.00000 1.00000; voxel to talairach voxel transform 1.10305 0.03383 0.00572 -18.70644; -0.03552 1.01628 0.17183 -16.49753; 0.00000 -0.20524 0.87702 37.13496; 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] = 1037 (min = 350, max = 1400), aspect = 0.49 (min = 0.10, max = 0.75) no need to search using seed (126, 121, 152), TAL = (2.0, 24.0, 7.0) talairach voxel to voxel transform 0.90561 -0.03014 0.00000 16.44341; 0.03044 0.94551 -0.18545 23.05470; 0.00712 0.22126 1.09683 -36.94708; 0.00000 0.00000 0.00000 1.00000; segmentation indicates cc at (126, 121, 152) --> (2.0, 24.0, 7.0) done. writing output to filled.mgz... filling took 1.0 minutes talairach cc position changed to (2.00, 24.00, 7.00) Erasing brainstem...done. MRImask(): AllowDiffGeom = 1 seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(20.00, 24.00, 7.00) SRC: (110.60, 112.56, 157.31) search lh wm seed point around talairach space (-16.00, 24.00, 7.00), SRC: (143.20, 113.66, 157.57) compute mri_fill using aseg Erasing Brain Stem and Cerebellum ... Define left and right masks using aseg: Building Voronoi diagram ... Using the Voronoi diagram for separating WM into two hemispheres ... Find the largest connected component for each hemisphere ... @#@FSTIME 2020:07:23:09:14:46 mri_fill N 8 e 62.98 S 1.45 U 61.51 P 99% M 968172 F 2 R 882162 W 0 c 18 w 65 I 1728 O 272 L 2.03 2.07 2.09 @#@FSLOADPOST 2020:07:23:09:15:49 mri_fill N 8 2.01 2.06 2.08 #-------------------------------------------- #@# Tessellate lh Thu Jul 23 09:15:49 EDT 2020 /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 5 found - 5 modified | TOTAL: 5 pass 2 (yz+): 0 found - 5 modified | TOTAL: 5 pass 1 (yz-): 6 found - 6 modified | TOTAL: 11 pass 2 (yz-): 0 found - 6 modified | TOTAL: 11 pass 1 (xz+): 1 found - 1 modified | TOTAL: 12 pass 2 (xz+): 0 found - 1 modified | TOTAL: 12 pass 1 (xz-): 0 found - 0 modified | TOTAL: 12 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 1 found - 1 modified | TOTAL: 1 pass 2 (yz+): 0 found - 1 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 0 found - 0 modified | TOTAL: 1 pass 1 (xz-): 0 found - 0 modified | TOTAL: 1 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 13 (out of 280163: 0.004640) Ambiguous edge configurations... mri_pretess done @#@FSTIME 2020:07:23:09:15:49 mri_pretess N 4 e 1.68 S 0.02 U 1.64 P 99% M 36948 F 0 R 9399 W 0 c 3 w 66 I 0 O 272 L 2.01 2.06 2.08 @#@FSLOADPOST 2020:07:23:09:15:51 mri_pretess N 4 2.01 2.06 2.08 mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix dev dev slice 30: 456 vertices, 513 faces slice 40: 4317 vertices, 4503 faces slice 50: 10840 vertices, 11087 faces slice 60: 18790 vertices, 19090 faces slice 70: 28094 vertices, 28418 faces slice 80: 37780 vertices, 38068 faces slice 90: 47181 vertices, 47516 faces slice 100: 57887 vertices, 58241 faces slice 110: 68223 vertices, 68604 faces slice 120: 78216 vertices, 78580 faces slice 130: 87969 vertices, 88341 faces slice 140: 97073 vertices, 97389 faces slice 150: 104626 vertices, 104878 faces slice 160: 110667 vertices, 110936 faces slice 170: 116991 vertices, 117227 faces slice 180: 122513 vertices, 122715 faces slice 190: 127172 vertices, 127342 faces slice 200: 130152 vertices, 130219 faces slice 210: 130332 vertices, 130362 faces slice 220: 130332 vertices, 130362 faces slice 230: 130332 vertices, 130362 faces slice 240: 130332 vertices, 130362 faces slice 250: 130332 vertices, 130362 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; @#@FSTIME 2020:07:23:09:15:51 mri_tessellate N 3 e 1.47 S 0.02 U 1.41 P 97% M 33316 F 2 R 8475 W 0 c 1 w 236 I 1680 O 6112 L 2.01 2.06 2.08 @#@FSLOADPOST 2020:07:23:09:15:52 mri_tessellate N 3 2.01 2.06 2.08 rm -f ../mri/filled-pretess255.mgz mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix counting number of connected components... 130332 voxel in cpt #1: X=-30 [v=130332,e=391086,f=260724] located at (-26.537327, -19.796358, 15.743931) For the whole surface: X=-30 [v=130332,e=391086,f=260724] One single component has been found nothing to do done @#@FSTIME 2020:07:23:09:15:52 mris_extract_main_component N 2 e 0.90 S 0.17 U 0.66 P 93% M 256096 F 4 R 72193 W 0 c 6 w 407 I 4360 O 9168 L 2.01 2.06 2.08 @#@FSLOADPOST 2020:07:23:09:15:53 mris_extract_main_component N 2 2.01 2.06 2.08 #-------------------------------------------- #@# Tessellate rh Thu Jul 23 09:15:53 EDT 2020 /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 6 found - 6 modified | TOTAL: 6 pass 2 (yz+): 0 found - 6 modified | TOTAL: 6 pass 1 (yz-): 5 found - 5 modified | TOTAL: 11 pass 2 (yz-): 0 found - 5 modified | TOTAL: 11 pass 1 (xz+): 0 found - 0 modified | TOTAL: 11 pass 1 (xz-): 0 found - 0 modified | TOTAL: 11 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 11 (out of 280977: 0.003915) Ambiguous edge configurations... mri_pretess done @#@FSTIME 2020:07:23:09:15:53 mri_pretess N 4 e 1.36 S 0.02 U 1.33 P 99% M 36952 F 0 R 9400 W 0 c 11 w 46 I 0 O 264 L 2.01 2.06 2.08 @#@FSLOADPOST 2020:07:23:09:15:55 mri_pretess N 4 2.01 2.06 2.08 mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix dev dev slice 30: 542 vertices, 612 faces slice 40: 4163 vertices, 4339 faces slice 50: 10875 vertices, 11127 faces slice 60: 19133 vertices, 19425 faces slice 70: 29004 vertices, 29373 faces slice 80: 38883 vertices, 39203 faces slice 90: 48793 vertices, 49155 faces slice 100: 59795 vertices, 60181 faces slice 110: 69772 vertices, 70136 faces slice 120: 79794 vertices, 80160 faces slice 130: 88930 vertices, 89266 faces slice 140: 97277 vertices, 97573 faces slice 150: 104146 vertices, 104401 faces slice 160: 110104 vertices, 110352 faces slice 170: 116596 vertices, 116838 faces slice 180: 122272 vertices, 122484 faces slice 190: 126915 vertices, 127087 faces slice 200: 130021 vertices, 130100 faces slice 210: 130352 vertices, 130378 faces slice 220: 130352 vertices, 130378 faces slice 230: 130352 vertices, 130378 faces slice 240: 130352 vertices, 130378 faces slice 250: 130352 vertices, 130378 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; @#@FSTIME 2020:07:23:09:15:55 mri_tessellate N 3 e 1.40 S 0.02 U 1.35 P 97% M 33292 F 0 R 8718 W 0 c 10 w 279 I 0 O 6120 L 2.01 2.06 2.08 @#@FSLOADPOST 2020:07:23:09:15:56 mri_tessellate N 3 2.01 2.06 2.08 rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 130352 voxel in cpt #1: X=-26 [v=130352,e=391134,f=260756] located at (26.122116, -20.380016, 18.557076) For the whole surface: X=-26 [v=130352,e=391134,f=260756] One single component has been found nothing to do done @#@FSTIME 2020:07:23:09:15:56 mris_extract_main_component N 2 e 0.90 S 0.13 U 0.72 P 95% M 256200 F 0 R 72224 W 0 c 7 w 403 I 0 O 9168 L 2.01 2.06 2.08 @#@FSLOADPOST 2020:07:23:09:15:57 mris_extract_main_component N 2 2.01 2.06 2.08 #-------------------------------------------- #@# Smooth1 lh Thu Jul 23 09:15:57 EDT 2020 /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/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... @#@FSTIME 2020:07:23:09:15:57 mris_smooth N 5 e 2.83 S 0.17 U 2.61 P 98% M 202820 F 0 R 98673 W 0 c 2 w 320 I 0 O 9168 L 2.01 2.06 2.08 @#@FSLOADPOST 2020:07:23:09:16:00 mris_smooth N 5 2.01 2.06 2.08 #-------------------------------------------- #@# Smooth1 rh Thu Jul 23 09:16:00 EDT 2020 /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/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... @#@FSTIME 2020:07:23:09:16:00 mris_smooth N 5 e 2.81 S 0.17 U 2.60 P 98% M 202900 F 0 R 99523 W 0 c 2 w 229 I 0 O 9176 L 2.01 2.06 2.08 @#@FSLOADPOST 2020:07:23:09:16:03 mris_smooth N 5 2.01 2.06 2.08 #-------------------------------------------- #@# Inflation1 lh Thu Jul 23 09:16:03 EDT 2020 /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/scripts mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Not saving sulc Reading ../surf/lh.smoothwm.nofix avg radius = 48.5 mm, total surface area = 71071 mm^2 step 000: RMS=0.145 (target=0.015) step 005: RMS=0.109 (target=0.015) step 010: RMS=0.079 (target=0.015) step 015: RMS=0.065 (target=0.015) step 020: RMS=0.055 (target=0.015) step 025: RMS=0.048 (target=0.015) step 030: RMS=0.042 (target=0.015) step 035: RMS=0.038 (target=0.015) step 040: RMS=0.035 (target=0.015) step 045: RMS=0.033 (target=0.015) step 050: RMS=0.032 (target=0.015) step 055: RMS=0.031 (target=0.015) step 060: RMS=0.031 (target=0.015) writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.3 minutes inflation complete. Not saving sulc mris_inflate utimesec 17.750079 mris_inflate stimesec 1.373160 mris_inflate ru_maxrss 202980 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 784034 mris_inflate ru_majflt 4 mris_inflate ru_nswap 0 mris_inflate ru_inblock 4328 mris_inflate ru_oublock 9176 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 308 mris_inflate ru_nivcsw 25 @#@FSTIME 2020:07:23:09:16:03 mris_inflate N 3 e 19.19 S 1.38 U 17.75 P 99% M 202980 F 4 R 784061 W 0 c 25 w 310 I 4328 O 9176 L 2.01 2.06 2.08 @#@FSLOADPOST 2020:07:23:09:16:22 mris_inflate N 3 1.94 2.04 2.07 #-------------------------------------------- #@# Inflation1 rh Thu Jul 23 09:16:22 EDT 2020 /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/scripts mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix Not saving sulc Reading ../surf/rh.smoothwm.nofix avg radius = 48.7 mm, total surface area = 71517 mm^2 step 000: RMS=0.143 (target=0.015) step 005: RMS=0.109 (target=0.015) step 010: RMS=0.079 (target=0.015) step 015: RMS=0.064 (target=0.015) step 020: RMS=0.054 (target=0.015) step 025: RMS=0.046 (target=0.015) step 030: RMS=0.041 (target=0.015) step 035: RMS=0.037 (target=0.015) step 040: RMS=0.034 (target=0.015) step 045: RMS=0.032 (target=0.015) step 050: RMS=0.031 (target=0.015) step 055: RMS=0.029 (target=0.015) step 060: RMS=0.028 (target=0.015) writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.3 minutes inflation complete. Not saving sulc mris_inflate utimesec 18.111637 mris_inflate stimesec 1.375200 mris_inflate ru_maxrss 203108 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 833485 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 9176 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 260 mris_inflate ru_nivcsw 16 @#@FSTIME 2020:07:23:09:16:22 mris_inflate N 3 e 19.55 S 1.40 U 18.11 P 99% M 203108 F 0 R 833511 W 0 c 16 w 261 I 0 O 9176 L 1.94 2.04 2.07 @#@FSLOADPOST 2020:07:23:09:16:42 mris_inflate N 3 1.96 2.04 2.07 #-------------------------------------------- #@# QSphere lh Thu Jul 23 09:16:42 EDT 2020 /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/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 version: dev available threads: 1 scaling brain by 0.295... inflating... projecting onto sphere... surface projected - minimizing metric distortion... vertex spacing 1.00 +- 0.59 (0.00-->7.36) (max @ vno 55541 --> 56600) face area 0.02 +- 0.03 (-0.20-->0.81) Entering MRISinflateToSphere() inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.745, avgs=0 005/300: dt: 0.9000, rms radial error=177.485, avgs=0 010/300: dt: 0.9000, rms radial error=176.926, avgs=0 015/300: dt: 0.9000, rms radial error=176.193, avgs=0 020/300: dt: 0.9000, rms radial error=175.357, avgs=0 025/300: dt: 0.9000, rms radial error=174.462, avgs=0 030/300: dt: 0.9000, rms radial error=173.536, avgs=0 035/300: dt: 0.9000, rms radial error=172.592, avgs=0 040/300: dt: 0.9000, rms radial error=171.640, avgs=0 045/300: dt: 0.9000, rms radial error=170.686, avgs=0 050/300: dt: 0.9000, rms radial error=169.732, avgs=0 055/300: dt: 0.9000, rms radial error=168.781, avgs=0 060/300: dt: 0.9000, rms radial error=167.834, avgs=0 065/300: dt: 0.9000, rms radial error=166.891, avgs=0 070/300: dt: 0.9000, rms radial error=165.953, avgs=0 075/300: dt: 0.9000, rms radial error=165.020, avgs=0 080/300: dt: 0.9000, rms radial error=164.092, avgs=0 085/300: dt: 0.9000, rms radial error=163.169, avgs=0 090/300: dt: 0.9000, rms radial error=162.251, avgs=0 095/300: dt: 0.9000, rms radial error=161.338, avgs=0 100/300: dt: 0.9000, rms radial error=160.430, avgs=0 105/300: dt: 0.9000, rms radial error=159.526, avgs=0 110/300: dt: 0.9000, rms radial error=158.628, avgs=0 115/300: dt: 0.9000, rms radial error=157.734, avgs=0 120/300: dt: 0.9000, rms radial error=156.846, avgs=0 125/300: dt: 0.9000, rms radial error=155.962, avgs=0 130/300: dt: 0.9000, rms radial error=155.084, avgs=0 135/300: dt: 0.9000, rms radial error=154.210, avgs=0 140/300: dt: 0.9000, rms radial error=153.342, avgs=0 145/300: dt: 0.9000, rms radial error=152.481, avgs=0 150/300: dt: 0.9000, rms radial error=151.626, avgs=0 155/300: dt: 0.9000, rms radial error=150.776, avgs=0 160/300: dt: 0.9000, rms radial error=149.930, avgs=0 165/300: dt: 0.9000, rms radial error=149.089, avgs=0 170/300: dt: 0.9000, rms radial error=148.252, avgs=0 175/300: dt: 0.9000, rms radial error=147.420, avgs=0 180/300: dt: 0.9000, rms radial error=146.592, avgs=0 185/300: dt: 0.9000, rms radial error=145.769, avgs=0 190/300: dt: 0.9000, rms radial error=144.951, avgs=0 195/300: dt: 0.9000, rms radial error=144.137, avgs=0 200/300: dt: 0.9000, rms radial error=143.327, avgs=0 205/300: dt: 0.9000, rms radial error=142.522, avgs=0 210/300: dt: 0.9000, rms radial error=141.721, avgs=0 215/300: dt: 0.9000, rms radial error=140.925, avgs=0 220/300: dt: 0.9000, rms radial error=140.133, avgs=0 225/300: dt: 0.9000, rms radial error=139.345, avgs=0 230/300: dt: 0.9000, rms radial error=138.562, avgs=0 235/300: dt: 0.9000, rms radial error=137.783, avgs=0 240/300: dt: 0.9000, rms radial error=137.009, avgs=0 245/300: dt: 0.9000, rms radial error=136.238, avgs=0 250/300: dt: 0.9000, rms radial error=135.472, avgs=0 255/300: dt: 0.9000, rms radial error=134.710, avgs=0 260/300: dt: 0.9000, rms radial error=133.953, avgs=0 265/300: dt: 0.9000, rms radial error=133.199, avgs=0 270/300: dt: 0.9000, rms radial error=132.450, avgs=0 275/300: dt: 0.9000, rms radial error=131.705, avgs=0 280/300: dt: 0.9000, rms radial error=130.964, avgs=0 285/300: dt: 0.9000, rms radial error=130.227, avgs=0 290/300: dt: 0.9000, rms radial error=129.495, avgs=0 295/300: dt: 0.9000, rms radial error=128.766, avgs=0 300/300: dt: 0.9000, rms radial error=128.041, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 15423.97 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/13 = 0.00042 epoch 2 (K=40.0), pass 1, starting sse = 2570.46 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/13 = 0.00030 epoch 3 (K=160.0), pass 1, starting sse = 252.44 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.17/18 = 0.00955 epoch 4 (K=640.0), pass 1, starting sse = 9.36 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.11/22 = 0.00487 final distance error %100000.00 writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.0417 hours FSRUNTIME@ mris_sphere 0.0417 hours 1 threads #VMPC# mris_sphere VmPeak 602432 mris_sphere done @#@FSTIME 2020:07:23:09:16:42 mris_sphere N 9 e 150.24 S 12.61 U 137.59 P 99% M 207868 F 0 R 6678188 W 0 c 39 w 342 I 1056 O 9176 L 1.96 2.04 2.07 @#@FSLOADPOST 2020:07:23:09:19:12 mris_sphere N 9 2.15 2.05 2.06 #-------------------------------------------- #@# QSphere rh Thu Jul 23 09:19:12 EDT 2020 /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/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 version: dev available threads: 1 scaling brain by 0.294... inflating... projecting onto sphere... surface projected - minimizing metric distortion... vertex spacing 1.01 +- 0.60 (0.00-->7.84) (max @ vno 93915 --> 93916) face area 0.02 +- 0.03 (-0.21-->0.52) Entering MRISinflateToSphere() inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.723, avgs=0 005/300: dt: 0.9000, rms radial error=177.462, avgs=0 010/300: dt: 0.9000, rms radial error=176.901, avgs=0 015/300: dt: 0.9000, rms radial error=176.165, avgs=0 020/300: dt: 0.9000, rms radial error=175.328, avgs=0 025/300: dt: 0.9000, rms radial error=174.432, avgs=0 030/300: dt: 0.9000, rms radial error=173.505, avgs=0 035/300: dt: 0.9000, rms radial error=172.561, avgs=0 040/300: dt: 0.9000, rms radial error=171.610, avgs=0 045/300: dt: 0.9000, rms radial error=170.656, avgs=0 050/300: dt: 0.9000, rms radial error=169.703, avgs=0 055/300: dt: 0.9000, rms radial error=168.754, avgs=0 060/300: dt: 0.9000, rms radial error=167.808, avgs=0 065/300: dt: 0.9000, rms radial error=166.867, avgs=0 070/300: dt: 0.9000, rms radial error=165.931, avgs=0 075/300: dt: 0.9000, rms radial error=165.000, avgs=0 080/300: dt: 0.9000, rms radial error=164.074, avgs=0 085/300: dt: 0.9000, rms radial error=163.153, avgs=0 090/300: dt: 0.9000, rms radial error=162.237, avgs=0 095/300: dt: 0.9000, rms radial error=161.326, avgs=0 100/300: dt: 0.9000, rms radial error=160.420, avgs=0 105/300: dt: 0.9000, rms radial error=159.519, avgs=0 110/300: dt: 0.9000, rms radial error=158.623, avgs=0 115/300: dt: 0.9000, rms radial error=157.732, avgs=0 120/300: dt: 0.9000, rms radial error=156.846, avgs=0 125/300: dt: 0.9000, rms radial error=155.964, avgs=0 130/300: dt: 0.9000, rms radial error=155.088, avgs=0 135/300: dt: 0.9000, rms radial error=154.216, avgs=0 140/300: dt: 0.9000, rms radial error=153.349, avgs=0 145/300: dt: 0.9000, rms radial error=152.487, avgs=0 150/300: dt: 0.9000, rms radial error=151.630, avgs=0 155/300: dt: 0.9000, rms radial error=150.777, avgs=0 160/300: dt: 0.9000, rms radial error=149.930, avgs=0 165/300: dt: 0.9000, rms radial error=149.087, avgs=0 170/300: dt: 0.9000, rms radial error=148.248, avgs=0 175/300: dt: 0.9000, rms radial error=147.415, avgs=0 180/300: dt: 0.9000, rms radial error=146.586, avgs=0 185/300: dt: 0.9000, rms radial error=145.761, avgs=0 190/300: dt: 0.9000, rms radial error=144.941, avgs=0 195/300: dt: 0.9000, rms radial error=144.125, avgs=0 200/300: dt: 0.9000, rms radial error=143.314, avgs=0 205/300: dt: 0.9000, rms radial error=142.508, avgs=0 210/300: dt: 0.9000, rms radial error=141.706, avgs=0 215/300: dt: 0.9000, rms radial error=140.908, avgs=0 220/300: dt: 0.9000, rms radial error=140.115, avgs=0 225/300: dt: 0.9000, rms radial error=139.327, avgs=0 230/300: dt: 0.9000, rms radial error=138.543, avgs=0 235/300: dt: 0.9000, rms radial error=137.765, avgs=0 240/300: dt: 0.9000, rms radial error=136.991, avgs=0 245/300: dt: 0.9000, rms radial error=136.222, avgs=0 250/300: dt: 0.9000, rms radial error=135.457, avgs=0 255/300: dt: 0.9000, rms radial error=134.696, avgs=0 260/300: dt: 0.9000, rms radial error=133.939, avgs=0 265/300: dt: 0.9000, rms radial error=133.187, avgs=0 270/300: dt: 0.9000, rms radial error=132.439, avgs=0 275/300: dt: 0.9000, rms radial error=131.694, avgs=0 280/300: dt: 0.9000, rms radial error=130.954, avgs=0 285/300: dt: 0.9000, rms radial error=130.219, avgs=0 290/300: dt: 0.9000, rms radial error=129.487, avgs=0 295/300: dt: 0.9000, rms radial error=128.759, avgs=0 300/300: dt: 0.9000, rms radial error=128.036, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 15441.40 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/13 = 0.00040 epoch 2 (K=40.0), pass 1, starting sse = 2592.08 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/13 = 0.00023 epoch 3 (K=160.0), pass 1, starting sse = 261.87 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.13/15 = 0.00848 epoch 4 (K=640.0), pass 1, starting sse = 11.45 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.20/23 = 0.00856 final distance error %100000.00 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.0408 hours FSRUNTIME@ mris_sphere 0.0408 hours 1 threads #VMPC# mris_sphere VmPeak 602564 mris_sphere done @#@FSTIME 2020:07:23:09:19:12 mris_sphere N 9 e 146.91 S 12.09 U 134.78 P 99% M 207996 F 0 R 6563256 W 0 c 203 w 267 I 0 O 9176 L 2.15 2.05 2.06 @#@FSLOADPOST 2020:07:23:09:21:39 mris_sphere N 9 2.00 2.01 2.05 #@# Fix Topology lh Thu Jul 23 09:21:39 EDT 2020 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 bert 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.premesh' dev dev before topology correction, eno=-30 (nv=130332, nf=260724, ne=391086, g=16) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 10 iterations marking ambiguous vertices... 2091 ambiguous faces found in tessellation segmenting defects... 21 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 3 into 2 -merging segment 4 into 2 -merging segment 20 into 19 18 defects to be corrected 0 vertices coincident reading input surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/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: -8.6162 (-4.3081) -vertex loglikelihood: -5.5745 (-2.7872) -normal dot loglikelihood: -3.6743 (-3.6743) -quad curv loglikelihood: -6.2347 (-3.1174) Total Loglikelihood : -24.0996 CORRECTING DEFECT 0 (vertices=54, convex hull=70, v0=2087) After retessellation of defect 0 (v0=2087), euler #=-17 (129058,386668,257593) : difference with theory (-15) = 2 CORRECTING DEFECT 1 (vertices=42, convex hull=79, v0=19691) After retessellation of defect 1 (v0=19691), euler #=-16 (129078,386763,257669) : difference with theory (-14) = 2 CORRECTING DEFECT 2 (vertices=344, convex hull=251, v0=45941) After retessellation of defect 2 (v0=45941), euler #=-13 (129123,387022,257886) : difference with theory (-13) = 0 CORRECTING DEFECT 3 (vertices=28, convex hull=64, v0=55288) After retessellation of defect 3 (v0=55288), euler #=-12 (129139,387094,257943) : difference with theory (-12) = 0 CORRECTING DEFECT 4 (vertices=49, convex hull=86, v0=71531) After retessellation of defect 4 (v0=71531), euler #=-11 (129169,387218,258038) : difference with theory (-11) = 0 CORRECTING DEFECT 5 (vertices=12, convex hull=20, v0=78792) After retessellation of defect 5 (v0=78792), euler #=-10 (129173,387236,258053) : difference with theory (-10) = 0 CORRECTING DEFECT 6 (vertices=6, convex hull=25, v0=83656) After retessellation of defect 6 (v0=83656), euler #=-9 (129175,387250,258066) : difference with theory (-9) = 0 CORRECTING DEFECT 7 (vertices=33, convex hull=60, v0=88693) After retessellation of defect 7 (v0=88693), euler #=-8 (129191,387326,258127) : difference with theory (-8) = 0 CORRECTING DEFECT 8 (vertices=62, convex hull=46, v0=93233) After retessellation of defect 8 (v0=93233), euler #=-7 (129201,387371,258163) : difference with theory (-7) = 0 CORRECTING DEFECT 9 (vertices=162, convex hull=60, v0=95066) After retessellation of defect 9 (v0=95066), euler #=-6 (129210,387419,258203) : difference with theory (-6) = 0 CORRECTING DEFECT 10 (vertices=60, convex hull=91, v0=104575) After retessellation of defect 10 (v0=104575), euler #=-5 (129245,387564,258314) : difference with theory (-5) = 0 CORRECTING DEFECT 11 (vertices=6, convex hull=16, v0=106196) After retessellation of defect 11 (v0=106196), euler #=-4 (129247,387572,258321) : difference with theory (-4) = 0 CORRECTING DEFECT 12 (vertices=59, convex hull=47, v0=108088) After retessellation of defect 12 (v0=108088), euler #=-4 (129265,387648,258379) : difference with theory (-3) = 1 CORRECTING DEFECT 13 (vertices=41, convex hull=78, v0=119195) After retessellation of defect 13 (v0=119195), euler #=-3 (129282,387731,258446) : difference with theory (-2) = 1 CORRECTING DEFECT 14 (vertices=43, convex hull=63, v0=121479) After retessellation of defect 14 (v0=121479), euler #=-2 (129306,387828,258520) : difference with theory (-1) = 1 CORRECTING DEFECT 15 (vertices=188, convex hull=46, v0=123521) After retessellation of defect 15 (v0=123521), euler #=-1 (129314,387871,258556) : difference with theory (0) = 1 CORRECTING DEFECT 16 (vertices=40, convex hull=77, v0=125293) After retessellation of defect 16 (v0=125293), euler #=0 (129337,387968,258631) : difference with theory (1) = 1 CORRECTING DEFECT 17 (vertices=57, convex hull=73, v0=125861) After retessellation of defect 17 (v0=125861), euler #=2 (129354,388056,258704) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.22 (0.13-->10.00) (max @ vno 48841 --> 53074) face area -nan +- -nan (1000.00-->-1.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.22 (0.13-->10.00) (max @ vno 48841 --> 53074) face area -nan +- -nan (1000.00-->-1.00) tessellation finished, orienting corrected surface... 62 mutations (32.8%), 127 crossovers (67.2%), 106 vertices were eliminated building final representation... 978 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=129354, nf=258704, ne=388056, g=0) writing corrected surface to /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.orig.premesh... 0.000 % of the vertices (0 vertices) exhibit an orientation change removing intersecting faces 000: 108 intersecting terminating search with 0 intersecting topology fixing took 1.4 minutes FSRUNTIME@ mris_fix_topology lh 0.0234 hours 1 threads #VMPC# mris_fix_topology VmPeak 884160 @#@FSTIME 2020:07:23:09:21:39 mris_fix_topology N 14 e 84.46 S 0.61 U 83.76 P 99% M 724440 F 3 R 505673 W 0 c 25 w 381 I 2392 O 12176 L 2.00 2.01 2.05 @#@FSLOADPOST 2020:07:23:09:23:04 mris_fix_topology N 14 2.03 2.02 2.05 #@# Fix Topology rh Thu Jul 23 09:23:04 EDT 2020 mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 bert rh 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.premesh' dev dev before topology correction, eno=-26 (nv=130352, nf=260756, ne=391134, g=14) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 10 iterations marking ambiguous vertices... 2212 ambiguous faces found in tessellation segmenting defects... 18 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 18 defects to be corrected 0 vertices coincident reading input surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.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: -8.4861 (-4.2431) -vertex loglikelihood: -5.5705 (-2.7853) -normal dot loglikelihood: -3.6533 (-3.6533) -quad curv loglikelihood: -6.1209 (-3.0604) Total Loglikelihood : -23.8309 CORRECTING DEFECT 0 (vertices=5, convex hull=22, v0=4656) After retessellation of defect 0 (v0=4656), euler #=-15 (129030,386574,257529) : difference with theory (-15) = 0 CORRECTING DEFECT 1 (vertices=21, convex hull=52, v0=4834) After retessellation of defect 1 (v0=4834), euler #=-14 (129043,386630,257573) : difference with theory (-14) = 0 CORRECTING DEFECT 2 (vertices=28, convex hull=62, v0=38214) After retessellation of defect 2 (v0=38214), euler #=-13 (129056,386695,257626) : difference with theory (-13) = 0 CORRECTING DEFECT 3 (vertices=678, convex hull=277, v0=47420) After retessellation of defect 3 (v0=47420), euler #=-12 (129070,386877,257795) : difference with theory (-12) = 0 CORRECTING DEFECT 4 (vertices=27, convex hull=79, v0=50717) After retessellation of defect 4 (v0=50717), euler #=-11 (129088,386960,257861) : difference with theory (-11) = 0 CORRECTING DEFECT 5 (vertices=38, convex hull=53, v0=51317) After retessellation of defect 5 (v0=51317), euler #=-10 (129102,387022,257910) : difference with theory (-10) = 0 CORRECTING DEFECT 6 (vertices=6, convex hull=18, v0=55920) After retessellation of defect 6 (v0=55920), euler #=-9 (129102,387025,257914) : difference with theory (-9) = 0 CORRECTING DEFECT 7 (vertices=23, convex hull=57, v0=57220) After retessellation of defect 7 (v0=57220), euler #=-8 (129111,387072,257953) : difference with theory (-8) = 0 CORRECTING DEFECT 8 (vertices=16, convex hull=33, v0=66156) After retessellation of defect 8 (v0=66156), euler #=-7 (129118,387101,257976) : difference with theory (-7) = 0 CORRECTING DEFECT 9 (vertices=202, convex hull=127, v0=70466) After retessellation of defect 9 (v0=70466), euler #=-6 (129137,387216,258073) : difference with theory (-6) = 0 CORRECTING DEFECT 10 (vertices=5, convex hull=27, v0=84338) After retessellation of defect 10 (v0=84338), euler #=-5 (129139,387228,258084) : difference with theory (-5) = 0 CORRECTING DEFECT 11 (vertices=35, convex hull=59, v0=90517) After retessellation of defect 11 (v0=90517), euler #=-4 (129154,387298,258140) : difference with theory (-4) = 0 CORRECTING DEFECT 12 (vertices=30, convex hull=58, v0=92433) After retessellation of defect 12 (v0=92433), euler #=-3 (129165,387353,258185) : difference with theory (-3) = 0 CORRECTING DEFECT 13 (vertices=83, convex hull=112, v0=93086) After retessellation of defect 13 (v0=93086), euler #=-2 (129192,387485,258291) : difference with theory (-2) = 0 CORRECTING DEFECT 14 (vertices=31, convex hull=54, v0=95452) After retessellation of defect 14 (v0=95452), euler #=-1 (129202,387536,258333) : difference with theory (-1) = 0 CORRECTING DEFECT 15 (vertices=8, convex hull=23, v0=97119) After retessellation of defect 15 (v0=97119), euler #=0 (129202,387542,258340) : difference with theory (0) = 0 CORRECTING DEFECT 16 (vertices=58, convex hull=80, v0=107865) After retessellation of defect 16 (v0=107865), euler #=1 (129229,387661,258433) : difference with theory (1) = 0 CORRECTING DEFECT 17 (vertices=28, convex hull=51, v0=122262) After retessellation of defect 17 (v0=122262), euler #=2 (129240,387714,258476) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.23 (0.09-->16.02) (max @ vno 51288 --> 51417) face area -nan +- -nan (1000.00-->-1.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.23 (0.09-->16.02) (max @ vno 51288 --> 51417) face area -nan +- -nan (1000.00-->-1.00) tessellation finished, orienting corrected surface... 77 mutations (34.4%), 147 crossovers (65.6%), 219 vertices were eliminated building final representation... 1112 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=129240, nf=258476, ne=387714, g=0) writing corrected surface to /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.orig.premesh... 0.000 % of the vertices (0 vertices) exhibit an orientation change removing intersecting faces 000: 113 intersecting terminating search with 0 intersecting topology fixing took 2.5 minutes FSRUNTIME@ mris_fix_topology rh 0.0414 hours 1 threads #VMPC# mris_fix_topology VmPeak 884344 @#@FSTIME 2020:07:23:09:23:04 mris_fix_topology N 14 e 149.17 S 0.67 U 148.43 P 99% M 724512 F 0 R 528659 W 0 c 47 w 444 I 0 O 12168 L 2.03 2.02 2.05 @#@FSLOADPOST 2020:07:23:09:25:33 mris_fix_topology N 14 2.06 2.05 2.05 mris_euler_number ../surf/lh.orig.premesh euler # = v-e+f = 2g-2: 129354 - 388056 + 258704 = 2 --> 0 holes F =2V-4: 258704 = 258708-4 (0) 2E=3F: 776112 = 776112 (0) total defect index = 0 mris_euler_number ../surf/rh.orig.premesh euler # = v-e+f = 2g-2: 129240 - 387714 + 258476 = 2 --> 0 holes F =2V-4: 258476 = 258480-4 (0) 2E=3F: 775428 = 775428 (0) total defect index = 0 Thu Jul 23 09:25:34 EDT 2020 setenv SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running cd /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/scripts /usr/local/freesurfer/dev/bin/defect2seg --s bert freesurfer-linux-centos7_x86_64-dev-20200723-04e3f95 defect2seg dev Linux nike 3.10.0-1062.7.1.el7.x86_64 #1 SMP Mon Dec 2 17:33:29 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux pid 5133 mri_label2vol --defects /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.orig.nofix /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.defect_labels /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/orig.mgz 1000 0 /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/surface.defects.mgz mri_label2vol supposed to be reproducible but seed not set Changing input type 0 to MRI_INT Converting defects to volume: offset=1000, merge=0 Writing to /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/surface.defects.mgz mris_defects_pointset -s /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.orig.nofix -d /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.defect_labels -o /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.defects.pointset Reading in surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.orig.nofix Reading in defect segmentation /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.defect_labels #VMPC# mris_defects_pointset 186628 mris_defects_pointset done mri_label2vol --defects /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.orig.nofix /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.defect_labels /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/surface.defects.mgz 2000 1 /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/surface.defects.mgz mri_label2vol supposed to be reproducible but seed not set Converting defects to volume: offset=2000, merge=1 Writing to /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/surface.defects.mgz mris_defects_pointset -s /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.orig.nofix -d /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.defect_labels -o /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.defects.pointset Reading in surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.orig.nofix Reading in defect segmentation /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.defect_labels #VMPC# mris_defects_pointset 186704 mris_defects_pointset done Started at Thu Jul 23 09:25:34 EDT 2020 Ended at Thu Jul 23 09:25:39 EDT 2020 Defect2seg-Run-Time-Sec 5 Defect2seg-Run-Time-Min 0.10 Defect2seg-Run-Time-Hours 0.00 tkmeditfv bert brain.finalsurfs.mgz -defect defect2seg Done @#@FSTIME 2020:07:23:09:25:34 defect2seg N 2 e 5.04 S 0.58 U 4.40 P 98% M 234036 F 7 R 240227 W 0 c 64 w 516 I 6784 O 584 L 2.06 2.05 2.05 @#@FSLOADPOST 2020:07:23:09:25:39 defect2seg N 2 2.05 2.05 2.05 mris_remesh --remesh --iters 3 --input /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.orig.premesh --output /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.orig iters = 3 standard remeshing without target adjusted l: 0.711637 remeshing to edge length 0.711637 with 3 iterations avg qual before : 0.893946 after: 0.970962 Removing intersections Remeshed surface quality stats nv0 = 129354 nv = 135579 1.04812 Area 271154 0.30311 0.03385 0.066817 0.5134 Corner 813462 60.00000 8.84073 14.106402 150.9197 Edge 406731 0.84469 0.08271 0.441825 1.2865 Hinge 406731 9.34304 9.57481 0.000000 133.7508 mris_remesh done @#@FSTIME 2020:07:23:09:25:39 mris_remesh N 7 e 26.20 S 0.77 U 25.37 P 99% M 716564 F 4 R 680556 W 0 c 8 w 212 I 4376 O 9536 L 2.05 2.05 2.05 @#@FSLOADPOST 2020:07:23:09:26:05 mris_remesh N 7 2.10 2.06 2.05 mris_remesh --remesh --iters 3 --input /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.orig.premesh --output /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.orig iters = 3 standard remeshing without target adjusted l: 0.712652 remeshing to edge length 0.712652 with 3 iterations avg qual before : 0.893456 after: 0.971079 Removing intersections Remeshed surface quality stats nv0 = 129240 nv = 135771 1.05053 Area 271538 0.30375 0.03376 0.064939 0.4761 Corner 814614 60.00000 8.81970 11.499300 156.1271 Edge 407307 0.84558 0.08264 0.427254 1.3095 Hinge 407307 9.25835 9.44791 0.000000 131.4200 mris_remesh done @#@FSTIME 2020:07:23:09:26:06 mris_remesh N 7 e 25.03 S 0.74 U 24.24 P 99% M 718404 F 0 R 654476 W 0 c 8 w 322 I 0 O 9552 L 2.10 2.06 2.05 @#@FSLOADPOST 2020:07:23:09:26:31 mris_remesh N 7 2.12 2.07 2.06 /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours writing corrected surface to ../surf/lh.orig @#@FSTIME 2020:07:23:09:26:31 mris_remove_intersection N 2 e 2.34 S 0.20 U 2.07 P 97% M 331680 F 4 R 143052 W 0 c 1 w 394 I 4360 O 9536 L 2.12 2.07 2.06 @#@FSLOADPOST 2020:07:23:09:26:33 mris_remove_intersection N 2 2.11 2.07 2.06 rm ../surf/lh.inflated rm: cannot remove '../surf/lh.inflated': No such file or directory /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours writing corrected surface to ../surf/rh.orig @#@FSTIME 2020:07:23:09:26:33 mris_remove_intersection N 2 e 2.35 S 0.21 U 2.09 P 97% M 333652 F 0 R 143722 W 0 c 3 w 329 I 0 O 9552 L 2.11 2.07 2.06 @#@FSLOADPOST 2020:07:23:09:26:35 mris_remove_intersection N 2 2.11 2.07 2.06 rm ../surf/rh.inflated rm: cannot remove '../surf/rh.inflated': No such file or directory #-------------------------------------------- #@# AutoDetGWStats lh Thu Jul 23 09:26:35 EDT 2020 cd /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh dev cd /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri setenv SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/lh.orig.premesh border white: 247646 voxels (1.48%) border gray 268901 voxels (1.60%) Reading in intensity volume brain.finalsurfs.mgz Reading in wm volume wm.mgz Reading in surf ../surf/lh.orig.premesh Auto detecting stats MRIclipBrightWM(): nthresh=19421, wmmin=5, clip=110 Binarizing thresholding at 5 computing class statistics... low=30, hi=110.000000 CCS WM (103.0): 103.2 +- 5.6 [70.0 --> 110.0] CCS GM (86.0) : 85.3 +- 9.6 [30.0 --> 110.0] white_mean = 103.158 +/- 5.63298, gray_mean = 85.3456 +/- 9.55652 using class modes intead of means, discounting robust sigmas.... MRIScomputeClassModes(): min=0 max=196 nbins=197 intensity peaks found at WM=106+-3.5, GM=82+-6.1 white_mode = 106, gray_mode = 82 std_scale = 1 Applying sanity checks, max_scale_down = 0.2 setting MIN_GRAY_AT_WHITE_BORDER to 72.4 (was 70.000000) setting MAX_BORDER_WHITE to 111.6 (was 105.000000) setting MIN_BORDER_WHITE to 82.0 (was 85.000000) setting MAX_CSF to 62.9 (was 40.000000) setting MAX_GRAY to 100.4 (was 95.000000) setting MAX_GRAY_AT_CSF_BORDER to 72.4 (was 75.000000) setting MIN_GRAY_AT_CSF_BORDER to 53.3 (was 40.000000) When placing the white surface white_border_hi = 111.633; white_border_low = 82; white_outside_low = 72.4435; white_inside_hi = 120; white_outside_hi = 111.633; When placing the pial surface pial_border_hi = 72.4435; pial_border_low = 53.3305; pial_outside_low = 10; pial_inside_hi = 100.367; pial_outside_hi = 67.6652; #VMPC# mris_autodet_gwstats VmPeak 368704 mris_autodet_gwstats done @#@FSTIME 2020:07:23:09:26:36 mris_autodet_gwstats N 8 e 3.94 S 0.15 U 3.76 P 99% M 229316 F 6 R 115510 W 0 c 2 w 39 I 5480 O 16 L 2.11 2.07 2.06 @#@FSLOADPOST 2020:07:23:09:26:39 mris_autodet_gwstats N 8 2.26 2.10 2.07 #-------------------------------------------- #@# AutoDetGWStats rh Thu Jul 23 09:26:39 EDT 2020 cd /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri mris_autodet_gwstats --o ../surf/autodet.gw.stats.rh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/rh.orig.premesh dev cd /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri setenv SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running mris_autodet_gwstats --o ../surf/autodet.gw.stats.rh.dat --i brain.finalsurfs.mgz --wm wm.mgz --surf ../surf/rh.orig.premesh border white: 247646 voxels (1.48%) border gray 268901 voxels (1.60%) Reading in intensity volume brain.finalsurfs.mgz Reading in wm volume wm.mgz Reading in surf ../surf/rh.orig.premesh Auto detecting stats MRIclipBrightWM(): nthresh=19421, wmmin=5, clip=110 Binarizing thresholding at 5 computing class statistics... low=30, hi=110.000000 CCS WM (103.0): 103.2 +- 5.6 [70.0 --> 110.0] CCS GM (86.0) : 85.3 +- 9.6 [30.0 --> 110.0] white_mean = 103.158 +/- 5.63298, gray_mean = 85.3456 +/- 9.55652 using class modes intead of means, discounting robust sigmas.... MRIScomputeClassModes(): min=0 max=196 nbins=197 intensity peaks found at WM=106+-3.5, GM=83+-6.1 white_mode = 106, gray_mode = 83 std_scale = 1 Applying sanity checks, max_scale_down = 0.2 setting MIN_GRAY_AT_WHITE_BORDER to 73.4 (was 70.000000) setting MAX_BORDER_WHITE to 111.6 (was 105.000000) setting MIN_BORDER_WHITE to 83.0 (was 85.000000) setting MAX_CSF to 63.9 (was 40.000000) setting MAX_GRAY to 100.4 (was 95.000000) setting MAX_GRAY_AT_CSF_BORDER to 73.4 (was 75.000000) setting MIN_GRAY_AT_CSF_BORDER to 54.3 (was 40.000000) When placing the white surface white_border_hi = 111.633; white_border_low = 83; white_outside_low = 73.4435; white_inside_hi = 120; white_outside_hi = 111.633; When placing the pial surface pial_border_hi = 73.4435; pial_border_low = 54.3305; pial_outside_low = 10; pial_inside_hi = 100.367; pial_outside_hi = 68.6652; #VMPC# mris_autodet_gwstats VmPeak 368624 mris_autodet_gwstats done @#@FSTIME 2020:07:23:09:26:40 mris_autodet_gwstats N 8 e 3.87 S 0.17 U 3.69 P 99% M 229296 F 0 R 115600 W 0 c 3 w 30 I 0 O 8 L 2.26 2.10 2.07 @#@FSLOADPOST 2020:07:23:09:26:43 mris_autodet_gwstats N 8 2.24 2.10 2.07 #-------------------------------------------- #@# WhitePreAparc lh Thu Jul 23 09:26:43 EDT 2020 cd /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --threads 1 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 dev dev cd /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri setenv SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --threads 1 --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 Reading in input surface ../surf/lh.orig Smoothing surface with 5 iterations Area 271154 0.26960 0.06221 0.002709 0.5794 Corner 813462 60.00000 9.30487 12.652481 143.1218 Edge 406731 0.79281 0.11234 0.071805 1.3420 Hinge 406731 6.26690 6.17075 0.000015 131.4432 Not reading in aparc Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=19421, wmmin=5, clip=110 MRIfindBrightNonWM(): 10149 bright non-wm voxels segmented. Masking bright non-wm for white surface MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Reading in seg volume aseg.presurf.mgz Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=0 removing 4 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6904, nmarked2=0, nripped=6904 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 67790: xyz = (-16.1384,-7.51003,62.1824) oxyz = (-16.1384,-7.51003,62.1824) wxzy = (-16.1384,-7.51003,62.1824) pxyz = (0,0,0) CBVO Creating mask 135579 n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=6904 removing 4 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=6904, nmarked2=0, nripped=6904 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 111.6329730; border_low = 82.0000000; outside_low = 72.4434810; outside_hi = 111.6329730; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=135579 Gdiag_no=-1 vno start=0, stop=135579 Replacing 255s with 0s #SI# sigma=2 had to be increased for 129 vertices, nripped=6904 mean border=89.8, 95 (95) missing vertices, mean dist 0.5 [0.7 (%29.7)->1.0 (%70.3))] %60 local maxima, %35 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.2707 min Finding expansion regions mean absolute distance = 0.90 +- 1.09 4461 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=2.0, host= nike, nav=4, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 000: dt: 0.0000, sse=1843786.8, rms=8.116 001: dt: 0.5000, sse=1092257.4, rms=6.067 (25.247%) 002: dt: 0.5000, sse=693120.2, rms=4.616 (23.922%) 003: dt: 0.5000, sse=471746.6, rms=3.560 (22.873%) 004: dt: 0.5000, sse=349427.2, rms=2.807 (21.158%) 005: dt: 0.5000, sse=285035.3, rms=2.307 (17.791%) 006: dt: 0.5000, sse=253516.4, rms=2.011 (12.841%) 007: dt: 0.5000, sse=239434.2, rms=1.852 (7.901%) 008: dt: 0.5000, sse=233122.8, rms=1.779 (3.928%) rms = 1.7357/1.7795, sse=230136.9/233122.8, time step reduction 1 of 3 to 0.250 0 0 1 009: dt: 0.5000, sse=230136.9, rms=1.736 (2.459%) 010: dt: 0.2500, sse=196331.7, rms=1.254 (27.759%) 011: dt: 0.2500, sse=190400.5, rms=1.182 (5.739%) rms = 1.1557/1.1819, sse=189208.1/190400.5, time step reduction 2 of 3 to 0.125 0 0 1 012: dt: 0.2500, sse=189208.1, rms=1.156 (2.216%) rms = 1.1366/1.1557, sse=188386.1/189208.1, time step reduction 3 of 3 to 0.062 0 0 1 013: dt: 0.1250, sse=188386.1, rms=1.137 (1.655%) maximum number of reductions reached, breaking from loop positioning took 1.1 minutes Iteration 1 ========================================= n_averages=2, current_sigma=1 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=6904 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=7129, nmarked2=15, nripped=7129 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 111.6329730; border_low = 82.0000000; outside_low = 72.4434810; outside_hi = 111.6329730; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=135579 Gdiag_no=-1 vno start=0, stop=135579 Replacing 255s with 0s #SI# sigma=1 had to be increased for 47 vertices, nripped=7129 mean border=92.2, 107 (59) missing vertices, mean dist -0.3 [0.5 (%72.4)->0.3 (%27.6))] %73 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1804 min Finding expansion regions mean absolute distance = 0.46 +- 0.72 4566 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=1.0, host= nike, nav=2, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=577279.3, rms=3.812 014: dt: 0.5000, sse=344024.4, rms=2.350 (38.363%) 015: dt: 0.5000, sse=278730.7, rms=1.725 (26.586%) 016: dt: 0.5000, sse=255187.5, rms=1.431 (17.064%) 017: dt: 0.5000, sse=245846.4, rms=1.312 (8.285%) rms = 1.2816/1.3122, sse=244182.4/245846.4, time step reduction 1 of 3 to 0.250 0 0 1 018: dt: 0.5000, sse=244182.4, rms=1.282 (2.332%) 019: dt: 0.2500, sse=227016.8, rms=0.936 (26.938%) 020: dt: 0.2500, sse=224286.0, rms=0.879 (6.082%) rms = 0.8598/0.8794, sse=224255.8/224286.0, time step reduction 2 of 3 to 0.125 0 0 1 021: dt: 0.2500, sse=224255.8, rms=0.860 (2.230%) rms = 0.8480/0.8598, sse=223558.0/224255.8, time step reduction 3 of 3 to 0.062 0 0 1 022: dt: 0.1250, sse=223558.0, rms=0.848 (1.372%) maximum number of reductions reached, breaking from loop positioning took 0.8 minutes Iteration 2 ========================================= n_averages=1, current_sigma=0.5 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=7129 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=7201, nmarked2=15, nripped=7201 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 111.6329730; border_low = 82.0000000; outside_low = 72.4434810; outside_hi = 111.6329730; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=135579 Gdiag_no=-1 vno start=0, stop=135579 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 94 vertices, nripped=7201 mean border=94.3, 102 (46) missing vertices, mean dist -0.2 [0.4 (%73.2)->0.2 (%26.8))] %84 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0972 min Finding expansion regions mean absolute distance = 0.33 +- 0.46 4864 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.5, host= nike, nav=1, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=397403.2, rms=2.795 023: dt: 0.5000, sse=253855.9, rms=1.487 (46.804%) 024: dt: 0.5000, sse=230261.3, rms=1.134 (23.747%) 025: dt: 0.5000, sse=227502.3, rms=1.061 (6.418%) rms = 1.0746/1.0610, sse=225630.5/227502.3, time step reduction 1 of 3 to 0.250 0 0 1 RMS increased, rejecting step 026: dt: 0.2500, sse=217197.5, rms=0.872 (17.848%) 027: dt: 0.2500, sse=213712.7, rms=0.786 (9.874%) rms = 0.7760/0.7856, sse=211694.8/213712.7, time step reduction 2 of 3 to 0.125 0 0 1 028: dt: 0.2500, sse=211694.8, rms=0.776 (1.211%) rms = 0.7700/0.7760, sse=211414.6/211694.8, time step reduction 3 of 3 to 0.062 0 0 1 029: dt: 0.1250, sse=211414.5, rms=0.770 (0.780%) maximum number of reductions reached, breaking from loop positioning took 0.6 minutes Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=7201 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=7223, nmarked2=15, nripped=7223 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 111.6329730; border_low = 82.0000000; outside_low = 72.4434810; outside_hi = 111.6329730; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=135579 Gdiag_no=-1 vno start=0, stop=135579 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 124 vertices, nripped=7223 mean border=94.9, 101 (44) missing vertices, mean dist -0.1 [0.3 (%58.2)->0.2 (%41.8))] %88 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0603 min Finding expansion regions mean absolute distance = 0.24 +- 0.35 4015 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host= nike, nav=0, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=229904.6, rms=1.218 030: dt: 0.5000, sse=206318.7, rms=0.731 (39.956%) rms = 0.8442/0.7314, sse=210225.4/206318.7, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 031: dt: 0.2500, sse=203492.9, rms=0.642 (12.196%) rms = 0.6301/0.6422, sse=202289.3/203492.9, time step reduction 2 of 3 to 0.125 0 0 1 032: dt: 0.2500, sse=202289.3, rms=0.630 (1.873%) rms = 0.6185/0.6301, sse=201584.4/202289.3, time step reduction 3 of 3 to 0.062 0 0 1 033: dt: 0.1250, sse=201584.4, rms=0.619 (1.845%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes Writing output to ../surf/lh.white.preaparc #ET# mris_place_surface 3.57 minutes #VMPC# mris_place_surfaces VmPeak 2253620 mris_place_surface done @#@FSTIME 2020:07:23:09:26:43 mris_place_surface N 18 e 221.91 S 1.69 U 220.10 P 99% M 1875372 F 3 R 1596998 W 0 c 1391 w 405 I 2400 O 9536 L 2.24 2.10 2.07 @#@FSLOADPOST 2020:07:23:09:30:25 mris_place_surface N 18 2.05 2.07 2.05 #-------------------------------------------- #@# WhitePreAparc rh Thu Jul 23 09:30:25 EDT 2020 cd /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --wm wm.mgz --threads 1 --invol brain.finalsurfs.mgz --rh --i ../surf/rh.orig --o ../surf/rh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 dev dev cd /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri setenv SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --wm wm.mgz --threads 1 --invol brain.finalsurfs.mgz --rh --i ../surf/rh.orig --o ../surf/rh.white.preaparc --white --seg aseg.presurf.mgz --nsmooth 5 Reading in input surface ../surf/rh.orig Smoothing surface with 5 iterations Area 271538 0.27075 0.06188 0.001144 0.6286 Corner 814614 60.00000 9.25895 6.606450 155.4068 Edge 407307 0.79452 0.11172 0.050935 1.3893 Hinge 407307 6.20494 6.07908 0.000034 118.7675 Not reading in aparc Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=19421, wmmin=5, clip=110 MRIfindBrightNonWM(): 10149 bright non-wm voxels segmented. Masking bright non-wm for white surface MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Reading in seg volume aseg.presurf.mgz Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=0 removing 3 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=7161, nmarked2=0, nripped=7161 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 67886: xyz = (42.4163,-8.508,46.1132) oxyz = (42.4163,-8.508,46.1132) wxzy = (42.4163,-8.508,46.1132) pxyz = (0,0,0) CBVO Creating mask 135771 n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=7161 removing 3 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=7161, nmarked2=0, nripped=7161 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 111.6329730; border_low = 83.0000000; outside_low = 73.4434810; outside_hi = 111.6329730; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=135771 Gdiag_no=-1 vno start=0, stop=135771 Replacing 255s with 0s #SI# sigma=2 had to be increased for 33 vertices, nripped=7161 mean border=90.2, 18 (18) missing vertices, mean dist 0.5 [0.7 (%29.5)->0.9 (%70.5))] %58 local maxima, %37 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.2645 min Finding expansion regions mean absolute distance = 0.88 +- 1.06 4488 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=2.0, host= nike, nav=4, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 000: dt: 0.0000, sse=1793060.8, rms=7.996 001: dt: 0.5000, sse=1051703.6, rms=5.934 (25.787%) 002: dt: 0.5000, sse=658371.4, rms=4.464 (24.763%) 003: dt: 0.5000, sse=443374.2, rms=3.398 (23.886%) 004: dt: 0.5000, sse=326227.9, rms=2.637 (22.390%) 005: dt: 0.5000, sse=264808.6, rms=2.126 (19.369%) 006: dt: 0.5000, sse=234376.9, rms=1.815 (14.664%) 007: dt: 0.5000, sse=219810.7, rms=1.639 (9.697%) 008: dt: 0.5000, sse=214959.8, rms=1.552 (5.262%) rms = 1.5110/1.5524, sse=211147.5/214959.8, time step reduction 1 of 3 to 0.250 0 0 1 009: dt: 0.5000, sse=211147.5, rms=1.511 (2.664%) 010: dt: 0.2500, sse=181389.6, rms=1.026 (32.098%) 011: dt: 0.2500, sse=178600.7, rms=0.966 (5.889%) rms = 0.9511/0.9656, sse=178147.7/178600.7, time step reduction 2 of 3 to 0.125 0 0 1 012: dt: 0.2500, sse=178147.7, rms=0.951 (1.504%) rms = 0.9418/0.9511, sse=177800.0/178147.7, time step reduction 3 of 3 to 0.062 0 0 1 013: dt: 0.1250, sse=177800.0, rms=0.942 (0.976%) maximum number of reductions reached, breaking from loop positioning took 1.1 minutes Iteration 1 ========================================= n_averages=2, current_sigma=1 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=7161 removing 3 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=7242, nmarked2=0, nripped=7242 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 111.6329730; border_low = 83.0000000; outside_low = 73.4434810; outside_hi = 111.6329730; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=135771 Gdiag_no=-1 vno start=0, stop=135771 Replacing 255s with 0s #SI# sigma=1 had to be increased for 30 vertices, nripped=7242 mean border=92.6, 49 (3) missing vertices, mean dist -0.3 [0.5 (%71.8)->0.2 (%28.2))] %72 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1791 min Finding expansion regions mean absolute distance = 0.46 +- 0.71 4455 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=1.0, host= nike, nav=2, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=568813.7, rms=3.772 014: dt: 0.5000, sse=342516.0, rms=2.341 (37.931%) 015: dt: 0.5000, sse=276905.0, rms=1.724 (26.350%) 016: dt: 0.5000, sse=251972.1, rms=1.416 (17.868%) 017: dt: 0.5000, sse=242148.3, rms=1.280 (9.617%) rms = 1.2346/1.2800, sse=239656.5/242148.3, time step reduction 1 of 3 to 0.250 0 0 1 018: dt: 0.5000, sse=239656.5, rms=1.235 (3.547%) 019: dt: 0.2500, sse=223012.4, rms=0.917 (25.725%) 020: dt: 0.2500, sse=221333.5, rms=0.867 (5.489%) rms = 0.8499/0.8667, sse=220786.5/221333.5, time step reduction 2 of 3 to 0.125 0 0 1 021: dt: 0.2500, sse=220786.5, rms=0.850 (1.940%) rms = 0.8394/0.8499, sse=220464.2/220786.5, time step reduction 3 of 3 to 0.062 0 0 1 022: dt: 0.1250, sse=220464.2, rms=0.839 (1.229%) maximum number of reductions reached, breaking from loop positioning took 0.8 minutes Iteration 2 ========================================= n_averages=1, current_sigma=0.5 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=7242 removing 3 vertices from ripped group in thread:0 removing 2 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=7307, nmarked2=0, nripped=7307 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 111.6329730; border_low = 83.0000000; outside_low = 73.4434810; outside_hi = 111.6329730; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=135771 Gdiag_no=-1 vno start=0, stop=135771 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 142 vertices, nripped=7307 mean border=94.6, 45 (0) missing vertices, mean dist -0.2 [0.4 (%73.3)->0.2 (%26.7))] %84 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0973 min Finding expansion regions mean absolute distance = 0.32 +- 0.45 4879 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.5, host= nike, nav=1, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=395343.0, rms=2.799 023: dt: 0.5000, sse=248896.3, rms=1.451 (48.158%) 024: dt: 0.5000, sse=226054.9, rms=1.088 (25.000%) 025: dt: 0.5000, sse=222712.4, rms=1.020 (6.276%) rms = 1.0261/1.0199, sse=225248.1/222712.4, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 026: dt: 0.2500, sse=215123.5, rms=0.853 (16.397%) 027: dt: 0.2500, sse=212230.5, rms=0.774 (9.197%) rms = 0.7661/0.7742, sse=212276.1/212230.6, time step reduction 2 of 3 to 0.125 0 1 1 028: dt: 0.2500, sse=212276.1, rms=0.766 (1.054%) rms = 0.7607/0.7661, sse=212066.7/212276.1, time step reduction 3 of 3 to 0.062 0 0 1 029: dt: 0.1250, sse=212066.7, rms=0.761 (0.701%) maximum number of reductions reached, breaking from loop positioning took 0.6 minutes Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Freezing midline and others Ripping frozen voxels INFO: rip surface needed but not specified, so using input surface Freezing midline and others Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures... which=1, fix_mtl=0, using annot = 0 #FML0# MRISripMidline(): nripped=7307 removing 4 vertices from ripped group in thread:0 removing 4 vertices from ripped group in thread:0 removing 3 vertices from ripped group in thread:0 #FML# MRISripMidline(): nmarked=7331, nmarked2=0, nripped=7331 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 247 MRISripSegs(): -2 2 0.5 ripped 0 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 111.6329730; border_low = 83.0000000; outside_low = 73.4434810; outside_hi = 111.6329730; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=135771 Gdiag_no=-1 vno start=0, stop=135771 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 148 vertices, nripped=7331 mean border=95.2, 61 (0) missing vertices, mean dist -0.1 [0.3 (%58.0)->0.2 (%42.0))] %88 local maxima, % 7 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0600 min Finding expansion regions mean absolute distance = 0.24 +- 0.33 3965 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host= nike, nav=0, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=229926.5, rms=1.203 030: dt: 0.5000, sse=205663.9, rms=0.698 (41.974%) rms = 0.8131/0.6978, sse=211209.2/205663.9, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 031: dt: 0.2500, sse=203021.0, rms=0.626 (10.243%) rms = 0.6153/0.6264, sse=202701.0/203021.0, time step reduction 2 of 3 to 0.125 0 0 1 032: dt: 0.2500, sse=202701.0, rms=0.615 (1.768%) rms = 0.6096/0.6153, sse=203097.3/202701.0, time step reduction 3 of 3 to 0.062 0 1 1 033: dt: 0.1250, sse=203097.3, rms=0.610 (0.926%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes Writing output to ../surf/rh.white.preaparc #ET# mris_place_surface 3.58 minutes #VMPC# mris_place_surfaces VmPeak 2249276 mris_place_surface done @#@FSTIME 2020:07:23:09:30:26 mris_place_surface N 18 e 222.71 S 1.59 U 221.08 P 99% M 1871040 F 0 R 1622784 W 0 c 67 w 352 I 0 O 9552 L 2.05 2.07 2.05 @#@FSLOADPOST 2020:07:23:09:34:08 mris_place_surface N 18 2.11 2.09 2.05 #-------------------------------------------- #@# CortexLabel lh Thu Jul 23 09:34:08 EDT 2020 cd /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri mri_label2label --label-cortex ../surf/lh.white.preaparc aseg.presurf.mgz 0 ../label/lh.cortex.label Generating cortex label... RemoveHipAmgy=0 NucAccIsMedialWall=0 mris->useRealRAS=0 11 non-cortical segments detected only using segment with 9183 vertices erasing segment 0 (vno[0] = 21077) erasing segment 1 (vno[0] = 23634) erasing segment 2 (vno[0] = 26819) erasing segment 4 (vno[0] = 69686) erasing segment 5 (vno[0] = 80738) erasing segment 6 (vno[0] = 81567) erasing segment 7 (vno[0] = 84424) erasing segment 8 (vno[0] = 98004) erasing segment 9 (vno[0] = 98530) erasing segment 10 (vno[0] = 130927) @#@FSTIME 2020:07:23:09:34:08 mri_label2label N 5 e 14.22 S 0.25 U 13.91 P 99% M 343756 F 1 R 178164 W 0 c 7 w 415 I 1448 O 10984 L 2.11 2.09 2.05 @#@FSLOADPOST 2020:07:23:09:34:23 mri_label2label N 5 2.16 2.10 2.06 #-------------------------------------------- #@# CortexLabel+HipAmyg lh Thu Jul 23 09:34:23 EDT 2020 cd /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri mri_label2label --label-cortex ../surf/lh.white.preaparc aseg.presurf.mgz 1 ../label/lh.cortex+hipamyg.label Generating cortex label... RemoveHipAmgy=1 NucAccIsMedialWall=0 mris->useRealRAS=0 15 non-cortical segments detected only using segment with 6852 vertices erasing segment 0 (vno[0] = 21077) erasing segment 1 (vno[0] = 23634) erasing segment 2 (vno[0] = 26819) erasing segment 4 (vno[0] = 44731) erasing segment 5 (vno[0] = 50010) erasing segment 6 (vno[0] = 57149) erasing segment 7 (vno[0] = 69686) erasing segment 8 (vno[0] = 80738) erasing segment 9 (vno[0] = 81567) erasing segment 10 (vno[0] = 84424) erasing segment 11 (vno[0] = 98004) erasing segment 12 (vno[0] = 98530) erasing segment 13 (vno[0] = 130927) erasing segment 14 (vno[0] = 132243) @#@FSTIME 2020:07:23:09:34:23 mri_label2label N 5 e 14.31 S 0.26 U 14.00 P 99% M 362756 F 0 R 182868 W 0 c 4 w 358 I 0 O 11168 L 2.16 2.10 2.06 @#@FSLOADPOST 2020:07:23:09:34:37 mri_label2label N 5 2.14 2.10 2.06 #-------------------------------------------- #@# CortexLabel rh Thu Jul 23 09:34:37 EDT 2020 cd /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri mri_label2label --label-cortex ../surf/rh.white.preaparc aseg.presurf.mgz 0 ../label/rh.cortex.label Generating cortex label... RemoveHipAmgy=0 NucAccIsMedialWall=0 mris->useRealRAS=0 6 non-cortical segments detected only using segment with 8917 vertices erasing segment 1 (vno[0] = 67996) erasing segment 2 (vno[0] = 71299) erasing segment 3 (vno[0] = 79957) erasing segment 4 (vno[0] = 80702) erasing segment 5 (vno[0] = 134336) @#@FSTIME 2020:07:23:09:34:37 mri_label2label N 5 e 15.12 S 0.23 U 14.83 P 99% M 320208 F 0 R 171161 W 0 c 97 w 499 I 0 O 10760 L 2.14 2.10 2.06 @#@FSLOADPOST 2020:07:23:09:34:52 mri_label2label N 5 2.11 2.09 2.06 #-------------------------------------------- #@# CortexLabel+HipAmyg rh Thu Jul 23 09:34:52 EDT 2020 cd /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri mri_label2label --label-cortex ../surf/rh.white.preaparc aseg.presurf.mgz 1 ../label/rh.cortex+hipamyg.label Generating cortex label... RemoveHipAmgy=1 NucAccIsMedialWall=0 mris->useRealRAS=0 12 non-cortical segments detected only using segment with 6679 vertices erasing segment 1 (vno[0] = 44841) erasing segment 2 (vno[0] = 45735) erasing segment 3 (vno[0] = 51250) erasing segment 4 (vno[0] = 54441) erasing segment 5 (vno[0] = 67996) erasing segment 6 (vno[0] = 71299) erasing segment 7 (vno[0] = 79957) erasing segment 8 (vno[0] = 80702) erasing segment 9 (vno[0] = 111170) erasing segment 10 (vno[0] = 126995) erasing segment 11 (vno[0] = 134336) @#@FSTIME 2020:07:23:09:34:52 mri_label2label N 5 e 15.15 S 0.25 U 14.85 P 99% M 348976 F 0 R 178757 W 0 c 5 w 363 I 0 O 10944 L 2.11 2.09 2.06 @#@FSLOADPOST 2020:07:23:09:35:07 mri_label2label N 5 2.08 2.09 2.05 #-------------------------------------------- #@# Smooth2 lh Thu Jul 23 09:35:07 EDT 2020 /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... @#@FSTIME 2020:07:23:09:35:07 mris_smooth N 7 e 3.15 S 0.15 U 2.95 P 98% M 204536 F 0 R 100805 W 0 c 4 w 340 I 0 O 9536 L 2.08 2.09 2.05 @#@FSLOADPOST 2020:07:23:09:35:11 mris_smooth N 7 2.08 2.09 2.05 #-------------------------------------------- #@# Smooth2 rh Thu Jul 23 09:35:11 EDT 2020 /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/scripts mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... @#@FSTIME 2020:07:23:09:35:11 mris_smooth N 7 e 3.23 S 0.18 U 3.00 P 98% M 204916 F 0 R 110396 W 0 c 3 w 239 I 0 O 9552 L 2.08 2.09 2.05 @#@FSLOADPOST 2020:07:23:09:35:14 mris_smooth N 7 1.99 2.07 2.05 #-------------------------------------------- #@# Inflation2 lh Thu Jul 23 09:35:14 EDT 2020 /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated Reading ../surf/lh.smoothwm avg radius = 48.4 mm, total surface area = 82629 mm^2 step 000: RMS=0.163 (target=0.015) step 005: RMS=0.111 (target=0.015) step 010: RMS=0.082 (target=0.015) step 015: RMS=0.066 (target=0.015) step 020: RMS=0.055 (target=0.015) step 025: RMS=0.046 (target=0.015) step 030: RMS=0.037 (target=0.015) step 035: RMS=0.031 (target=0.015) step 040: RMS=0.027 (target=0.015) step 045: RMS=0.023 (target=0.015) step 050: RMS=0.021 (target=0.015) step 055: RMS=0.019 (target=0.015) step 060: RMS=0.018 (target=0.015) writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc inflation complete. inflation took 0.4 minutes mris_inflate utimesec 21.546473 mris_inflate stimesec 1.270850 mris_inflate ru_maxrss 204668 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 756818 mris_inflate ru_majflt 1 mris_inflate ru_nswap 0 mris_inflate ru_inblock 72 mris_inflate ru_oublock 10608 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 380 mris_inflate ru_nivcsw 7 @#@FSTIME 2020:07:23:09:35:14 mris_inflate N 2 e 22.88 S 1.28 U 21.54 P 99% M 204668 F 1 R 756844 W 0 c 7 w 382 I 72 O 10616 L 1.99 2.07 2.05 @#@FSLOADPOST 2020:07:23:09:35:37 mris_inflate N 2 1.93 2.05 2.04 #-------------------------------------------- #@# Inflation2 rh Thu Jul 23 09:35:37 EDT 2020 /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated Reading ../surf/rh.smoothwm avg radius = 48.8 mm, total surface area = 82657 mm^2 step 000: RMS=0.161 (target=0.015) step 005: RMS=0.110 (target=0.015) step 010: RMS=0.081 (target=0.015) step 015: RMS=0.065 (target=0.015) step 020: RMS=0.054 (target=0.015) step 025: RMS=0.045 (target=0.015) step 030: RMS=0.038 (target=0.015) step 035: RMS=0.032 (target=0.015) step 040: RMS=0.027 (target=0.015) step 045: RMS=0.023 (target=0.015) step 050: RMS=0.021 (target=0.015) step 055: RMS=0.020 (target=0.015) step 060: RMS=0.018 (target=0.015) writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc inflation complete. inflation took 0.4 minutes mris_inflate utimesec 23.818872 mris_inflate stimesec 1.365221 mris_inflate ru_maxrss 204948 mris_inflate ru_ixrss 0 mris_inflate ru_idrss 0 mris_inflate ru_isrss 0 mris_inflate ru_minflt 848332 mris_inflate ru_majflt 0 mris_inflate ru_nswap 0 mris_inflate ru_inblock 0 mris_inflate ru_oublock 10616 mris_inflate ru_msgsnd 0 mris_inflate ru_msgrcv 0 mris_inflate ru_nsignals 0 mris_inflate ru_nvcsw 451 mris_inflate ru_nivcsw 123 @#@FSTIME 2020:07:23:09:35:37 mris_inflate N 2 e 25.25 S 1.38 U 23.81 P 99% M 204948 F 0 R 848358 W 0 c 123 w 452 I 0 O 10616 L 1.93 2.05 2.04 @#@FSLOADPOST 2020:07:23:09:36:02 mris_inflate N 2 1.95 2.04 2.04 #-------------------------------------------- #@# Curv .H and .K lh Thu Jul 23 09:36:02 EDT 2020 /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf mris_curvature -w -seed 1234 lh.white.preaparc setting seed for random number generator to 1234 total integrated curvature = 17.190*4pi (216.015) --> -16 handles ICI = 141.1, FI = 1287.9, variation=20677.556 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...done. @#@FSTIME 2020:07:23:09:36:02 mris_curvature N 4 e 1.61 S 0.10 U 1.48 P 98% M 151332 F 0 R 46323 W 0 c 12 w 86 I 0 O 2128 L 1.95 2.04 2.04 @#@FSLOADPOST 2020:07:23:09:36:04 mris_curvature N 4 1.96 2.04 2.04 rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H rm -f lh.white.K ln -s lh.white.preaparc.K lh.white.K mris_curvature -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated setting seed for random number generator to 1234 normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 233 vertices thresholded to be in k1 ~ [-0.15 0.57], k2 ~ [-0.09 0.06] total integrated curvature = 0.685*4pi (8.604) --> 0 handles ICI = 1.6, FI = 8.9, variation=156.884 121 vertices thresholded to be in [-0.01 0.01] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 155 vertices thresholded to be in [-0.10 0.25] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.016, std = 0.022 done. @#@FSTIME 2020:07:23:09:36:04 mris_curvature N 12 e 47.11 S 0.54 U 46.55 P 99% M 363484 F 0 R 252230 W 0 c 64 w 121 I 0 O 2128 L 1.96 2.04 2.04 @#@FSLOADPOST 2020:07:23:09:36:51 mris_curvature N 12 2.11 2.07 2.05 #-------------------------------------------- #@# Curv .H and .K rh Thu Jul 23 09:36:51 EDT 2020 /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf mris_curvature -w -seed 1234 rh.white.preaparc setting seed for random number generator to 1234 total integrated curvature = 16.552*4pi (208.000) --> -16 handles ICI = 137.0, FI = 1251.7, variation=20100.048 writing Gaussian curvature to ./rh.white.preaparc.K...done. writing mean curvature to ./rh.white.preaparc.H...done. @#@FSTIME 2020:07:23:09:36:51 mris_curvature N 4 e 1.67 S 0.10 U 1.54 P 98% M 151500 F 0 R 46381 W 0 c 2 w 68 I 0 O 2128 L 2.11 2.07 2.05 @#@FSLOADPOST 2020:07:23:09:36:53 mris_curvature N 4 2.10 2.07 2.05 rm -f rh.white.H ln -s rh.white.preaparc.H rh.white.H rm -f rh.white.K ln -s rh.white.preaparc.K rh.white.K mris_curvature -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated setting seed for random number generator to 1234 normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 242 vertices thresholded to be in k1 ~ [-0.20 0.26], k2 ~ [-0.11 0.06] total integrated curvature = 0.631*4pi (7.927) --> 0 handles ICI = 1.5, FI = 9.0, variation=156.501 130 vertices thresholded to be in [-0.01 0.02] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.001 140 vertices thresholded to be in [-0.13 0.14] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.016, std = 0.022 done. @#@FSTIME 2020:07:23:09:36:53 mris_curvature N 12 e 46.93 S 0.38 U 46.54 P 99% M 363932 F 0 R 258636 W 0 c 14 w 74 I 0 O 2128 L 2.10 2.07 2.05 @#@FSLOADPOST 2020:07:23:09:37:40 mris_curvature N 12 2.05 2.06 2.05 #-------------------------------------------- #@# Sphere lh Thu Jul 23 09:37:40 EDT 2020 /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/scripts mris_sphere -seed 1234 ../surf/lh.inflated ../surf/lh.sphere setting seed for random number genererator to 1234 version: dev available threads: 1 reading original vertex positions... projecting onto sphere... surface projected - minimizing metric distortion... scaling brain by 0.273... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host= nike, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 1234 singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %20.29 pass 1: epoch 2 of 3 starting distance error %20.31 unfolding complete - removing small folds... starting distance error %20.25 removing remaining folds... final distance error %20.25 MRISunfold() return, current seed 1234 -01: dt=0.0000, 78 negative triangles VmPeak 669696 098: dt=0.9900, 78 negative triangles 099: dt=0.9900, 45 negative triangles 100: dt=0.9900, 35 negative triangles 101: dt=0.9900, 30 negative triangles 102: dt=0.9900, 32 negative triangles 103: dt=0.9900, 33 negative triangles 104: dt=0.9900, 27 negative triangles 105: dt=0.9900, 23 negative triangles 106: dt=0.9900, 13 negative triangles 107: dt=0.9900, 15 negative triangles 108: dt=0.9900, 7 negative triangles 109: dt=0.9900, 9 negative triangles 110: dt=0.9900, 7 negative triangles 111: dt=0.9900, 7 negative triangles 112: dt=0.9900, 6 negative triangles 113: dt=0.9900, 1 negative triangles 114: dt=0.9900, 4 negative triangles 115: dt=0.9900, 4 negative triangles writing spherical brain to ../surf/lh.sphere spherical transformation took 0.1275 hours FSRUNTIME@ mris_sphere 0.1275 hours 1 threads #VMPC# mris_sphere VmPeak 669696 mris_sphere done @#@FSTIME 2020:07:23:09:37:40 mris_sphere N 4 e 459.20 S 14.42 U 444.77 P 99% M 275220 F 0 R 7694901 W 0 c 122 w 356 I 0 O 9544 L 2.05 2.06 2.05 @#@FSLOADPOST 2020:07:23:09:45:19 mris_sphere N 4 2.08 2.06 2.05 #-------------------------------------------- #@# Sphere rh Thu Jul 23 09:45:19 EDT 2020 /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/scripts mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 version: dev available threads: 1 reading original vertex positions... projecting onto sphere... surface projected - minimizing metric distortion... scaling brain by 0.272... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host= nike, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 1234 singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form singular matrix in quadratic form -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %20.35 pass 1: epoch 2 of 3 starting distance error %20.35 unfolding complete - removing small folds... starting distance error %20.23 removing remaining folds... final distance error %20.26 MRISunfold() return, current seed 1234 -01: dt=0.0000, 13 negative triangles VmPeak 670052 183: dt=0.9900, 13 negative triangles 184: dt=0.9900, 10 negative triangles 185: dt=0.9900, 12 negative triangles 186: dt=0.9900, 12 negative triangles 187: dt=0.9900, 11 negative triangles 188: dt=0.9900, 8 negative triangles 189: dt=0.9900, 9 negative triangles 190: dt=0.9900, 8 negative triangles 191: dt=0.9900, 7 negative triangles 192: dt=0.9900, 9 negative triangles 193: dt=0.9900, 8 negative triangles 194: dt=0.9900, 6 negative triangles 195: dt=0.9900, 6 negative triangles 196: dt=0.9900, 5 negative triangles 197: dt=0.9900, 3 negative triangles 198: dt=0.9900, 5 negative triangles 199: dt=0.9900, 4 negative triangles 200: dt=0.9900, 5 negative triangles 201: dt=0.9900, 1 negative triangles 202: dt=0.9900, 3 negative triangles writing spherical brain to ../surf/rh.sphere spherical transformation took 0.1921 hours FSRUNTIME@ mris_sphere 0.1921 hours 1 threads #VMPC# mris_sphere VmPeak 670052 mris_sphere done @#@FSTIME 2020:07:23:09:45:19 mris_sphere N 4 e 691.75 S 27.23 U 664.53 P 100% M 275576 F 0 R 14214961 W 0 c 176 w 352 I 0 O 9560 L 2.08 2.06 2.05 @#@FSLOADPOST 2020:07:23:09:56:51 mris_sphere N 4 2.06 2.10 2.06 #-------------------------------------------- #@# Surf Reg lh Thu Jul 23 09:56:51 EDT 2020 /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/scripts mris_register -curv ../surf/lh.sphere /usr/local/freesurfer/dev/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg using smoothwm curvature for final alignment cwd /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/scripts cmdline mris_register -curv ../surf/lh.sphere /usr/local/freesurfer/dev/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) dev dev reading surface from ../surf/lh.sphere... reading template parameterization from /usr/local/freesurfer/dev/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host= nike, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 0 randomSeed 0 tol=5.0e-01, sigma=0.0, host= nike, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading lh.sulc tol=1.0e+00, sigma=0.5, host= nike, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization curvature mean = 0.000, std = 5.399 curvature mean = 0.023, std = 0.818 curvature mean = 0.010, std = 0.862 Starting MRISrigidBodyAlignGlobal() Starting new MRISrigidBodyAlignGlobal_findMinSSE() new MRISrigidBodyAlignGlobal_findMinSSE min @ (1.50, -10.50, 4.00) sse = 256028.8, elapsed since starting=0.4015 min MRISrigidBodyAlignGlobal() done 0.40 min curvature mean = 0.014, std = 0.846 curvature mean = 0.005, std = 0.949 curvature mean = 0.013, std = 0.856 curvature mean = 0.002, std = 0.980 curvature mean = 0.013, std = 0.858 curvature mean = 0.000, std = 0.993 2 Reading smoothwm curvature mean = -0.018, std = 0.247 curvature mean = 0.044, std = 0.249 curvature mean = 0.052, std = 0.401 curvature mean = 0.042, std = 0.306 curvature mean = 0.024, std = 0.614 curvature mean = 0.041, std = 0.333 curvature mean = 0.012, std = 0.753 curvature mean = 0.041, std = 0.345 curvature mean = 0.003, std = 0.850 MRISregister() return, current seed 0 writing registered surface to ../surf/lh.sphere.reg... -01: dt=0.0000, 0 negative triangles VmPeak 652600 registration took 0.12 hours #VMPC# mris_register VmPeak 652600 FSRUNTIME@ mris_register 0.1214 hours 1 threads @#@FSTIME 2020:07:23:09:56:51 mris_register N 4 e 437.22 S 15.06 U 422.12 P 99% M 258224 F 1 R 7715012 W 0 c 286 w 328 I 7608 O 9544 L 2.06 2.10 2.06 @#@FSLOADPOST 2020:07:23:10:04:08 mris_register N 4 2.18 2.17 2.10 ln -sf lh.sphere.reg lh.fsaverage.sphere.reg #-------------------------------------------- #@# Surf Reg rh Thu Jul 23 10:04:08 EDT 2020 /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/scripts mris_register -curv ../surf/rh.sphere /usr/local/freesurfer/dev/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment cwd /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/scripts cmdline mris_register -curv ../surf/rh.sphere /usr/local/freesurfer/dev/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg 0 inflated.H 1 sulc 2 smoothwm (computed) dev dev reading surface from ../surf/rh.sphere... reading template parameterization from /usr/local/freesurfer/dev/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host= nike, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 1 randomSeed 0 tol=5.0e-01, sigma=0.0, host= nike, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading rh.sulc tol=1.0e+00, sigma=0.5, host= nike, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization curvature mean = 0.000, std = 5.439 curvature mean = 0.030, std = 0.811 curvature mean = 0.011, std = 0.865 Starting MRISrigidBodyAlignGlobal() Starting new MRISrigidBodyAlignGlobal_findMinSSE() new MRISrigidBodyAlignGlobal_findMinSSE min @ (7.50, -10.50, 5.50) sse = 270446.6, elapsed since starting=0.3935 min MRISrigidBodyAlignGlobal() done 0.39 min curvature mean = 0.012, std = 0.828 curvature mean = 0.005, std = 0.950 curvature mean = 0.010, std = 0.838 curvature mean = 0.002, std = 0.981 curvature mean = 0.009, std = 0.840 curvature mean = 0.000, std = 0.993 2 Reading smoothwm curvature mean = -0.018, std = 0.241 curvature mean = 0.040, std = 0.243 curvature mean = 0.051, std = 0.412 curvature mean = 0.036, std = 0.300 curvature mean = 0.025, std = 0.623 curvature mean = 0.035, std = 0.327 curvature mean = 0.012, std = 0.763 curvature mean = 0.035, std = 0.339 curvature mean = 0.003, std = 0.859 MRISregister() return, current seed 0 -01: dt=0.0000, 13 negative triangles VmPeak 651864 113: dt=0.9900, 13 negative triangles 114: dt=0.9900, 11 negative triangles 115: dt=0.9900, 11 negative triangles 116: dt=0.9900, 11 negative triangles 117: dt=0.9900, 8 negative triangles 118: dt=0.9900, 9 negative triangles 119: dt=0.9900, 9 negative triangles 120: dt=0.9900, 11 negative triangles 121: dt=0.9900, 7 negative triangles 122: dt=0.9900, 8 negative triangles 123: dt=0.9900, 7 negative triangles 124: dt=0.9900, 7 negative triangles 125: dt=0.9900, 7 negative triangles 126: dt=0.9900, 7 negative triangles 127: dt=0.9900, 7 negative triangles 128: dt=0.9900, 4 negative triangles 129: dt=0.9900, 5 negative triangles 130: dt=0.9900, 4 negative triangles 131: dt=0.9900, 3 negative triangles 132: dt=0.9900, 7 negative triangles 133: dt=0.9900, 3 negative triangles writing registered surface to ../surf/rh.sphere.reg... registration took 0.14 hours #VMPC# mris_register VmPeak 651864 FSRUNTIME@ mris_register 0.1402 hours 1 threads @#@FSTIME 2020:07:23:10:04:08 mris_register N 4 e 504.83 S 17.99 U 486.82 P 99% M 257680 F 0 R 9235968 W 0 c 175 w 430 I 5584 O 9552 L 2.18 2.17 2.10 @#@FSLOADPOST 2020:07:23:10:12:33 mris_register N 4 2.10 2.09 2.09 ln -sf rh.sphere.reg rh.fsaverage.sphere.reg #-------------------------------------------- #@# Jacobian white lh Thu Jul 23 10:12:33 EDT 2020 /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/scripts mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white reading surface from ../surf/lh.white.preaparc... writing curvature file ../surf/lh.jacobian_white @#@FSTIME 2020:07:23:10:12:33 mris_jacobian N 3 e 1.11 S 0.14 U 0.95 P 98% M 204132 F 0 R 66629 W 0 c 2 w 48 I 0 O 1064 L 2.10 2.09 2.09 @#@FSLOADPOST 2020:07:23:10:12:35 mris_jacobian N 3 2.10 2.09 2.09 #-------------------------------------------- #@# Jacobian white rh Thu Jul 23 10:12:35 EDT 2020 /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/scripts mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white reading surface from ../surf/rh.white.preaparc... writing curvature file ../surf/rh.jacobian_white @#@FSTIME 2020:07:23:10:12:35 mris_jacobian N 3 e 1.12 S 0.16 U 0.95 P 99% M 204368 F 0 R 66725 W 0 c 2 w 32 I 0 O 1064 L 2.10 2.09 2.09 @#@FSLOADPOST 2020:07:23:10:12:36 mris_jacobian N 3 2.10 2.09 2.09 #-------------------------------------------- #@# AvgCurv lh Thu Jul 23 10:12:36 EDT 2020 /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/scripts mrisp_paint -a 5 /usr/local/freesurfer/dev/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/lh.sphere.reg... reading template parameterization from /usr/local/freesurfer/dev/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/lh.avg_curv... @#@FSTIME 2020:07:23:10:12:36 mrisp_paint N 5 e 0.90 S 0.12 U 0.77 P 98% M 156328 F 0 R 47585 W 0 c 1 w 47 I 0 O 1064 L 2.10 2.09 2.09 @#@FSLOADPOST 2020:07:23:10:12:37 mrisp_paint N 5 2.10 2.09 2.09 #-------------------------------------------- #@# AvgCurv rh Thu Jul 23 10:12:37 EDT 2020 /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/scripts mrisp_paint -a 5 /usr/local/freesurfer/dev/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/rh.sphere.reg... reading template parameterization from /usr/local/freesurfer/dev/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif... writing curvature file to ../surf/rh.avg_curv... @#@FSTIME 2020:07:23:10:12:37 mrisp_paint N 5 e 1.04 S 0.11 U 0.91 P 99% M 156544 F 0 R 47653 W 0 c 4 w 28 I 0 O 1064 L 2.10 2.09 2.09 @#@FSLOADPOST 2020:07:23:10:12:38 mrisp_paint N 5 2.09 2.09 2.09 #----------------------------------------- #@# Cortical Parc lh Thu Jul 23 10:12:38 EDT 2020 /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 bert lh ../surf/lh.sphere.reg /usr/local/freesurfer/dev/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline dev dev reading atlas from /usr/local/freesurfer/dev/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.8 using min determinant for regularization = 0.006 0 singular and 342 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1438 labels changed using aseg relabeling using gibbs priors... 000: 3023 changed, 135579 examined... 001: 692 changed, 12839 examined... 002: 149 changed, 3859 examined... 003: 63 changed, 868 examined... 004: 27 changed, 364 examined... 005: 9 changed, 165 examined... 006: 4 changed, 47 examined... 007: 2 changed, 27 examined... 008: 4 changed, 10 examined... 009: 1 changed, 15 examined... 010: 0 changed, 6 examined... 227 labels changed using aseg 000: 99 total segments, 56 labels (126 vertices) changed 001: 43 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 6 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1634 vertices marked for relabeling... 1634 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 10 seconds. @#@FSTIME 2020:07:23:10:12:38 mris_ca_label N 11 e 10.29 S 0.85 U 9.37 P 99% M 1135856 F 2 R 608051 W 0 c 5 w 114 I 64920 O 2128 L 2.09 2.09 2.09 @#@FSLOADPOST 2020:07:23:10:12:48 mris_ca_label N 11 2.08 2.09 2.09 #----------------------------------------- #@# Cortical Parc rh Thu Jul 23 10:12:48 EDT 2020 /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 bert rh ../surf/rh.sphere.reg /usr/local/freesurfer/dev/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline dev dev reading atlas from /usr/local/freesurfer/dev/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.7 using min determinant for regularization = 0.004 0 singular and 309 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1411 labels changed using aseg relabeling using gibbs priors... 000: 2799 changed, 135771 examined... 001: 640 changed, 12048 examined... 002: 138 changed, 3640 examined... 003: 46 changed, 878 examined... 004: 12 changed, 285 examined... 005: 3 changed, 85 examined... 006: 0 changed, 21 examined... 173 labels changed using aseg 000: 86 total segments, 49 labels (233 vertices) changed 001: 37 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 2 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 1553 vertices marked for relabeling... 1553 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 11 seconds. @#@FSTIME 2020:07:23:10:12:48 mris_ca_label N 11 e 10.65 S 0.92 U 9.67 P 99% M 1073108 F 0 R 584695 W 0 c 56 w 62 I 36352 O 2128 L 2.08 2.09 2.09 @#@FSLOADPOST 2020:07:23:10:12:59 mris_ca_label N 11 2.14 2.10 2.10 #-------------------------------------------- #@# WhiteSurfs lh Thu Jul 23 10:12:59 EDT 2020 cd /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --threads 1 --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.white.preaparc --o ../surf/lh.white --white --nsmooth 0 --rip-label ../label/lh.cortex.label --rip-bg --rip-surf ../surf/lh.white.preaparc --aparc ../label/lh.aparc.annot dev dev cd /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri setenv SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --threads 1 --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.white.preaparc --o ../surf/lh.white --white --nsmooth 0 --rip-label ../label/lh.cortex.label --rip-bg --rip-surf ../surf/lh.white.preaparc --aparc ../label/lh.aparc.annot Reading in input surface ../surf/lh.white.preaparc Not smoothing input surface Area 271154 0.33209 0.11112 0.002178 2.0610 Corner 813462 60.00000 13.14595 0.474024 173.4273 Edge 406731 0.88539 0.18733 0.043764 3.5554 Hinge 406731 9.62613 9.96255 0.000035 179.8928 Reading in aparc ../label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=19421, wmmin=5, clip=110 MRIfindBrightNonWM(): 10149 bright non-wm voxels segmented. Masking bright non-wm for white surface MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Reading in seg volume aseg.presurf.mgz Ripping frozen voxels Ripping vertices not in label ../label/lh.cortex.label Reading in ripping surface ../surf/lh.white.preaparc Reading in aparc ../label/lh.aparc.annot for ripsurf reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Ripping BG MRISripBasalGanglia(): -2 2 0.5 ripped 362 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 67790: xyz = (-16.2661,-7.71317,62.2264) oxyz = (-16.2661,-7.71317,62.2264) wxzy = (-16.2661,-7.71317,62.2264) pxyz = (0,0,0) CBVO Creating mask 135579 n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 111.6329730; border_low = 82.0000000; outside_low = 72.4434810; outside_hi = 111.6329730; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=135579 Gdiag_no=-1 vno start=0, stop=135579 Replacing 255s with 0s #SI# sigma=2 had to be increased for 108 vertices, nripped=9786 mean border=89.6, 51 (51) missing vertices, mean dist 0.5 [1.4 (%12.1)->0.7 (%87.9))] %56 local maxima, %36 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.2498 min Finding expansion regions mean absolute distance = 0.82 +- 1.03 2576 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=2.0, host= nike, nav=4, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 000: dt: 0.0000, sse=1243050.5, rms=6.483 001: dt: 0.5000, sse=585425.4, rms=3.999 (38.320%) 002: dt: 0.5000, sse=350892.6, rms=2.581 (35.450%) 003: dt: 0.5000, sse=275825.6, rms=1.910 (26.017%) 004: dt: 0.5000, sse=249508.6, rms=1.601 (16.167%) 005: dt: 0.5000, sse=240181.2, rms=1.472 (8.040%) 006: dt: 0.5000, sse=236578.4, rms=1.411 (4.179%) rms = 1.3925/1.4107, sse=235862.1/236578.4, time step reduction 1 of 3 to 0.250 0 0 1 007: dt: 0.5000, sse=235862.1, rms=1.392 (1.290%) 008: dt: 0.2500, sse=218545.7, rms=1.085 (22.118%) rms = 1.0445/1.0845, sse=216128.2/218545.7, time step reduction 2 of 3 to 0.125 0 0 1 009: dt: 0.2500, sse=216128.2, rms=1.044 (3.693%) rms = 1.0335/1.0445, sse=215690.1/216128.2, time step reduction 3 of 3 to 0.062 0 0 1 010: dt: 0.1250, sse=215690.1, rms=1.033 (1.051%) maximum number of reductions reached, breaking from loop positioning took 0.9 minutes Iteration 1 ========================================= n_averages=2, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 111.6329730; border_low = 82.0000000; outside_low = 72.4434810; outside_hi = 111.6329730; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=135579 Gdiag_no=-1 vno start=0, stop=135579 Replacing 255s with 0s #SI# sigma=1 had to be increased for 54 vertices, nripped=9786 mean border=92.1, 25 (4) missing vertices, mean dist -0.3 [0.6 (%71.7)->0.2 (%28.3))] %71 local maxima, %22 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1784 min Finding expansion regions mean absolute distance = 0.46 +- 0.73 4411 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=1.0, host= nike, nav=2, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=548665.9, rms=3.692 011: dt: 0.5000, sse=335729.4, rms=2.285 (38.121%) 012: dt: 0.5000, sse=275339.7, rms=1.689 (26.075%) 013: dt: 0.5000, sse=255062.8, rms=1.409 (16.599%) 014: dt: 0.5000, sse=245356.2, rms=1.279 (9.169%) rms = 1.2438/1.2794, sse=243061.3/245356.2, time step reduction 1 of 3 to 0.250 0 0 1 015: dt: 0.5000, sse=243061.3, rms=1.244 (2.785%) 016: dt: 0.2500, sse=227337.2, rms=0.942 (24.271%) rms = 0.8960/0.9419, sse=225224.9/227337.2, time step reduction 2 of 3 to 0.125 0 0 1 017: dt: 0.2500, sse=225224.9, rms=0.896 (4.878%) rms = 0.8838/0.8960, sse=227407.0/225224.9, time step reduction 3 of 3 to 0.062 0 1 1 018: dt: 0.1250, sse=227407.0, rms=0.884 (1.358%) maximum number of reductions reached, breaking from loop positioning took 0.7 minutes Iteration 2 ========================================= n_averages=1, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 111.6329730; border_low = 82.0000000; outside_low = 72.4434810; outside_hi = 111.6329730; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=135579 Gdiag_no=-1 vno start=0, stop=135579 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 105 vertices, nripped=9786 mean border=94.2, 53 (2) missing vertices, mean dist -0.2 [0.4 (%73.8)->0.2 (%26.2))] %83 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0969 min Finding expansion regions mean absolute distance = 0.33 +- 0.46 4173 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.5, host= nike, nav=1, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=400783.4, rms=2.838 019: dt: 0.5000, sse=256120.7, rms=1.527 (46.191%) 020: dt: 0.5000, sse=234233.3, rms=1.150 (24.713%) 021: dt: 0.5000, sse=228193.0, rms=1.065 (7.357%) rms = 1.0676/1.0650, sse=229870.7/228193.0, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 022: dt: 0.2500, sse=220429.1, rms=0.896 (15.894%) 023: dt: 0.2500, sse=218236.4, rms=0.815 (9.047%) rms = 0.8084/0.8147, sse=218560.3/218236.4, time step reduction 2 of 3 to 0.125 0 1 1 024: dt: 0.2500, sse=218560.3, rms=0.808 (0.777%) rms = 0.8014/0.8084, sse=218512.2/218560.3, time step reduction 3 of 3 to 0.062 0 0 1 025: dt: 0.1250, sse=218512.2, rms=0.801 (0.860%) maximum number of reductions reached, breaking from loop positioning took 0.6 minutes Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 111.6329730; border_low = 82.0000000; outside_low = 72.4434810; outside_hi = 111.6329730; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=135579 Gdiag_no=-1 vno start=0, stop=135579 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 116 vertices, nripped=9786 mean border=94.9, 48 (2) missing vertices, mean dist -0.1 [0.3 (%58.3)->0.2 (%41.7))] %86 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0600 min Finding expansion regions mean absolute distance = 0.24 +- 0.34 3894 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host= nike, nav=0, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=235972.8, rms=1.233 026: dt: 0.5000, sse=211719.8, rms=0.767 (37.811%) rms = 0.8609/0.7668, sse=213457.2/211719.8, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 027: dt: 0.2500, sse=207833.2, rms=0.683 (10.945%) rms = 0.6676/0.6828, sse=206418.2/207833.2, time step reduction 2 of 3 to 0.125 0 0 1 028: dt: 0.2500, sse=206418.2, rms=0.668 (2.228%) rms = 0.6536/0.6676, sse=205653.5/206418.2, time step reduction 3 of 3 to 0.062 0 0 1 029: dt: 0.1250, sse=205653.5, rms=0.654 (2.106%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes Writing output to ../surf/lh.white #ET# mris_place_surface 3.23 minutes #VMPC# mris_place_surfaces VmPeak 2190056 mris_place_surface done @#@FSTIME 2020:07:23:10:12:59 mris_place_surface N 25 e 202.39 S 1.97 U 200.37 P 99% M 1811960 F 0 R 1576695 W 0 c 1057 w 296 I 0 O 9536 L 2.14 2.10 2.10 @#@FSLOADPOST 2020:07:23:10:16:21 mris_place_surface N 25 2.07 2.08 2.09 #-------------------------------------------- #@# WhiteSurfs rh Thu Jul 23 10:16:21 EDT 2020 cd /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --threads 1 --wm wm.mgz --invol brain.finalsurfs.mgz --rh --i ../surf/rh.white.preaparc --o ../surf/rh.white --white --nsmooth 0 --rip-label ../label/rh.cortex.label --rip-bg --rip-surf ../surf/rh.white.preaparc --aparc ../label/rh.aparc.annot dev dev cd /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri setenv SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --threads 1 --wm wm.mgz --invol brain.finalsurfs.mgz --rh --i ../surf/rh.white.preaparc --o ../surf/rh.white --white --nsmooth 0 --rip-label ../label/rh.cortex.label --rip-bg --rip-surf ../surf/rh.white.preaparc --aparc ../label/rh.aparc.annot Reading in input surface ../surf/rh.white.preaparc Not smoothing input surface Area 271538 0.33105 0.10906 0.001144 1.7977 Corner 814614 60.00000 13.04172 0.365649 178.2758 Edge 407307 0.88370 0.18299 0.044022 3.4915 Hinge 407307 9.56024 9.81936 0.000020 179.6736 Reading in aparc ../label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=19421, wmmin=5, clip=110 MRIfindBrightNonWM(): 10149 bright non-wm voxels segmented. Masking bright non-wm for white surface MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Reading in seg volume aseg.presurf.mgz Ripping frozen voxels Ripping vertices not in label ../label/rh.cortex.label Reading in ripping surface ../surf/rh.white.preaparc Reading in aparc ../label/rh.aparc.annot for ripsurf reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Ripping BG MRISripBasalGanglia(): -2 2 0.5 ripped 459 Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 67886: xyz = (42.8987,-8.53,46.534) oxyz = (42.8987,-8.53,46.534) wxzy = (42.8987,-8.53,46.534) pxyz = (0,0,0) CBVO Creating mask 135771 n_averages 4 Iteration 0 ========================================= n_averages=4, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 111.6329730; border_low = 83.0000000; outside_low = 73.4434810; outside_hi = 111.6329730; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=135771 Gdiag_no=-1 vno start=0, stop=135771 Replacing 255s with 0s #SI# sigma=2 had to be increased for 105 vertices, nripped=9624 mean border=90.0, 36 (36) missing vertices, mean dist 0.5 [1.3 (%12.5)->0.7 (%87.5))] %54 local maxima, %39 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.2458 min Finding expansion regions mean absolute distance = 0.82 +- 1.02 2358 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=2.0, host= nike, nav=4, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 000: dt: 0.0000, sse=1210056.0, rms=6.363 001: dt: 0.5000, sse=562241.4, rms=3.870 (39.180%) 002: dt: 0.5000, sse=336238.0, rms=2.454 (36.592%) 003: dt: 0.5000, sse=266415.4, rms=1.807 (26.357%) 004: dt: 0.5000, sse=244934.8, rms=1.534 (15.130%) 005: dt: 0.5000, sse=238297.2, rms=1.442 (5.998%) rms = 1.4178/1.4417, sse=236978.0/238297.2, time step reduction 1 of 3 to 0.250 0 0 1 006: dt: 0.5000, sse=236978.0, rms=1.418 (1.657%) 007: dt: 0.2500, sse=222866.5, rms=1.184 (16.475%) rms = 1.1438/1.1842, sse=220922.7/222866.5, time step reduction 2 of 3 to 0.125 0 0 1 008: dt: 0.2500, sse=220922.7, rms=1.144 (3.409%) rms = 1.1312/1.1438, sse=220359.7/220922.7, time step reduction 3 of 3 to 0.062 0 0 1 009: dt: 0.1250, sse=220359.7, rms=1.131 (1.109%) maximum number of reductions reached, breaking from loop positioning took 0.8 minutes Iteration 1 ========================================= n_averages=2, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 111.6329730; border_low = 83.0000000; outside_low = 73.4434810; outside_hi = 111.6329730; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=135771 Gdiag_no=-1 vno start=0, stop=135771 Replacing 255s with 0s #SI# sigma=1 had to be increased for 56 vertices, nripped=9624 mean border=92.5, 72 (12) missing vertices, mean dist -0.3 [0.5 (%70.7)->0.2 (%29.3))] %70 local maxima, %23 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1745 min Finding expansion regions mean absolute distance = 0.45 +- 0.71 3513 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=1.0, host= nike, nav=2, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=537157.3, rms=3.633 010: dt: 0.5000, sse=335960.4, rms=2.288 (37.021%) 011: dt: 0.5000, sse=275847.4, rms=1.704 (25.515%) 012: dt: 0.5000, sse=253033.2, rms=1.404 (17.615%) 013: dt: 0.5000, sse=242717.9, rms=1.254 (10.665%) rms = 1.2137/1.2542, sse=241261.3/242717.9, time step reduction 1 of 3 to 0.250 0 0 1 014: dt: 0.5000, sse=241261.3, rms=1.214 (3.234%) 015: dt: 0.2500, sse=225747.6, rms=0.938 (22.682%) rms = 0.9011/0.9384, sse=224138.6/225747.6, time step reduction 2 of 3 to 0.125 0 0 1 016: dt: 0.2500, sse=224138.6, rms=0.901 (3.969%) rms = 0.8868/0.9011, sse=223761.6/224138.6, time step reduction 3 of 3 to 0.062 0 0 1 017: dt: 0.1250, sse=223761.6, rms=0.887 (1.595%) maximum number of reductions reached, breaking from loop positioning took 0.7 minutes Iteration 2 ========================================= n_averages=1, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 111.6329730; border_low = 83.0000000; outside_low = 73.4434810; outside_hi = 111.6329730; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=135771 Gdiag_no=-1 vno start=0, stop=135771 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 117 vertices, nripped=9624 mean border=94.6, 81 (7) missing vertices, mean dist -0.2 [0.4 (%73.7)->0.2 (%26.3))] %83 local maxima, %10 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0956 min Finding expansion regions mean absolute distance = 0.33 +- 0.45 4946 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.5, host= nike, nav=1, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=397965.1, rms=2.838 018: dt: 0.5000, sse=253807.1, rms=1.507 (46.898%) 019: dt: 0.5000, sse=228827.8, rms=1.135 (24.658%) 020: dt: 0.5000, sse=224973.1, rms=1.052 (7.347%) rms = 1.0425/1.0520, sse=224038.6/224973.1, time step reduction 1 of 3 to 0.250 0 0 1 021: dt: 0.5000, sse=224038.6, rms=1.043 (0.894%) 022: dt: 0.2500, sse=214844.1, rms=0.833 (20.068%) rms = 0.8107/0.8333, sse=213549.7/214844.1, time step reduction 2 of 3 to 0.125 0 0 1 023: dt: 0.2500, sse=213549.7, rms=0.811 (2.710%) rms = 0.8055/0.8107, sse=213187.7/213549.7, time step reduction 3 of 3 to 0.062 0 0 1 024: dt: 0.1250, sse=213187.7, rms=0.805 (0.649%) maximum number of reductions reached, breaking from loop positioning took 0.6 minutes Iteration 3 ========================================= n_averages=0, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 120.0000000; border_hi = 111.6329730; border_low = 83.0000000; outside_low = 73.4434810; outside_hi = 111.6329730; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 1 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=135771 Gdiag_no=-1 vno start=0, stop=135771 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 136 vertices, nripped=9624 mean border=95.2, 113 (7) missing vertices, mean dist -0.1 [0.3 (%58.0)->0.2 (%42.0))] %86 local maxima, % 6 large gradients and % 0 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0588 min Finding expansion regions mean absolute distance = 0.24 +- 0.33 3684 vertices more than 2 sigmas from mean. Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host= nike, nav=0, nbrs=2, l_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=229651.3, rms=1.220 025: dt: 0.5000, sse=208377.9, rms=0.751 (38.452%) rms = 0.8497/0.7511, sse=212397.5/208377.9, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 026: dt: 0.2500, sse=205513.6, rms=0.685 (8.736%) rms = 0.6698/0.6854, sse=204415.1/205513.6, time step reduction 2 of 3 to 0.125 0 0 1 027: dt: 0.2500, sse=204415.1, rms=0.670 (2.278%) rms = 0.6623/0.6698, sse=204100.5/204415.1, time step reduction 3 of 3 to 0.062 0 0 1 028: dt: 0.1250, sse=204100.5, rms=0.662 (1.120%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes Writing output to ../surf/rh.white #ET# mris_place_surface 3.05 minutes #VMPC# mris_place_surfaces VmPeak 2182904 mris_place_surface done @#@FSTIME 2020:07:23:10:16:22 mris_place_surface N 25 e 190.82 S 1.61 U 189.17 P 99% M 1804844 F 0 R 1523892 W 0 c 59 w 452 I 0 O 9552 L 2.07 2.08 2.09 @#@FSLOADPOST 2020:07:23:10:19:32 mris_place_surface N 25 2.06 2.08 2.09 #-------------------------------------------- #@# T1PialSurf lh Thu Jul 23 10:19:32 EDT 2020 cd /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --threads 1 --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.white --o ../surf/lh.pial.T1 --pial --nsmooth 0 --rip-label ../label/lh.cortex+hipamyg.label --pin-medial-wall ../label/lh.cortex.label --aparc ../label/lh.aparc.annot --repulse-surf ../surf/lh.white --white-surf ../surf/lh.white dev dev cd /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri setenv SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --seg aseg.presurf.mgz --threads 1 --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.white --o ../surf/lh.pial.T1 --pial --nsmooth 0 --rip-label ../label/lh.cortex+hipamyg.label --pin-medial-wall ../label/lh.cortex.label --aparc ../label/lh.aparc.annot --repulse-surf ../surf/lh.white --white-surf ../surf/lh.white Reading in input surface ../surf/lh.white Not smoothing input surface Area 271154 0.33405 0.12507 0.001587 2.0610 Corner 813462 60.00000 14.62118 1.211944 176.6051 Edge 406731 0.88959 0.20809 0.043764 3.5554 Hinge 406731 9.70093 10.19214 0.000006 179.8928 Reading white surface coordinates from ../surf/lh.white Reading repulsion surface coordinates from ../surf/lh.white Reading in aparc ../label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=19421, wmmin=5, clip=110 MRIfindBrightNonWM(): 10149 bright non-wm voxels segmented. Masking bright non-wm for pial surface mid_gray = 76.8487 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Reading in seg volume aseg.presurf.mgz Ripping frozen voxels Ripping vertices not in label ../label/lh.cortex+hipamyg.label INFO: rip surface needed but not specified, so using input surface Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 67790: xyz = (-16.4185,-7.98803,62.1462) oxyz = (-16.4185,-7.98803,62.1462) wxzy = (-16.4185,-7.98803,62.1462) pxyz = (-16.4185,-7.98803,62.1462) CBVO Creating mask 135579 n_averages 16 Iteration 0 ========================================= n_averages=16, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 100.3670270; border_hi = 72.4434810; border_low = 53.3304520; outside_low = 10.0000000; outside_hi = 67.6652220; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=135579 Gdiag_no=-1 vno start=0, stop=135579 Replacing 255s with 0s #SI# sigma=2 had to be increased for 168 vertices, nripped=7317 mean border=70.0, 94 (94) missing vertices, mean dist 1.9 [1.1 (%0.0)->2.9 (%100.0))] %17 local maxima, %44 large gradients and %33 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1913 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=2.0, host= nike, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 0 randomSeed 0 000: dt: 0.0000, sse=17055750.0, rms=25.650 001: dt: 0.5000, sse=13028924.0, rms=22.379 (12.752%) 002: dt: 0.5000, sse=9959623.0, rms=19.521 (12.774%) 003: dt: 0.5000, sse=7781980.0, rms=17.205 (11.861%) 004: dt: 0.5000, sse=6282089.0, rms=15.408 (10.445%) 005: dt: 0.5000, sse=5177766.5, rms=13.936 (9.552%) 006: dt: 0.5000, sse=4264506.0, rms=12.589 (9.671%) 007: dt: 0.5000, sse=3432211.5, rms=11.219 (10.877%) 008: dt: 0.5000, sse=2660127.5, rms=9.779 (12.840%) 009: dt: 0.5000, sse=1962361.2, rms=8.263 (15.498%) 010: dt: 0.5000, sse=1383538.4, rms=6.752 (18.291%) 011: dt: 0.5000, sse=983023.3, rms=5.465 (19.054%) 012: dt: 0.5000, sse=751932.1, rms=4.559 (16.588%) 013: dt: 0.5000, sse=634797.4, rms=4.020 (11.819%) 014: dt: 0.5000, sse=578052.4, rms=3.729 (7.246%) 015: dt: 0.5000, sse=552475.0, rms=3.588 (3.784%) 016: dt: 0.5000, sse=537849.6, rms=3.502 (2.377%) rms = 3.4537/3.5023, sse=529890.8/537849.6, time step reduction 1 of 3 to 0.250 0 0 1 017: dt: 0.5000, sse=529890.8, rms=3.454 (1.387%) 018: dt: 0.2500, sse=404220.2, rms=2.618 (24.189%) 019: dt: 0.2500, sse=379138.8, rms=2.419 (7.600%) rms = 2.3719/2.4193, sse=373689.0/379138.9, time step reduction 2 of 3 to 0.125 0 0 1 020: dt: 0.2500, sse=373689.0, rms=2.372 (1.960%) 021: dt: 0.1250, sse=362542.9, rms=2.274 (4.113%) rms = 2.2523/2.2743, sse=360117.3/362543.0, time step reduction 3 of 3 to 0.062 0 0 1 022: dt: 0.1250, sse=360117.2, rms=2.252 (0.969%) maximum number of reductions reached, breaking from loop positioning took 1.7 minutes Iteration 1 ========================================= n_averages=8, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 100.3670270; border_hi = 72.4434810; border_low = 53.3304520; outside_low = 10.0000000; outside_hi = 67.6652220; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=135579 Gdiag_no=-1 vno start=0, stop=135579 Replacing 255s with 0s #SI# sigma=1 had to be increased for 7838 vertices, nripped=7317 mean border=68.7, 1253 (19) missing vertices, mean dist 0.1 [0.1 (%45.4)->0.4 (%54.6))] %34 local maxima, %33 large gradients and %27 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0544 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=1.0, host= nike, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=523218.2, rms=3.134 023: dt: 0.5000, sse=504253.8, rms=3.008 (4.036%) rms = 3.1102/3.0078, sse=517519.0/504253.8, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 024: dt: 0.2500, sse=435475.5, rms=2.519 (16.235%) 025: dt: 0.2500, sse=409266.2, rms=2.309 (8.368%) 026: dt: 0.2500, sse=402852.2, rms=2.252 (2.437%) rms = 2.2154/2.2523, sse=398772.5/402852.2, time step reduction 2 of 3 to 0.125 0 0 1 027: dt: 0.2500, sse=398772.5, rms=2.215 (1.641%) 028: dt: 0.1250, sse=391329.5, rms=2.145 (3.161%) rms = 2.1300/2.1453, sse=389754.3/391329.5, time step reduction 3 of 3 to 0.062 0 0 1 029: dt: 0.1250, sse=389754.3, rms=2.130 (0.715%) maximum number of reductions reached, breaking from loop positioning took 0.6 minutes Iteration 2 ========================================= n_averages=4, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 100.3670270; border_hi = 72.4434810; border_low = 53.3304520; outside_low = 10.0000000; outside_hi = 67.6652220; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=135579 Gdiag_no=-1 vno start=0, stop=135579 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 8816 vertices, nripped=7317 mean border=68.0, 1568 (14) missing vertices, mean dist 0.1 [0.1 (%44.7)->0.3 (%55.3))] %46 local maxima, %20 large gradients and %27 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0311 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.5, host= nike, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=428906.1, rms=2.444 rms = 2.6584/2.4443, sse=457132.0/428906.1, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 030: dt: 0.2500, sse=404059.3, rms=2.234 (8.615%) 031: dt: 0.2500, sse=394697.5, rms=2.149 (3.790%) rms = 2.1281/2.1491, sse=392315.1/394697.5, time step reduction 2 of 3 to 0.125 0 0 1 032: dt: 0.2500, sse=392315.1, rms=2.128 (0.974%) 033: dt: 0.1250, sse=386660.7, rms=2.073 (2.575%) rms = 2.0579/2.0733, sse=385012.0/386660.7, time step reduction 3 of 3 to 0.062 0 0 1 034: dt: 0.1250, sse=385012.0, rms=2.058 (0.743%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes Iteration 3 ========================================= n_averages=2, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 100.3670270; border_hi = 72.4434810; border_low = 53.3304520; outside_low = 10.0000000; outside_hi = 67.6652220; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=135579 Gdiag_no=-1 vno start=0, stop=135579 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 7759 vertices, nripped=7317 mean border=67.5, 3243 (11) missing vertices, mean dist 0.1 [0.2 (%46.6)->0.3 (%53.4))] %50 local maxima, %16 large gradients and %26 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0203 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host= nike, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=400278.1, rms=2.201 rms = 2.3909/2.2006, sse=421949.0/400278.1, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 035: dt: 0.2500, sse=389166.2, rms=2.098 (4.658%) rms = 2.0515/2.0981, sse=383971.1/389166.2, time step reduction 2 of 3 to 0.125 0 0 1 036: dt: 0.2500, sse=383971.1, rms=2.052 (2.218%) rms = 2.0131/2.0515, sse=380113.7/383971.1, time step reduction 3 of 3 to 0.062 0 0 1 037: dt: 0.1250, sse=380113.7, rms=2.013 (1.875%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes Pinning medial wall to white surface removing intersecting faces 000: 8 intersecting 001: 4 intersecting terminating search with 0 intersecting Writing output to ../surf/lh.pial.T1 #ET# mris_place_surface 3.44 minutes #VMPC# mris_place_surfaces VmPeak 1479816 mris_place_surface done @#@FSTIME 2020:07:23:10:19:32 mris_place_surface N 28 e 214.25 S 1.06 U 213.15 P 99% M 1101680 F 0 R 994636 W 0 c 64 w 420 I 0 O 9536 L 2.06 2.08 2.09 @#@FSLOADPOST 2020:07:23:10:23:07 mris_place_surface N 28 2.06 2.06 2.08 #-------------------------------------------- #@# T1PialSurf rh Thu Jul 23 10:23:07 EDT 2020 cd /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --threads 1 --wm wm.mgz --invol brain.finalsurfs.mgz --rh --i ../surf/rh.white --o ../surf/rh.pial.T1 --pial --nsmooth 0 --rip-label ../label/rh.cortex+hipamyg.label --pin-medial-wall ../label/rh.cortex.label --aparc ../label/rh.aparc.annot --repulse-surf ../surf/rh.white --white-surf ../surf/rh.white dev dev cd /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri setenv SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --seg aseg.presurf.mgz --threads 1 --wm wm.mgz --invol brain.finalsurfs.mgz --rh --i ../surf/rh.white --o ../surf/rh.pial.T1 --pial --nsmooth 0 --rip-label ../label/rh.cortex+hipamyg.label --pin-medial-wall ../label/rh.cortex.label --aparc ../label/rh.aparc.annot --repulse-surf ../surf/rh.white --white-surf ../surf/rh.white Reading in input surface ../surf/rh.white Not smoothing input surface Area 271538 0.33283 0.12142 0.001111 2.2111 Corner 814614 60.00000 14.31050 0.327048 178.6043 Edge 407307 0.88750 0.20135 0.040327 3.5567 Hinge 407307 9.63861 10.01213 0.000034 179.6736 Reading white surface coordinates from ../surf/rh.white Reading repulsion surface coordinates from ../surf/rh.white Reading in aparc ../label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=19421, wmmin=5, clip=110 MRIfindBrightNonWM(): 10149 bright non-wm voxels segmented. Masking bright non-wm for pial surface mid_gray = 77.3487 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Reading in seg volume aseg.presurf.mgz Ripping frozen voxels Ripping vertices not in label ../label/rh.cortex+hipamyg.label INFO: rip surface needed but not specified, so using input surface Ripping WMSA Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 MRISripSegs(): -2 2 0.5 ripped 0 vertex 67886: xyz = (42.8429,-8.62863,46.5325) oxyz = (42.8429,-8.62863,46.5325) wxzy = (42.8429,-8.62863,46.5325) pxyz = (42.8429,-8.62863,46.5325) CBVO Creating mask 135771 n_averages 16 Iteration 0 ========================================= n_averages=16, current_sigma=2 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 100.3670270; border_hi = 73.4434810; border_low = 54.3304520; outside_low = 10.0000000; outside_hi = 68.6652220; sigma = 2; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=135771 Gdiag_no=-1 vno start=0, stop=135771 Replacing 255s with 0s #SI# sigma=2 had to be increased for 144 vertices, nripped=7092 mean border=71.0, 92 (92) missing vertices, mean dist 1.9 [1.5 (%0.0)->2.8 (%100.0))] %18 local maxima, %46 large gradients and %31 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.1923 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=2.0, host= nike, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 100 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 000: dt: 0.0000, sse=16193984.0, rms=24.946 001: dt: 0.5000, sse=12344434.0, rms=21.740 (12.853%) 002: dt: 0.5000, sse=9428321.0, rms=18.952 (12.822%) 003: dt: 0.5000, sse=7378470.5, rms=16.716 (11.802%) 004: dt: 0.5000, sse=5977341.0, rms=14.994 (10.296%) 005: dt: 0.5000, sse=4940344.0, rms=13.579 (9.437%) 006: dt: 0.5000, sse=4068448.2, rms=12.263 (9.695%) 007: dt: 0.5000, sse=3263016.2, rms=10.906 (11.068%) 008: dt: 0.5000, sse=2512692.8, rms=9.467 (13.188%) 009: dt: 0.5000, sse=1843171.6, rms=7.967 (15.844%) 010: dt: 0.5000, sse=1297986.6, rms=6.494 (18.489%) 011: dt: 0.5000, sse=913616.4, rms=5.210 (19.782%) 012: dt: 0.5000, sse=695062.1, rms=4.310 (17.263%) 013: dt: 0.5000, sse=588665.0, rms=3.794 (11.985%) 014: dt: 0.5000, sse=546382.4, rms=3.565 (6.022%) 015: dt: 0.5000, sse=522985.9, rms=3.431 (3.775%) 016: dt: 0.5000, sse=512465.1, rms=3.367 (1.860%) rms = 3.3198/3.3668, sse=505109.1/512465.1, time step reduction 1 of 3 to 0.250 0 0 1 017: dt: 0.5000, sse=505109.2, rms=3.320 (1.395%) 018: dt: 0.2500, sse=383347.7, rms=2.475 (25.452%) 019: dt: 0.2500, sse=358687.2, rms=2.268 (8.348%) 020: dt: 0.2500, sse=353165.2, rms=2.217 (2.248%) rms = 2.1900/2.2173, sse=350249.3/353165.2, time step reduction 2 of 3 to 0.125 0 0 1 021: dt: 0.2500, sse=350249.3, rms=2.190 (1.231%) 022: dt: 0.1250, sse=342289.2, rms=2.115 (3.442%) rms = 2.1033/2.1146, sse=341177.3/342289.2, time step reduction 3 of 3 to 0.062 0 0 1 023: dt: 0.1250, sse=341177.3, rms=2.103 (0.535%) maximum number of reductions reached, breaking from loop positioning took 1.8 minutes Iteration 1 ========================================= n_averages=8, current_sigma=1 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 100.3670270; border_hi = 73.4434810; border_low = 54.3304520; outside_low = 10.0000000; outside_hi = 68.6652220; sigma = 1; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=135771 Gdiag_no=-1 vno start=0, stop=135771 Replacing 255s with 0s #SI# sigma=1 had to be increased for 7363 vertices, nripped=7092 mean border=69.6, 1395 (17) missing vertices, mean dist 0.1 [0.1 (%44.2)->0.4 (%55.8))] %36 local maxima, %32 large gradients and %25 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0553 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=1.0, host= nike, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=506518.3, rms=3.044 024: dt: 0.5000, sse=474033.9, rms=2.823 (7.291%) rms = 2.9744/2.8225, sse=494021.2/474033.9, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 025: dt: 0.2500, sse=408677.0, rms=2.326 (17.584%) 026: dt: 0.2500, sse=385011.3, rms=2.121 (8.837%) 027: dt: 0.2500, sse=378476.1, rms=2.059 (2.922%) rms = 2.0377/2.0587, sse=376352.5/378476.0, time step reduction 2 of 3 to 0.125 0 0 1 028: dt: 0.2500, sse=376352.5, rms=2.038 (1.017%) 029: dt: 0.1250, sse=370069.7, rms=1.974 (3.130%) rms = 1.9624/1.9740, sse=368934.4/370069.6, time step reduction 3 of 3 to 0.062 0 0 1 030: dt: 0.1250, sse=368934.4, rms=1.962 (0.586%) maximum number of reductions reached, breaking from loop positioning took 0.6 minutes Iteration 2 ========================================= n_averages=4, current_sigma=0.5 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 100.3670270; border_hi = 73.4434810; border_low = 54.3304520; outside_low = 10.0000000; outside_hi = 68.6652220; sigma = 0.5; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=135771 Gdiag_no=-1 vno start=0, stop=135771 Replacing 255s with 0s #SI# sigma=0.5 had to be increased for 8352 vertices, nripped=7092 mean border=68.9, 1517 (15) missing vertices, mean dist 0.1 [0.1 (%43.6)->0.3 (%56.4))] %49 local maxima, %19 large gradients and %25 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0318 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.5, host= nike, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=414084.4, rms=2.352 rms = 2.5381/2.3520, sse=437933.9/414084.4, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 031: dt: 0.2500, sse=384055.0, rms=2.085 (11.348%) 032: dt: 0.2500, sse=372531.4, rms=1.973 (5.384%) rms = 1.9456/1.9729, sse=369690.0/372531.4, time step reduction 2 of 3 to 0.125 0 0 1 033: dt: 0.2500, sse=369690.0, rms=1.946 (1.383%) rms = 1.9008/1.9456, sse=365470.9/369690.0, time step reduction 3 of 3 to 0.062 0 0 1 034: dt: 0.1250, sse=365470.9, rms=1.901 (2.299%) maximum number of reductions reached, breaking from loop positioning took 0.4 minutes Iteration 3 ========================================= n_averages=2, current_sigma=0.25 Computing target border values Entering MRIScomputeBorderValues_new(): inside_hi = 100.3670270; border_hi = 73.4434810; border_low = 54.3304520; outside_low = 10.0000000; outside_hi = 68.6652220; sigma = 0.25; max_thickness = 10; step_size=0.5; STEP_SIZE=0.1; which = 2 thresh = 0 flags = 0 CBVfindFirstPeakD1=0 CBVfindFirstPeakD2=0 nvertices=135771 Gdiag_no=-1 vno start=0, stop=135771 Replacing 255s with 0s #SI# sigma=0.25 had to be increased for 7247 vertices, nripped=7092 mean border=68.3, 3192 (12) missing vertices, mean dist 0.0 [0.2 (%46.8)->0.3 (%53.2))] %53 local maxima, %15 large gradients and %25 min vals, 0 gradients ignored nFirstPeakD1 0 MRIScomputeBorderValues_new() finished in 0.0207 min Averaging target values for 5 iterations... Positioning Surface: tspring = 0.3, nspring = 0.3, spring = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0 Positioning pial surface Entering MRISpositionSurface() max_mm = 0.3 MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5 parms->check_tol = 0, niterations = 100 tol=1.0e-04, sigma=0.2, host= nike, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 000: dt: 0.0000, sse=380574.2, rms=2.055 rms = 2.2468/2.0555, sse=401044.5/380574.2, time step reduction 1 of 3 to 0.250 0 1 1 RMS increased, rejecting step 035: dt: 0.2500, sse=368980.8, rms=1.941 (5.570%) rms = 1.8928/1.9410, sse=363965.3/368980.8, time step reduction 2 of 3 to 0.125 0 0 1 036: dt: 0.2500, sse=363965.3, rms=1.893 (2.484%) rms = 1.8566/1.8928, sse=360591.3/363965.3, time step reduction 3 of 3 to 0.062 0 0 1 037: dt: 0.1250, sse=360591.3, rms=1.857 (1.909%) maximum number of reductions reached, breaking from loop positioning took 0.3 minutes Pinning medial wall to white surface removing intersecting faces 000: 19 intersecting 001: 5 intersecting 002: 4 intersecting step 1 with no progress (num=12, old_num=4) 003: 12 intersecting 004: 8 intersecting step 1 with no progress (num=20, old_num=8) 005: 20 intersecting terminating search with 0 intersecting Writing output to ../surf/rh.pial.T1 #ET# mris_place_surface 3.56 minutes #VMPC# mris_place_surfaces VmPeak 1489812 mris_place_surface done @#@FSTIME 2020:07:23:10:23:07 mris_place_surface N 28 e 221.91 S 1.50 U 220.37 P 99% M 1111816 F 0 R 1140244 W 0 c 68 w 289 I 0 O 9552 L 2.06 2.06 2.08 @#@FSLOADPOST 2020:07:23:10:26:49 mris_place_surface N 28 2.04 2.05 2.06 #@# white curv lh Thu Jul 23 10:26:49 EDT 2020 cd /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri mris_place_surface --curv-map ../surf/lh.white 2 10 ../surf/lh.curv insurf ../surf/lh.white, nbrs 2, curvature_avgs 10 writing curvature file ../surf/lh.curv @#@FSTIME 2020:07:23:10:26:49 mris_place_surface N 5 e 1.97 S 0.13 U 1.82 P 99% M 182348 F 0 R 54173 W 0 c 3 w 48 I 0 O 1064 L 2.04 2.05 2.06 @#@FSLOADPOST 2020:07:23:10:26:51 mris_place_surface N 5 2.04 2.05 2.06 #@# white area lh Thu Jul 23 10:26:51 EDT 2020 cd /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri mris_place_surface --area-map ../surf/lh.white ../surf/lh.area writing curvature file ../surf/lh.area @#@FSTIME 2020:07:23:10:26:51 mris_place_surface N 3 e 0.89 S 0.12 U 0.76 P 99% M 182348 F 0 R 54159 W 0 c 1 w 42 I 0 O 1064 L 2.04 2.05 2.06 @#@FSLOADPOST 2020:07:23:10:26:52 mris_place_surface N 3 2.04 2.05 2.06 #@# pial curv lh Thu Jul 23 10:26:52 EDT 2020 cd /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri mris_place_surface --curv-map ../surf/lh.pial 2 10 ../surf/lh.curv.pial insurf ../surf/lh.pial, nbrs 2, curvature_avgs 10 writing curvature file ../surf/lh.curv.pial @#@FSTIME 2020:07:23:10:26:52 mris_place_surface N 5 e 1.89 S 0.12 U 1.75 P 99% M 182348 F 0 R 54173 W 0 c 3 w 34 I 0 O 1064 L 2.04 2.05 2.06 @#@FSLOADPOST 2020:07:23:10:26:54 mris_place_surface N 5 2.04 2.05 2.06 #@# pial area lh Thu Jul 23 10:26:54 EDT 2020 cd /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial writing curvature file ../surf/lh.area.pial @#@FSTIME 2020:07:23:10:26:54 mris_place_surface N 3 e 0.88 S 0.11 U 0.76 P 99% M 182348 F 0 R 54159 W 0 c 1 w 48 I 0 O 1064 L 2.04 2.05 2.06 @#@FSLOADPOST 2020:07:23:10:26:55 mris_place_surface N 3 2.04 2.05 2.06 #@# thickness lh Thu Jul 23 10:26:55 EDT 2020 cd /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness 0 of 135579 vertices processed 25000 of 135579 vertices processed 50000 of 135579 vertices processed 75000 of 135579 vertices processed 100000 of 135579 vertices processed 125000 of 135579 vertices processed 0 of 135579 vertices processed 25000 of 135579 vertices processed 50000 of 135579 vertices processed 75000 of 135579 vertices processed 100000 of 135579 vertices processed 125000 of 135579 vertices processed thickness calculation complete, 43:467 truncations. 63749 vertices at 0 distance 115636 vertices at 1 distance 59991 vertices at 2 distance 20433 vertices at 3 distance 7144 vertices at 4 distance 2660 vertices at 5 distance 932 vertices at 6 distance 340 vertices at 7 distance 117 vertices at 8 distance 48 vertices at 9 distance 19 vertices at 10 distance 21 vertices at 11 distance 13 vertices at 12 distance 6 vertices at 13 distance 10 vertices at 14 distance 9 vertices at 15 distance 18 vertices at 16 distance 3 vertices at 17 distance 3 vertices at 18 distance 3 vertices at 19 distance 3 vertices at 20 distance writing curvature file ../surf/lh.thickness @#@FSTIME 2020:07:23:10:26:55 mris_place_surface N 6 e 32.78 S 0.32 U 32.45 P 99% M 182384 F 0 R 160103 W 0 c 11 w 35 I 0 O 1064 L 2.04 2.05 2.06 @#@FSLOADPOST 2020:07:23:10:27:28 mris_place_surface N 6 2.05 2.04 2.06 #@# area and vertex vol lh Thu Jul 23 10:27:28 EDT 2020 cd /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri mris_place_surface --thickness ../surf/lh.white ../surf/lh.pial 20 5 ../surf/lh.thickness /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_convert --volume bert lh /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.volume masking with /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/label/lh.cortex.label Total face volume 243626 Total vertex volume 243384 (mask=0) #@# bert lh 243384 vertexvol Done @#@FSTIME 2020:07:23:10:27:28 vertexvol N 4 e 1.83 S 0.22 U 1.57 P 98% M 306324 F 0 R 97289 W 0 c 9 w 211 I 984 O 3192 L 2.05 2.04 2.06 @#@FSLOADPOST 2020:07:23:10:27:30 vertexvol N 4 2.05 2.04 2.06 #@# white curv rh Thu Jul 23 10:27:30 EDT 2020 cd /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri mris_place_surface --curv-map ../surf/rh.white 2 10 ../surf/rh.curv insurf ../surf/rh.white, nbrs 2, curvature_avgs 10 writing curvature file ../surf/rh.curv @#@FSTIME 2020:07:23:10:27:30 mris_place_surface N 5 e 2.15 S 0.14 U 2.00 P 99% M 182780 F 0 R 56291 W 0 c 9 w 42 I 0 O 1064 L 2.05 2.04 2.06 @#@FSLOADPOST 2020:07:23:10:27:32 mris_place_surface N 5 2.05 2.04 2.06 #@# white area rh Thu Jul 23 10:27:32 EDT 2020 cd /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri mris_place_surface --area-map ../surf/rh.white ../surf/rh.area writing curvature file ../surf/rh.area @#@FSTIME 2020:07:23:10:27:32 mris_place_surface N 3 e 0.90 S 0.12 U 0.77 P 99% M 182780 F 0 R 54240 W 0 c 1 w 48 I 0 O 1064 L 2.05 2.04 2.06 @#@FSLOADPOST 2020:07:23:10:27:33 mris_place_surface N 3 2.05 2.04 2.06 #@# pial curv rh Thu Jul 23 10:27:33 EDT 2020 cd /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri mris_place_surface --curv-map ../surf/rh.pial 2 10 ../surf/rh.curv.pial insurf ../surf/rh.pial, nbrs 2, curvature_avgs 10 writing curvature file ../surf/rh.curv.pial @#@FSTIME 2020:07:23:10:27:33 mris_place_surface N 5 e 1.89 S 0.12 U 1.75 P 99% M 182780 F 0 R 54253 W 0 c 4 w 28 I 0 O 1064 L 2.05 2.04 2.06 @#@FSLOADPOST 2020:07:23:10:27:35 mris_place_surface N 5 2.04 2.04 2.05 #@# pial area rh Thu Jul 23 10:27:35 EDT 2020 cd /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri mris_place_surface --area-map ../surf/rh.pial ../surf/rh.area.pial writing curvature file ../surf/rh.area.pial @#@FSTIME 2020:07:23:10:27:35 mris_place_surface N 3 e 0.92 S 0.13 U 0.78 P 99% M 182784 F 0 R 54240 W 0 c 1 w 31 I 0 O 1064 L 2.04 2.04 2.05 @#@FSLOADPOST 2020:07:23:10:27:36 mris_place_surface N 3 2.04 2.04 2.05 #@# thickness rh Thu Jul 23 10:27:36 EDT 2020 cd /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness 0 of 135771 vertices processed 25000 of 135771 vertices processed 50000 of 135771 vertices processed 75000 of 135771 vertices processed 100000 of 135771 vertices processed 125000 of 135771 vertices processed 0 of 135771 vertices processed 25000 of 135771 vertices processed 50000 of 135771 vertices processed 75000 of 135771 vertices processed 100000 of 135771 vertices processed 125000 of 135771 vertices processed thickness calculation complete, 74:348 truncations. 64864 vertices at 0 distance 117055 vertices at 1 distance 59896 vertices at 2 distance 19472 vertices at 3 distance 6480 vertices at 4 distance 2375 vertices at 5 distance 873 vertices at 6 distance 285 vertices at 7 distance 87 vertices at 8 distance 43 vertices at 9 distance 29 vertices at 10 distance 19 vertices at 11 distance 15 vertices at 12 distance 12 vertices at 13 distance 5 vertices at 14 distance 4 vertices at 15 distance 6 vertices at 16 distance 7 vertices at 17 distance 8 vertices at 18 distance 2 vertices at 19 distance 5 vertices at 20 distance writing curvature file ../surf/rh.thickness @#@FSTIME 2020:07:23:10:27:36 mris_place_surface N 6 e 32.69 S 0.20 U 32.48 P 99% M 182780 F 0 R 148558 W 0 c 11 w 55 I 0 O 1064 L 2.04 2.04 2.05 @#@FSLOADPOST 2020:07:23:10:28:08 mris_place_surface N 6 2.02 2.04 2.05 #@# area and vertex vol rh Thu Jul 23 10:28:09 EDT 2020 cd /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri mris_place_surface --thickness ../surf/rh.white ../surf/rh.pial 20 5 ../surf/rh.thickness /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_convert --volume bert rh /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.volume masking with /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/label/rh.cortex.label Total face volume 241323 Total vertex volume 241099 (mask=0) #@# bert rh 241099 vertexvol Done @#@FSTIME 2020:07:23:10:28:09 vertexvol N 4 e 1.84 S 0.21 U 1.60 P 98% M 306744 F 0 R 97417 W 0 c 10 w 221 I 0 O 3192 L 2.02 2.04 2.05 @#@FSLOADPOST 2020:07:23:10:28:10 vertexvol N 4 2.02 2.04 2.05 #----------------------------------------- #@# Curvature Stats lh Thu Jul 23 10:28:10 EDT 2020 /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm bert lh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/lh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ bert/lh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vno faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 237 ] Gb_filter = 0 @#@FSTIME 2020:07:23:10:28:10 mris_curvature_stats N 11 e 2.75 S 0.17 U 2.51 P 97% M 182564 F 1 R 91419 W 0 c 2 w 293 I 40 O 8552 L 2.02 2.04 2.05 @#@FSLOADPOST 2020:07:23:10:28:13 mris_curvature_stats N 11 2.02 2.04 2.05 #----------------------------------------- #@# Curvature Stats rh Thu Jul 23 10:28:13 EDT 2020 /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm bert rh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/rh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ bert/rh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vno faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 243 ] Gb_filter = 0 @#@FSTIME 2020:07:23:10:28:13 mris_curvature_stats N 11 e 2.70 S 0.16 U 2.47 P 97% M 182728 F 0 R 91557 W 0 c 1 w 291 I 0 O 8552 L 2.02 2.04 2.05 @#@FSLOADPOST 2020:07:23:10:28:16 mris_curvature_stats N 11 2.02 2.04 2.05 #-------------------------------------------- #@# Cortical ribbon mask Thu Jul 23 10:28:16 EDT 2020 /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri mris_volmask --aseg_name aseg.presurf --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon bert SUBJECTS_DIR is /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running loading input data... Running hemis serially Processing left hemi computing distance to left white surface computing distance to left pial surface Processing right hemi computing distance to right white surface computing distance to right pial surface hemi masks overlap voxels = 88 writing volume /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/ribbon.mgz mris_volmask took 4.87 minutes writing ribbon files @#@FSTIME 2020:07:23:10:28:16 mris_volmask N 12 e 292.20 S 2.06 U 290.14 P 100% M 982884 F 1 R 1346300 W 0 c 122 w 80 I 824 O 872 L 2.02 2.04 2.05 @#@FSLOADPOST 2020:07:23:10:33:08 mris_volmask N 12 2.11 2.07 2.05 #----------------------------------------- #@# Cortical Parc 2 lh Thu Jul 23 10:33:08 EDT 2020 /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 bert lh ../surf/lh.sphere.reg /usr/local/freesurfer/dev/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline dev dev reading atlas from /usr/local/freesurfer/dev/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 3.0 using min determinant for regularization = 0.088 0 singular and 0 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 110 labels changed using aseg relabeling using gibbs priors... 000: 8959 changed, 135579 examined... 001: 2102 changed, 35072 examined... 002: 608 changed, 11124 examined... 003: 227 changed, 3335 examined... 004: 114 changed, 1330 examined... 005: 56 changed, 655 examined... 006: 29 changed, 321 examined... 007: 14 changed, 167 examined... 008: 6 changed, 89 examined... 009: 2 changed, 34 examined... 010: 0 changed, 13 examined... 56 labels changed using aseg 000: 230 total segments, 146 labels (2513 vertices) changed 001: 94 total segments, 10 labels (26 vertices) changed 002: 84 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 50 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1123 vertices marked for relabeling... 1123 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 14 seconds. @#@FSTIME 2020:07:23:10:33:08 mris_ca_label N 11 e 14.49 S 1.43 U 13.02 P 99% M 1778652 F 0 R 986465 W 0 c 6 w 128 I 42432 O 2128 L 2.11 2.07 2.05 @#@FSLOADPOST 2020:07:23:10:33:23 mris_ca_label N 11 2.09 2.07 2.05 #----------------------------------------- #@# Cortical Parc 2 rh Thu Jul 23 10:33:23 EDT 2020 /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 bert rh ../surf/rh.sphere.reg /usr/local/freesurfer/dev/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline dev dev reading atlas from /usr/local/freesurfer/dev/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 1.4 using min determinant for regularization = 0.021 0 singular and 0 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 31 labels changed using aseg relabeling using gibbs priors... 000: 8698 changed, 135771 examined... 001: 1961 changed, 34306 examined... 002: 579 changed, 10504 examined... 003: 230 changed, 3373 examined... 004: 98 changed, 1330 examined... 005: 53 changed, 596 examined... 006: 32 changed, 318 examined... 007: 20 changed, 203 examined... 008: 11 changed, 115 examined... 009: 12 changed, 63 examined... 010: 6 changed, 70 examined... 011: 2 changed, 36 examined... 012: 0 changed, 12 examined... 15 labels changed using aseg 000: 225 total segments, 141 labels (1788 vertices) changed 001: 95 total segments, 11 labels (15 vertices) changed 002: 84 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 30 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 1091 vertices marked for relabeling... 1091 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 14 seconds. @#@FSTIME 2020:07:23:10:33:23 mris_ca_label N 11 e 14.40 S 1.42 U 12.95 P 99% M 1757708 F 0 R 983360 W 0 c 17 w 65 I 42776 O 2128 L 2.09 2.07 2.05 @#@FSLOADPOST 2020:07:23:10:33:37 mris_ca_label N 11 2.00 2.05 2.05 #----------------------------------------- #@# Cortical Parc 3 lh Thu Jul 23 10:33:37 EDT 2020 /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 bert lh ../surf/lh.sphere.reg /usr/local/freesurfer/dev/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.DKTatlas.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline dev dev reading atlas from /usr/local/freesurfer/dev/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 1.4 using min determinant for regularization = 0.020 0 singular and 383 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 1954 labels changed using aseg relabeling using gibbs priors... 000: 2027 changed, 135579 examined... 001: 469 changed, 9433 examined... 002: 122 changed, 2646 examined... 003: 46 changed, 760 examined... 004: 34 changed, 276 examined... 005: 30 changed, 177 examined... 006: 32 changed, 166 examined... 007: 21 changed, 148 examined... 008: 12 changed, 105 examined... 009: 15 changed, 77 examined... 010: 8 changed, 80 examined... 011: 5 changed, 53 examined... 012: 4 changed, 35 examined... 013: 2 changed, 29 examined... 014: 4 changed, 14 examined... 015: 2 changed, 19 examined... 016: 2 changed, 14 examined... 017: 2 changed, 14 examined... 018: 1 changed, 16 examined... 019: 1 changed, 8 examined... 020: 1 changed, 7 examined... 021: 1 changed, 7 examined... 022: 1 changed, 7 examined... 023: 0 changed, 7 examined... 345 labels changed using aseg 000: 45 total segments, 12 labels (158 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 16 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 753 vertices marked for relabeling... 753 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas.annot... classification took 0 minutes and 11 seconds. @#@FSTIME 2020:07:23:10:33:37 mris_ca_label N 11 e 10.71 S 0.70 U 9.96 P 99% M 890356 F 0 R 541516 W 0 c 8 w 109 I 42976 O 2128 L 2.00 2.05 2.05 @#@FSLOADPOST 2020:07:23:10:33:48 mris_ca_label N 11 1.93 2.03 2.04 #----------------------------------------- #@# Cortical Parc 3 rh Thu Jul 23 10:33:48 EDT 2020 /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 bert rh ../surf/rh.sphere.reg /usr/local/freesurfer/dev/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.DKTatlas.annot setting seed for random number generator to 1234 using ../mri/aseg.presurf.mgz aseg volume to correct midline dev dev reading atlas from /usr/local/freesurfer/dev/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs... reading color table from GCSA file.... average std = 0.9 using min determinant for regularization = 0.009 0 singular and 325 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 2141 labels changed using aseg relabeling using gibbs priors... 000: 1977 changed, 135771 examined... 001: 466 changed, 9297 examined... 002: 126 changed, 2623 examined... 003: 62 changed, 789 examined... 004: 37 changed, 362 examined... 005: 23 changed, 195 examined... 006: 19 changed, 121 examined... 007: 14 changed, 101 examined... 008: 10 changed, 76 examined... 009: 8 changed, 58 examined... 010: 2 changed, 41 examined... 011: 3 changed, 14 examined... 012: 0 changed, 16 examined... 320 labels changed using aseg 000: 40 total segments, 7 labels (59 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 6 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 844 vertices marked for relabeling... 844 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas.annot... classification took 0 minutes and 10 seconds. @#@FSTIME 2020:07:23:10:33:48 mris_ca_label N 11 e 10.50 S 0.69 U 9.79 P 99% M 866808 F 0 R 535800 W 0 c 7 w 104 I 42952 O 2128 L 1.93 2.03 2.04 @#@FSLOADPOST 2020:07:23:10:33:59 mris_ca_label N 11 1.95 2.03 2.04 #----------------------------------------- #@# WM/GM Contrast lh Thu Jul 23 10:33:59 EDT 2020 /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/scripts pctsurfcon --s bert --lh-only Log file is /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/scripts/pctsurfcon.log Thu Jul 23 10:33:59 EDT 2020 setenv SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running cd /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/scripts /usr/local/freesurfer/dev/bin/pctsurfcon pctsurfcon dev Linux nike 3.10.0-1062.7.1.el7.x86_64 #1 SMP Mon Dec 2 17:33:29 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer/dev mri_vol2surf --mov /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/tmp.pctsurfcon.22018/lh.wm.mgh --regheader bert --cortex srcvol = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/label/lh.cortex.label Reading surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 -1 -1 -1 using old Done mapping volume to surface Number of source voxels hit = 78911 Masking with /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/label/lh.cortex.label Writing to /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/tmp.pctsurfcon.22018/lh.wm.mgh Dim: 135579 1 1 mri_vol2surf --mov /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/tmp.pctsurfcon.22018/lh.gm.mgh --projfrac 0.3 --regheader bert --cortex srcvol = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/label/lh.cortex.label Reading surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.white Done reading source surface Reading thickness /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 92113 Masking with /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/label/lh.cortex.label Writing to /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/tmp.pctsurfcon.22018/lh.gm.mgh Dim: 135579 1 1 mri_concat /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/tmp.pctsurfcon.22018/lh.wm.mgh /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/tmp.pctsurfcon.22018/lh.gm.mgh --paired-diff-norm --mul 100 --o /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.w-g.pct.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing Combining pairs nframes = 1 Multiplying by 100.000000 Writing to /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.w-g.pct.mgh mri_segstats --in /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.w-g.pct.mgh --annot bert lh aparc --sum /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/stats/lh.w-g.pct.stats --snr dev cwd cmdline mri_segstats --in /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.w-g.pct.mgh --annot bert lh aparc --sum /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/stats/lh.w-g.pct.stats --snr sysname Linux hostname nike machine x86_64 user ah221 whitesurfname white UseRobust 0 Constructing seg from annotation Reading annotation /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Seg base 1000 Loading /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.w-g.pct.mgh Vertex Area is 0.668094 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation Reporting on 35 segmentations Using PrintSegStat mri_segstats done Cleaning up @#@FSTIME 2020:07:23:10:33:59 pctsurfcon N 3 e 4.27 S 0.47 U 3.73 P 98% M 290028 F 4 R 218437 W 0 c 26 w 393 I 2320 O 3392 L 1.95 2.03 2.04 @#@FSLOADPOST 2020:07:23:10:34:03 pctsurfcon N 3 1.95 2.03 2.04 #----------------------------------------- #@# WM/GM Contrast rh Thu Jul 23 10:34:03 EDT 2020 /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/scripts pctsurfcon --s bert --rh-only Log file is /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/scripts/pctsurfcon.log Thu Jul 23 10:34:03 EDT 2020 setenv SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running cd /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/scripts /usr/local/freesurfer/dev/bin/pctsurfcon pctsurfcon dev Linux nike 3.10.0-1062.7.1.el7.x86_64 #1 SMP Mon Dec 2 17:33:29 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer/dev mri_vol2surf --mov /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/tmp.pctsurfcon.22100/rh.wm.mgh --regheader bert --cortex srcvol = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/label/rh.cortex.label Reading surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 -1 -1 -1 using old Done mapping volume to surface Number of source voxels hit = 79165 Masking with /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/label/rh.cortex.label Writing to /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/tmp.pctsurfcon.22100/rh.wm.mgh Dim: 135771 1 1 mri_vol2surf --mov /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/tmp.pctsurfcon.22100/rh.gm.mgh --projfrac 0.3 --regheader bert --cortex srcvol = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/orig.mgz as target reference. -------- original matrix ----------- 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/label/rh.cortex.label Reading surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.white Done reading source surface Reading thickness /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 92441 Masking with /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/label/rh.cortex.label Writing to /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/tmp.pctsurfcon.22100/rh.gm.mgh Dim: 135771 1 1 mri_concat /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/tmp.pctsurfcon.22100/rh.wm.mgh /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/tmp.pctsurfcon.22100/rh.gm.mgh --paired-diff-norm --mul 100 --o /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.w-g.pct.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing Combining pairs nframes = 1 Multiplying by 100.000000 Writing to /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.w-g.pct.mgh mri_segstats --in /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.w-g.pct.mgh --annot bert rh aparc --sum /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/stats/rh.w-g.pct.stats --snr dev cwd cmdline mri_segstats --in /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.w-g.pct.mgh --annot bert rh aparc --sum /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/stats/rh.w-g.pct.stats --snr sysname Linux hostname nike machine x86_64 user ah221 whitesurfname white UseRobust 0 Constructing seg from annotation Reading annotation /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Seg base 2000 Loading /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.w-g.pct.mgh Vertex Area is 0.66566 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation Reporting on 35 segmentations Using PrintSegStat mri_segstats done Cleaning up @#@FSTIME 2020:07:23:10:34:03 pctsurfcon N 3 e 4.56 S 0.52 U 3.97 P 98% M 290244 F 0 R 219020 W 0 c 47 w 497 I 0 O 3392 L 1.95 2.03 2.04 @#@FSLOADPOST 2020:07:23:10:34:08 pctsurfcon N 3 1.95 2.03 2.04 #----------------------------------------- #@# Relabel Hypointensities Thu Jul 23 10:34:08 EDT 2020 /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz reading input surface ../surf/lh.white... relabeling lh hypointensities... 2640 voxels changed to hypointensity... reading input surface ../surf/rh.white... relabeling rh hypointensities... 2799 voxels changed to hypointensity... 5395 hypointense voxels neighboring cortex changed @#@FSTIME 2020:07:23:10:34:08 mri_relabel_hypointensities N 3 e 16.03 S 0.73 U 15.28 P 99% M 469724 F 2 R 548304 W 0 c 5 w 58 I 1320 O 672 L 1.95 2.03 2.04 @#@FSLOADPOST 2020:07:23:10:34:24 mri_relabel_hypointensities N 3 1.96 2.03 2.04 #----------------------------------------- #@# APas-to-ASeg Thu Jul 23 10:34:24 EDT 2020 /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri mri_surf2volseg --o aseg.mgz --i aseg.presurf.hypos.mgz --fix-presurf-with-ribbon /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/ribbon.mgz --threads 1 --lh-cortex-mask /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/label/lh.cortex.label --lh-white /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.white --lh-pial /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.pial --rh-cortex-mask /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/label/rh.cortex.label --rh-white /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.white --rh-pial /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.pial SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running outvol aseg.mgz 24 avail.processors, using 1 Loading aseg.presurf.hypos.mgz Loading /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/ribbon.mgz Loading /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.white Loading /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.pial Loading /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/label/lh.cortex.label Loading /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.white Loading /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.pial Loading /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/label/rh.cortex.label Done loading 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nrelabeled = 174283 ndotcheck = 0 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 1052692 mri_surf2volseg done @#@FSTIME 2020:07:23:10:34:24 mri_surf2volseg N 20 e 8.64 S 0.62 U 8.00 P 99% M 892564 F 1 R 501035 W 0 c 4 w 106 I 792 O 712 L 1.96 2.03 2.04 @#@FSLOADPOST 2020:07:23:10:34:33 mri_surf2volseg N 20 1.97 2.03 2.04 mri_brainvol_stats bert ComputeBrainVolumeStats2 VoxelVol=1, KeepCSF=1 #CBVS2 MaskVol 1790604.0 #CBVS2 BrainSegVol 1218716.0 #CBVS2 BrainSegVolNotVent 1199901.0 #CBVS2 SupraTentVol 1061977.0 #CBVS2 SupraTentVolNotVent 1043162.0 #CBVS2 lhCtxGM 243789.7 #CBVS2 rhCtxGM 241529.2 #CBVS2 lhCerebralWM 249386.5 #CBVS2 rhCerebralWM 248273.5 #CBVS2 SubCortGMVol 61321.0 #CBVS2 CerebellumVol 156739.0 #CBVS2 CerebellumGMVol 127113.0 #CBVS2 VentChorVol 15249.0 #CBVS2 3rd4th5thCSF 3566.0 #CBVS2 AllCSF 18815.0 #CBVS2 CCVol 4905.0 @#@FSTIME 2020:07:23:10:34:33 mri_brainvol_stats N 1 e 4.50 S 0.24 U 4.22 P 99% M 219204 F 6 R 192322 W 0 c 3 w 64 I 6200 O 8 L 1.97 2.03 2.04 @#@FSLOADPOST 2020:07:23:10:34:37 mri_brainvol_stats N 1 1.97 2.03 2.04 #----------------------------------------- #@# AParc-to-ASeg aparc Thu Jul 23 10:34:37 EDT 2020 /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri mri_surf2volseg --o aparc+aseg.mgz --label-cortex --i aseg.mgz --threads 1 --lh-annot /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/label/lh.aparc.annot 1000 --lh-cortex-mask /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/label/lh.cortex.label --lh-white /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.white --lh-pial /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.pial --rh-annot /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/label/rh.aparc.annot 2000 --rh-cortex-mask /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/label/rh.cortex.label --rh-white /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.white --rh-pial /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.pial SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running outvol aparc+aseg.mgz 24 avail.processors, using 1 Loading aseg.mgz Loading /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.white Loading /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.pial Loading /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 9424 vertices from lh hemi Loading /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Loading /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.white Loading /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.pial Loading /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 9165 vertices from rh hemi Loading /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Done loading 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 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/autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/label/lh.aparc.a2009s.annot 11100 --lh-cortex-mask /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/label/lh.cortex.label --lh-white /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.white --lh-pial /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.pial --rh-annot /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/label/rh.aparc.a2009s.annot 12100 --rh-cortex-mask /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/label/rh.cortex.label --rh-white /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.white --rh-pial /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.pial SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running outvol aparc.a2009s+aseg.mgz 24 avail.processors, using 1 Loading aseg.mgz Loading /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.white Loading /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.pial Loading /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 9424 vertices from lh hemi Loading /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/label/lh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2009.txt) reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2009.txt) Loading /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.white Loading /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.pial Loading /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 9165 vertices from rh hemi Loading /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/label/rh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2009.txt) reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2009.txt) Done loading 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 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/autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/label/lh.aparc.DKTatlas.annot 1000 --lh-cortex-mask /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/label/lh.cortex.label --lh-white /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.white --lh-pial /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.pial --rh-annot /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/label/rh.aparc.DKTatlas.annot 2000 --rh-cortex-mask /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/label/rh.cortex.label --rh-white /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.white --rh-pial /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.pial SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running outvol aparc.DKTatlas+aseg.mgz 24 avail.processors, using 1 Loading aseg.mgz Loading /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.white Loading /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.pial Loading /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 9424 vertices from lh hemi Loading /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/label/lh.aparc.DKTatlas.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Loading /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.white Loading /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.pial Loading /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 9165 vertices from rh hemi Loading /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/label/rh.aparc.DKTatlas.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Done loading 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nrelabeled = 484151 ndotcheck = 22377 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 1036780 mri_surf2volseg done @#@FSTIME 2020:07:23:10:39:16 mri_surf2volseg N 25 e 138.83 S 0.81 U 138.01 P 99% M 877952 F 0 R 811005 W 0 c 64 w 170 I 0 O 816 L 2.06 2.05 2.05 @#@FSLOADPOST 2020:07:23:10:41:35 mri_surf2volseg N 25 2.10 2.06 2.05 #----------------------------------------- #@# WMParc Thu Jul 23 10:41:35 EDT 2020 /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri mri_surf2volseg --o wmparc.mgz --label-wm --i aparc+aseg.mgz --threads 1 --lh-annot /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/label/lh.aparc.annot 3000 --lh-cortex-mask /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/label/lh.cortex.label --lh-white /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.white --lh-pial /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.pial --rh-annot /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/label/rh.aparc.annot 4000 --rh-cortex-mask /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/label/rh.cortex.label --rh-white /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.white --rh-pial /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.pial SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running outvol wmparc.mgz 24 avail.processors, using 1 Loading aparc+aseg.mgz Loading /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.white Loading /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.pial Loading /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/label/lh.cortex.label Ripping lh vertices labeled not in lh.cortex.label ripped 9424 vertices from lh hemi Loading /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Loading /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.white Loading /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.pial Loading /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/label/rh.cortex.label Ripping rh vertices labeled not in rh.cortex.label ripped 9165 vertices from rh hemi Loading /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Done loading 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nrelabeled = 492755 ndotcheck = 4051 Starting Surf2VolSeg free free done #VMPC# mri_surf2volseg VmPeak 1036892 mri_surf2volseg done @#@FSTIME 2020:07:23:10:41:35 mri_surf2volseg N 25 e 51.94 S 0.70 U 51.22 P 99% M 877948 F 0 R 634349 W 0 c 14 w 161 I 0 O 928 L 2.10 2.06 2.05 @#@FSLOADPOST 2020:07:23:10:42:27 mri_surf2volseg N 25 2.16 2.08 2.06 mri_segstats --seed 1234 --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject bert --surf-wm-vol --ctab /usr/local/freesurfer/dev/WMParcStatsLUT.txt --etiv setting seed for random number genererator to 1234 dev cwd cmdline mri_segstats --seed 1234 --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject bert --surf-wm-vol --ctab /usr/local/freesurfer/dev/WMParcStatsLUT.txt --etiv sysname Linux hostname nike machine x86_64 user ah221 whitesurfname white UseRobust 0 atlas_icv (eTIV) = 1518149 mm^3 (det: 1.283211 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 390 segmentations Computing statistics for each segmentation Reporting on 70 segmentations Using PrintSegStat mri_segstats done @#@FSTIME 2020:07:23:10:42:27 mri_segstats N 24 e 276.98 S 0.58 U 276.41 P 100% M 236028 F 0 R 654392 W 0 c 90 w 93 I 56 O 32 L 2.16 2.08 2.06 @#@FSLOADPOST 2020:07:23:10:47:04 mri_segstats N 24 2.14 2.10 2.06 #----------------------------------------- #@# Parcellation Stats lh Thu Jul 23 10:47:04 EDT 2020 /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab bert lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/wm.mgz... reading input surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.white... reading input pial surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.pial... reading input white surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 243626 Total vertex volume 243384 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1518149 mm^3 (det: 1.283211 ) 1270 852 2487 2.862 0.449 0.108 0.019 10 0.9 bankssts 966 598 1449 2.386 0.475 0.105 0.012 9 0.6 caudalanteriorcingulate 2848 1878 5740 2.775 0.485 0.109 0.020 23 2.4 caudalmiddlefrontal 2731 1798 3138 1.724 0.451 0.136 0.031 32 3.6 cuneus 609 401 1582 3.041 0.679 0.096 0.023 3 0.5 entorhinal 4420 2958 8444 2.598 0.604 0.117 0.025 43 4.4 fusiform 5125 3642 10753 2.654 0.474 0.122 0.026 55 5.5 inferiorparietal 4917 3522 12058 2.910 0.627 0.131 0.029 58 5.9 inferiortemporal 1459 955 2209 2.051 0.721 0.110 0.022 16 1.2 isthmuscingulate 7752 5183 12744 2.263 0.575 0.136 0.032 90 10.2 lateraloccipital 3839 2692 8126 2.770 0.628 0.130 0.029 47 4.6 lateralorbitofrontal 4633 3105 5624 1.748 0.510 0.121 0.028 47 5.5 lingual 3111 2234 6636 2.625 0.678 0.117 0.027 48 3.5 medialorbitofrontal 4958 3375 11981 3.026 0.579 0.117 0.023 51 5.0 middletemporal 1023 627 1735 2.392 0.552 0.064 0.011 3 0.4 parahippocampal 2308 1399 3642 2.431 0.603 0.095 0.020 13 1.9 paracentral 2335 1583 5113 2.908 0.500 0.108 0.018 18 1.8 parsopercularis 1035 669 2360 2.960 0.666 0.125 0.030 14 1.3 parsorbitalis 2309 1562 4598 2.739 0.490 0.111 0.019 20 1.8 parstriangularis 1876 1282 1679 1.490 0.370 0.127 0.032 20 2.3 pericalcarine 6006 3709 9177 2.220 0.670 0.096 0.021 42 4.9 postcentral 1713 1185 3152 2.407 0.634 0.115 0.021 18 1.6 posteriorcingulate 7264 4573 14052 2.865 0.718 0.105 0.023 46 7.3 precentral 5543 3716 9067 2.363 0.530 0.117 0.025 50 5.8 precuneus 937 639 2292 2.958 0.640 0.125 0.024 11 1.0 rostralanteriorcingulate 8338 5874 16449 2.512 0.513 0.124 0.028 98 9.6 rostralmiddlefrontal 10706 7098 23742 2.987 0.565 0.108 0.021 83 9.1 superiorfrontal 7870 5189 13870 2.393 0.525 0.116 0.022 77 7.2 superiorparietal 6207 4170 13240 2.859 0.558 0.105 0.020 50 5.1 superiortemporal 6651 4590 13833 2.745 0.506 0.117 0.021 64 6.1 supramarginal 375 265 1070 2.922 0.491 0.142 0.037 6 0.5 frontalpole 642 516 2757 3.601 0.651 0.166 0.048 11 1.3 temporalpole 750 494 1286 2.488 0.577 0.131 0.026 8 0.7 transversetemporal 3629 2375 7303 3.116 0.651 0.094 0.019 22 2.9 insula @#@FSTIME 2020:07:23:10:47:04 mris_anatomical_stats N 14 e 12.78 S 0.38 U 12.31 P 99% M 474468 F 2 R 290552 W 0 c 17 w 246 I 1968 O 296 L 2.14 2.10 2.06 @#@FSLOADPOST 2020:07:23:10:47:16 mris_anatomical_stats N 14 2.12 2.09 2.06 mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab bert lh pial computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/wm.mgz... reading input surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.pial... reading input pial surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.pial... reading input white surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 243626 Total vertex volume 243384 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1518149 mm^3 (det: 1.283211 ) 1270 844 2487 2.862 0.449 0.116 0.026 17 1.4 bankssts 966 664 1449 2.386 0.475 0.140 0.049 72 1.7 caudalanteriorcingulate 2848 2197 5740 2.775 0.485 0.118 0.024 50 2.8 caudalmiddlefrontal 2731 2010 3138 1.724 0.451 0.139 0.033 77 3.8 cuneus 609 657 1582 3.041 0.679 0.207 0.053 13 1.6 entorhinal 4420 3516 8444 2.598 0.604 0.134 0.035 73 6.4 fusiform 5125 4385 10753 2.654 0.474 0.140 0.034 2125 6.2 inferiorparietal 4917 4621 12058 2.910 0.627 0.164 0.042 116 9.2 inferiortemporal 1459 1244 2209 2.051 0.721 0.161 0.052 29 3.0 isthmuscingulate 7752 6127 12744 2.263 0.575 0.135 0.031 233 10.2 lateraloccipital 3839 3263 8126 2.770 0.628 0.154 0.039 100 6.5 lateralorbitofrontal 4633 3605 5624 1.748 0.510 0.128 0.034 61 6.3 lingual 3111 2908 6636 2.625 0.678 0.175 0.053 151 8.7 medialorbitofrontal 4958 4493 11981 3.026 0.579 0.141 0.030 115 6.6 middletemporal 1023 839 1735 2.392 0.552 0.129 0.029 7 1.6 parahippocampal 2308 1570 3642 2.431 0.603 0.093 0.017 15 1.7 paracentral 2335 1909 5113 2.908 0.500 0.130 0.027 25 2.9 parsopercularis 1035 928 2360 2.960 0.666 0.133 0.031 12 1.2 parsorbitalis 2309 1796 4598 2.739 0.490 0.128 0.027 36 2.6 parstriangularis 1876 1059 1679 1.490 0.370 0.102 0.029 42 2.0 pericalcarine 6006 4575 9177 2.220 0.670 0.108 0.020 55 5.0 postcentral 1713 1418 3152 2.407 0.634 0.141 0.033 33 2.5 posteriorcingulate 7264 5165 14052 2.865 0.718 0.101 0.022 76 6.6 precentral 5543 3970 9067 2.363 0.530 0.124 0.030 97 6.5 precuneus 937 891 2292 2.958 0.640 0.172 0.039 68 1.6 rostralanteriorcingulate 8338 6964 16449 2.512 0.513 0.139 0.029 365 9.9 rostralmiddlefrontal 10706 8490 23742 2.987 0.565 0.119 0.024 145 10.3 superiorfrontal 7870 6247 13870 2.393 0.525 0.126 0.030 98 7.9 superiorparietal 6207 4902 13240 2.859 0.558 0.125 0.029 107 7.6 superiortemporal 6651 5402 13833 2.745 0.506 0.133 0.049 122 7.8 supramarginal 375 472 1070 2.922 0.491 0.174 0.033 4 0.4 frontalpole 642 1043 2757 3.601 0.651 0.226 0.051 8 1.5 temporalpole 750 591 1286 2.488 0.577 0.113 0.025 4 0.8 transversetemporal 3629 2225 7303 3.116 0.651 0.118 0.036 80 4.8 insula @#@FSTIME 2020:07:23:10:47:17 mris_anatomical_stats N 14 e 12.62 S 0.37 U 12.18 P 99% M 474468 F 0 R 290133 W 0 c 4 w 214 I 0 O 296 L 2.12 2.09 2.06 @#@FSLOADPOST 2020:07:23:10:47:29 mris_anatomical_stats N 14 2.18 2.10 2.06 #----------------------------------------- #@# Parcellation Stats rh Thu Jul 23 10:47:29 EDT 2020 /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab bert rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/wm.mgz... reading input surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.white... reading input pial surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.pial... reading input white surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 241323 Total vertex volume 241099 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1518149 mm^3 (det: 1.283211 ) 1112 729 1917 2.562 0.486 0.090 0.016 6 0.7 bankssts 1254 836 2276 2.336 0.642 0.121 0.018 15 1.1 caudalanteriorcingulate 2699 1767 5298 2.845 0.496 0.104 0.020 18 2.3 caudalmiddlefrontal 2374 1550 2839 1.755 0.501 0.128 0.030 26 3.1 cuneus 533 345 1677 3.237 0.657 0.104 0.028 4 0.6 entorhinal 4060 2813 7546 2.527 0.537 0.117 0.024 42 4.1 fusiform 7107 4975 14861 2.656 0.464 0.119 0.024 73 6.9 inferiorparietal 4336 3100 10726 2.880 0.644 0.129 0.028 51 4.9 inferiortemporal 1221 819 1936 2.144 0.722 0.113 0.025 14 1.1 isthmuscingulate 8313 5650 12972 2.107 0.551 0.131 0.030 94 10.1 lateraloccipital 3845 2744 8194 2.787 0.680 0.124 0.028 41 4.5 lateralorbitofrontal 4777 3117 6296 1.931 0.569 0.124 0.031 53 6.4 lingual 3415 2357 6569 2.532 0.677 0.115 0.024 39 3.5 medialorbitofrontal 4974 3495 11799 2.839 0.573 0.118 0.024 54 5.0 middletemporal 1052 647 1725 2.448 0.625 0.075 0.014 5 0.5 parahippocampal 2445 1503 3703 2.395 0.502 0.108 0.025 18 2.4 paracentral 1908 1300 4052 2.890 0.451 0.111 0.021 15 1.6 parsopercularis 1358 942 3399 2.853 0.649 0.124 0.025 15 1.4 parsorbitalis 2701 1833 5267 2.563 0.480 0.113 0.022 24 2.4 parstriangularis 1923 1283 1962 1.729 0.594 0.114 0.025 14 1.9 pericalcarine 6305 3890 9342 2.182 0.658 0.097 0.020 44 5.1 postcentral 1759 1244 3346 2.445 0.633 0.125 0.024 19 1.9 posteriorcingulate 7794 4760 14699 2.819 0.676 0.104 0.023 56 7.7 precentral 5874 3908 9986 2.455 0.496 0.109 0.021 47 5.1 precuneus 981 672 2256 2.705 0.656 0.126 0.023 12 1.0 rostralanteriorcingulate 8238 5682 16672 2.567 0.495 0.124 0.026 89 9.0 rostralmiddlefrontal 9443 6230 20891 3.012 0.559 0.110 0.023 72 9.0 superiorfrontal 8150 5324 14051 2.371 0.528 0.112 0.021 73 6.9 superiorparietal 5300 3537 11367 2.902 0.534 0.101 0.020 40 4.3 superiortemporal 5637 3847 11060 2.693 0.492 0.115 0.021 52 5.1 supramarginal 488 353 1257 2.669 0.487 0.132 0.025 7 0.5 frontalpole 554 408 2233 3.849 0.442 0.153 0.041 7 0.9 temporalpole 506 303 824 2.428 0.388 0.111 0.024 4 0.4 transversetemporal 4170 2767 8103 2.992 0.723 0.107 0.024 35 4.1 insula @#@FSTIME 2020:07:23:10:47:29 mris_anatomical_stats N 14 e 12.70 S 0.38 U 12.25 P 99% M 475108 F 0 R 290732 W 0 c 6 w 225 I 0 O 296 L 2.18 2.10 2.06 @#@FSLOADPOST 2020:07:23:10:47:42 mris_anatomical_stats N 14 2.15 2.10 2.06 mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab bert rh pial computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/wm.mgz... reading input surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.pial... reading input pial surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.pial... reading input white surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 241323 Total vertex volume 241099 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1518149 mm^3 (det: 1.283211 ) 1112 732 1917 2.562 0.486 0.116 0.027 12 1.3 bankssts 1254 1070 2276 2.336 0.642 0.148 0.049 31 1.9 caudalanteriorcingulate 2699 1833 5298 2.845 0.496 0.106 0.023 32 2.5 caudalmiddlefrontal 2374 1844 2839 1.755 0.501 0.133 0.035 51 3.5 cuneus 533 708 1677 3.237 0.657 0.271 0.067 13 2.0 entorhinal 4060 3183 7546 2.527 0.537 0.137 0.036 68 6.0 fusiform 7107 6080 14861 2.656 0.464 0.136 0.028 995 8.3 inferiorparietal 4336 4214 10726 2.880 0.644 0.156 0.036 135 6.2 inferiortemporal 1221 1009 1936 2.144 0.722 0.181 1.595 -114 1.9 isthmuscingulate 8313 6704 12972 2.107 0.551 0.138 0.031 154 11.4 lateraloccipital 3845 3266 8194 2.787 0.680 0.148 0.037 62 5.8 lateralorbitofrontal 4777 3606 6296 1.931 0.569 0.127 0.035 72 6.2 lingual 3415 2911 6569 2.532 0.677 0.137 0.031 43 4.3 medialorbitofrontal 4974 4664 11799 2.839 0.573 0.145 0.032 90 6.7 middletemporal 1052 793 1725 2.448 0.625 0.148 0.040 15 2.2 parahippocampal 2445 1594 3703 2.395 0.502 0.101 0.021 24 2.0 paracentral 1908 1460 4052 2.890 0.451 0.117 0.027 21 2.2 parsopercularis 1358 1383 3399 2.853 0.649 0.155 0.032 20 1.8 parsorbitalis 2701 2228 5267 2.563 0.480 0.126 0.023 42 2.6 parstriangularis 1923 1096 1962 1.729 0.594 0.101 0.023 20 1.9 pericalcarine 6305 4702 9342 2.182 0.658 0.106 0.020 46 5.2 postcentral 1759 1444 3346 2.445 0.633 0.146 0.035 42 2.5 posteriorcingulate 7794 5486 14699 2.819 0.676 0.104 0.020 7933 6.1 precentral 5874 4227 9986 2.455 0.496 0.117 0.025 59 6.2 precuneus 981 987 2256 2.705 0.656 0.184 0.047 56 1.9 rostralanteriorcingulate 8238 7061 16672 2.567 0.495 0.143 0.029 149 10.3 rostralmiddlefrontal 9443 7408 20891 3.012 0.559 0.123 0.026 154 9.6 superiorfrontal 8150 6299 14051 2.371 0.528 0.120 0.024 99 7.4 superiorparietal 5300 4211 11367 2.902 0.534 0.121 0.026 124 5.9 superiortemporal 5637 4225 11060 2.693 0.492 0.125 0.027 119 6.3 supramarginal 488 579 1257 2.669 0.487 0.186 0.028 7 0.7 frontalpole 554 763 2233 3.849 0.442 0.186 0.043 6 0.9 temporalpole 506 386 824 2.428 0.388 0.118 0.031 8 0.5 transversetemporal 4170 2595 8103 2.992 0.723 0.124 0.032 96 5.8 insula @#@FSTIME 2020:07:23:10:47:42 mris_anatomical_stats N 14 e 12.79 S 0.41 U 12.31 P 99% M 475108 F 0 R 305839 W 0 c 37 w 218 I 0 O 296 L 2.15 2.10 2.06 @#@FSLOADPOST 2020:07:23:10:47:55 mris_anatomical_stats N 14 2.04 2.08 2.05 #----------------------------------------- #@# Parcellation Stats 2 lh Thu Jul 23 10:47:55 EDT 2020 /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.a2009s.stats -b -a ../label/lh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab bert lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/wm.mgz... reading input surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.white... reading input pial surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.pial... reading input white surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 243626 Total vertex volume 243384 (mask=0) reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2009.txt) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1518149 mm^3 (det: 1.283211 ) 1243 876 2277 2.458 0.389 0.128 0.026 13 1.4 G_and_S_frontomargin 1903 1309 3525 2.428 0.541 0.138 0.030 24 2.2 G_and_S_occipital_inf 1813 1058 2818 2.286 0.601 0.107 0.026 13 2.0 G_and_S_paracentral 1294 927 3333 3.053 0.487 0.142 0.029 17 1.5 G_and_S_subcentral 867 633 2299 2.755 0.572 0.155 0.039 14 1.4 G_and_S_transv_frontopol 2450 1632 5001 2.820 0.494 0.109 0.020 23 2.1 G_and_S_cingul-Ant 1166 756 1896 2.558 0.503 0.090 0.012 6 0.6 G_and_S_cingul-Mid-Ant 1390 944 2462 2.546 0.459 0.096 0.017 8 1.0 G_and_S_cingul-Mid-Post 506 350 1273 2.909 0.520 0.133 0.030 7 0.5 G_cingul-Post-dorsal 309 199 604 2.248 0.599 0.135 0.032 5 0.4 G_cingul-Post-ventral 2369 1541 2861 1.689 0.476 0.143 0.035 30 3.5 G_cuneus 1302 909 3386 2.980 0.450 0.118 0.021 13 1.2 G_front_inf-Opercular 462 295 1181 2.878 0.358 0.115 0.023 7 0.4 G_front_inf-Orbital 1273 858 3213 2.911 0.433 0.123 0.022 16 1.1 G_front_inf-Triangul 4280 3037 10670 2.761 0.556 0.132 0.030 61 5.2 G_front_middle 7642 5028 19001 3.124 0.556 0.119 0.025 75 7.7 G_front_sup 656 429 1548 3.288 0.647 0.105 0.027 6 0.6 G_Ins_lg_and_S_cent_ins 748 504 2403 3.657 0.633 0.099 0.020 7 0.6 G_insular_short 2038 1441 4787 2.680 0.446 0.147 0.033 33 2.8 G_occipital_middle 1236 797 2399 2.475 0.586 0.104 0.020 10 0.9 G_occipital_sup 1834 1221 4127 2.732 0.590 0.128 0.029 24 2.1 G_oc-temp_lat-fusifor 3254 2181 4113 1.692 0.525 0.135 0.034 41 4.8 G_oc-temp_med-Lingual 1231 779 2885 2.754 0.700 0.091 0.023 8 1.1 G_oc-temp_med-Parahip 2197 1540 5929 3.020 0.708 0.135 0.036 35 3.2 G_orbital 1924 1409 4930 2.832 0.404 0.140 0.030 26 2.2 G_pariet_inf-Angular 3167 2218 7748 2.855 0.536 0.125 0.024 36 3.2 G_pariet_inf-Supramar 3076 2053 6467 2.499 0.574 0.127 0.026 42 3.1 G_parietal_sup 2323 1304 3763 2.298 0.583 0.095 0.025 18 2.3 G_postcentral 2862 1644 6833 3.112 0.803 0.104 0.025 22 3.1 G_precentral 2661 1813 5409 2.401 0.543 0.126 0.027 31 2.9 G_precuneus 832 704 2477 2.726 0.570 0.133 0.037 21 1.3 G_rectus 798 519 1486 2.835 0.810 0.108 0.036 8 1.2 G_subcallosal 643 408 1282 2.702 0.612 0.141 0.028 9 0.7 G_temp_sup-G_T_transv 2317 1586 6395 3.056 0.571 0.130 0.028 31 2.6 G_temp_sup-Lateral 540 406 1589 3.383 0.548 0.105 0.024 4 0.6 G_temp_sup-Plan_polar 1091 766 2217 2.690 0.492 0.106 0.018 9 0.8 G_temp_sup-Plan_tempo 2596 1936 7814 3.046 0.610 0.150 0.036 42 3.9 G_temporal_inf 2656 1803 7643 3.143 0.506 0.126 0.029 37 3.1 G_temporal_middle 449 291 574 2.399 0.359 0.083 0.012 1 0.2 Lat_Fis-ant-Horizont 419 281 620 2.895 0.466 0.104 0.018 2 0.4 Lat_Fis-ant-Vertical 1290 834 1779 2.834 0.426 0.107 0.019 8 1.2 Lat_Fis-post 2096 1324 3000 2.026 0.584 0.138 0.040 26 3.3 Pole_occipital 1544 1137 5439 3.347 0.761 0.135 0.033 20 2.0 Pole_temporal 2576 1748 2495 1.644 0.509 0.118 0.028 23 3.0 S_calcarine 3134 2092 3840 2.133 0.701 0.092 0.017 12 2.3 S_central 1117 721 1470 2.298 0.458 0.083 0.013 4 0.6 S_cingul-Marginalis 518 353 873 2.878 0.364 0.108 0.018 3 0.4 S_circular_insula_ant 1689 1069 2452 2.857 0.554 0.082 0.013 6 0.9 S_circular_insula_inf 1919 1211 2704 2.809 0.391 0.081 0.013 6 1.0 S_circular_insula_sup 872 594 1679 2.832 0.699 0.108 0.021 6 0.8 S_collat_transv_ant 477 327 446 1.661 0.395 0.134 0.028 4 0.6 S_collat_transv_post 2288 1563 4374 2.584 0.572 0.100 0.017 16 1.5 S_front_inf 1498 1057 2103 2.228 0.406 0.115 0.025 12 1.6 S_front_middle 2529 1667 4094 2.637 0.417 0.087 0.013 12 1.4 S_front_sup 460 315 740 2.490 0.394 0.073 0.007 1 0.2 S_interm_prim-Jensen 2974 1973 4230 2.363 0.447 0.102 0.017 17 2.2 S_intrapariet_and_P_trans 1210 822 1527 2.221 0.461 0.122 0.026 9 1.3 S_oc_middle_and_Lunatus 1011 673 1320 2.158 0.396 0.094 0.016 6 0.7 S_oc_sup_and_transversal 684 459 1053 2.431 0.465 0.118 0.021 6 0.7 S_occipital_ant 999 653 1426 2.555 0.359 0.091 0.014 4 0.6 S_oc-temp_lat 2219 1456 2763 2.163 0.401 0.091 0.015 11 1.3 S_oc-temp_med_and_Lingual 395 290 631 2.595 0.381 0.135 0.020 5 0.5 S_orbital_lateral 647 445 975 2.356 0.736 0.106 0.014 7 0.4 S_orbital_med-olfact 1473 1026 2484 2.518 0.571 0.132 0.030 15 2.0 S_orbital-H_Shaped 2645 1739 3593 2.279 0.542 0.114 0.021 20 2.5 S_parieto_occipital 1245 750 941 1.660 0.518 0.107 0.017 17 0.9 S_pericallosal 3346 2251 4931 2.256 0.511 0.109 0.021 25 3.0 S_postcentral 1528 995 2269 2.679 0.428 0.104 0.018 9 1.3 S_precentral-inf-part 1252 819 1876 2.781 0.488 0.095 0.017 6 1.0 S_precentral-sup-part 646 456 935 2.307 0.573 0.117 0.017 5 0.6 S_suborbital 773 533 1113 2.329 0.459 0.114 0.024 5 0.8 S_subparietal 1717 1202 2903 2.789 0.588 0.112 0.020 10 1.6 S_temporal_inf 5175 3494 9220 2.715 0.444 0.102 0.018 35 3.9 S_temporal_sup 392 270 468 2.177 0.550 0.107 0.013 3 0.3 S_temporal_transverse @#@FSTIME 2020:07:23:10:47:55 mris_anatomical_stats N 14 e 13.42 S 0.43 U 12.85 P 99% M 474468 F 0 R 334722 W 0 c 33 w 386 I 0 O 632 L 2.04 2.08 2.05 @#@FSLOADPOST 2020:07:23:10:48:08 mris_anatomical_stats N 14 2.11 2.09 2.06 #----------------------------------------- #@# Parcellation Stats 2 rh Thu Jul 23 10:48:08 EDT 2020 /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab bert rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/wm.mgz... reading input surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.white... reading input pial surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.pial... reading input white surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 241323 Total vertex volume 241099 (mask=0) reading colortable from annotation file... colortable with 76 entries read (originally Simple_surface_labels2009.txt) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1518149 mm^3 (det: 1.283211 ) 1104 797 2298 2.540 0.522 0.128 0.029 11 1.3 G_and_S_frontomargin 1302 922 2469 2.375 0.485 0.129 0.028 14 1.4 G_and_S_occipital_inf 1653 963 2373 2.175 0.550 0.116 0.030 15 2.0 G_and_S_paracentral 1388 974 3225 2.907 0.526 0.135 0.026 16 1.5 G_and_S_subcentral 1157 848 2907 2.709 0.498 0.133 0.028 16 1.3 G_and_S_transv_frontopol 3454 2335 6843 2.852 0.523 0.114 0.022 31 3.1 G_and_S_cingul-Ant 1497 1012 2868 2.729 0.487 0.098 0.017 10 1.2 G_and_S_cingul-Mid-Ant 1528 1058 2782 2.583 0.448 0.106 0.021 10 1.4 G_and_S_cingul-Mid-Post 402 294 1072 2.782 0.448 0.140 0.034 6 0.6 G_cingul-Post-dorsal 270 186 651 2.764 0.723 0.133 0.029 4 0.3 G_cingul-Post-ventral 2251 1451 2588 1.666 0.478 0.129 0.031 27 2.9 G_cuneus 1172 802 3283 3.052 0.372 0.119 0.023 13 1.0 G_front_inf-Opercular 483 342 1357 2.910 0.386 0.138 0.032 8 0.6 G_front_inf-Orbital 1227 850 3013 2.734 0.436 0.129 0.027 15 1.3 G_front_inf-Triangul 3527 2396 9519 2.911 0.472 0.135 0.030 51 4.4 G_front_middle 5892 3855 14971 3.123 0.568 0.119 0.027 58 6.6 G_front_sup 703 462 1599 3.263 0.746 0.106 0.025 7 0.5 G_Ins_lg_and_S_cent_ins 696 492 2274 3.581 0.782 0.123 0.029 11 1.0 G_insular_short 2056 1512 5017 2.582 0.480 0.140 0.032 32 2.6 G_occipital_middle 1601 1034 2654 2.128 0.566 0.118 0.027 16 1.7 G_occipital_sup 1804 1253 3942 2.525 0.491 0.123 0.027 25 2.0 G_oc-temp_lat-fusifor 2783 1785 4025 1.938 0.606 0.132 0.036 38 4.2 G_oc-temp_med-Lingual 1182 736 2981 2.868 0.786 0.103 0.028 10 1.2 G_oc-temp_med-Parahip 2598 1892 7756 3.087 0.694 0.131 0.031 37 3.2 G_orbital 2694 1955 7080 2.855 0.442 0.142 0.033 42 3.3 G_pariet_inf-Angular 2601 1834 6525 2.930 0.409 0.131 0.027 34 3.0 G_pariet_inf-Supramar 2606 1727 5875 2.623 0.520 0.127 0.025 34 2.5 G_parietal_sup 2306 1276 3653 2.287 0.635 0.094 0.023 17 2.0 G_postcentral 3187 1740 6993 3.067 0.695 0.103 0.027 28 3.5 G_precentral 2884 1912 5488 2.393 0.501 0.116 0.022 31 2.6 G_precuneus 1136 826 2597 2.350 0.680 0.126 0.033 17 1.6 G_rectus 507 337 832 2.590 0.868 0.120 0.038 6 0.8 G_subcallosal 398 218 760 2.656 0.438 0.111 0.029 4 0.4 G_temp_sup-G_T_transv 1693 1153 4925 3.158 0.514 0.123 0.027 19 1.9 G_temp_sup-Lateral 848 566 1850 3.120 0.695 0.102 0.025 5 0.8 G_temp_sup-Plan_polar 705 507 1533 2.855 0.631 0.090 0.017 5 0.4 G_temp_sup-Plan_tempo 2421 1750 6706 2.883 0.649 0.135 0.032 36 3.0 G_temporal_inf 2854 2062 8136 2.973 0.539 0.130 0.027 40 3.3 G_temporal_middle 500 331 603 2.134 0.312 0.085 0.010 2 0.2 Lat_Fis-ant-Horizont 255 178 336 2.413 0.398 0.114 0.018 1 0.3 Lat_Fis-ant-Vertical 1531 978 1931 2.482 0.520 0.099 0.017 8 1.1 Lat_Fis-post 3724 2451 4915 1.839 0.569 0.143 0.037 47 5.6 Pole_occipital 1678 1261 5882 3.362 0.704 0.146 0.034 23 2.4 Pole_temporal 2342 1595 2506 1.804 0.577 0.106 0.023 15 2.1 S_calcarine 3071 2016 3835 2.180 0.764 0.095 0.019 14 2.5 S_central 1430 952 2145 2.483 0.507 0.096 0.015 7 1.0 S_cingul-Marginalis 614 405 958 2.994 0.475 0.102 0.019 3 0.5 S_circular_insula_ant 1298 824 1833 2.851 0.444 0.080 0.011 4 0.7 S_circular_insula_inf 1639 1054 2418 2.729 0.450 0.085 0.013 5 1.0 S_circular_insula_sup 830 568 1584 2.820 0.643 0.111 0.018 7 0.8 S_collat_transv_ant 552 378 694 2.131 0.400 0.139 0.032 5 0.8 S_collat_transv_post 2202 1473 3333 2.474 0.451 0.107 0.022 14 2.1 S_front_inf 2152 1432 3130 2.385 0.384 0.104 0.019 13 1.5 S_front_middle 2143 1444 3759 2.687 0.539 0.106 0.019 14 1.8 S_front_sup 486 325 690 2.628 0.471 0.099 0.014 2 0.3 S_interm_prim-Jensen 3698 2461 5688 2.436 0.445 0.107 0.018 26 2.9 S_intrapariet_and_P_trans 1287 861 1648 2.261 0.452 0.109 0.019 8 1.1 S_oc_middle_and_Lunatus 1317 850 1394 1.857 0.386 0.101 0.018 8 0.9 S_oc_sup_and_transversal 672 447 900 2.328 0.381 0.104 0.018 4 0.6 S_occipital_ant 845 605 1520 2.720 0.455 0.117 0.023 6 0.8 S_oc-temp_lat 2274 1469 2927 2.348 0.428 0.089 0.014 10 1.3 S_oc-temp_med_and_Lingual 561 359 649 2.261 0.485 0.102 0.017 3 0.4 S_orbital_lateral 907 630 1310 2.289 0.651 0.106 0.018 6 0.6 S_orbital_med-olfact 1473 1068 2427 2.485 0.513 0.129 0.030 15 2.0 S_orbital-H_Shaped 2424 1592 3464 2.465 0.482 0.104 0.021 14 2.2 S_parieto_occipital 1559 953 1252 1.661 0.367 0.119 0.018 21 1.2 S_pericallosal 2762 1799 3714 2.270 0.476 0.093 0.015 13 1.8 S_postcentral 2002 1302 3148 2.676 0.393 0.092 0.015 9 1.4 S_precentral-inf-part 1148 757 1577 2.478 0.459 0.112 0.021 8 1.0 S_precentral-sup-part 354 240 578 2.535 0.636 0.098 0.015 2 0.2 S_suborbital 848 590 1423 2.396 0.524 0.111 0.021 6 0.7 S_subparietal 1275 858 1752 2.500 0.406 0.115 0.020 7 1.3 S_temporal_inf 5818 3867 9221 2.522 0.426 0.091 0.014 30 3.5 S_temporal_sup 365 238 532 2.670 0.422 0.098 0.012 2 0.2 S_temporal_transverse @#@FSTIME 2020:07:23:10:48:08 mris_anatomical_stats N 14 e 13.40 S 0.39 U 12.87 P 99% M 475108 F 0 R 290423 W 0 c 18 w 385 I 0 O 632 L 2.11 2.09 2.06 @#@FSLOADPOST 2020:07:23:10:48:22 mris_anatomical_stats N 14 2.10 2.09 2.06 #----------------------------------------- #@# Parcellation Stats 3 lh Thu Jul 23 10:48:22 EDT 2020 /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas.stats -b -a ../label/lh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab bert lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot. reading volume /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/wm.mgz... reading input surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.white... reading input pial surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.pial... reading input white surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 243626 Total vertex volume 243384 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.DKTatlas.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1518149 mm^3 (det: 1.283211 ) 1811 1130 3047 2.571 0.522 0.101 0.014 15 1.1 caudalanteriorcingulate 3034 1998 6129 2.778 0.484 0.109 0.020 24 2.6 caudalmiddlefrontal 3579 2350 4538 1.870 0.542 0.132 0.030 40 4.6 cuneus 505 335 1479 3.149 0.667 0.096 0.023 3 0.4 entorhinal 4178 2753 7375 2.526 0.596 0.115 0.024 39 4.0 fusiform 5296 3731 10548 2.619 0.462 0.120 0.025 54 5.5 inferiorparietal 4898 3546 12717 2.956 0.632 0.134 0.030 61 6.1 inferiortemporal 1438 940 2182 2.062 0.727 0.109 0.022 15 1.2 isthmuscingulate 7677 5122 12847 2.289 0.566 0.134 0.031 87 9.8 lateraloccipital 4161 2954 9087 2.754 0.660 0.135 0.032 58 5.6 lateralorbitofrontal 4751 3188 5779 1.749 0.517 0.123 0.029 50 5.9 lingual 2489 1822 5616 2.605 0.689 0.115 0.027 39 2.8 medialorbitofrontal 6294 4275 14366 2.953 0.588 0.115 0.023 61 6.1 middletemporal 1083 667 1820 2.377 0.549 0.066 0.011 4 0.4 parahippocampal 2673 1614 4320 2.484 0.610 0.093 0.020 14 2.2 paracentral 2200 1488 4824 2.901 0.508 0.109 0.018 18 1.7 parsopercularis 1162 759 2334 2.778 0.474 0.101 0.018 9 0.9 parsorbitalis 2740 1854 5622 2.758 0.490 0.110 0.020 26 2.2 parstriangularis 1847 1269 1646 1.486 0.364 0.126 0.031 19 2.2 pericalcarine 6955 4335 10548 2.235 0.662 0.100 0.021 51 5.9 postcentral 1890 1297 3306 2.383 0.621 0.113 0.020 19 1.7 posteriorcingulate 7213 4546 13950 2.873 0.713 0.105 0.023 45 7.2 precentral 5337 3561 8872 2.370 0.520 0.116 0.024 48 5.2 precuneus 1389 928 2860 2.875 0.624 0.119 0.023 15 1.4 rostralanteriorcingulate 5855 4104 11411 2.540 0.566 0.126 0.029 72 7.0 rostralmiddlefrontal 11668 7894 26234 2.925 0.590 0.114 0.023 104 11.1 superiorfrontal 6290 4186 11328 2.415 0.523 0.117 0.023 64 5.9 superiorparietal 7662 5233 17535 2.927 0.586 0.111 0.022 68 7.1 superiortemporal 6184 4268 13143 2.771 0.508 0.117 0.022 60 5.5 supramarginal 749 494 1272 2.463 0.577 0.131 0.026 8 0.7 transversetemporal 3147 2067 6649 3.167 0.633 0.091 0.016 18 2.1 insula @#@FSTIME 2020:07:23:10:48:22 mris_anatomical_stats N 14 e 13.16 S 0.67 U 12.43 P 99% M 474468 F 0 R 361487 W 0 c 25 w 205 I 0 O 272 L 2.10 2.09 2.06 @#@FSLOADPOST 2020:07:23:10:48:35 mris_anatomical_stats N 14 2.07 2.08 2.05 #----------------------------------------- #@# Parcellation Stats 3 rh Thu Jul 23 10:48:35 EDT 2020 /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/scripts mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas.stats -b -a ../label/rh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab bert rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot. reading volume /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/wm.mgz... reading input surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.white... reading input pial surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.pial... reading input white surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. Using TH3 vertex volume calc Total face volume 241323 Total vertex volume 241099 (mask=0) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/tanha_002/users/greve/fsdev.build/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.DKTatlas.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1518149 mm^3 (det: 1.283211 ) 1349 898 2409 2.340 0.637 0.122 0.019 16 1.2 caudalanteriorcingulate 2730 1795 5387 2.833 0.509 0.105 0.020 18 2.2 caudalmiddlefrontal 3010 1943 3737 1.876 0.551 0.123 0.028 32 3.7 cuneus 512 330 1628 3.246 0.670 0.111 0.030 4 0.6 entorhinal 3763 2572 6704 2.510 0.513 0.116 0.024 38 3.6 fusiform 6943 4844 14335 2.646 0.470 0.119 0.024 71 6.7 inferiorparietal 4645 3343 11646 2.868 0.649 0.129 0.028 57 5.4 inferiortemporal 1205 809 1916 2.158 0.723 0.112 0.025 13 1.1 isthmuscingulate 8402 5721 12928 2.086 0.549 0.132 0.030 96 10.4 lateraloccipital 4414 3225 9870 2.765 0.696 0.134 0.032 55 5.9 lateralorbitofrontal 4642 3026 6149 1.936 0.565 0.122 0.031 50 6.1 lingual 2631 1841 5246 2.491 0.731 0.116 0.027 30 2.9 medialorbitofrontal 5819 4061 13330 2.809 0.571 0.116 0.023 59 5.6 middletemporal 1134 704 1871 2.447 0.632 0.078 0.015 6 0.6 parahippocampal 2514 1550 3856 2.396 0.508 0.109 0.025 19 2.6 paracentral 2311 1578 4857 2.867 0.454 0.114 0.022 19 2.0 parsopercularis 1249 865 3045 2.910 0.497 0.119 0.025 13 1.3 parsorbitalis 2532 1703 4736 2.522 0.461 0.115 0.022 23 2.3 parstriangularis 1865 1248 1913 1.729 0.598 0.112 0.025 12 1.8 pericalcarine 6987 4329 10589 2.219 0.670 0.099 0.020 50 5.8 postcentral 1817 1281 3412 2.453 0.629 0.124 0.024 19 1.9 posteriorcingulate 7623 4647 14600 2.843 0.669 0.102 0.023 54 7.4 precentral 5954 3965 10131 2.435 0.500 0.110 0.021 49 5.2 precuneus 1350 911 2652 2.606 0.663 0.122 0.023 15 1.4 rostralanteriorcingulate 5856 3995 11664 2.547 0.527 0.122 0.025 60 6.0 rostralmiddlefrontal 12553 8367 27070 2.902 0.571 0.113 0.023 108 12.1 superiorfrontal 6754 4432 11946 2.392 0.512 0.112 0.021 62 5.8 superiorparietal 6697 4493 15064 2.949 0.590 0.106 0.022 53 5.9 superiortemporal 5430 3713 10616 2.688 0.496 0.114 0.021 48 4.9 supramarginal 510 302 843 2.449 0.391 0.108 0.023 4 0.4 transversetemporal 3405 2237 6947 3.117 0.660 0.098 0.018 26 2.6 insula @#@FSTIME 2020:07:23:10:48:35 mris_anatomical_stats N 14 e 12.50 S 0.39 U 12.04 P 99% M 475108 F 0 R 289857 W 0 c 7 w 205 I 0 O 272 L 2.07 2.08 2.05 @#@FSLOADPOST 2020:07:23:10:48:48 mris_anatomical_stats N 14 2.06 2.08 2.05 #-------------------------------------------- #@# ASeg Stats Thu Jul 23 10:48:48 EDT 2020 /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert mri_segstats --seed 1234 --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /usr/local/freesurfer/dev/ASegStatsLUT.txt --subject bert setting seed for random number genererator to 1234 dev cwd cmdline mri_segstats --seed 1234 --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /usr/local/freesurfer/dev/ASegStatsLUT.txt --subject bert sysname Linux hostname nike machine x86_64 user ah221 whitesurfname white UseRobust 0 atlas_icv (eTIV) = 1518149 mm^3 (det: 1.283211 ) Computing euler number orig.nofix lheno = -30, rheno = -26 orig.nofix lhholes = 16, rhholes = 14 Loading mri/aseg.mgz Getting Brain Volume Statistics Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 50 segmentations Computing statistics for each segmentation Reporting on 45 segmentations Using PrintSegStat mri_segstats done @#@FSTIME 2020:07:23:10:48:48 mri_segstats N 32 e 150.10 S 0.39 U 149.70 P 100% M 287576 F 0 R 422414 W 0 c 58 w 103 I 0 O 24 L 2.06 2.08 2.05 @#@FSLOADPOST 2020:07:23:10:51:18 mri_segstats N 32 2.07 2.07 2.05 /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/label INFO: fsaverage subject does not exist in SUBJECTS_DIR INFO: Creating symlink to fsaverage subject... cd /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running; ln -s /usr/local/freesurfer/dev/subjects/fsaverage; cd - #-------------------------------------------- #@# BA_exvivo Labels lh Thu Jul 23 10:51:18 EDT 2020 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.BA1_exvivo.label --trgsubject bert --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.BA1_exvivo.label srcsubject = fsaverage trgsubject = bert trglabel = ./lh.BA1_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4129 nlabel points Performing mapping from target back to the source label 135579 Number of reverse mapping hits = 93 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.label 4222 mri_label2label: Done @#@FSTIME 2020:07:23:10:51:18 mri_label2label N 12 e 5.89 S 0.44 U 5.30 P 97% M 552372 F 0 R 310031 W 0 c 3 w 94 I 17624 O 264 L 2.07 2.07 2.05 @#@FSLOADPOST 2020:07:23:10:51:24 mri_label2label N 12 2.06 2.06 2.05 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.BA2_exvivo.label --trgsubject bert --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.BA2_exvivo.label srcsubject = fsaverage trgsubject = bert trglabel = ./lh.BA2_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 7909 nlabel points Performing mapping from target back to the source label 135579 Number of reverse mapping hits = 263 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.label 8172 mri_label2label: Done @#@FSTIME 2020:07:23:10:51:24 mri_label2label N 12 e 6.72 S 0.44 U 6.24 P 99% M 552644 F 0 R 342360 W 0 c 4 w 37 I 632 O 512 L 2.06 2.06 2.05 @#@FSLOADPOST 2020:07:23:10:51:31 mri_label2label N 12 2.05 2.06 2.05 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.BA3a_exvivo.label --trgsubject bert --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = bert trglabel = ./lh.BA3a_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4077 nlabel points Performing mapping from target back to the source label 135579 Number of reverse mapping hits = 28 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.label 4105 mri_label2label: Done @#@FSTIME 2020:07:23:10:51:31 mri_label2label N 12 e 6.16 S 0.69 U 5.43 P 99% M 552368 F 0 R 309919 W 0 c 37 w 31 I 320 O 232 L 2.05 2.06 2.05 @#@FSLOADPOST 2020:07:23:10:51:37 mri_label2label N 12 2.05 2.06 2.05 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.BA3b_exvivo.label --trgsubject bert --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = bert trglabel = ./lh.BA3b_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5983 nlabel points Performing mapping from target back to the source label 135579 Number of reverse mapping hits = 97 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.label 6080 mri_label2label: Done @#@FSTIME 2020:07:23:10:51:37 mri_label2label N 12 e 6.22 S 0.45 U 5.73 P 99% M 552504 F 0 R 310941 W 0 c 4 w 32 I 472 O 352 L 2.05 2.06 2.05 @#@FSLOADPOST 2020:07:23:10:51:43 mri_label2label N 12 2.12 2.08 2.05 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.BA4a_exvivo.label --trgsubject bert --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = bert trglabel = ./lh.BA4a_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5784 nlabel points Performing mapping from target back to the source label 135579 Number of reverse mapping hits = 202 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.label 5986 mri_label2label: Done @#@FSTIME 2020:07:23:10:51:43 mri_label2label N 12 e 6.19 S 0.47 U 5.68 P 99% M 552492 F 0 R 362033 W 0 c 4 w 34 I 456 O 376 L 2.12 2.08 2.05 @#@FSLOADPOST 2020:07:23:10:51:49 mri_label2label N 12 2.11 2.08 2.05 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.BA4p_exvivo.label --trgsubject bert --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = bert trglabel = ./lh.BA4p_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4070 nlabel points Performing mapping from target back to the source label 135579 Number of reverse mapping hits = 138 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.label 4208 mri_label2label: Done @#@FSTIME 2020:07:23:10:51:49 mri_label2label N 12 e 5.74 S 0.43 U 5.26 P 99% M 552368 F 0 R 316068 W 0 c 3 w 42 I 320 O 256 L 2.11 2.08 2.05 @#@FSLOADPOST 2020:07:23:10:51:55 mri_label2label N 12 2.10 2.07 2.05 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.BA6_exvivo.label --trgsubject bert --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.BA6_exvivo.label srcsubject = fsaverage trgsubject = bert trglabel = ./lh.BA6_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 13589 nlabel points Performing mapping from target back to the source label 135579 Number of reverse mapping hits = 332 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.label 13921 mri_label2label: Done @#@FSTIME 2020:07:23:10:51:55 mri_label2label N 12 e 8.04 S 0.46 U 7.53 P 99% M 553048 F 0 R 357572 W 0 c 4 w 40 I 1056 O 848 L 2.10 2.07 2.05 @#@FSLOADPOST 2020:07:23:10:52:03 mri_label2label N 12 2.09 2.07 2.05 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.BA44_exvivo.label --trgsubject bert --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.BA44_exvivo.label srcsubject = fsaverage trgsubject = bert trglabel = ./lh.BA44_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4181 nlabel points Performing mapping from target back to the source label 135579 Number of reverse mapping hits = 110 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.label 4291 mri_label2label: Done @#@FSTIME 2020:07:23:10:52:03 mri_label2label N 12 e 6.19 S 0.69 U 5.46 P 99% M 552380 F 0 R 309744 W 0 c 10 w 32 I 328 O 264 L 2.09 2.07 2.05 @#@FSLOADPOST 2020:07:23:10:52:09 mri_label2label N 12 2.08 2.07 2.05 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.BA45_exvivo.label --trgsubject bert --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.BA45_exvivo.label srcsubject = fsaverage trgsubject = bert trglabel = ./lh.BA45_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3422 nlabel points Performing mapping from target back to the source label 135579 Number of reverse mapping hits = 677 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.label 4099 mri_label2label: Done @#@FSTIME 2020:07:23:10:52:09 mri_label2label N 12 e 6.01 S 0.60 U 5.40 P 99% M 552348 F 0 R 307490 W 0 c 5 w 33 I 272 O 328 L 2.08 2.07 2.05 @#@FSLOADPOST 2020:07:23:10:52:15 mri_label2label N 12 2.07 2.07 2.05 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.V1_exvivo.label --trgsubject bert --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.V1_exvivo.label srcsubject = fsaverage trgsubject = bert trglabel = ./lh.V1_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4641 nlabel points Performing mapping from target back to the source label 135579 Number of reverse mapping hits = 1076 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.label 5717 mri_label2label: Done @#@FSTIME 2020:07:23:10:52:16 mri_label2label N 12 e 6.00 S 0.42 U 5.54 P 99% M 552440 F 0 R 313278 W 0 c 3 w 33 I 376 O 456 L 2.07 2.07 2.05 @#@FSLOADPOST 2020:07:23:10:52:22 mri_label2label N 12 2.06 2.07 2.05 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.V2_exvivo.label --trgsubject bert --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.V2_exvivo.label srcsubject = fsaverage trgsubject = bert trglabel = ./lh.V2_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 8114 nlabel points Performing mapping from target back to the source label 135579 Number of reverse mapping hits = 2720 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.label 10834 mri_label2label: Done @#@FSTIME 2020:07:23:10:52:22 mri_label2label N 12 e 7.08 S 0.47 U 6.57 P 99% M 552748 F 0 R 355014 W 0 c 3 w 49 I 664 O 880 L 2.06 2.07 2.05 @#@FSLOADPOST 2020:07:23:10:52:29 mri_label2label N 12 2.05 2.07 2.05 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.MT_exvivo.label --trgsubject bert --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.MT_exvivo.label srcsubject = fsaverage trgsubject = bert trglabel = ./lh.MT_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2018 nlabel points Performing mapping from target back to the source label 135579 Number of reverse mapping hits = 353 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.label 2371 mri_label2label: Done @#@FSTIME 2020:07:23:10:52:29 mri_label2label N 12 e 5.73 S 0.71 U 4.99 P 99% M 552248 F 0 R 315952 W 0 c 29 w 31 I 168 O 184 L 2.05 2.07 2.05 @#@FSLOADPOST 2020:07:23:10:52:34 mri_label2label N 12 1.97 2.05 2.04 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject bert --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = bert trglabel = ./lh.entorhinal_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 1290 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1290 nlabel points Performing mapping from target back to the source label 135579 Number of reverse mapping hits = 34 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.label 1324 mri_label2label: Done @#@FSTIME 2020:07:23:10:52:34 mri_label2label N 12 e 4.98 S 0.42 U 4.53 P 99% M 552164 F 0 R 311041 W 0 c 35 w 31 I 120 O 88 L 1.97 2.05 2.04 @#@FSLOADPOST 2020:07:23:10:52:39 mri_label2label N 12 1.97 2.05 2.04 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject bert --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = bert trglabel = ./lh.perirhinal_exvivo.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 1199 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1199 nlabel points Performing mapping from target back to the source label 135579 Number of reverse mapping hits = 25 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.label 1224 mri_label2label: Done @#@FSTIME 2020:07:23:10:52:40 mri_label2label N 12 e 5.29 S 0.67 U 4.60 P 99% M 552156 F 0 R 360084 W 0 c 31 w 29 I 112 O 80 L 1.97 2.05 2.04 @#@FSLOADPOST 2020:07:23:10:52:45 mri_label2label N 12 1.97 2.05 2.04 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.FG1.mpm.vpnl.label --trgsubject bert --trglabel ./lh.FG1.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.FG1.mpm.vpnl.label srcsubject = fsaverage trgsubject = bert trglabel = ./lh.FG1.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 414 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 414 nlabel points Performing mapping from target back to the source label 135579 Number of reverse mapping hits = 111 Checking for and removing duplicates Writing label file ./lh.FG1.mpm.vpnl.label 525 mri_label2label: Done @#@FSTIME 2020:07:23:10:52:45 mri_label2label N 12 e 4.71 S 0.42 U 4.26 P 99% M 552112 F 0 R 281327 W 0 c 4 w 28 I 40 O 48 L 1.97 2.05 2.04 @#@FSLOADPOST 2020:07:23:10:52:50 mri_label2label N 12 1.98 2.05 2.04 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.FG2.mpm.vpnl.label --trgsubject bert --trglabel ./lh.FG2.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.FG2.mpm.vpnl.label srcsubject = fsaverage trgsubject = bert trglabel = ./lh.FG2.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 703 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 703 nlabel points Performing mapping from target back to the source label 135579 Number of reverse mapping hits = 141 Checking for and removing duplicates Writing label file ./lh.FG2.mpm.vpnl.label 844 mri_label2label: Done @#@FSTIME 2020:07:23:10:52:50 mri_label2label N 12 e 4.79 S 0.43 U 4.33 P 99% M 552136 F 0 R 291865 W 0 c 5 w 30 I 72 O 72 L 1.98 2.05 2.04 @#@FSLOADPOST 2020:07:23:10:52:54 mri_label2label N 12 1.98 2.04 2.04 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.FG3.mpm.vpnl.label --trgsubject bert --trglabel ./lh.FG3.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.FG3.mpm.vpnl.label srcsubject = fsaverage trgsubject = bert trglabel = ./lh.FG3.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 1873 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1873 nlabel points Performing mapping from target back to the source label 135579 Number of reverse mapping hits = 122 Checking for and removing duplicates Writing label file ./lh.FG3.mpm.vpnl.label 1995 mri_label2label: Done @#@FSTIME 2020:07:23:10:52:54 mri_label2label N 12 e 5.22 S 0.44 U 4.70 P 98% M 552208 F 0 R 310542 W 0 c 3 w 41 I 176 O 152 L 1.98 2.04 2.04 @#@FSLOADPOST 2020:07:23:10:53:00 mri_label2label N 12 1.98 2.04 2.04 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.FG4.mpm.vpnl.label --trgsubject bert --trglabel ./lh.FG4.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.FG4.mpm.vpnl.label srcsubject = fsaverage trgsubject = bert trglabel = ./lh.FG4.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 2101 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2101 nlabel points Performing mapping from target back to the source label 135579 Number of reverse mapping hits = 377 Checking for and removing duplicates Writing label file ./lh.FG4.mpm.vpnl.label 2478 mri_label2label: Done @#@FSTIME 2020:07:23:10:53:00 mri_label2label N 12 e 5.28 S 0.44 U 4.81 P 99% M 552236 F 0 R 309919 W 0 c 6 w 33 I 200 O 208 L 1.98 2.04 2.04 @#@FSLOADPOST 2020:07:23:10:53:05 mri_label2label N 12 1.98 2.04 2.04 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.hOc1.mpm.vpnl.label --trgsubject bert --trglabel ./lh.hOc1.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.hOc1.mpm.vpnl.label srcsubject = fsaverage trgsubject = bert trglabel = ./lh.hOc1.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 3877 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3877 nlabel points Performing mapping from target back to the source label 135579 Number of reverse mapping hits = 822 Checking for and removing duplicates Writing label file ./lh.hOc1.mpm.vpnl.label 4699 mri_label2label: Done @#@FSTIME 2020:07:23:10:53:05 mri_label2label N 12 e 5.79 S 0.46 U 5.29 P 99% M 552384 F 0 R 312329 W 0 c 4 w 33 I 360 O 368 L 1.98 2.04 2.04 @#@FSLOADPOST 2020:07:23:10:53:11 mri_label2label N 12 1.98 2.04 2.04 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.hOc2.mpm.vpnl.label --trgsubject bert --trglabel ./lh.hOc2.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.hOc2.mpm.vpnl.label srcsubject = fsaverage trgsubject = bert trglabel = ./lh.hOc2.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 2919 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2919 nlabel points Performing mapping from target back to the source label 135579 Number of reverse mapping hits = 1136 Checking for and removing duplicates Writing label file ./lh.hOc2.mpm.vpnl.label 4055 mri_label2label: Done @#@FSTIME 2020:07:23:10:53:11 mri_label2label N 12 e 5.56 S 0.44 U 5.08 P 99% M 552340 F 0 R 315860 W 0 c 3 w 32 I 272 O 336 L 1.98 2.04 2.04 @#@FSLOADPOST 2020:07:23:10:53:17 mri_label2label N 12 1.98 2.04 2.04 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.hOc3v.mpm.vpnl.label --trgsubject bert --trglabel ./lh.hOc3v.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.hOc3v.mpm.vpnl.label srcsubject = fsaverage trgsubject = bert trglabel = ./lh.hOc3v.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 1286 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1286 nlabel points Performing mapping from target back to the source label 135579 Number of reverse mapping hits = 615 Checking for and removing duplicates Writing label file ./lh.hOc3v.mpm.vpnl.label 1901 mri_label2label: Done @#@FSTIME 2020:07:23:10:53:17 mri_label2label N 12 e 5.05 S 0.44 U 4.58 P 99% M 552196 F 0 R 359488 W 0 c 4 w 31 I 128 O 176 L 1.98 2.04 2.04 @#@FSLOADPOST 2020:07:23:10:53:22 mri_label2label N 12 1.99 2.04 2.04 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.hOc4v.mpm.vpnl.label --trgsubject bert --trglabel ./lh.hOc4v.mpm.vpnl.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.hOc4v.mpm.vpnl.label srcsubject = fsaverage trgsubject = bert trglabel = ./lh.hOc4v.mpm.vpnl.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 1006 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1006 nlabel points Performing mapping from target back to the source label 135579 Number of reverse mapping hits = 350 Checking for and removing duplicates Writing label file ./lh.hOc4v.mpm.vpnl.label 1356 mri_label2label: Done @#@FSTIME 2020:07:23:10:53:22 mri_label2label N 12 e 4.94 S 0.43 U 4.49 P 99% M 552156 F 0 R 306141 W 0 c 3 w 34 I 96 O 120 L 1.99 2.04 2.04 @#@FSLOADPOST 2020:07:23:10:53:27 mri_label2label N 12 1.99 2.04 2.04 mris_label2annot --s bert --ctab /usr/local/freesurfer/dev/average/colortable_vpnl.txt --hemi lh --a mpm.vpnl --maxstatwinner --noverbose --l lh.FG1.mpm.vpnl.label --l lh.FG2.mpm.vpnl.label --l lh.FG3.mpm.vpnl.label --l lh.FG4.mpm.vpnl.label --l lh.hOc1.mpm.vpnl.label --l lh.hOc2.mpm.vpnl.label --l lh.hOc3v.mpm.vpnl.label --l lh.hOc4v.mpm.vpnl.label Reading ctab /usr/local/freesurfer/dev/average/colortable_vpnl.txt Number of ctab entries 9 dev cwd /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/label cmdline mris_label2annot --s bert --ctab /usr/local/freesurfer/dev/average/colortable_vpnl.txt --hemi lh --a mpm.vpnl --maxstatwinner --noverbose --l lh.FG1.mpm.vpnl.label --l lh.FG2.mpm.vpnl.label --l lh.FG3.mpm.vpnl.label --l lh.FG4.mpm.vpnl.label --l lh.hOc1.mpm.vpnl.label --l lh.hOc2.mpm.vpnl.label --l lh.hOc3v.mpm.vpnl.label --l lh.hOc4v.mpm.vpnl.label sysname Linux hostname nike machine x86_64 user ah221 subject bert hemi lh SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running ColorTable /usr/local/freesurfer/dev/average/colortable_vpnl.txt AnnotName mpm.vpnl nlables 8 LabelThresh 0 0.000000 Loading /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.orig 1 1376057 FG1 2 16711935 FG2 3 16711680 FG3 4 1705837 FG4 5 25600 hOc1 6 255 hOc2 7 16776960 hOc3v 8 65535 hOc4v Mapping unhit to unknown Found 119178 unhit vertices Writing annot to /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/label/lh.mpm.vpnl.annot @#@FSTIME 2020:07:23:10:53:27 mris_label2annot N 26 e 0.82 S 0.11 U 0.67 P 96% M 153788 F 0 R 47002 W 0 c 2 w 155 I 8 O 2120 L 1.99 2.04 2.04 @#@FSLOADPOST 2020:07:23:10:53:27 mris_label2annot N 26 1.99 2.04 2.04 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject bert --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert trglabel = ./lh.BA1_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 1014 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1014 nlabel points Performing mapping from target back to the source label 135579 Number of reverse mapping hits = 22 Checking for and removing duplicates Writing label file ./lh.BA1_exvivo.thresh.label 1036 mri_label2label: Done @#@FSTIME 2020:07:23:10:53:28 mri_label2label N 12 e 5.54 S 0.70 U 4.81 P 99% M 552156 F 0 R 308398 W 0 c 6 w 34 I 96 O 72 L 1.99 2.04 2.04 @#@FSLOADPOST 2020:07:23:10:53:33 mri_label2label N 12 1.99 2.04 2.04 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject bert --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert trglabel = ./lh.BA2_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 2092 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2092 nlabel points Performing mapping from target back to the source label 135579 Number of reverse mapping hits = 47 Checking for and removing duplicates Writing label file ./lh.BA2_exvivo.thresh.label 2139 mri_label2label: Done @#@FSTIME 2020:07:23:10:53:33 mri_label2label N 12 e 5.19 S 0.45 U 4.72 P 99% M 552228 F 0 R 314181 W 0 c 36 w 31 I 192 O 136 L 1.99 2.04 2.04 @#@FSLOADPOST 2020:07:23:10:53:38 mri_label2label N 12 1.99 2.04 2.04 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject bert --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert trglabel = ./lh.BA3a_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 1504 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1504 nlabel points Performing mapping from target back to the source label 135579 Number of reverse mapping hits = 7 Checking for and removing duplicates Writing label file ./lh.BA3a_exvivo.thresh.label 1511 mri_label2label: Done @#@FSTIME 2020:07:23:10:53:38 mri_label2label N 12 e 5.43 S 0.71 U 4.67 P 99% M 552188 F 0 R 316014 W 0 c 20 w 29 I 136 O 88 L 1.99 2.04 2.04 @#@FSLOADPOST 2020:07:23:10:53:44 mri_label2label N 12 2.07 2.06 2.05 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject bert --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert trglabel = ./lh.BA3b_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 1996 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1996 nlabel points Performing mapping from target back to the source label 135579 Number of reverse mapping hits = 32 Checking for and removing duplicates Writing label file ./lh.BA3b_exvivo.thresh.label 2028 mri_label2label: Done @#@FSTIME 2020:07:23:10:53:44 mri_label2label N 12 e 5.24 S 0.45 U 4.73 P 98% M 552216 F 0 R 309970 W 0 c 4 w 31 I 184 O 128 L 2.07 2.06 2.05 @#@FSLOADPOST 2020:07:23:10:53:49 mri_label2label N 12 2.06 2.06 2.05 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject bert --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert trglabel = ./lh.BA4a_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 2319 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2319 nlabel points Performing mapping from target back to the source label 135579 Number of reverse mapping hits = 118 Checking for and removing duplicates Writing label file ./lh.BA4a_exvivo.thresh.label 2437 mri_label2label: Done @#@FSTIME 2020:07:23:10:53:49 mri_label2label N 12 e 5.26 S 0.43 U 4.81 P 99% M 552248 F 0 R 358673 W 0 c 4 w 32 I 208 O 168 L 2.06 2.06 2.05 @#@FSLOADPOST 2020:07:23:10:53:54 mri_label2label N 12 2.06 2.05 2.05 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject bert --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert trglabel = ./lh.BA4p_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 1549 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1549 nlabel points Performing mapping from target back to the source label 135579 Number of reverse mapping hits = 31 Checking for and removing duplicates Writing label file ./lh.BA4p_exvivo.thresh.label 1580 mri_label2label: Done @#@FSTIME 2020:07:23:10:53:54 mri_label2label N 12 e 5.08 S 0.40 U 4.66 P 99% M 552168 F 0 R 309762 W 0 c 6 w 32 I 144 O 96 L 2.06 2.05 2.05 @#@FSLOADPOST 2020:07:23:10:54:00 mri_label2label N 12 2.05 2.05 2.05 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject bert --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert trglabel = ./lh.BA6_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 7035 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 7035 nlabel points Performing mapping from target back to the source label 135579 Number of reverse mapping hits = 116 Checking for and removing duplicates Writing label file ./lh.BA6_exvivo.thresh.label 7151 mri_label2label: Done @#@FSTIME 2020:07:23:10:54:00 mri_label2label N 12 e 6.48 S 0.47 U 5.96 P 99% M 552576 F 0 R 326149 W 0 c 4 w 47 I 616 O 424 L 2.05 2.05 2.05 @#@FSLOADPOST 2020:07:23:10:54:06 mri_label2label N 12 2.05 2.05 2.05 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject bert --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert trglabel = ./lh.BA44_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 1912 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1912 nlabel points Performing mapping from target back to the source label 135579 Number of reverse mapping hits = 41 Checking for and removing duplicates Writing label file ./lh.BA44_exvivo.thresh.label 1953 mri_label2label: Done @#@FSTIME 2020:07:23:10:54:06 mri_label2label N 12 e 5.57 S 0.71 U 4.84 P 99% M 552224 F 0 R 315582 W 0 c 20 w 29 I 168 O 120 L 2.05 2.05 2.05 @#@FSLOADPOST 2020:07:23:10:54:12 mri_label2label N 12 2.05 2.05 2.05 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject bert --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert trglabel = ./lh.BA45_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 1151 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1151 nlabel points Performing mapping from target back to the source label 135579 Number of reverse mapping hits = 280 Checking for and removing duplicates Writing label file ./lh.BA45_exvivo.thresh.label 1431 mri_label2label: Done @#@FSTIME 2020:07:23:10:54:12 mri_label2label N 12 e 5.17 S 0.56 U 4.58 P 99% M 552172 F 0 R 310042 W 0 c 10 w 30 I 104 O 120 L 2.05 2.05 2.05 @#@FSLOADPOST 2020:07:23:10:54:17 mri_label2label N 12 2.04 2.05 2.05 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject bert --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert trglabel = ./lh.V1_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 3405 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3405 nlabel points Performing mapping from target back to the source label 135579 Number of reverse mapping hits = 679 Checking for and removing duplicates Writing label file ./lh.V1_exvivo.thresh.label 4084 mri_label2label: Done @#@FSTIME 2020:07:23:10:54:17 mri_label2label N 12 e 6.16 S 0.64 U 5.49 P 99% M 552352 F 0 R 307701 W 0 c 13 w 31 I 304 O 328 L 2.04 2.05 2.05 @#@FSLOADPOST 2020:07:23:10:54:23 mri_label2label N 12 2.04 2.05 2.05 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject bert --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert trglabel = ./lh.V2_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 3334 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3334 nlabel points Performing mapping from target back to the source label 135579 Number of reverse mapping hits = 1225 Checking for and removing duplicates Writing label file ./lh.V2_exvivo.thresh.label 4559 mri_label2label: Done @#@FSTIME 2020:07:23:10:54:23 mri_label2label N 12 e 6.20 S 0.67 U 5.49 P 99% M 552360 F 0 R 309892 W 0 c 6 w 37 I 296 O 376 L 2.04 2.05 2.05 @#@FSLOADPOST 2020:07:23:10:54:29 mri_label2label N 12 2.03 2.05 2.05 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject bert --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert trglabel = ./lh.MT_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 513 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 513 nlabel points Performing mapping from target back to the source label 135579 Number of reverse mapping hits = 85 Checking for and removing duplicates Writing label file ./lh.MT_exvivo.thresh.label 598 mri_label2label: Done @#@FSTIME 2020:07:23:10:54:29 mri_label2label N 12 e 4.72 S 0.43 U 4.27 P 99% M 552136 F 0 R 281838 W 0 c 3 w 33 I 48 O 48 L 2.03 2.05 2.05 @#@FSLOADPOST 2020:07:23:10:54:34 mri_label2label N 12 2.03 2.05 2.05 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject bert --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert trglabel = ./lh.entorhinal_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 470 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 470 nlabel points Performing mapping from target back to the source label 135579 Number of reverse mapping hits = 10 Checking for and removing duplicates Writing label file ./lh.entorhinal_exvivo.thresh.label 480 mri_label2label: Done @#@FSTIME 2020:07:23:10:54:34 mri_label2label N 12 e 4.69 S 0.40 U 4.26 P 99% M 552112 F 0 R 283666 W 0 c 35 w 34 I 48 O 32 L 2.03 2.05 2.05 @#@FSLOADPOST 2020:07:23:10:54:39 mri_label2label N 12 2.03 2.05 2.05 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject bert --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/lh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert trglabel = ./lh.perirhinal_exvivo.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 450 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 450 nlabel points Performing mapping from target back to the source label 135579 Number of reverse mapping hits = 8 Checking for and removing duplicates Writing label file ./lh.perirhinal_exvivo.thresh.label 458 mri_label2label: Done @#@FSTIME 2020:07:23:10:54:39 mri_label2label N 12 e 4.75 S 0.43 U 4.26 P 98% M 552120 F 0 R 282273 W 0 c 5 w 27 I 48 O 32 L 2.03 2.05 2.05 @#@FSLOADPOST 2020:07:23:10:54:44 mri_label2label N 12 2.11 2.06 2.05 mris_label2annot --s bert --hemi lh --ctab /usr/local/freesurfer/dev/average/colortable_BA.txt --l lh.BA1_exvivo.label --l lh.BA2_exvivo.label --l lh.BA3a_exvivo.label --l lh.BA3b_exvivo.label --l lh.BA4a_exvivo.label --l lh.BA4p_exvivo.label --l lh.BA6_exvivo.label --l lh.BA44_exvivo.label --l lh.BA45_exvivo.label --l lh.V1_exvivo.label --l lh.V2_exvivo.label --l lh.MT_exvivo.label --l lh.perirhinal_exvivo.label --l lh.entorhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose Reading ctab /usr/local/freesurfer/dev/average/colortable_BA.txt Number of ctab entries 15 dev cwd /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/label cmdline mris_label2annot --s bert --hemi lh --ctab /usr/local/freesurfer/dev/average/colortable_BA.txt --l lh.BA1_exvivo.label --l lh.BA2_exvivo.label --l lh.BA3a_exvivo.label --l lh.BA3b_exvivo.label --l lh.BA4a_exvivo.label --l lh.BA4p_exvivo.label --l lh.BA6_exvivo.label --l lh.BA44_exvivo.label --l lh.BA45_exvivo.label --l lh.V1_exvivo.label --l lh.V2_exvivo.label --l lh.MT_exvivo.label --l lh.perirhinal_exvivo.label --l lh.entorhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose sysname Linux hostname nike machine x86_64 user ah221 subject bert hemi lh SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running ColorTable /usr/local/freesurfer/dev/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 94371 unhit vertices Writing annot to /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/label/lh.BA_exvivo.annot @#@FSTIME 2020:07:23:10:54:44 mris_label2annot N 38 e 0.85 S 0.12 U 0.70 P 96% M 154132 F 0 R 47205 W 0 c 2 w 227 I 8 O 2120 L 2.11 2.06 2.05 @#@FSLOADPOST 2020:07:23:10:54:45 mris_label2annot N 38 2.11 2.06 2.05 mris_label2annot --s bert --hemi lh --ctab /usr/local/freesurfer/dev/average/colortable_BA.txt --l lh.BA1_exvivo.thresh.label --l lh.BA2_exvivo.thresh.label --l lh.BA3a_exvivo.thresh.label --l lh.BA3b_exvivo.thresh.label --l lh.BA4a_exvivo.thresh.label --l lh.BA4p_exvivo.thresh.label --l lh.BA6_exvivo.thresh.label --l lh.BA44_exvivo.thresh.label --l lh.BA45_exvivo.thresh.label --l lh.V1_exvivo.thresh.label --l lh.V2_exvivo.thresh.label --l lh.MT_exvivo.thresh.label --l lh.perirhinal_exvivo.thresh.label --l lh.entorhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose Reading ctab /usr/local/freesurfer/dev/average/colortable_BA.txt Number of ctab entries 15 dev cwd /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/label cmdline mris_label2annot --s bert --hemi lh --ctab /usr/local/freesurfer/dev/average/colortable_BA.txt --l lh.BA1_exvivo.thresh.label --l lh.BA2_exvivo.thresh.label --l lh.BA3a_exvivo.thresh.label --l lh.BA3b_exvivo.thresh.label --l lh.BA4a_exvivo.thresh.label --l lh.BA4p_exvivo.thresh.label --l lh.BA6_exvivo.thresh.label --l lh.BA44_exvivo.thresh.label --l lh.BA45_exvivo.thresh.label --l lh.V1_exvivo.thresh.label --l lh.V2_exvivo.thresh.label --l lh.MT_exvivo.thresh.label --l lh.perirhinal_exvivo.thresh.label --l lh.entorhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose sysname Linux hostname nike machine x86_64 user ah221 subject bert hemi lh SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running ColorTable /usr/local/freesurfer/dev/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 111567 unhit vertices Writing annot to /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/label/lh.BA_exvivo.thresh.annot @#@FSTIME 2020:07:23:10:54:45 mris_label2annot N 38 e 0.79 S 0.11 U 0.65 P 96% M 153772 F 0 R 47114 W 0 c 3 w 191 I 0 O 2120 L 2.11 2.06 2.05 @#@FSLOADPOST 2020:07:23:10:54:46 mris_label2annot N 38 2.11 2.06 2.05 mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.stats -b -a ./lh.BA_exvivo.annot -c ./BA_exvivo.ctab bert lh white computing statistics for each annotation in ./lh.BA_exvivo.annot. reading volume /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/wm.mgz... reading input surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.white... reading input pial surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.pial... reading input white surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 243626 Total vertex volume 243384 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /usr/local/freesurfer/dev/average/colortable_BA.txt) Saving annotation colortable ./BA_exvivo.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1518149 mm^3 (det: 1.283211 ) 1121 591 1986 2.456 0.544 0.106 0.031 11 1.2 BA1_exvivo 4107 2664 6183 2.294 0.526 0.104 0.021 30 3.6 BA2_exvivo 1047 716 1021 1.896 0.428 0.125 0.025 7 1.1 BA3a_exvivo 2258 1442 3183 1.982 0.653 0.093 0.019 15 1.9 BA3b_exvivo 1760 1099 2966 2.478 0.818 0.103 0.024 10 2.0 BA4a_exvivo 1409 869 2258 2.787 0.665 0.093 0.023 6 1.4 BA4p_exvivo 8652 5374 19426 3.082 0.596 0.102 0.021 61 7.3 BA6_exvivo 2144 1446 4681 2.875 0.491 0.116 0.021 19 2.0 BA44_exvivo 3293 2296 7096 2.734 0.515 0.124 0.024 35 3.4 BA45_exvivo 3506 2328 3545 1.546 0.461 0.126 0.032 36 4.6 V1_exvivo 8697 5809 11604 1.911 0.557 0.135 0.034 99 12.5 V2_exvivo 2008 1362 3442 2.531 0.421 0.128 0.024 21 2.0 MT_exvivo 635 411 1048 2.593 0.618 0.086 0.016 3 0.3 perirhinal_exvivo 571 375 1448 2.722 0.963 0.086 0.022 3 0.5 entorhinal_exvivo @#@FSTIME 2020:07:23:10:54:46 mris_anatomical_stats N 12 e 5.36 S 0.42 U 4.90 P 99% M 470028 F 0 R 269683 W 0 c 6 w 152 I 0 O 136 L 2.11 2.06 2.05 @#@FSLOADPOST 2020:07:23:10:54:51 mris_anatomical_stats N 12 2.10 2.06 2.05 mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.thresh.stats -b -a ./lh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab bert lh white computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot. reading volume /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/wm.mgz... reading input surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.white... reading input pial surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.pial... reading input white surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/lh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 243626 Total vertex volume 243384 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /usr/local/freesurfer/dev/average/colortable_BA.txt) Saving annotation colortable ./BA_exvivo.thresh.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1518149 mm^3 (det: 1.283211 ) 689 346 1220 2.499 0.558 0.111 0.035 8 0.9 BA1_exvivo 1512 931 2229 2.246 0.522 0.085 0.015 7 1.0 BA2_exvivo 882 596 801 1.840 0.356 0.128 0.027 6 1.0 BA3a_exvivo 1365 858 1476 1.661 0.445 0.070 0.012 4 0.7 BA3b_exvivo 1768 1074 2881 2.583 0.833 0.096 0.023 8 1.8 BA4a_exvivo 1080 706 1650 2.602 0.634 0.101 0.025 5 1.3 BA4p_exvivo 4802 2829 10485 3.108 0.631 0.096 0.021 31 4.0 BA6_exvivo 1390 947 2967 2.824 0.470 0.117 0.021 13 1.2 BA44_exvivo 1332 926 3076 2.848 0.473 0.125 0.023 14 1.2 BA45_exvivo 3729 2469 3779 1.536 0.450 0.122 0.031 37 4.7 V1_exvivo 4330 2885 5379 1.808 0.522 0.141 0.037 55 6.9 V2_exvivo 527 372 1166 2.660 0.472 0.138 0.028 7 0.7 MT_exvivo 251 167 479 2.858 0.493 0.073 0.011 1 0.1 perirhinal_exvivo 355 229 928 2.871 0.706 0.076 0.016 1 0.3 entorhinal_exvivo @#@FSTIME 2020:07:23:10:54:51 mris_anatomical_stats N 12 e 4.95 S 0.36 U 4.56 P 99% M 470028 F 0 R 240685 W 0 c 3 w 135 I 0 O 136 L 2.10 2.06 2.05 @#@FSLOADPOST 2020:07:23:10:54:56 mris_anatomical_stats N 12 2.09 2.06 2.05 #-------------------------------------------- #@# BA_exvivo Labels rh Thu Jul 23 10:54:56 EDT 2020 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.BA1_exvivo.label --trgsubject bert --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.BA1_exvivo.label srcsubject = fsaverage trgsubject = bert trglabel = ./rh.BA1_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3962 nlabel points Performing mapping from target back to the source label 135771 Number of reverse mapping hits = 181 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.label 4143 mri_label2label: Done @#@FSTIME 2020:07:23:10:54:56 mri_label2label N 12 e 5.87 S 0.46 U 5.28 P 97% M 552788 F 0 R 310289 W 0 c 4 w 54 I 17600 O 264 L 2.09 2.06 2.05 @#@FSLOADPOST 2020:07:23:10:55:02 mri_label2label N 12 2.08 2.06 2.05 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.BA2_exvivo.label --trgsubject bert --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.BA2_exvivo.label srcsubject = fsaverage trgsubject = bert trglabel = ./rh.BA2_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6687 nlabel points Performing mapping from target back to the source label 135771 Number of reverse mapping hits = 256 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.label 6943 mri_label2label: Done @#@FSTIME 2020:07:23:10:55:02 mri_label2label N 12 e 6.39 S 0.44 U 5.90 P 99% M 552980 F 0 R 312982 W 0 c 42 w 49 I 520 O 432 L 2.08 2.06 2.05 @#@FSLOADPOST 2020:07:23:10:55:08 mri_label2label N 12 2.07 2.06 2.05 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.BA3a_exvivo.label --trgsubject bert --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.BA3a_exvivo.label srcsubject = fsaverage trgsubject = bert trglabel = ./rh.BA3a_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3980 nlabel points Performing mapping from target back to the source label 135771 Number of reverse mapping hits = 29 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.label 4009 mri_label2label: Done @#@FSTIME 2020:07:23:10:55:08 mri_label2label N 12 e 5.71 S 0.42 U 5.26 P 99% M 552780 F 0 R 310378 W 0 c 4 w 39 I 312 O 216 L 2.07 2.06 2.05 @#@FSLOADPOST 2020:07:23:10:55:14 mri_label2label N 12 2.06 2.06 2.05 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.BA3b_exvivo.label --trgsubject bert --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.BA3b_exvivo.label srcsubject = fsaverage trgsubject = bert trglabel = ./rh.BA3b_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4522 nlabel points Performing mapping from target back to the source label 135771 Number of reverse mapping hits = 138 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.label 4660 mri_label2label: Done @#@FSTIME 2020:07:23:10:55:14 mri_label2label N 12 e 5.89 S 0.46 U 5.39 P 99% M 552828 F 0 R 362786 W 0 c 2 w 33 I 352 O 280 L 2.06 2.06 2.05 @#@FSLOADPOST 2020:07:23:10:55:20 mri_label2label N 12 2.06 2.05 2.05 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.BA4a_exvivo.label --trgsubject bert --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.BA4a_exvivo.label srcsubject = fsaverage trgsubject = bert trglabel = ./rh.BA4a_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5747 nlabel points Performing mapping from target back to the source label 135771 Number of reverse mapping hits = 269 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.label 6016 mri_label2label: Done @#@FSTIME 2020:07:23:10:55:20 mri_label2label N 12 e 6.17 S 0.47 U 5.66 P 99% M 552916 F 0 R 362906 W 0 c 3 w 35 I 440 O 376 L 2.06 2.05 2.05 @#@FSLOADPOST 2020:07:23:10:55:26 mri_label2label N 12 2.05 2.05 2.05 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.BA4p_exvivo.label --trgsubject bert --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.BA4p_exvivo.label srcsubject = fsaverage trgsubject = bert trglabel = ./rh.BA4p_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4473 nlabel points Performing mapping from target back to the source label 135771 Number of reverse mapping hits = 153 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.label 4626 mri_label2label: Done @#@FSTIME 2020:07:23:10:55:26 mri_label2label N 12 e 5.86 S 0.41 U 5.40 P 99% M 552824 F 0 R 315706 W 0 c 2 w 35 I 344 O 272 L 2.05 2.05 2.05 @#@FSLOADPOST 2020:07:23:10:55:32 mri_label2label N 12 2.05 2.05 2.05 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.BA6_exvivo.label --trgsubject bert --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.BA6_exvivo.label srcsubject = fsaverage trgsubject = bert trglabel = ./rh.BA6_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 12256 nlabel points Performing mapping from target back to the source label 135771 Number of reverse mapping hits = 485 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.label 12741 mri_label2label: Done @#@FSTIME 2020:07:23:10:55:32 mri_label2label N 12 e 7.77 S 0.44 U 7.28 P 99% M 553384 F 0 R 354189 W 0 c 57 w 62 I 936 O 728 L 2.05 2.05 2.05 @#@FSLOADPOST 2020:07:23:10:55:40 mri_label2label N 12 2.04 2.05 2.05 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.BA44_exvivo.label --trgsubject bert --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.BA44_exvivo.label srcsubject = fsaverage trgsubject = bert trglabel = ./rh.BA44_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6912 nlabel points Performing mapping from target back to the source label 135771 Number of reverse mapping hits = 617 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.label 7529 mri_label2label: Done @#@FSTIME 2020:07:23:10:55:40 mri_label2label N 12 e 6.46 S 0.45 U 5.97 P 99% M 553012 F 0 R 361116 W 0 c 44 w 57 I 528 O 512 L 2.04 2.05 2.05 @#@FSLOADPOST 2020:07:23:10:55:47 mri_label2label N 12 2.04 2.05 2.05 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.BA45_exvivo.label --trgsubject bert --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.BA45_exvivo.label srcsubject = fsaverage trgsubject = bert trglabel = ./rh.BA45_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5355 nlabel points Performing mapping from target back to the source label 135771 Number of reverse mapping hits = 853 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.label 6208 mri_label2label: Done @#@FSTIME 2020:07:23:10:55:47 mri_label2label N 12 e 6.07 S 0.43 U 5.63 P 99% M 552916 F 0 R 361578 W 0 c 40 w 39 I 416 O 472 L 2.04 2.05 2.05 @#@FSLOADPOST 2020:07:23:10:55:53 mri_label2label N 12 2.04 2.05 2.05 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.V1_exvivo.label --trgsubject bert --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.V1_exvivo.label srcsubject = fsaverage trgsubject = bert trglabel = ./rh.V1_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4727 nlabel points Performing mapping from target back to the source label 135771 Number of reverse mapping hits = 1135 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.label 5862 mri_label2label: Done @#@FSTIME 2020:07:23:10:55:53 mri_label2label N 12 e 6.02 S 0.44 U 5.57 P 99% M 552880 F 0 R 311645 W 0 c 4 w 36 I 376 O 456 L 2.04 2.05 2.05 @#@FSLOADPOST 2020:07:23:10:55:59 mri_label2label N 12 2.03 2.05 2.05 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.V2_exvivo.label --trgsubject bert --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.V2_exvivo.label srcsubject = fsaverage trgsubject = bert trglabel = ./rh.V2_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 8016 nlabel points Performing mapping from target back to the source label 135771 Number of reverse mapping hits = 2587 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.label 10603 mri_label2label: Done @#@FSTIME 2020:07:23:10:55:59 mri_label2label N 12 e 7.02 S 0.47 U 6.52 P 99% M 553160 F 0 R 359064 W 0 c 4 w 41 I 640 O 840 L 2.03 2.05 2.05 @#@FSLOADPOST 2020:07:23:10:56:06 mri_label2label N 12 2.03 2.05 2.05 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.MT_exvivo.label --trgsubject bert --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.MT_exvivo.label srcsubject = fsaverage trgsubject = bert trglabel = ./rh.MT_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1932 nlabel points Performing mapping from target back to the source label 135771 Number of reverse mapping hits = 248 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.label 2180 mri_label2label: Done @#@FSTIME 2020:07:23:10:56:06 mri_label2label N 12 e 5.21 S 0.46 U 4.71 P 99% M 552640 F 0 R 359173 W 0 c 3 w 36 I 160 O 160 L 2.03 2.05 2.05 @#@FSLOADPOST 2020:07:23:10:56:11 mri_label2label N 12 2.03 2.04 2.05 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject bert --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.entorhinal_exvivo.label srcsubject = fsaverage trgsubject = bert trglabel = ./rh.entorhinal_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 1038 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1038 nlabel points Performing mapping from target back to the source label 135771 Number of reverse mapping hits = 26 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.label 1064 mri_label2label: Done @#@FSTIME 2020:07:23:10:56:11 mri_label2label N 12 e 4.90 S 0.43 U 4.44 P 99% M 552556 F 0 R 360351 W 0 c 3 w 36 I 96 O 72 L 2.03 2.04 2.05 @#@FSLOADPOST 2020:07:23:10:56:16 mri_label2label N 12 2.02 2.04 2.05 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject bert --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.perirhinal_exvivo.label srcsubject = fsaverage trgsubject = bert trglabel = ./rh.perirhinal_exvivo.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 752 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 752 nlabel points Performing mapping from target back to the source label 135771 Number of reverse mapping hits = 22 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.label 774 mri_label2label: Done @#@FSTIME 2020:07:23:10:56:16 mri_label2label N 12 e 4.79 S 0.42 U 4.35 P 99% M 552528 F 0 R 288134 W 0 c 33 w 30 I 72 O 56 L 2.02 2.04 2.05 @#@FSLOADPOST 2020:07:23:10:56:21 mri_label2label N 12 2.02 2.04 2.05 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.FG1.mpm.vpnl.label --trgsubject bert --trglabel ./rh.FG1.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.FG1.mpm.vpnl.label srcsubject = fsaverage trgsubject = bert trglabel = ./rh.FG1.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 541 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 541 nlabel points Performing mapping from target back to the source label 135771 Number of reverse mapping hits = 212 Checking for and removing duplicates Writing label file ./rh.FG1.mpm.vpnl.label 753 mri_label2label: Done @#@FSTIME 2020:07:23:10:56:21 mri_label2label N 12 e 4.77 S 0.40 U 4.34 P 99% M 552508 F 0 R 281102 W 0 c 3 w 30 I 56 O 72 L 2.02 2.04 2.05 @#@FSLOADPOST 2020:07:23:10:56:26 mri_label2label N 12 2.02 2.04 2.05 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.FG2.mpm.vpnl.label --trgsubject bert --trglabel ./rh.FG2.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.FG2.mpm.vpnl.label srcsubject = fsaverage trgsubject = bert trglabel = ./rh.FG2.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 721 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 721 nlabel points Performing mapping from target back to the source label 135771 Number of reverse mapping hits = 215 Checking for and removing duplicates Writing label file ./rh.FG2.mpm.vpnl.label 936 mri_label2label: Done @#@FSTIME 2020:07:23:10:56:26 mri_label2label N 12 e 4.82 S 0.41 U 4.38 P 99% M 552532 F 0 R 282242 W 0 c 6 w 41 I 72 O 80 L 2.02 2.04 2.05 @#@FSLOADPOST 2020:07:23:10:56:31 mri_label2label N 12 2.02 2.04 2.05 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.FG3.mpm.vpnl.label --trgsubject bert --trglabel ./rh.FG3.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.FG3.mpm.vpnl.label srcsubject = fsaverage trgsubject = bert trglabel = ./rh.FG3.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 1523 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1523 nlabel points Performing mapping from target back to the source label 135771 Number of reverse mapping hits = 248 Checking for and removing duplicates Writing label file ./rh.FG3.mpm.vpnl.label 1771 mri_label2label: Done @#@FSTIME 2020:07:23:10:56:31 mri_label2label N 12 e 5.09 S 0.43 U 4.63 P 99% M 552600 F 0 R 309955 W 0 c 2 w 32 I 144 O 144 L 2.02 2.04 2.05 @#@FSLOADPOST 2020:07:23:10:56:36 mri_label2label N 12 2.02 2.04 2.05 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.FG4.mpm.vpnl.label --trgsubject bert --trglabel ./rh.FG4.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.FG4.mpm.vpnl.label srcsubject = fsaverage trgsubject = bert trglabel = ./rh.FG4.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 1586 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1586 nlabel points Performing mapping from target back to the source label 135771 Number of reverse mapping hits = 161 Checking for and removing duplicates Writing label file ./rh.FG4.mpm.vpnl.label 1747 mri_label2label: Done @#@FSTIME 2020:07:23:10:56:36 mri_label2label N 12 e 5.08 S 0.46 U 4.60 P 99% M 552608 F 0 R 359376 W 0 c 2 w 37 I 152 O 128 L 2.02 2.04 2.05 @#@FSLOADPOST 2020:07:23:10:56:41 mri_label2label N 12 2.02 2.04 2.05 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.hOc1.mpm.vpnl.label --trgsubject bert --trglabel ./rh.hOc1.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.hOc1.mpm.vpnl.label srcsubject = fsaverage trgsubject = bert trglabel = ./rh.hOc1.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 3667 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3667 nlabel points Performing mapping from target back to the source label 135771 Number of reverse mapping hits = 768 Checking for and removing duplicates Writing label file ./rh.hOc1.mpm.vpnl.label 4435 mri_label2label: Done @#@FSTIME 2020:07:23:10:56:41 mri_label2label N 12 e 5.72 S 0.43 U 5.27 P 99% M 552792 F 0 R 364260 W 0 c 3 w 33 I 328 O 344 L 2.02 2.04 2.05 @#@FSLOADPOST 2020:07:23:10:56:47 mri_label2label N 12 2.01 2.04 2.05 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.hOc2.mpm.vpnl.label --trgsubject bert --trglabel ./rh.hOc2.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.hOc2.mpm.vpnl.label srcsubject = fsaverage trgsubject = bert trglabel = ./rh.hOc2.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 2719 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2719 nlabel points Performing mapping from target back to the source label 135771 Number of reverse mapping hits = 840 Checking for and removing duplicates Writing label file ./rh.hOc2.mpm.vpnl.label 3559 mri_label2label: Done @#@FSTIME 2020:07:23:10:56:47 mri_label2label N 12 e 5.47 S 0.46 U 5.00 P 99% M 552712 F 0 R 365935 W 0 c 3 w 40 I 248 O 288 L 2.01 2.04 2.05 @#@FSLOADPOST 2020:07:23:10:56:52 mri_label2label N 12 2.01 2.04 2.05 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.hOc3v.mpm.vpnl.label --trgsubject bert --trglabel ./rh.hOc3v.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.hOc3v.mpm.vpnl.label srcsubject = fsaverage trgsubject = bert trglabel = ./rh.hOc3v.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 1228 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1228 nlabel points Performing mapping from target back to the source label 135771 Number of reverse mapping hits = 573 Checking for and removing duplicates Writing label file ./rh.hOc3v.mpm.vpnl.label 1801 mri_label2label: Done @#@FSTIME 2020:07:23:10:56:52 mri_label2label N 12 e 5.04 S 0.44 U 4.58 P 99% M 552600 F 0 R 359228 W 0 c 3 w 32 I 112 O 152 L 2.01 2.04 2.05 @#@FSLOADPOST 2020:07:23:10:56:57 mri_label2label N 12 2.01 2.04 2.05 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.hOc4v.mpm.vpnl.label --trgsubject bert --trglabel ./rh.hOc4v.mpm.vpnl.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.hOc4v.mpm.vpnl.label srcsubject = fsaverage trgsubject = bert trglabel = ./rh.hOc4v.mpm.vpnl.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 1025 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1025 nlabel points Performing mapping from target back to the source label 135771 Number of reverse mapping hits = 468 Checking for and removing duplicates Writing label file ./rh.hOc4v.mpm.vpnl.label 1493 mri_label2label: Done @#@FSTIME 2020:07:23:10:56:57 mri_label2label N 12 e 4.97 S 0.45 U 4.50 P 99% M 552596 F 0 R 359912 W 0 c 3 w 31 I 96 O 128 L 2.01 2.04 2.05 @#@FSLOADPOST 2020:07:23:10:57:02 mri_label2label N 12 2.01 2.04 2.05 mris_label2annot --s bert --ctab /usr/local/freesurfer/dev/average/colortable_vpnl.txt --hemi rh --a mpm.vpnl --maxstatwinner --noverbose --l rh.FG1.mpm.vpnl.label --l rh.FG2.mpm.vpnl.label --l rh.FG3.mpm.vpnl.label --l rh.FG4.mpm.vpnl.label --l rh.hOc1.mpm.vpnl.label --l rh.hOc2.mpm.vpnl.label --l rh.hOc3v.mpm.vpnl.label --l rh.hOc4v.mpm.vpnl.label Reading ctab /usr/local/freesurfer/dev/average/colortable_vpnl.txt Number of ctab entries 9 dev cwd /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/label cmdline mris_label2annot --s bert --ctab /usr/local/freesurfer/dev/average/colortable_vpnl.txt --hemi rh --a mpm.vpnl --maxstatwinner --noverbose --l rh.FG1.mpm.vpnl.label --l rh.FG2.mpm.vpnl.label --l rh.FG3.mpm.vpnl.label --l rh.FG4.mpm.vpnl.label --l rh.hOc1.mpm.vpnl.label --l rh.hOc2.mpm.vpnl.label --l rh.hOc3v.mpm.vpnl.label --l rh.hOc4v.mpm.vpnl.label sysname Linux hostname nike machine x86_64 user ah221 subject bert hemi rh SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running ColorTable /usr/local/freesurfer/dev/average/colortable_vpnl.txt AnnotName mpm.vpnl nlables 8 LabelThresh 0 0.000000 Loading /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.orig 1 1376057 FG1 2 16711935 FG2 3 16711680 FG3 4 1705837 FG4 5 25600 hOc1 6 255 hOc2 7 16776960 hOc3v 8 65535 hOc4v Mapping unhit to unknown Found 120470 unhit vertices Writing annot to /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/label/rh.mpm.vpnl.annot @#@FSTIME 2020:07:23:10:57:02 mris_label2annot N 26 e 0.77 S 0.10 U 0.65 P 97% M 153744 F 0 R 47118 W 0 c 1 w 176 I 0 O 2128 L 2.01 2.04 2.05 @#@FSLOADPOST 2020:07:23:10:57:03 mris_label2annot N 26 2.01 2.04 2.05 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject bert --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.BA1_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert trglabel = ./rh.BA1_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 876 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 876 nlabel points Performing mapping from target back to the source label 135771 Number of reverse mapping hits = 70 Checking for and removing duplicates Writing label file ./rh.BA1_exvivo.thresh.label 946 mri_label2label: Done @#@FSTIME 2020:07:23:10:57:03 mri_label2label N 12 e 4.88 S 0.44 U 4.42 P 99% M 552548 F 0 R 360651 W 0 c 2 w 30 I 80 O 72 L 2.01 2.04 2.05 @#@FSLOADPOST 2020:07:23:10:57:08 mri_label2label N 12 2.01 2.04 2.05 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject bert --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.BA2_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert trglabel = ./rh.BA2_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 2688 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2688 nlabel points Performing mapping from target back to the source label 135771 Number of reverse mapping hits = 46 Checking for and removing duplicates Writing label file ./rh.BA2_exvivo.thresh.label 2734 mri_label2label: Done @#@FSTIME 2020:07:23:10:57:08 mri_label2label N 12 e 5.37 S 0.44 U 4.92 P 99% M 552680 F 0 R 313010 W 0 c 40 w 39 I 240 O 168 L 2.01 2.04 2.05 @#@FSLOADPOST 2020:07:23:10:57:13 mri_label2label N 12 2.01 2.04 2.05 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject bert --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.BA3a_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert trglabel = ./rh.BA3a_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 1698 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1698 nlabel points Performing mapping from target back to the source label 135771 Number of reverse mapping hits = 14 Checking for and removing duplicates Writing label file ./rh.BA3a_exvivo.thresh.label 1712 mri_label2label: Done @#@FSTIME 2020:07:23:10:57:13 mri_label2label N 12 e 5.10 S 0.45 U 4.64 P 99% M 552600 F 0 R 311224 W 0 c 3 w 28 I 152 O 96 L 2.01 2.04 2.05 @#@FSLOADPOST 2020:07:23:10:57:19 mri_label2label N 12 2.01 2.04 2.05 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject bert --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.BA3b_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert trglabel = ./rh.BA3b_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 2183 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2183 nlabel points Performing mapping from target back to the source label 135771 Number of reverse mapping hits = 44 Checking for and removing duplicates Writing label file ./rh.BA3b_exvivo.thresh.label 2227 mri_label2label: Done @#@FSTIME 2020:07:23:10:57:19 mri_label2label N 12 e 5.33 S 0.46 U 4.86 P 99% M 552660 F 0 R 312596 W 0 c 22 w 35 I 192 O 136 L 2.01 2.04 2.05 @#@FSLOADPOST 2020:07:23:10:57:24 mri_label2label N 12 2.01 2.04 2.05 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject bert --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.BA4a_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert trglabel = ./rh.BA4a_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 1388 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1388 nlabel points Performing mapping from target back to the source label 135771 Number of reverse mapping hits = 51 Checking for and removing duplicates Writing label file ./rh.BA4a_exvivo.thresh.label 1439 mri_label2label: Done @#@FSTIME 2020:07:23:10:57:24 mri_label2label N 12 e 5.42 S 0.68 U 4.71 P 99% M 552604 F 0 R 309855 W 0 c 5 w 29 I 120 O 96 L 2.01 2.04 2.05 @#@FSLOADPOST 2020:07:23:10:57:29 mri_label2label N 12 2.01 2.04 2.05 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject bert --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.BA4p_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert trglabel = ./rh.BA4p_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 1489 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1489 nlabel points Performing mapping from target back to the source label 135771 Number of reverse mapping hits = 18 Checking for and removing duplicates Writing label file ./rh.BA4p_exvivo.thresh.label 1507 mri_label2label: Done @#@FSTIME 2020:07:23:10:57:30 mri_label2label N 12 e 5.46 S 0.75 U 4.69 P 99% M 552608 F 0 R 312970 W 0 c 22 w 32 I 136 O 96 L 2.01 2.04 2.05 @#@FSLOADPOST 2020:07:23:10:57:35 mri_label2label N 12 2.01 2.04 2.05 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject bert --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.BA6_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert trglabel = ./rh.BA6_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 6959 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6959 nlabel points Performing mapping from target back to the source label 135771 Number of reverse mapping hits = 211 Checking for and removing duplicates Writing label file ./rh.BA6_exvivo.thresh.label 7170 mri_label2label: Done @#@FSTIME 2020:07:23:10:57:35 mri_label2label N 12 e 6.44 S 0.44 U 5.97 P 99% M 553000 F 0 R 303342 W 0 c 8 w 34 I 592 O 400 L 2.01 2.04 2.05 @#@FSLOADPOST 2020:07:23:10:57:41 mri_label2label N 12 2.01 2.04 2.05 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject bert --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.BA44_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert trglabel = ./rh.BA44_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 1012 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1012 nlabel points Performing mapping from target back to the source label 135771 Number of reverse mapping hits = 83 Checking for and removing duplicates Writing label file ./rh.BA44_exvivo.thresh.label 1095 mri_label2label: Done @#@FSTIME 2020:07:23:10:57:42 mri_label2label N 12 e 5.29 S 0.54 U 4.74 P 99% M 552560 F 0 R 308217 W 0 c 9 w 33 I 88 O 80 L 2.01 2.04 2.05 @#@FSLOADPOST 2020:07:23:10:57:47 mri_label2label N 12 2.01 2.03 2.05 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject bert --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.BA45_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert trglabel = ./rh.BA45_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 1178 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1178 nlabel points Performing mapping from target back to the source label 135771 Number of reverse mapping hits = 177 Checking for and removing duplicates Writing label file ./rh.BA45_exvivo.thresh.label 1355 mri_label2label: Done @#@FSTIME 2020:07:23:10:57:47 mri_label2label N 12 e 4.96 S 0.44 U 4.51 P 99% M 552580 F 0 R 324152 W 0 c 3 w 30 I 104 O 112 L 2.01 2.03 2.05 @#@FSLOADPOST 2020:07:23:10:57:52 mri_label2label N 12 2.00 2.03 2.05 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject bert --trglabel ./rh.V1_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.V1_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert trglabel = ./rh.V1_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 3232 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3232 nlabel points Performing mapping from target back to the source label 135771 Number of reverse mapping hits = 630 Checking for and removing duplicates Writing label file ./rh.V1_exvivo.thresh.label 3862 mri_label2label: Done @#@FSTIME 2020:07:23:10:57:52 mri_label2label N 12 e 5.58 S 0.45 U 5.12 P 99% M 552732 F 0 R 364875 W 0 c 3 w 40 I 280 O 296 L 2.00 2.03 2.05 @#@FSLOADPOST 2020:07:23:10:57:57 mri_label2label N 12 2.00 2.03 2.05 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject bert --trglabel ./rh.V2_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.V2_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert trglabel = ./rh.V2_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 3437 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3437 nlabel points Performing mapping from target back to the source label 135771 Number of reverse mapping hits = 1127 Checking for and removing duplicates Writing label file ./rh.V2_exvivo.thresh.label 4564 mri_label2label: Done @#@FSTIME 2020:07:23:10:57:58 mri_label2label N 12 e 5.69 S 0.46 U 5.22 P 99% M 552772 F 0 R 364380 W 0 c 2 w 37 I 296 O 368 L 2.00 2.03 2.05 @#@FSLOADPOST 2020:07:23:10:58:03 mri_label2label N 12 2.00 2.03 2.05 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject bert --trglabel ./rh.MT_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.MT_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert trglabel = ./rh.MT_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 268 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 268 nlabel points Performing mapping from target back to the source label 135771 Number of reverse mapping hits = 20 Checking for and removing duplicates Writing label file ./rh.MT_exvivo.thresh.label 288 mri_label2label: Done @#@FSTIME 2020:07:23:10:58:03 mri_label2label N 12 e 4.87 S 0.48 U 4.37 P 99% M 552508 F 0 R 357308 W 0 c 31 w 27 I 24 O 24 L 2.00 2.03 2.05 @#@FSLOADPOST 2020:07:23:10:58:08 mri_label2label N 12 2.00 2.03 2.05 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject bert --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.entorhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert trglabel = ./rh.entorhinal_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 694 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 694 nlabel points Performing mapping from target back to the source label 135771 Number of reverse mapping hits = 9 Checking for and removing duplicates Writing label file ./rh.entorhinal_exvivo.thresh.label 703 mri_label2label: Done @#@FSTIME 2020:07:23:10:58:08 mri_label2label N 12 e 4.78 S 0.43 U 4.34 P 99% M 552528 F 0 R 361543 W 0 c 35 w 29 I 64 O 48 L 2.00 2.03 2.05 @#@FSLOADPOST 2020:07:23:10:58:13 mri_label2label N 12 2.00 2.03 2.05 mri_label2label --srcsubject fsaverage --srclabel /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject bert --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface srclabel = /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/label/rh.perirhinal_exvivo.thresh.label srcsubject = fsaverage trgsubject = bert trglabel = ./rh.perirhinal_exvivo.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running FREESURFER_HOME /usr/local/freesurfer/dev Loading source label. Found 291 points in source label. Starting surface-based mapping Reading source registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.white Reading target registration /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 291 nlabel points Performing mapping from target back to the source label 135771 Number of reverse mapping hits = 5 Checking for and removing duplicates Writing label file ./rh.perirhinal_exvivo.thresh.label 296 mri_label2label: Done @#@FSTIME 2020:07:23:10:58:13 mri_label2label N 12 e 4.63 S 0.39 U 4.22 P 99% M 552500 F 0 R 283666 W 0 c 6 w 31 I 32 O 24 L 2.00 2.03 2.05 @#@FSLOADPOST 2020:07:23:10:58:18 mri_label2label N 12 2.00 2.03 2.05 mris_label2annot --s bert --hemi rh --ctab /usr/local/freesurfer/dev/average/colortable_BA.txt --l rh.BA1_exvivo.label --l rh.BA2_exvivo.label --l rh.BA3a_exvivo.label --l rh.BA3b_exvivo.label --l rh.BA4a_exvivo.label --l rh.BA4p_exvivo.label --l rh.BA6_exvivo.label --l rh.BA44_exvivo.label --l rh.BA45_exvivo.label --l rh.V1_exvivo.label --l rh.V2_exvivo.label --l rh.MT_exvivo.label --l rh.perirhinal_exvivo.label --l rh.entorhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose Reading ctab /usr/local/freesurfer/dev/average/colortable_BA.txt Number of ctab entries 15 dev cwd /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/label cmdline mris_label2annot --s bert --hemi rh --ctab /usr/local/freesurfer/dev/average/colortable_BA.txt --l rh.BA1_exvivo.label --l rh.BA2_exvivo.label --l rh.BA3a_exvivo.label --l rh.BA3b_exvivo.label --l rh.BA4a_exvivo.label --l rh.BA4p_exvivo.label --l rh.BA6_exvivo.label --l rh.BA44_exvivo.label --l rh.BA45_exvivo.label --l rh.V1_exvivo.label --l rh.V2_exvivo.label --l rh.MT_exvivo.label --l rh.perirhinal_exvivo.label --l rh.entorhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose sysname Linux hostname nike machine x86_64 user ah221 subject bert hemi rh SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running ColorTable /usr/local/freesurfer/dev/average/colortable_BA.txt AnnotName BA_exvivo nlables 14 LabelThresh 0 0.000000 Loading /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 94689 unhit vertices Writing annot to /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/label/rh.BA_exvivo.annot @#@FSTIME 2020:07:23:10:58:18 mris_label2annot N 38 e 0.85 S 0.12 U 0.70 P 96% M 154292 F 0 R 47275 W 0 c 2 w 223 I 0 O 2128 L 2.00 2.03 2.05 @#@FSLOADPOST 2020:07:23:10:58:19 mris_label2annot N 38 2.00 2.03 2.05 mris_label2annot --s bert --hemi rh --ctab /usr/local/freesurfer/dev/average/colortable_BA.txt --l rh.BA1_exvivo.thresh.label --l rh.BA2_exvivo.thresh.label --l rh.BA3a_exvivo.thresh.label --l rh.BA3b_exvivo.thresh.label --l rh.BA4a_exvivo.thresh.label --l rh.BA4p_exvivo.thresh.label --l rh.BA6_exvivo.thresh.label --l rh.BA44_exvivo.thresh.label --l rh.BA45_exvivo.thresh.label --l rh.V1_exvivo.thresh.label --l rh.V2_exvivo.thresh.label --l rh.MT_exvivo.thresh.label --l rh.perirhinal_exvivo.thresh.label --l rh.entorhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose Reading ctab /usr/local/freesurfer/dev/average/colortable_BA.txt Number of ctab entries 15 dev cwd /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/label cmdline mris_label2annot --s bert --hemi rh --ctab /usr/local/freesurfer/dev/average/colortable_BA.txt --l rh.BA1_exvivo.thresh.label --l rh.BA2_exvivo.thresh.label --l rh.BA3a_exvivo.thresh.label --l rh.BA3b_exvivo.thresh.label --l rh.BA4a_exvivo.thresh.label --l rh.BA4p_exvivo.thresh.label --l rh.BA6_exvivo.thresh.label --l rh.BA44_exvivo.thresh.label --l rh.BA45_exvivo.thresh.label --l rh.V1_exvivo.thresh.label --l rh.V2_exvivo.thresh.label --l rh.MT_exvivo.thresh.label --l rh.perirhinal_exvivo.thresh.label --l rh.entorhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose sysname Linux hostname nike machine x86_64 user ah221 subject bert hemi rh SUBJECTS_DIR /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running ColorTable /usr/local/freesurfer/dev/average/colortable_BA.txt AnnotName BA_exvivo.thresh nlables 14 LabelThresh 0 0.000000 Loading /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.orig 1 1530880 BA1_exvivo 2 16749699 BA2_exvivo 3 16711680 BA3a_exvivo 4 3368703 BA3b_exvivo 5 1376196 BA4a_exvivo 6 13382655 BA4p_exvivo 7 10036737 BA6_exvivo 8 2490521 BA44_exvivo 9 39283 BA45_exvivo 10 3993 V1_exvivo 11 8508928 V2_exvivo 12 10027163 MT_exvivo 13 16422433 perirhinal_exvivo 14 16392598 entorhinal_exvivo Mapping unhit to unknown Found 113173 unhit vertices Writing annot to /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/label/rh.BA_exvivo.thresh.annot @#@FSTIME 2020:07:23:10:58:19 mris_label2annot N 38 e 0.77 S 0.10 U 0.64 P 96% M 153976 F 0 R 47195 W 0 c 1 w 214 I 72 O 2128 L 2.00 2.03 2.05 @#@FSLOADPOST 2020:07:23:10:58:19 mris_label2annot N 38 2.00 2.03 2.05 mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.stats -b -a ./rh.BA_exvivo.annot -c ./BA_exvivo.ctab bert rh white computing statistics for each annotation in ./rh.BA_exvivo.annot. reading volume /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/wm.mgz... reading input surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.white... reading input pial surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.pial... reading input white surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 241323 Total vertex volume 241099 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /usr/local/freesurfer/dev/average/colortable_BA.txt) Saving annotation colortable ./BA_exvivo.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1518149 mm^3 (det: 1.283211 ) 1056 533 1813 2.423 0.558 0.109 0.029 12 1.2 BA1_exvivo 3431 2163 5080 2.323 0.524 0.095 0.017 19 2.4 BA2_exvivo 1051 731 1015 1.825 0.392 0.126 0.028 8 1.2 BA3a_exvivo 1971 1222 2416 1.771 0.609 0.091 0.020 12 1.6 BA3b_exvivo 1738 1024 2954 2.631 0.670 0.114 0.031 15 2.5 BA4a_exvivo 1293 847 2135 2.705 0.664 0.101 0.026 7 1.4 BA4p_exvivo 7272 4422 15139 2.958 0.644 0.103 0.022 51 6.7 BA6_exvivo 3746 2487 7804 2.856 0.478 0.102 0.018 26 2.8 BA44_exvivo 4631 3181 9634 2.621 0.520 0.121 0.024 46 4.9 BA45_exvivo 3682 2377 4246 1.719 0.598 0.116 0.028 32 4.4 V1_exvivo 8511 5689 11146 1.887 0.528 0.137 0.034 104 11.9 V2_exvivo 1829 1269 3247 2.509 0.393 0.114 0.022 15 1.7 MT_exvivo 347 229 626 2.721 0.582 0.102 0.019 2 0.2 perirhinal_exvivo 524 341 1555 3.128 0.655 0.092 0.021 3 0.5 entorhinal_exvivo @#@FSTIME 2020:07:23:10:58:19 mris_anatomical_stats N 12 e 5.60 S 0.43 U 5.13 P 99% M 470660 F 0 R 270855 W 0 c 7 w 155 I 0 O 136 L 2.00 2.03 2.05 @#@FSLOADPOST 2020:07:23:10:58:25 mris_anatomical_stats N 12 2.00 2.03 2.05 mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b -a ./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab bert rh white computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot. reading volume /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/mri/wm.mgz... reading input surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.white... reading input pial surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.pial... reading input white surface /autofs/cluster/freesurfer/test/recons/linux/bert/dev/running/bert/surf/rh.white... INFO: using TH3 volume calc INFO: assuming MGZ format for volumes. Using TH3 vertex volume calc Total face volume 241323 Total vertex volume 241099 (mask=0) reading colortable from annotation file... colortable with 15 entries read (originally /usr/local/freesurfer/dev/average/colortable_BA.txt) Saving annotation colortable ./BA_exvivo.thresh.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name atlas_icv (eTIV) = 1518149 mm^3 (det: 1.283211 ) 725 354 1168 2.383 0.524 0.100 0.024 6 0.7 BA1_exvivo 1877 1141 2928 2.378 0.519 0.083 0.015 9 1.1 BA2_exvivo 960 659 884 1.853 0.409 0.128 0.029 7 1.2 BA3a_exvivo 1549 971 1616 1.641 0.496 0.078 0.014 6 0.9 BA3b_exvivo 1038 614 1456 2.312 0.621 0.130 0.041 11 2.0 BA4a_exvivo 1046 694 1747 2.769 0.695 0.099 0.026 6 1.1 BA4p_exvivo 4663 2779 9282 2.905 0.670 0.099 0.021 32 3.9 BA6_exvivo 889 624 2238 2.969 0.370 0.117 0.022 8 0.8 BA44_exvivo 1237 855 2866 2.710 0.453 0.120 0.024 13 1.2 BA45_exvivo 3506 2269 3981 1.722 0.600 0.113 0.027 28 3.9 V1_exvivo 4352 2893 5057 1.704 0.507 0.144 0.040 60 7.2 V2_exvivo 233 165 509 2.462 0.337 0.135 0.029 3 0.3 MT_exvivo 29 18 62 3.107 0.732 0.101 0.028 0 0.0 perirhinal_exvivo 494 328 1325 3.086 0.575 0.092 0.019 2 0.4 entorhinal_exvivo @#@FSTIME 2020:07:23:10:58:25 mris_anatomical_stats N 12 e 4.93 S 0.35 U 4.55 P 99% M 470660 F 0 R 241119 W 0 c 3 w 138 I 0 O 144 L 2.00 2.03 2.05 @#@FSLOADPOST 2020:07:23:10:58:30 mris_anatomical_stats N 12 2.00 2.03 2.05 Started at Thu Jul 23 06:00:05 EDT 2020 Ended at Thu Jul 23 10:58:30 EDT 2020 #@#%# recon-all-run-time-hours 4.974 recon-all -s bert finished without error at Thu Jul 23 10:58:30 EDT 2020 #New# invocation of recon-all Wed May 26 18:10:22 CST 2021 cd /home/liubing/FreeSurfer/freesurfer/subjects/bert setenv SUBJECTS_DIR /home/liubing/FreeSurfer/freesurfer/subjects /home/liubing/FreeSurfer/freesurfer/bin/recon-all -all -s bert subjid bert setenv SUBJECTS_DIR /home/liubing/FreeSurfer/freesurfer/subjects FREESURFER_HOME /home/liubing/FreeSurfer/freesurfer Actual FREESURFER_HOME /home/liubing/FreeSurfer/freesurfer build-stamp.txt: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 Linux HEUBME.com 4.18.0-193.28.1.el8_2.x86_64 #1 SMP Thu Oct 22 00:20:22 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize unlimited memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 512146 maxlocks unlimited maxsignal 512146 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 125Gi 14Gi 27Gi 858Mi 83Gi 108Gi Swap: 7.7Gi 49Mi 7.7Gi ######################################## program versions used 7.1.1 (freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551) 7.1.1 ProgramName: lta_convert ProgramArguments: lta_convert -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_and ProgramArguments: mri_and -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_annotation2label ProgramArguments: mri_annotation2label -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_aparc2aseg ProgramArguments: mri_aparc2aseg -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surf2volseg ProgramArguments: mri_surf2volseg -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_binarize ProgramArguments: mri_binarize -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_ca_label ProgramArguments: mri_ca_label -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_ca_normalize ProgramArguments: mri_ca_normalize -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_ca_register ProgramArguments: mri_ca_register -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_cc ProgramArguments: mri_cc -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_compute_overlap ProgramArguments: mri_compute_overlap -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_compute_seg_overlap ProgramArguments: mri_compute_seg_overlap -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_concat ProgramArguments: mri_concat -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_concatenate_lta ProgramArguments: mri_concatenate_lta -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_diff ProgramArguments: mri_diff -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_edit_wm_with_aseg ProgramArguments: mri_edit_wm_with_aseg -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_em_register ProgramArguments: mri_em_register -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_fill ProgramArguments: mri_fill -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_fuse_segmentations ProgramArguments: mri_fuse_segmentations -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_fwhm ProgramArguments: mri_fwhm -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_gcut ProgramArguments: mri_gcut -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_info ProgramArguments: mri_info -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_label2label ProgramArguments: mri_label2label -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_label2vol ProgramArguments: mri_label2vol -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_log_likelihood ProgramArguments: mri_log_likelihood -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_mask ProgramArguments: mri_mask -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_matrix_multiply ProgramArguments: mri_matrix_multiply -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_normalize ProgramArguments: mri_normalize -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_normalize_tp2 ProgramArguments: mri_normalize_tp2 -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_or ProgramArguments: mri_or -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_relabel_hypointensities ProgramArguments: mri_relabel_hypointensities -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_relabel_nonwm_hypos ProgramArguments: mri_relabel_nonwm_hypos -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_remove_neck ProgramArguments: mri_remove_neck -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 7.1.1 ProgramName: mri_robust_register ProgramArguments: mri_robust_register -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 7.1.1 ProgramName: mri_robust_template ProgramArguments: mri_robust_template -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_anatomical_stats ProgramArguments: mris_anatomical_stats -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_ca_label ProgramArguments: mris_ca_label -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_calc ProgramArguments: mris_calc -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_convert ProgramArguments: mris_convert -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_curvature ProgramArguments: mris_curvature -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_curvature_stats ProgramArguments: mris_curvature_stats -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_diff ProgramArguments: mris_diff -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_divide_parcellation ProgramArguments: mris_divide_parcellation -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_segment ProgramArguments: mri_segment -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_segstats ProgramArguments: mri_segstats -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_euler_number ProgramArguments: mris_euler_number -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_fix_topology ProgramArguments: mris_fix_topology -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_jacobian ProgramArguments: mris_jacobian -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_label2annot ProgramArguments: mris_label2annot -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_left_right_register ProgramArguments: mris_left_right_register -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_place_surface ProgramArguments: mris_place_surface -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mrisp_paint ProgramArguments: mrisp_paint -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_register ProgramArguments: mris_register -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_smooth ProgramArguments: mris_smooth -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_sphere ProgramArguments: mris_sphere -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_surface_stats ProgramArguments: mris_surface_stats -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_stats2seg ProgramArguments: mri_stats2seg -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_thickness ProgramArguments: mris_thickness -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_thickness_diff ProgramArguments: mris_thickness_diff -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surf2surf ProgramArguments: mri_surf2surf -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surf2vol ProgramArguments: mri_surf2vol -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surfcluster ProgramArguments: mri_surfcluster -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_volmask ProgramArguments: mris_volmask -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_tessellate ProgramArguments: mri_tessellate -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_vol2surf ProgramArguments: mri_vol2surf -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_vol2vol ProgramArguments: mri_vol2vol -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_voldiff ProgramArguments: mri_voldiff -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_watershed ProgramArguments: mri_watershed -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: tkregister2 ProgramArguments: tkregister2_cmdl -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 mri_motion_correct.fsl 7.1.1 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:10:22-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 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 /home/liubing/FreeSurfer/freesurfer/average GCA RB_all_2020-01-02.gca GCASkull RB_all_withskull_2020_01_02.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /home/liubing/FreeSurfer/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #-------------------------------------------- #@# MotionCor Wed May 26 18:10:22 CST 2021 Found 3 runs /home/liubing/FreeSurfer/freesurfer/subjects/bert/mri/orig/001.mgz /home/liubing/FreeSurfer/freesurfer/subjects/bert/mri/orig/002.mgz /home/liubing/FreeSurfer/freesurfer/subjects/bert/mri/orig/003.mgz Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... /home/liubing/FreeSurfer/freesurfer/subjects/bert mri_robust_template --mov /home/liubing/FreeSurfer/freesurfer/subjects/bert/mri/orig/001.mgz /home/liubing/FreeSurfer/freesurfer/subjects/bert/mri/orig/002.mgz /home/liubing/FreeSurfer/freesurfer/subjects/bert/mri/orig/003.mgz --average 1 --template /home/liubing/FreeSurfer/freesurfer/subjects/bert/mri/rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --iscaleout /home/liubing/FreeSurfer/freesurfer/subjects/bert/mri/orig/001-iscale.txt /home/liubing/FreeSurfer/freesurfer/subjects/bert/mri/orig/002-iscale.txt /home/liubing/FreeSurfer/freesurfer/subjects/bert/mri/orig/003-iscale.txt --subsample 200 --lta /home/liubing/FreeSurfer/freesurfer/subjects/bert/mri/orig/001.lta /home/liubing/FreeSurfer/freesurfer/subjects/bert/mri/orig/002.lta /home/liubing/FreeSurfer/freesurfer/subjects/bert/mri/orig/003.lta 7.1.1 --mov: Using /home/liubing/FreeSurfer/freesurfer/subjects/bert/mri/orig/001.mgz as movable/source volume. --mov: Using /home/liubing/FreeSurfer/freesurfer/subjects/bert/mri/orig/002.mgz as movable/source volume. --mov: Using /home/liubing/FreeSurfer/freesurfer/subjects/bert/mri/orig/003.mgz as movable/source volume. Total: 3 input volumes --average: Using method 1 for template computation. --template: Using /home/liubing/FreeSurfer/freesurfer/subjects/bert/mri/rawavg.mgz as template output volume. --satit: Will estimate SAT iteratively! --inittp: Using TP 1 as target for initialization --fixtp: Will map everything to init TP! --noit: Will output only first template (no iterations)! --iscale: Enabling intensity scaling! --iscaleout: Will perform intensity scaling and output results --subsample: Will subsample if size is larger than 200 on all axes! --lta: Will output LTA transforms Setting iscale ... reading source '/home/liubing/FreeSurfer/freesurfer/subjects/bert/mri/orig/001.mgz'... error parsing license file, expected 4 values -------------------------------------------------------------------------- GNU libc version: 2.28 ERROR: Systems running GNU glibc version greater than 2.15 require a newly formatted license file (it's free). Please download a new one from the following page: http://surfer.nmr.mgh.harvard.edu/registration.html -------------------------------------------------------------------------- Command exited with non-zero status 255 @#@FSTIME 2021:05:26:18:10:23 mri_robust_template N 24 e 0.00 S 0.00 U 0.00 P 50% M 5604 F 0 R 204 W 0 c 0 w 1 I 0 O 0 L 0.75 1.15 1.09 @#@FSLOADPOST 2021:05:26:18:10:23 mri_robust_template N 24 0.75 1.15 1.09 Linux HEUBME.com 4.18.0-193.28.1.el8_2.x86_64 #1 SMP Thu Oct 22 00:20:22 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux recon-all -s bert exited with ERRORS at Wed May 26 18:10:23 CST 2021 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting #New# invocation of recon-all Wed May 26 18:11:21 CST 2021 cd /home/liubing/FreeSurfer/freesurfer/subjects/bert setenv SUBJECTS_DIR /home/liubing/FreeSurfer/freesurfer/subjects /home/liubing/FreeSurfer/freesurfer/bin/recon-all -all -s bert subjid bert setenv SUBJECTS_DIR /home/liubing/FreeSurfer/freesurfer/subjects FREESURFER_HOME /home/liubing/FreeSurfer/freesurfer Actual FREESURFER_HOME /home/liubing/FreeSurfer/freesurfer build-stamp.txt: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 Linux HEUBME.com 4.18.0-193.28.1.el8_2.x86_64 #1 SMP Thu Oct 22 00:20:22 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize unlimited memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 512146 maxlocks unlimited maxsignal 512146 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 125Gi 14Gi 27Gi 849Mi 83Gi 108Gi Swap: 7.7Gi 49Mi 7.7Gi ######################################## program versions used 7.1.1 (freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551) 7.1.1 ProgramName: lta_convert ProgramArguments: lta_convert -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:11:21-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_and ProgramArguments: mri_and -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:11:21-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_annotation2label ProgramArguments: mri_annotation2label -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:11:21-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_aparc2aseg ProgramArguments: mri_aparc2aseg -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:11:21-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surf2volseg ProgramArguments: mri_surf2volseg -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:11:21-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_binarize ProgramArguments: mri_binarize -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:11:21-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_ca_label ProgramArguments: mri_ca_label -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:11:21-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_ca_normalize ProgramArguments: mri_ca_normalize -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:11:21-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_ca_register ProgramArguments: mri_ca_register -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:11:21-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_cc ProgramArguments: mri_cc -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:11:21-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_compute_overlap ProgramArguments: mri_compute_overlap -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:11:21-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_compute_seg_overlap ProgramArguments: mri_compute_seg_overlap -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:11:21-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_concat ProgramArguments: mri_concat -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:11:21-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_concatenate_lta ProgramArguments: mri_concatenate_lta -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:11:21-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 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freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_em_register ProgramArguments: mri_em_register -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:11:21-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_fill ProgramArguments: mri_fill -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:11:21-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_fuse_segmentations ProgramArguments: mri_fuse_segmentations -all-info 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ProgramName: mri_info ProgramArguments: mri_info -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:11:21-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_label2label ProgramArguments: mri_label2label -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:11:21-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_label2vol ProgramArguments: mri_label2vol -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:11:21-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux 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freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_normalize ProgramArguments: mri_normalize -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:11:21-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_normalize_tp2 ProgramArguments: mri_normalize_tp2 -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:11:21-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_or ProgramArguments: mri_or -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:11:21-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_relabel_hypointensities ProgramArguments: mri_relabel_hypointensities -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:11:21-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_relabel_nonwm_hypos ProgramArguments: mri_relabel_nonwm_hypos -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:11:21-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 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BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_anatomical_stats ProgramArguments: mris_anatomical_stats -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:11:21-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_ca_label ProgramArguments: mris_ca_label -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:11:21-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_calc ProgramArguments: mris_calc 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freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_segment ProgramArguments: mri_segment -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:11:21-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_segstats ProgramArguments: mri_segstats -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:11:21-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_euler_number ProgramArguments: mris_euler_number -all-info 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CompilerVersion: 4.8.5 ProgramName: mris_surface_stats ProgramArguments: mris_surface_stats -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:11:21-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_stats2seg ProgramArguments: mri_stats2seg -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:11:21-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_thickness ProgramArguments: mris_thickness -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:11:21-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_thickness_diff ProgramArguments: mris_thickness_diff -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:11:21-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_topo_fixer ProgramArguments: mris_topo_fixer -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:11:21-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surf2surf ProgramArguments: mri_surf2surf -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:11:21-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surf2vol ProgramArguments: mri_surf2vol -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:11:21-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_surfcluster ProgramArguments: mri_surfcluster -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:11:21-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mris_volmask ProgramArguments: mris_volmask -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:11:21-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_tessellate ProgramArguments: mri_tessellate -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:11:21-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_vol2surf ProgramArguments: mri_vol2surf -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:11:21-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_vol2vol ProgramArguments: mri_vol2vol -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:11:21-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_voldiff ProgramArguments: mri_voldiff -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:11:21-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: mri_watershed ProgramArguments: mri_watershed -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:11:21-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 ProgramName: tkregister2 ProgramArguments: tkregister2_cmdl -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:11:21-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 mri_motion_correct.fsl 7.1.1 mri_convert -all-info ProgramName: mri_convert ProgramArguments: mri_convert -all-info ProgramVersion: 7.1.1 TimeStamp: 2021/05/26-10:11:21-GMT BuildTime: Jul 23 2020 11:55:54 BuildStamp: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 User: liubing Machine: HEUBME.com Platform: Linux PlatformVersion: 4.18.0-193.28.1.el8_2.x86_64 CompilerName: GCC CompilerVersion: 4.8.5 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 /home/liubing/FreeSurfer/freesurfer/average GCA RB_all_2020-01-02.gca GCASkull RB_all_withskull_2020_01_02.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /home/liubing/FreeSurfer/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #-------------------------------------------- #@# MotionCor Wed May 26 18:11:22 CST 2021 Found 3 runs /home/liubing/FreeSurfer/freesurfer/subjects/bert/mri/orig/001.mgz /home/liubing/FreeSurfer/freesurfer/subjects/bert/mri/orig/002.mgz /home/liubing/FreeSurfer/freesurfer/subjects/bert/mri/orig/003.mgz Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... /home/liubing/FreeSurfer/freesurfer/subjects/bert mri_robust_template --mov /home/liubing/FreeSurfer/freesurfer/subjects/bert/mri/orig/001.mgz /home/liubing/FreeSurfer/freesurfer/subjects/bert/mri/orig/002.mgz /home/liubing/FreeSurfer/freesurfer/subjects/bert/mri/orig/003.mgz --average 1 --template /home/liubing/FreeSurfer/freesurfer/subjects/bert/mri/rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --iscaleout /home/liubing/FreeSurfer/freesurfer/subjects/bert/mri/orig/001-iscale.txt /home/liubing/FreeSurfer/freesurfer/subjects/bert/mri/orig/002-iscale.txt /home/liubing/FreeSurfer/freesurfer/subjects/bert/mri/orig/003-iscale.txt --subsample 200 --lta /home/liubing/FreeSurfer/freesurfer/subjects/bert/mri/orig/001.lta /home/liubing/FreeSurfer/freesurfer/subjects/bert/mri/orig/002.lta /home/liubing/FreeSurfer/freesurfer/subjects/bert/mri/orig/003.lta 7.1.1 --mov: Using /home/liubing/FreeSurfer/freesurfer/subjects/bert/mri/orig/001.mgz as movable/source volume. --mov: Using /home/liubing/FreeSurfer/freesurfer/subjects/bert/mri/orig/002.mgz as movable/source volume. --mov: Using /home/liubing/FreeSurfer/freesurfer/subjects/bert/mri/orig/003.mgz as movable/source volume. Total: 3 input volumes --average: Using method 1 for template computation. --template: Using /home/liubing/FreeSurfer/freesurfer/subjects/bert/mri/rawavg.mgz as template output volume. --satit: Will estimate SAT iteratively! --inittp: Using TP 1 as target for initialization --fixtp: Will map everything to init TP! --noit: Will output only first template (no iterations)! --iscale: Enabling intensity scaling! --iscaleout: Will perform intensity scaling and output results --subsample: Will subsample if size is larger than 200 on all axes! --lta: Will output LTA transforms Setting iscale ... reading source '/home/liubing/FreeSurfer/freesurfer/subjects/bert/mri/orig/001.mgz'... converting source '/home/liubing/FreeSurfer/freesurfer/subjects/bert/mri/orig/001.mgz' to bspline ... MRItoBSpline degree 3 reading source '/home/liubing/FreeSurfer/freesurfer/subjects/bert/mri/orig/002.mgz'... converting source '/home/liubing/FreeSurfer/freesurfer/subjects/bert/mri/orig/002.mgz' to bspline ... MRItoBSpline degree 3 reading source '/home/liubing/FreeSurfer/freesurfer/subjects/bert/mri/orig/003.mgz'... converting source '/home/liubing/FreeSurfer/freesurfer/subjects/bert/mri/orig/003.mgz' to bspline ... MRItoBSpline degree 3 MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) : [init] ========================= TP 2 to TP 1 ============================== Register TP 2 ( /home/liubing/FreeSurfer/freesurfer/subjects/bert/mri/orig/002.mgz ) to TP 1 ( /home/liubing/FreeSurfer/freesurfer/subjects/bert/mri/orig/001.mgz ) - Max Resolution used: 2 -- gpS ( 64 , 64 , 64 ) -- gpT ( 64 , 64 , 64 ) - running loop to estimate saturation parameter: [init] ========================= TP 3 to TP 1 ============================== Register TP 3 ( /home/liubing/FreeSurfer/freesurfer/subjects/bert/mri/orig/003.mgz ) to TP 1 ( /home/liubing/FreeSurfer/freesurfer/subjects/bert/mri/orig/001.mgz ) - Max Resolution used: 2 -- gpS ( 64 , 64 , 64 ) -- gpT ( 64 , 64 , 64 ) - running loop to estimate saturation parameter: * WARNING: TP 2 to 1 did not converge !! mapping movs and creating initial template... allow intensity scaling using median -- Template : (1, 1, 1)mm and (256, 256, 256) voxels. Writing final template: /home/liubing/FreeSurfer/freesurfer/subjects/bert/mri/rawavg.mgz Writing final transforms (warps etc.)... Determinant( lta[ 0 ]) : 1 Determinant( lta[ 1 ]) : 1 Determinant( lta[ 2 ]) : 1 registration took 1 minutes and 30 seconds. Thank you for using RobustTemplate! If you find it useful and use it for a publication, please cite: Within-Subject Template Estimation for Unbiased Longitudinal Image Analysis M. Reuter, N.J. Schmansky, H.D. Rosas, B. Fischl. NeuroImage 2012. http://dx.doi.org/10.1016/j.neuroimage.2012.02.084 http://reuter.mit.edu/papers/reuter-long12.pdf @#@FSTIME 2021:05:26:18:11:22 mri_robust_template N 24 e 89.70 S 1.19 U 88.26 P 99% M 1528632 F 0 R 186757 W 0 c 161 w 9 I 0 O 89120 L 0.58 1.02 1.05 @#@FSLOADPOST 2021:05:26:18:12:52 mri_robust_template N 24 1.17 1.10 1.07 /home/liubing/FreeSurfer/freesurfer/subjects/bert mri_convert /home/liubing/FreeSurfer/freesurfer/subjects/bert/mri/rawavg.mgz /home/liubing/FreeSurfer/freesurfer/subjects/bert/mri/orig.mgz --conform mri_convert /home/liubing/FreeSurfer/freesurfer/subjects/bert/mri/rawavg.mgz /home/liubing/FreeSurfer/freesurfer/subjects/bert/mri/orig.mgz --conform reading from /home/liubing/FreeSurfer/freesurfer/subjects/bert/mri/rawavg.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 float to uchar (noscale = 0)... MRIchangeType: Building histogram 0 265.402 1000, flo=0, fhi=0.999, dest_type=0 writing to /home/liubing/FreeSurfer/freesurfer/subjects/bert/mri/orig.mgz... @#@FSTIME 2021:05:26:18:12:52 mri_convert N 3 e 4.40 S 0.01 U 4.37 P 99% M 88852 F 0 R 1650 W 0 c 18 w 2 I 0 O 12472 L 1.17 1.10 1.07 @#@FSLOADPOST 2021:05:26:18:12:56 mri_convert N 3 1.17 1.10 1.07 mri_add_xform_to_header -c /home/liubing/FreeSurfer/freesurfer/subjects/bert/mri/transforms/talairach.xfm /home/liubing/FreeSurfer/freesurfer/subjects/bert/mri/orig.mgz /home/liubing/FreeSurfer/freesurfer/subjects/bert/mri/orig.mgz INFO: extension is mgz @#@FSTIME 2021:05:26:18:12:56 mri_add_xform_to_header N 4 e 1.13 S 0.00 U 1.11 P 99% M 22808 F 0 R 963 W 0 c 14 w 2 I 0 O 12472 L 1.17 1.10 1.07 @#@FSLOADPOST 2021:05:26:18:12:57 mri_add_xform_to_header N 4 1.15 1.10 1.07 #-------------------------------------------- #@# Talairach Wed May 26 18:12:57 CST 2021 /home/liubing/FreeSurfer/freesurfer/subjects/bert/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50 /usr/local/ashs_Linux64_rev103_20140612/ext/Linux/bin/bc /home/liubing/FreeSurfer/freesurfer/subjects/bert/mri /home/liubing/FreeSurfer/freesurfer/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50 nIters 1 mri_nu_correct.mni 7.1.1 Linux HEUBME.com 4.18.0-193.28.1.el8_2.x86_64 #1 SMP Thu Oct 22 00:20:22 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux Wed May 26 18:12:57 CST 2021 Found /dev/shm , will use for temp dir tmpdir is /dev/shm/tmp.mri_nu_correct.mni.810169 cd /home/liubing/FreeSurfer/freesurfer/subjects/bert/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o /dev/shm/tmp.mri_nu_correct.mni.810169/nu0.mgz Using shrink factor: 4 mri_convert /dev/shm/tmp.mri_nu_correct.mni.810169/nu0.mgz orig_nu.mgz --like orig.mgz --conform mri_convert /dev/shm/tmp.mri_nu_correct.mni.810169/nu0.mgz orig_nu.mgz --like orig.mgz --conform reading from /dev/shm/tmp.mri_nu_correct.mni.810169/nu0.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) INFO: transform src into the like-volume: orig.mgz writing to orig_nu.mgz... Wed May 26 18:15:43 CST 2021 mri_nu_correct.mni done @#@FSTIME 2021:05:26:18:12:57 mri_nu_correct.mni N 12 e 165.92 S 0.07 U 165.71 P 99% M 503048 F 0 R 20950 W 0 c 190 w 109 I 0 O 11824 L 1.15 1.10 1.07 @#@FSLOADPOST 2021:05:26:18:15:43 mri_nu_correct.mni N 12 1.21 1.12 1.08 talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... Started at Wed May 26 18:15:43 CST 2021 Ended at Wed May 26 18:16:09 CST 2021 talairach_avi done @#@FSTIME 2021:05:26:18:15:43 talairach_avi N 4 e 26.12 S 0.36 U 19.72 P 76% M 255692 F 0 R 27998 W 0 c 621 w 144 I 0 O 295248 L 1.21 1.12 1.08 @#@FSLOADPOST 2021:05:26:18:16:10 talairach_avi N 4 1.13 1.11 1.08 INFO: transforms/talairach.xfm already exists! The new transforms/talairach.auto.xfm will not be copied to transforms/talairach.xfm This is done to retain any edits made to transforms/talairach.xfm Add the -clean-tal flag to recon-all to overwrite transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Wed May 26 18:16:10 CST 2021 /home/liubing/FreeSurfer/freesurfer/subjects/bert/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7826, pval=0.8469 >= threshold=0.0050) @#@FSTIME 2021:05:26:18:16:10 talairach_afd N 4 e 0.00 S 0.00 U 0.00 P 100% M 5264 F 0 R 197 W 0 c 1 w 1 I 0 O 0 L 1.13 1.11 1.08 @#@FSLOADPOST 2021:05:26:18:16:10 talairach_afd N 4 1.13 1.11 1.08 awk -f /home/liubing/FreeSurfer/freesurfer/bin/extract_talairach_avi_QA.awk /home/liubing/FreeSurfer/freesurfer/subjects/bert/mri/transforms/talairach_avi.log tal_QC_AZS /home/liubing/FreeSurfer/freesurfer/subjects/bert/mri/transforms/talairach_avi.log TalAviQA: 0.97389 z-score: #-------------------------------------------- #@# Nu Intensity Correction Wed May 26 18:16:10 CST 2021 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4 /usr/local/ashs_Linux64_rev103_20140612/ext/Linux/bin/bc /home/liubing/FreeSurfer/freesurfer/subjects/bert/mri /home/liubing/FreeSurfer/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 --ants-n4 nIters 2 mri_nu_correct.mni 7.1.1 Linux HEUBME.com 4.18.0-193.28.1.el8_2.x86_64 #1 SMP Thu Oct 22 00:20:22 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux Wed May 26 18:16:10 CST 2021 Found /dev/shm , will use for temp dir tmpdir is /dev/shm/tmp.mri_nu_correct.mni.810474 cd /home/liubing/FreeSurfer/freesurfer/subjects/bert/mri AntsN4BiasFieldCorrectionFs -i orig.mgz -o /dev/shm/tmp.mri_nu_correct.mni.810474/nu0.mgz Using shrink factor: 4 mri_binarize --i /dev/shm/tmp.mri_nu_correct.mni.810474/nu0.mgz --min -1 --o /dev/shm/tmp.mri_nu_correct.mni.810474/ones.mgz 7.1.1 cwd /home/liubing/FreeSurfer/freesurfer/subjects/bert/mri cmdline mri_binarize --i /dev/shm/tmp.mri_nu_correct.mni.810474/nu0.mgz --min -1 --o /dev/shm/tmp.mri_nu_correct.mni.810474/ones.mgz sysname Linux hostname HEUBME.com machine x86_64 user liubing input /dev/shm/tmp.mri_nu_correct.mni.810474/nu0.mgz frame 0 nErode3d 0 nErode2d 0 output /dev/shm/tmp.mri_nu_correct.mni.810474/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.810474/ones.mgz --i orig.mgz --sum /dev/shm/tmp.mri_nu_correct.mni.810474/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.810474/input.mean.dat 7.1.1 cwd cmdline mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.810474/ones.mgz --i orig.mgz --sum /dev/shm/tmp.mri_nu_correct.mni.810474/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.810474/input.mean.dat sysname Linux hostname HEUBME.com machine x86_64 user liubing whitesurfname white UseRobust 0 Loading /dev/shm/tmp.mri_nu_correct.mni.810474/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.810474/input.mean.dat mri_segstats done mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.810474/ones.mgz --i /dev/shm/tmp.mri_nu_correct.mni.810474/nu0.mgz --sum /dev/shm/tmp.mri_nu_correct.mni.810474/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.810474/output.mean.dat 7.1.1 cwd cmdline mri_segstats --id 1 --seg /dev/shm/tmp.mri_nu_correct.mni.810474/ones.mgz --i /dev/shm/tmp.mri_nu_correct.mni.810474/nu0.mgz --sum /dev/shm/tmp.mri_nu_correct.mni.810474/sum.junk --avgwf /dev/shm/tmp.mri_nu_correct.mni.810474/output.mean.dat sysname Linux hostname HEUBME.com machine x86_64 user liubing whitesurfname white UseRobust 0 Loading /dev/shm/tmp.mri_nu_correct.mni.810474/ones.mgz Loading /dev/shm/tmp.mri_nu_correct.mni.810474/nu0.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.810474/output.mean.dat mri_segstats done Missing parameters. Usage: bc inputImageFile inputSegmentationFile side PathToTrainingFiles outputSegmentationFile side = 0 (left side) or else (right side) mris_calc -o /dev/shm/tmp.mri_nu_correct.mni.810474/nu0.mgz /dev/shm/tmp.mri_nu_correct.mni.810474/nu0.mgz mul Segmentation fault (core dumped) Command exited with non-zero status 1 @#@FSTIME 2021:05:26:18:16:10 mri_nu_correct.mni N 9 e 176.34 S 0.27 U 175.39 P 99% M 503024 F 0 R 31379 W 0 c 3897 w 137 I 0 O 16 L 1.13 1.11 1.08 @#@FSLOADPOST 2021:05:26:18:19:06 mri_nu_correct.mni N 9 1.37 1.21 1.12 Linux HEUBME.com 4.18.0-193.28.1.el8_2.x86_64 #1 SMP Thu Oct 22 00:20:22 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux recon-all -s bert exited with ERRORS at Wed May 26 18:19:06 CST 2021 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting